Created
October 3, 2014 01:48
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installation from vagrant fails tests
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| christophes-pro:bcbio pfaucon$ sh vagrant_osx.sh | |
| --2014-10-02 15:45:03-- https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/vm/Vagrantfile | |
| Resolving raw.github.com... 23.235.47.133 | |
| Connecting to raw.github.com|23.235.47.133|:443... connected. | |
| HTTP request sent, awaiting response... 301 Moved Permanently | |
| Location: https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/scripts/vm/Vagrantfile [following] | |
| --2014-10-02 15:45:04-- https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/scripts/vm/Vagrantfile | |
| Resolving raw.githubusercontent.com... 23.235.47.133 | |
| Connecting to raw.githubusercontent.com|23.235.47.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 572 [text/plain] | |
| Saving to: 'Vagrantfile' | |
| 100%[========================================================================================================================>] 572 --.-K/s in 0s | |
| 2014-10-02 15:45:05 (49.6 MB/s) - 'Vagrantfile' saved [572/572] | |
| --2014-10-02 15:45:05-- https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/vm/bootstrap.sh | |
| Resolving raw.github.com... 23.235.47.133 | |
| Connecting to raw.github.com|23.235.47.133|:443... connected. | |
| HTTP request sent, awaiting response... 301 Moved Permanently | |
| Location: https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/scripts/vm/bootstrap.sh [following] | |
| --2014-10-02 15:45:06-- https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/scripts/vm/bootstrap.sh | |
| Resolving raw.githubusercontent.com... 23.235.47.133 | |
| Connecting to raw.githubusercontent.com|23.235.47.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 358 [text/plain] | |
| Saving to: 'bootstrap.sh' | |
| 100%[========================================================================================================================>] 358 --.-K/s in 0s | |
| 2014-10-02 15:45:06 (31.0 MB/s) - 'bootstrap.sh' saved [358/358] | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Bringing machine 'default' up with 'virtualbox' provider... | |
| ==> default: Importing base box 'ubuntu/trusty64'... | |
| ==> default: Matching MAC address for NAT networking... | |
| ==> default: Checking if box 'ubuntu/trusty64' is up to date... | |
| ==> default: Setting the name of the VM: bcbio_default_1412289929640_3166 | |
| ==> default: Clearing any previously set forwarded ports... | |
| ==> default: Clearing any previously set network interfaces... | |
| ==> default: Preparing network interfaces based on configuration... | |
| default: Adapter 1: nat | |
| ==> default: Forwarding ports... | |
| default: 8090 => 8090 (adapter 1) | |
| default: 22 => 2222 (adapter 1) | |
| ==> default: Running 'pre-boot' VM customizations... | |
| ==> default: Booting VM... | |
| ==> default: Waiting for machine to boot. This may take a few minutes... | |
| default: SSH address: 127.0.0.1:2222 | |
| default: SSH username: vagrant | |
| default: SSH auth method: private key | |
| default: Warning: Connection timeout. Retrying... | |
| ==> default: Machine booted and ready! | |
| ==> default: Checking for guest additions in VM... | |
| ==> default: Mounting shared folders... | |
| default: /vagrant => /Volumes/WORK/vagrant/bcbio | |
| ==> default: Running provisioner: shell... | |
| default: Running: /var/folders/v3/j6lsstb54rq_b_6y_7l692ch0000gn/T/vagrant-shell20141002-2430-xkotjx.sh | |
| ==> default: Ign http://security.ubuntu.com trusty-security InRelease | |
| ==> default: Ign http://archive.ubuntu.com trusty InRelease | |
| ==> default: Get:1 http://security.ubuntu.com trusty-security Release.gpg [933 B] | |
| ==> default: Ign http://archive.ubuntu.com trusty-updates InRelease | |
| ==> default: Hit http://archive.ubuntu.com trusty Release.gpg | |
| ==> default: Get:2 http://security.ubuntu.com trusty-security Release [59.7 kB] | |
| ==> default: Get:3 http://archive.ubuntu.com trusty-updates Release.gpg [933 B] | |
| ==> default: Hit http://archive.ubuntu.com trusty Release | |
| ==> default: Get:4 http://archive.ubuntu.com trusty-updates Release [59.7 kB] | |
| ==> default: Get:5 http://security.ubuntu.com trusty-security/main Sources [46.3 kB] | |
| ==> default: Get:6 http://security.ubuntu.com trusty-security/universe Sources [10.8 kB] | |
| ==> default: Get:7 http://archive.ubuntu.com trusty/main Sources [1,064 kB] | |
| ==> default: Get:8 http://security.ubuntu.com trusty-security/main amd64 Packages [146 kB] | |
| ==> default: Get:9 http://security.ubuntu.com trusty-security/universe amd64 Packages [49.0 kB] | |
| ==> default: Get:10 http://security.ubuntu.com trusty-security/main Translation-en [70.7 kB] | |
| ==> default: Get:11 http://security.ubuntu.com trusty-security/universe Translation-en [28.7 kB] | |
| ==> default: Get:12 http://archive.ubuntu.com trusty/universe Sources [6,399 kB] | |
| ==> default: Hit http://archive.ubuntu.com trusty/main amd64 Packages | |
| ==> default: Hit http://archive.ubuntu.com trusty/universe amd64 Packages | |
| ==> default: Hit http://archive.ubuntu.com trusty/main Translation-en | |
| ==> default: Hit http://archive.ubuntu.com trusty/universe Translation-en | |
| ==> default: Get:13 http://archive.ubuntu.com trusty-updates/main Sources [125 kB] | |
| ==> default: Get:14 http://archive.ubuntu.com trusty-updates/universe Sources [86.2 kB] | |
| ==> default: Get:15 http://archive.ubuntu.com trusty-updates/main amd64 Packages [337 kB] | |
| ==> default: Get:16 http://archive.ubuntu.com trusty-updates/universe amd64 Packages [208 kB] | |
| ==> default: Get:17 http://archive.ubuntu.com trusty-updates/main Translation-en [150 kB] | |
| ==> default: Get:18 http://archive.ubuntu.com trusty-updates/universe Translation-en [105 kB] | |
| ==> default: Ign http://archive.ubuntu.com trusty/main Translation-en_US | |
| ==> default: Ign http://archive.ubuntu.com trusty/universe Translation-en_US | |
| ==> default: Fetched 8,947 kB in 13s (675 kB/s) | |
| ==> default: Reading package lists... | |
| ==> default: Reading package lists... | |
| ==> default: Building dependency tree... | |
| ==> default: Reading state information... | |
| ==> default: wget is already the newest version. | |
| ==> default: curl is already the newest version. | |
| ==> default: The following extra packages will be installed: | |
| ==> default: dpkg-dev g++ g++-4.8 git-man libalgorithm-diff-perl | |
| ==> default: libalgorithm-diff-xs-perl libalgorithm-merge-perl libdpkg-perl liberror-perl | |
| ==> default: libfile-fcntllock-perl libstdc++-4.8-dev | |
| ==> default: Suggested packages: | |
| ==> default: debian-keyring g++-multilib g++-4.8-multilib gcc-4.8-doc libstdc++6-4.8-dbg | |
| ==> default: git-daemon-run git-daemon-sysvinit git-doc git-el git-email git-gui gitk | |
| ==> default: gitweb git-arch git-bzr git-cvs git-mediawiki git-svn libstdc++-4.8-doc | |
| ==> default: The following NEW packages will be installed: | |
| ==> default: build-essential dpkg-dev g++ g++-4.8 git git-man libalgorithm-diff-perl | |
| ==> default: libalgorithm-diff-xs-perl libalgorithm-merge-perl libdpkg-perl liberror-perl | |
| ==> default: libfile-fcntllock-perl libstdc++-4.8-dev python-setuptools zlib1g-dev | |
| ==> default: 0 upgraded, 15 newly installed, 0 to remove and 28 not upgraded. | |
| ==> default: Need to get 12.8 MB of archives. | |
| ==> default: After this operation, 56.2 MB of additional disk space will be used. | |
| ==> default: Get:1 http://archive.ubuntu.com/ubuntu/ trusty/main libstdc++-4.8-dev amd64 4.8.2-19ubuntu1 [1,050 kB] | |
| ==> default: Get:2 http://archive.ubuntu.com/ubuntu/ trusty/main g++-4.8 amd64 4.8.2-19ubuntu1 [7,038 kB] | |
| ==> default: Get:3 http://archive.ubuntu.com/ubuntu/ trusty/main g++ amd64 4:4.8.2-1ubuntu6 [1,490 B] | |
| ==> default: Get:4 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libdpkg-perl all 1.17.5ubuntu5.3 [179 kB] | |
| ==> default: Get:5 http://archive.ubuntu.com/ubuntu/ trusty-updates/main dpkg-dev all 1.17.5ubuntu5.3 [726 kB] | |
| ==> default: Get:6 http://archive.ubuntu.com/ubuntu/ trusty/main build-essential amd64 11.6ubuntu6 [4,838 B] | |
| ==> default: Get:7 http://archive.ubuntu.com/ubuntu/ trusty/main liberror-perl all 0.17-1.1 [21.1 kB] | |
| ==> default: Get:8 http://archive.ubuntu.com/ubuntu/ trusty/main git-man all 1:1.9.1-1 [698 kB] | |
| ==> default: Get:9 http://archive.ubuntu.com/ubuntu/ trusty/main git amd64 1:1.9.1-1 [2,555 kB] | |
| ==> default: Get:10 http://archive.ubuntu.com/ubuntu/ trusty/main libalgorithm-diff-perl all 1.19.02-3 [50.0 kB] | |
| ==> default: Get:11 http://archive.ubuntu.com/ubuntu/ trusty/main libalgorithm-diff-xs-perl amd64 0.04-2build4 [12.6 kB] | |
| ==> default: Get:12 http://archive.ubuntu.com/ubuntu/ trusty/main libalgorithm-merge-perl all 0.08-2 [12.7 kB] | |
| ==> default: Get:13 http://archive.ubuntu.com/ubuntu/ trusty/main libfile-fcntllock-perl amd64 0.14-2build1 [15.9 kB] | |
| ==> default: Get:14 http://archive.ubuntu.com/ubuntu/ trusty/main python-setuptools all 3.3-1ubuntu1 [230 kB] | |
| ==> default: Get:15 http://archive.ubuntu.com/ubuntu/ trusty/main zlib1g-dev amd64 1:1.2.8.dfsg-1ubuntu1 [183 kB] | |
| ==> default: dpkg-preconfigure: unable to re-open stdin: No such file or directory | |
| ==> default: Fetched 12.8 MB in 14s (884 kB/s) | |
| ==> default: Selecting previously unselected package libstdc++-4.8-dev:amd64. | |
| ==> default: (Reading database ... 60931 files and directories currently installed.) | |
| ==> default: Preparing to unpack .../libstdc++-4.8-dev_4.8.2-19ubuntu1_amd64.deb ... | |
| ==> default: Unpacking libstdc++-4.8-dev:amd64 (4.8.2-19ubuntu1) ... | |
| ==> default: Selecting previously unselected package g++-4.8. | |
| ==> default: Preparing to unpack .../g++-4.8_4.8.2-19ubuntu1_amd64.deb ... | |
| ==> default: Unpacking g++-4.8 (4.8.2-19ubuntu1) ... | |
| ==> default: Selecting previously unselected package g++. | |
| ==> default: Preparing to unpack .../g++_4%3a4.8.2-1ubuntu6_amd64.deb ... | |
| ==> default: Unpacking g++ (4:4.8.2-1ubuntu6) ... | |
| ==> default: Selecting previously unselected package libdpkg-perl. | |
| ==> default: Preparing to unpack .../libdpkg-perl_1.17.5ubuntu5.3_all.deb ... | |
| ==> default: Unpacking libdpkg-perl (1.17.5ubuntu5.3) ... | |
| ==> default: Selecting previously unselected package dpkg-dev. | |
| ==> default: Preparing to unpack .../dpkg-dev_1.17.5ubuntu5.3_all.deb ... | |
| ==> default: Unpacking dpkg-dev (1.17.5ubuntu5.3) ... | |
| ==> default: Selecting previously unselected package build-essential. | |
| ==> default: Preparing to unpack .../build-essential_11.6ubuntu6_amd64.deb ... | |
| ==> default: Unpacking build-essential (11.6ubuntu6) ... | |
| ==> default: Selecting previously unselected package liberror-perl. | |
| ==> default: Preparing to unpack .../liberror-perl_0.17-1.1_all.deb ... | |
| ==> default: Unpacking liberror-perl (0.17-1.1) ... | |
| ==> default: Selecting previously unselected package git-man. | |
| ==> default: Preparing to unpack .../git-man_1%3a1.9.1-1_all.deb ... | |
| ==> default: Unpacking git-man (1:1.9.1-1) ... | |
| ==> default: Selecting previously unselected package git. | |
| ==> default: Preparing to unpack .../git_1%3a1.9.1-1_amd64.deb ... | |
| ==> default: Unpacking git (1:1.9.1-1) ... | |
| ==> default: Selecting previously unselected package libalgorithm-diff-perl. | |
| ==> default: Preparing to unpack .../libalgorithm-diff-perl_1.19.02-3_all.deb ... | |
| ==> default: Unpacking libalgorithm-diff-perl (1.19.02-3) ... | |
| ==> default: Selecting previously unselected package libalgorithm-diff-xs-perl. | |
| ==> default: Preparing to unpack .../libalgorithm-diff-xs-perl_0.04-2build4_amd64.deb ... | |
| ==> default: Unpacking libalgorithm-diff-xs-perl (0.04-2build4) ... | |
| ==> default: Selecting previously unselected package libalgorithm-merge-perl. | |
| ==> default: Preparing to unpack .../libalgorithm-merge-perl_0.08-2_all.deb ... | |
| ==> default: Unpacking libalgorithm-merge-perl (0.08-2) ... | |
| ==> default: Selecting previously unselected package libfile-fcntllock-perl. | |
| ==> default: Preparing to unpack .../libfile-fcntllock-perl_0.14-2build1_amd64.deb ... | |
| ==> default: Unpacking libfile-fcntllock-perl (0.14-2build1) ... | |
| ==> default: Selecting previously unselected package python-setuptools. | |
| ==> default: Preparing to unpack .../python-setuptools_3.3-1ubuntu1_all.deb ... | |
| ==> default: Unpacking python-setuptools (3.3-1ubuntu1) ... | |
| ==> default: Selecting previously unselected package zlib1g-dev:amd64. | |
| ==> default: Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-1ubuntu1_amd64.deb ... | |
| ==> default: Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-1ubuntu1) ... | |
| ==> default: Processing triggers for man-db (2.6.7.1-1) ... | |
| ==> default: Setting up libstdc++-4.8-dev:amd64 (4.8.2-19ubuntu1) ... | |
| ==> default: Setting up g++-4.8 (4.8.2-19ubuntu1) ... | |
| ==> default: Setting up g++ (4:4.8.2-1ubuntu6) ... | |
| ==> default: update-alternatives: | |
| ==> default: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode | |
| ==> default: Setting up libdpkg-perl (1.17.5ubuntu5.3) ... | |
| ==> default: Setting up dpkg-dev (1.17.5ubuntu5.3) ... | |
| ==> default: Setting up build-essential (11.6ubuntu6) ... | |
| ==> default: Setting up liberror-perl (0.17-1.1) ... | |
| ==> default: Setting up git-man (1:1.9.1-1) ... | |
| ==> default: Setting up git (1:1.9.1-1) ... | |
| ==> default: Setting up libalgorithm-diff-perl (1.19.02-3) ... | |
| ==> default: Setting up libalgorithm-diff-xs-perl (0.04-2build4) ... | |
| ==> default: Setting up libalgorithm-merge-perl (0.08-2) ... | |
| ==> default: Setting up libfile-fcntllock-perl (0.14-2build1) ... | |
| ==> default: Setting up python-setuptools (3.3-1ubuntu1) ... | |
| ==> default: Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-1ubuntu1) ... | |
| ==> default: --2014-10-02 22:46:22-- https://raw.github.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py | |
| ==> default: Resolving raw.github.com (raw.github.com)... | |
| ==> default: 199.27.79.133 | |
| ==> default: Connecting to raw.github.com (raw.github.com)|199.27.79.133|:443... | |
| ==> default: connected. | |
| ==> default: HTTP request sent, awaiting response... | |
| ==> default: 301 Moved Permanently | |
| ==> default: Location: https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py [following] | |
| ==> default: --2014-10-02 22:46:28-- https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py | |
| ==> default: Resolving raw.githubusercontent.com (raw.githubusercontent.com)... | |
| ==> default: 199.27.79.133 | |
| ==> default: Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|199.27.79.133|:443... | |
| ==> default: connected. | |
| ==> default: HTTP request sent, awaiting response... | |
| ==> default: 200 OK | |
| ==> default: Length: | |
| ==> default: 11954 | |
| ==> default: (12K) | |
| ==> default: [text/plain] | |
| ==> default: Saving to: ‘bcbio_nextgen_install.py’ | |
| ==> default: | |
| ==> default: 0K | |
| ==> default: | |
| ==> default: . | |
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| ==> default: 100% 6.90M=0.002s | |
| ==> default: | |
| ==> default: 2014-10-02 22:46:28 (6.90 MB/s) - ‘bcbio_nextgen_install.py’ saved [11954/11954] | |
| Your VM is all set up. You can connect to the VM by typing 'vagrant ssh'. | |
| You can complete the setup by doing the following: | |
| vagrant ssh | |
| cd tmp | |
| python bcbio_nextgen_install.py /usr/local/share/bcbio-nextgen --tooldir=/usr/local --genomes GRCh37 --aligners bwa --sudo | |
| You might have to answer a few questions during the install process, but other | |
| than that it should be all set! | |
| christophes-pro:bcbio pfaucon$ vagrant ssh | |
| /Applications/Vagrant/bin/../embedded/gems/gems/vagrant-1.6.5/lib/vagrant/pre-rubygems.rb:31: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| /Applications/Vagrant/embedded/gems/gems/bundler-1.6.6/lib/bundler/runtime.rb:222: warning: Insecure world writable dir /Users/pfaucon/bin/FDK in PATH, mode 040777 | |
| Welcome to Ubuntu 14.04.1 LTS (GNU/Linux 3.13.0-35-generic x86_64) | |
| * Documentation: https://help.ubuntu.com/ | |
| System information as of Thu Oct 2 22:45:45 UTC 2014 | |
| System load: 0.23 Processes: 87 | |
| Usage of /: 2.7% of 39.34GB Users logged in: 0 | |
| Memory usage: 15% IP address for eth0: 10.0.2.15 | |
| Swap usage: 0% | |
| Graph this data and manage this system at: | |
| https://landscape.canonical.com/ | |
| Get cloud support with Ubuntu Advantage Cloud Guest: | |
| http://www.ubuntu.com/business/services/cloud | |
| 0 packages can be updated. | |
| 0 updates are security updates. | |
| vagrant@vagrant-ubuntu-trusty-64:~$ python bcbio_nextgen_install.py /usr/local/share/bcbio-nextgen --tooldir=/usr/local --genomes hg19 --aligners bwa --sudo | |
| python: can't open file 'bcbio_nextgen_install.py': [Errno 2] No such file or directory | |
| vagrant@vagrant-ubuntu-trusty-64:~$ cd tmp | |
| vagrant@vagrant-ubuntu-trusty-64:~/tmp$ python bcbio_nextgen_install.py /usr/local/share/bcbio-nextgen --tooldir=/usr/local --genomes hg19 --aligners bwa --sudo | |
| Checking required dependencies | |
| git version 1.9.1 | |
| Installing isolated base python installation | |
| --2014-10-02 22:50:08-- http://repo.continuum.io/miniconda/Miniconda-3.5.5-Linux-x86_64.sh | |
| Resolving repo.continuum.io (repo.continuum.io)... 54.231.0.60 | |
| Connecting to repo.continuum.io (repo.continuum.io)|54.231.0.60|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 20736312 (20M) [application/x-sh] | |
| Saving to: ‘Miniconda-3.5.5-Linux-x86_64.sh’ | |
| 100%[========================================================================================================================>] 20,736,312 2.81MB/s in 9.8s | |
| 2014-10-02 22:50:23 (2.02 MB/s) - ‘Miniconda-3.5.5-Linux-x86_64.sh’ saved [20736312/20736312] | |
| PREFIX=/usr/local/share/bcbio-nextgen/anaconda | |
| installing: python-2.7.7-0 ... | |
| installing: openssl-1.0.1h-0 ... | |
| installing: pycosat-0.6.1-py27_0 ... | |
| installing: pyyaml-3.11-py27_0 ... | |
| installing: readline-6.2-2 ... | |
| installing: requests-2.3.0-py27_0 ... | |
| installing: sqlite-3.8.4.1-0 ... | |
| installing: system-5.8-1 ... | |
| installing: tk-8.5.15-0 ... | |
| installing: yaml-0.1.4-0 ... | |
| installing: zlib-1.2.7-0 ... | |
| installing: conda-3.5.5-py27_0 ... | |
| Python 2.7.7 :: Continuum Analytics, Inc. | |
| creating default environment... | |
| installation finished. | |
| Installing bcbio-nextgen | |
| Fetching package metadata: .. | |
| Solving package specifications: . | |
| Package plan for installation in environment /usr/local/share/bcbio-nextgen/anaconda: | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| conda-3.7.0 | py27_0 154 KB | |
| numpy-1.9.0 | py27_0 7.7 MB | |
| openssl-1.0.1h | 1 2.5 MB | |
| python-2.7.8 | 1 11.9 MB | |
| requests-2.4.1 | py27_0 577 KB | |
| ------------------------------------------------------------ | |
| Total: 22.8 MB | |
| The following packages will be UN-linked: | |
| package | build | |
| ---------------------------|----------------- | |
| conda-3.5.5 | py27_0 | |
| openssl-1.0.1h | 0 | |
| python-2.7.7 | 0 | |
| requests-2.3.0 | py27_0 | |
| The following packages will be linked: | |
| package | build | |
| ---------------------------|----------------- | |
| conda-3.7.0 | py27_0 hard-link | |
| numpy-1.9.0 | py27_0 hard-link | |
| openssl-1.0.1h | 1 hard-link | |
| python-2.7.8 | 1 hard-link | |
| requests-2.4.1 | py27_0 hard-link | |
| Fetching packages ... | |
| conda-3.7.0-py 100% |##################################################################################################################| Time: 0:00:00 414.42 kB/s | |
| numpy-1.9.0-py 100% |##################################################################################################################| Time: 0:00:03 2.03 MB/s | |
| openssl-1.0.1h 100% |##################################################################################################################| Time: 0:00:02 1.19 MB/s | |
| python-2.7.8-1 100% |##################################################################################################################| Time: 0:00:03 3.80 MB/s | |
| requests-2.4.1 100% |##################################################################################################################| Time: 0:00:00 898.69 kB/s | |
| Extracting packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Unlinking packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Linking packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Fetching package metadata: ... | |
| Solving package specifications: ............... | |
| Package plan for installation in environment /usr/local/share/bcbio-nextgen/anaconda: | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| biopython-1.64 | np18py27_0 2.1 MB | |
| boto-2.32.1 | py27_0 1.2 MB | |
| bx-python-0.7.2 | np18py27_1 1.7 MB | |
| cairo-1.12.2 | 2 568 KB | |
| cpat-1.2.1 | np18py27_1 2.1 MB | |
| cython-0.21 | py27_0 5.0 MB | |
| dateutil-2.1 | py27_2 227 KB | |
| freetype-2.4.10 | 0 2.0 MB | |
| ipython-2.2.0 | py27_0 2.8 MB | |
| libpng-1.5.13 | 1 152 KB | |
| libsodium-0.4.5 | 0 529 KB | |
| libxml2-2.9.0 | 0 3.9 MB | |
| libxslt-1.1.28 | 0 1.1 MB | |
| lxml-3.4.0 | py27_0 2.7 MB | |
| matplotlib-1.4.0 | np18py27_0 44.7 MB | |
| msgpack-python-0.4.1 | py27_0 203 KB | |
| nose-1.3.4 | py27_0 189 KB | |
| numpy-1.8.2 | py27_0 7.3 MB | |
| pandas-0.14.1 | np18py27_0 9.0 MB | |
| patsy-0.2.1 | np18py27_0 221 KB | |
| pip-1.5.6 | py27_0 1.3 MB | |
| pixman-0.26.2 | 0 1.9 MB | |
| py2cairo-1.10.0 | py27_1 36 KB | |
| pycrypto-2.6.1 | py27_0 443 KB | |
| pyparsing-2.0.1 | py27_0 62 KB | |
| pyqt-4.10.4 | py27_0 4.4 MB | |
| pysam-0.8.0 | py27_0 4.8 MB | |
| pytz-2014.7 | py27_0 175 KB | |
| pyvcf-0.6.7 | py27_0 50 KB | |
| pyzmq-14.3.1 | py27_0 585 KB | |
| qt-4.8.5 | 0 32.8 MB | |
| reportlab-3.1.8 | py27_0 2.2 MB | |
| scipy-0.14.0 | np18py27_0 29.6 MB | |
| setuptools-5.8 | py27_0 426 KB | |
| sip-4.15.5 | py27_0 243 KB | |
| six-1.8.0 | py27_0 15 KB | |
| sqlalchemy-0.9.7 | py27_0 1.2 MB | |
| ssl_match_hostname-3.4.0.2 | py27_0 6 KB | |
| statsmodels-0.5.0 | np18py27_0 5.7 MB | |
| toolz-0.7.0 | py27_9 110 KB | |
| tornado-4.0.2 | py27_0 456 KB | |
| zeromq-4.0.4 | 0 2.4 MB | |
| ------------------------------------------------------------ | |
| Total: 176.6 MB | |
| The following NEW packages will be INSTALLED: | |
| biopython: 1.64-np18py27_0 | |
| boto: 2.32.1-py27_0 | |
| bx-python: 0.7.2-np18py27_1 | |
| cairo: 1.12.2-2 | |
| cpat: 1.2.1-np18py27_1 | |
| cython: 0.21-py27_0 | |
| dateutil: 2.1-py27_2 | |
| freetype: 2.4.10-0 | |
| ipython: 2.2.0-py27_0 | |
| libpng: 1.5.13-1 | |
| libsodium: 0.4.5-0 | |
| libxml2: 2.9.0-0 | |
| libxslt: 1.1.28-0 | |
| lxml: 3.4.0-py27_0 | |
| matplotlib: 1.4.0-np18py27_0 | |
| msgpack-python: 0.4.1-py27_0 | |
| nose: 1.3.4-py27_0 | |
| pandas: 0.14.1-np18py27_0 | |
| patsy: 0.2.1-np18py27_0 | |
| pip: 1.5.6-py27_0 | |
| pixman: 0.26.2-0 | |
| py2cairo: 1.10.0-py27_1 | |
| pycrypto: 2.6.1-py27_0 | |
| pyparsing: 2.0.1-py27_0 | |
| pyqt: 4.10.4-py27_0 | |
| pysam: 0.8.0-py27_0 | |
| pytz: 2014.7-py27_0 | |
| pyvcf: 0.6.7-py27_0 | |
| pyzmq: 14.3.1-py27_0 | |
| qt: 4.8.5-0 | |
| reportlab: 3.1.8-py27_0 | |
| scipy: 0.14.0-np18py27_0 | |
| setuptools: 5.8-py27_0 | |
| sip: 4.15.5-py27_0 | |
| six: 1.8.0-py27_0 | |
| sqlalchemy: 0.9.7-py27_0 | |
| ssl_match_hostname: 3.4.0.2-py27_0 | |
| statsmodels: 0.5.0-np18py27_0 | |
| toolz: 0.7.0-py27_9 | |
| tornado: 4.0.2-py27_0 | |
| zeromq: 4.0.4-0 | |
| The following packages will be DOWNGRADED: | |
| numpy: 1.9.0-py27_0 --> 1.8.2-py27_0 | |
| Fetching packages ... | |
| biopython-1.64 100% |##################################################################################################################| Time: 0:00:01 2.21 MB/s | |
| boto-2.32.1-py 100% |##################################################################################################################| Time: 0:00:01 647.47 kB/s | |
| bx-python-0.7. 100% |##################################################################################################################| Time: 0:00:00 2.02 MB/s | |
| cairo-1.12.2-2 100% |##################################################################################################################| Time: 0:00:00 885.35 kB/s | |
| cpat-1.2.1-np1 100% |##################################################################################################################| Time: 0:00:00 2.30 MB/s | |
| cython-0.21-py 100% |##################################################################################################################| Time: 0:00:03 1.37 MB/s | |
| dateutil-2.1-p 100% |##################################################################################################################| Time: 0:00:01 179.08 kB/s | |
| freetype-2.4.1 100% |##################################################################################################################| Time: 0:00:01 2.07 MB/s | |
| ipython-2.2.0- 100% |##################################################################################################################| Time: 0:00:01 2.80 MB/s | |
| libpng-1.5.13- 100% |##################################################################################################################| Time: 0:00:00 409.93 kB/s | |
| libsodium-0.4. 100% |##################################################################################################################| Time: 0:00:00 798.49 kB/s | |
| libxml2-2.9.0- 100% |##################################################################################################################| Time: 0:00:04 869.78 kB/s | |
| libxslt-1.1.28 100% |##################################################################################################################| Time: 0:00:00 1.26 MB/s | |
| lxml-3.4.0-py2 100% |##################################################################################################################| Time: 0:00:02 1.04 MB/s | |
| matplotlib-1.4 100% |##################################################################################################################| Time: 0:00:11 4.06 MB/s | |
| msgpack-python 100% |##################################################################################################################| Time: 0:00:00 548.22 kB/s | |
| nose-1.3.4-py2 100% |##################################################################################################################| Time: 0:00:00 522.00 kB/s | |
| numpy-1.8.2-py 100% |##################################################################################################################| Time: 0:00:02 3.58 MB/s | |
| pandas-0.14.1- 100% |##################################################################################################################| Time: 0:00:05 1.68 MB/s | |
| patsy-0.2.1-np 100% |##################################################################################################################| Time: 0:00:01 201.71 kB/s | |
| pip-1.5.6-py27 100% |##################################################################################################################| Time: 0:00:02 589.46 kB/s | |
| pixman-0.26.2- 100% |##################################################################################################################| Time: 0:00:01 1.30 MB/s | |
| py2cairo-1.10. 100% |##################################################################################################################| Time: 0:00:00 201.56 kB/s | |
| pycrypto-2.6.1 100% |##################################################################################################################| Time: 0:00:02 204.62 kB/s | |
| pyparsing-2.0. 100% |##################################################################################################################| Time: 0:00:00 113.84 kB/s | |
| pyqt-4.10.4-py 100% |##################################################################################################################| Time: 0:00:01 3.05 MB/s | |
| pysam-0.8.0-py 100% |##################################################################################################################| Time: 0:00:03 1.49 MB/s | |
| pytz-2014.7-py 100% |##################################################################################################################| Time: 0:00:00 468.27 kB/s | |
| pyvcf-0.6.7-py 100% |##################################################################################################################| Time: 0:00:00 273.79 kB/s | |
| pyzmq-14.3.1-p 100% |##################################################################################################################| Time: 0:00:02 210.12 kB/s | |
| qt-4.8.5-0.tar 100% |##################################################################################################################| Time: 0:00:10 3.24 MB/s | |
| reportlab-3.1. 100% |##################################################################################################################| Time: 0:00:01 1.18 MB/s | |
| scipy-0.14.0-n 100% |##################################################################################################################| Time: 0:00:10 3.03 MB/s | |
| setuptools-5.8 100% |##################################################################################################################| Time: 0:00:00 649.99 kB/s | |
| sip-4.15.5-py2 100% |##################################################################################################################| Time: 0:00:00 431.81 kB/s | |
| six-1.8.0-py27 100% |##################################################################################################################| Time: 0:00:00 57.12 kB/s | |
| sqlalchemy-0.9 100% |##################################################################################################################| Time: 0:00:00 1.24 MB/s | |
| ssl_match_host 100% |##################################################################################################################| Time: 0:00:00 13.43 MB/s | |
| statsmodels-0. 100% |##################################################################################################################| Time: 0:00:02 2.34 MB/s | |
| toolz-0.7.0-py 100% |##################################################################################################################| Time: 0:00:00 398.61 kB/s | |
| tornado-4.0.2- 100% |##################################################################################################################| Time: 0:00:01 314.69 kB/s | |
| zeromq-4.0.4-0 100% |##################################################################################################################| Time: 0:00:01 1.26 MB/s | |
| Extracting packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Unlinking packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Linking packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Downloading/unpacking fabric | |
| Downloading Fabric-1.10.0.tar.gz (208kB): 208kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/fabric/setup.py) egg_info for package fabric | |
| warning: no previously-included files matching '*' found under directory 'sites/docs/_build' | |
| warning: no previously-included files matching '*' found under directory 'sites/www/_build' | |
| warning: no previously-included files matching '*.pyc' found under directory 'tests' | |
| warning: no previously-included files matching '*.pyo' found under directory 'tests' | |
| Downloading/unpacking paramiko>=1.10 (from fabric) | |
| Downloading paramiko-1.15.1-py2.py3-none-any.whl (165kB): 165kB downloaded | |
| Requirement already satisfied (use --upgrade to upgrade): pycrypto>=2.1,!=2.4 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from paramiko>=1.10->fabric) | |
| Downloading/unpacking ecdsa>=0.11 (from paramiko>=1.10->fabric) | |
| Downloading ecdsa-0.11.tar.gz (45kB): 45kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/ecdsa/setup.py) egg_info for package ecdsa | |
| Installing collected packages: fabric, paramiko, ecdsa | |
| Running setup.py install for fabric | |
| warning: no previously-included files matching '*' found under directory 'sites/docs/_build' | |
| warning: no previously-included files matching '*' found under directory 'sites/www/_build' | |
| warning: no previously-included files matching '*.pyc' found under directory 'tests' | |
| warning: no previously-included files matching '*.pyo' found under directory 'tests' | |
| Installing fab script to /usr/local/share/bcbio-nextgen/anaconda/bin | |
| Running setup.py install for ecdsa | |
| Successfully installed fabric paramiko ecdsa | |
| Cleaning up... | |
| Requirement already satisfied (use --upgrade to upgrade): biopython>=1.61 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 1)) | |
| Requirement already satisfied (use --upgrade to upgrade): boto>=2.9.6 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 2)) | |
| Requirement already satisfied (use --upgrade to upgrade): Cython>=0.19 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 3)) | |
| Requirement already satisfied (use --upgrade to upgrade): ipython>=2.0.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 4)) | |
| Downloading/unpacking ipython-cluster-helper>=0.3.3 (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 5)) | |
| Downloading ipython-cluster-helper-0.3.3.tar.gz | |
| Running setup.py (path:/tmp/pip_build_vagrant/ipython-cluster-helper/setup.py) egg_info for package ipython-cluster-helper | |
| Downloading/unpacking Logbook>=0.6.0 (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 6)) | |
| Downloading Logbook-0.7.0.tar.gz (147kB): 147kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/Logbook/setup.py) egg_info for package Logbook | |
| warning: no files found matching 'logbook/_speedups.c' | |
| Requirement already satisfied (use --upgrade to upgrade): lxml>=3.3.5 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 7)) | |
| Requirement already satisfied (use --upgrade to upgrade): nose>=1.3.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 8)) | |
| Requirement already satisfied (use --upgrade to upgrade): pysam>=0.7.7 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 9)) | |
| Requirement already satisfied (use --upgrade to upgrade): pyzmq>=2.2.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 10)) | |
| Requirement already satisfied (use --upgrade to upgrade): PyYAML>=3.10 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 11)) | |
| Requirement already satisfied (use --upgrade to upgrade): toolz>=0.6.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 12)) | |
| Requirement already satisfied (use --upgrade to upgrade): tornado>=3.1.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 13)) | |
| Downloading/unpacking bioblend>=0.4.3 (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 15)) | |
| Downloading bioblend-0.5.1.tar.gz (114kB): 114kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/bioblend/setup.py) egg_info for package bioblend | |
| warning: no previously-included files matching '*.swp' found anywhere in distribution | |
| warning: no previously-included files matching '.gitignore' found anywhere in distribution | |
| Downloading/unpacking cutadapt==1.4.2 (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 16)) | |
| Downloading cutadapt-1.4.2.tar.gz (347kB): 347kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/cutadapt/setup.py) egg_info for package cutadapt | |
| Requirement already satisfied (use --upgrade to upgrade): fabric>=1.7.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 17)) | |
| Downloading/unpacking gffutils>=0.8.1 (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 18)) | |
| Downloading gffutils-0.8.2.tar.gz (1.4MB): 1.4MB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/gffutils/setup.py) egg_info for package gffutils | |
| package init file 'gffutils/scripts/__init__.py' not found (or not a regular file) | |
| warning: no files found matching '*.rst' under directory 'docs/source' | |
| warning: no files found matching '*.py' under directory 'docs/source' | |
| warning: no files found matching '*' under directory 'docs/source/images' | |
| warning: no files found matching '*' under directory 'doc/source/_templates' | |
| warning: no files found matching 'docs/Makefile' | |
| warning: no files found matching 'docs/make.bat' | |
| warning: no files found matching 'gffutils/test/data/t.py' | |
| Downloading/unpacking HTSeq>=0.5.4p5 (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 19)) | |
| Downloading HTSeq-0.6.1p1.tar.gz (226kB): 226kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/HTSeq/setup.py) egg_info for package HTSeq | |
| Downloading/unpacking joblib>=0.7.0d (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 20)) | |
| Downloading joblib-0.8.3_r1-py2.py3-none-any.whl (77kB): 77kB downloaded | |
| Downloading/unpacking openpyxl>=1.6.1,<2.0.0 (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 21)) | |
| Downloading openpyxl-1.8.6-py2.py3-none-any.whl (190kB): 190kB downloaded | |
| Downloading/unpacking prettyplotlib>=0.1.7 (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 22)) | |
| Downloading prettyplotlib-0.1.7.tar.gz (697kB): 697kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/prettyplotlib/setup.py) egg_info for package prettyplotlib | |
| Downloading/unpacking psutil>=1.2.0 (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 23)) | |
| Downloading psutil-2.1.3.tar.gz (224kB): 224kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/psutil/setup.py) egg_info for package psutil | |
| warning: no previously-included files matching '*' found under directory 'docs/_build' | |
| Downloading/unpacking pybedtools>=0.6.2 (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 24)) | |
| Downloading pybedtools-0.6.7.tar.gz (42.2MB): 42.2MB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/pybedtools/setup.py) egg_info for package pybedtools | |
| Requirement already satisfied (use --upgrade to upgrade): PyVCF>=0.6.7 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 25)) | |
| Downloading/unpacking sh>=1.07 (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 26)) | |
| Downloading sh-1.09.tar.gz | |
| Running setup.py (path:/tmp/pip_build_vagrant/sh/setup.py) egg_info for package sh | |
| Downloading/unpacking arvados-python-client>=0.1.1405019228.4a7ca04 (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 27)) | |
| Downloading arvados-python-client-0.1.1412281922.89e7c75.tar.gz (62kB): 62kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/arvados-python-client/setup.py) egg_info for package arvados-python-client | |
| fatal: Not a git repository (or any of the parent directories): .git | |
| Downloading/unpacking chanjo>=2.0.2 (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 28)) | |
| Downloading chanjo-2.1.2-py2.py3-none-any.whl (49kB): 49kB downloaded | |
| Requirement already satisfied (use --upgrade to upgrade): msgpack-python>=0.4.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 29)) | |
| Downloading/unpacking bcbio-nextgen==0.8.2 (from -r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 30)) | |
| Downloading bcbio-nextgen-0.8.2.tar.gz (266kB): 266kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/bcbio-nextgen/setup.py) egg_info for package bcbio-nextgen | |
| fatal: Not a git repository (or any of the parent directories): .git | |
| warning: no files found matching 'config/*.ini' | |
| Downloading/unpacking netifaces>=0.10.3 (from ipython-cluster-helper>=0.3.3->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 5)) | |
| Downloading netifaces-0.10.4.tar.gz | |
| Running setup.py (path:/tmp/pip_build_vagrant/netifaces/setup.py) egg_info for package netifaces | |
| Requirement already satisfied (use --upgrade to upgrade): requests>=1.1.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bioblend>=0.4.3->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 15)) | |
| Downloading/unpacking poster (from bioblend>=0.4.3->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 15)) | |
| Downloading poster-0.8.1.tar.gz | |
| Running setup.py (path:/tmp/pip_build_vagrant/poster/setup.py) egg_info for package poster | |
| Requirement already satisfied (use --upgrade to upgrade): paramiko>=1.10 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from fabric>=1.7.0->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 17)) | |
| Requirement already satisfied (use --upgrade to upgrade): six in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from gffutils>=0.8.1->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 18)) | |
| Downloading/unpacking argh (from gffutils>=0.8.1->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 18)) | |
| Downloading argh-0.25.0.tar.gz | |
| Running setup.py (path:/tmp/pip_build_vagrant/argh/setup.py) egg_info for package argh | |
| Downloading/unpacking argcomplete (from gffutils>=0.8.1->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 18)) | |
| Downloading argcomplete-0.8.1.tar.gz | |
| Running setup.py (path:/tmp/pip_build_vagrant/argcomplete/setup.py) egg_info for package argcomplete | |
| Downloading/unpacking simplejson (from gffutils>=0.8.1->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 18)) | |
| Downloading simplejson-3.6.4.tar.gz (73kB): 73kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/simplejson/setup.py) egg_info for package simplejson | |
| Requirement already satisfied (use --upgrade to upgrade): matplotlib>=1.2.1 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from prettyplotlib>=0.1.7->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 22)) | |
| Downloading/unpacking brewer2mpl>=1.3.1 (from prettyplotlib>=0.1.7->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 22)) | |
| Downloading brewer2mpl-1.4.1-py2.py3-none-any.whl | |
| Downloading/unpacking distribute (from PyVCF>=0.6.7->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 25)) | |
| Downloading distribute-0.7.3.zip (145kB): 145kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/distribute/setup.py) egg_info for package distribute | |
| Downloading/unpacking python-gflags (from arvados-python-client>=0.1.1405019228.4a7ca04->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 27)) | |
| Downloading python-gflags-2.0.tar.gz (65kB): 65kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/python-gflags/setup.py) egg_info for package python-gflags | |
| Downloading/unpacking google-api-python-client (from arvados-python-client>=0.1.1405019228.4a7ca04->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 27)) | |
| Downloading google-api-python-client-1.2.tar.gz (74kB): 74kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/google-api-python-client/setup.py) egg_info for package google-api-python-client | |
| warning: no files found matching '*.json' under directory 'apiclient' | |
| Downloading/unpacking httplib2 (from arvados-python-client>=0.1.1405019228.4a7ca04->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 27)) | |
| Downloading httplib2-0.9.tar.gz (204kB): 204kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/httplib2/setup.py) egg_info for package httplib2 | |
| Downloading/unpacking urllib3 (from arvados-python-client>=0.1.1405019228.4a7ca04->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 27)) | |
| Downloading urllib3-1.9.1.tar.gz (171kB): 171kB downloaded | |
| Running setup.py (path:/tmp/pip_build_vagrant/urllib3/setup.py) egg_info for package urllib3 | |
| warning: no previously-included files matching '*' found under directory 'docs/_build' | |
| Downloading/unpacking ws4py (from arvados-python-client>=0.1.1405019228.4a7ca04->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 27)) | |
| Downloading ws4py-0.3.4.tar.gz | |
| Running setup.py (path:/tmp/pip_build_vagrant/ws4py/setup.py) egg_info for package ws4py | |
| Requirement already satisfied (use --upgrade to upgrade): numpy in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from chanjo>=2.0.2->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 28)) | |
| Downloading/unpacking Click (from chanjo>=2.0.2->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 28)) | |
| Downloading click-3.3-py2.py3-none-any.whl (58kB): 58kB downloaded | |
| Requirement already satisfied (use --upgrade to upgrade): setuptools in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/setuptools-5.8-py2.7.egg (from chanjo>=2.0.2->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 28)) | |
| Requirement already satisfied (use --upgrade to upgrade): sqlalchemy>=0.8.2 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from chanjo>=2.0.2->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 28)) | |
| Downloading/unpacking path.py (from chanjo>=2.0.2->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 28)) | |
| Downloading path.py-6.2.zip | |
| Running setup.py (path:/tmp/pip_build_vagrant/path.py/setup.py) egg_info for package path.py | |
| Downloading/unpacking toml (from chanjo>=2.0.2->-r https://raw.githubusercontent.com/chapmanb/bcbio-nextgen/master/requirements.txt (line 28)) | |
| Downloading toml-0.8.2.tar.gz | |
| Running setup.py (path:/tmp/pip_build_vagrant/toml/setup.py) egg_info for package toml | |
| Installing collected packages: ipython-cluster-helper, Logbook, bioblend, cutadapt, gffutils, HTSeq, joblib, openpyxl, prettyplotlib, psutil, pybedtools, sh, arvados-python-client, chanjo, bcbio-nextgen, netifaces, poster, argh, argcomplete, simplejson, brewer2mpl, python-gflags, google-api-python-client, httplib2, urllib3, ws4py, Click, path.py, toml, distribute | |
| Running setup.py install for ipython-cluster-helper | |
| Running setup.py install for Logbook | |
| warning: no files found matching 'logbook/_speedups.c' | |
| Running setup.py install for bioblend | |
| warning: no previously-included files matching '*.swp' found anywhere in distribution | |
| warning: no previously-included files matching '.gitignore' found anywhere in distribution | |
| Running setup.py install for cutadapt | |
| skipping 'cutadapt/_align.c' Cython extension (up-to-date) | |
| building 'cutadapt._align' extension | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c cutadapt/_align.c -o build/temp.linux-x86_64-2.7/cutadapt/_align.o | |
| gcc -pthread -shared build/temp.linux-x86_64-2.7/cutadapt/_align.o -L/usr/local/share/bcbio-nextgen/anaconda/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/cutadapt/_align.so | |
| skipping 'cutadapt/_qualtrim.c' Cython extension (up-to-date) | |
| building 'cutadapt._qualtrim' extension | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c cutadapt/_qualtrim.c -o build/temp.linux-x86_64-2.7/cutadapt/_qualtrim.o | |
| gcc -pthread -shared build/temp.linux-x86_64-2.7/cutadapt/_qualtrim.o -L/usr/local/share/bcbio-nextgen/anaconda/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/cutadapt/_qualtrim.so | |
| skipping 'cutadapt/_seqio.c' Cython extension (up-to-date) | |
| building 'cutadapt._seqio' extension | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c cutadapt/_seqio.c -o build/temp.linux-x86_64-2.7/cutadapt/_seqio.o | |
| gcc -pthread -shared build/temp.linux-x86_64-2.7/cutadapt/_seqio.o -L/usr/local/share/bcbio-nextgen/anaconda/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/cutadapt/_seqio.so | |
| changing mode of build/scripts-2.7/cutadapt from 664 to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/cutadapt to 775 | |
| Running setup.py install for gffutils | |
| package init file 'gffutils/scripts/__init__.py' not found (or not a regular file) | |
| changing mode of build/scripts-2.7/gffutils-cli from 664 to 775 | |
| warning: no files found matching '*.rst' under directory 'docs/source' | |
| warning: no files found matching '*.py' under directory 'docs/source' | |
| warning: no files found matching '*' under directory 'docs/source/images' | |
| warning: no files found matching '*' under directory 'doc/source/_templates' | |
| warning: no files found matching 'docs/Makefile' | |
| warning: no files found matching 'docs/make.bat' | |
| warning: no files found matching 'gffutils/test/data/t.py' | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/gffutils-cli to 775 | |
| Running setup.py install for HTSeq | |
| building 'HTSeq._HTSeq' extension | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/numpy/core/include -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c src/_HTSeq.c -o build/temp.linux-x86_64-2.7/src/_HTSeq.o -w | |
| gcc -pthread -shared build/temp.linux-x86_64-2.7/src/_HTSeq.o -L/usr/local/share/bcbio-nextgen/anaconda/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/HTSeq/_HTSeq.so | |
| building 'HTSeq._StepVector' extension | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c src/StepVector_wrap.cxx -o build/temp.linux-x86_64-2.7/src/StepVector_wrap.o -w | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| c++ -pthread -shared build/temp.linux-x86_64-2.7/src/StepVector_wrap.o -L/usr/local/share/bcbio-nextgen/anaconda/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/HTSeq/_StepVector.so | |
| changing mode of build/scripts-2.7/htseq-qa from 664 to 775 | |
| changing mode of build/scripts-2.7/htseq-count from 664 to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/htseq-count to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/htseq-qa to 775 | |
| Running setup.py install for prettyplotlib | |
| Running setup.py install for psutil | |
| building '_psutil_linux' extension | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c psutil/_psutil_linux.c -o build/temp.linux-x86_64-2.7/psutil/_psutil_linux.o | |
| gcc -pthread -shared build/temp.linux-x86_64-2.7/psutil/_psutil_linux.o -L/usr/local/share/bcbio-nextgen/anaconda/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/_psutil_linux.so | |
| building '_psutil_posix' extension | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c psutil/_psutil_posix.c -o build/temp.linux-x86_64-2.7/psutil/_psutil_posix.o | |
| gcc -pthread -shared build/temp.linux-x86_64-2.7/psutil/_psutil_posix.o -L/usr/local/share/bcbio-nextgen/anaconda/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/_psutil_posix.so | |
| warning: no previously-included files matching '*' found under directory 'docs/_build' | |
| Running setup.py install for pybedtools | |
| skipping 'pybedtools/cbedtools.cpp' Cython extension (up-to-date) | |
| building 'pybedtools.cbedtools' extension | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc/ -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c pybedtools/cbedtools.cpp -o build/temp.linux-x86_64-2.7/pybedtools/cbedtools.o | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc/ -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c src/fileType.cpp -o build/temp.linux-x86_64-2.7/src/fileType.o | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc/ -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c src/bedFile.cpp -o build/temp.linux-x86_64-2.7/src/bedFile.o | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc/ -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c src/gzstream.cpp -o build/temp.linux-x86_64-2.7/src/gzstream.o | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| c++ -pthread -shared build/temp.linux-x86_64-2.7/pybedtools/cbedtools.o build/temp.linux-x86_64-2.7/src/fileType.o build/temp.linux-x86_64-2.7/src/bedFile.o build/temp.linux-x86_64-2.7/src/gzstream.o -L/usr/local/share/bcbio-nextgen/anaconda/lib -lstdc++ -lz -lpython2.7 -o build/lib.linux-x86_64-2.7/pybedtools/cbedtools.so | |
| skipping 'pybedtools/featurefuncs.cpp' Cython extension (up-to-date) | |
| skipping 'pybedtools/cbedtools.cpp' Cython extension (up-to-date) | |
| building 'pybedtools.featurefuncs' extension | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc/ -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c pybedtools/featurefuncs.cpp -o build/temp.linux-x86_64-2.7/pybedtools/featurefuncs.o | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc/ -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c pybedtools/cbedtools.cpp -o build/temp.linux-x86_64-2.7/pybedtools/cbedtools.o | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc/ -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c src/fileType.cpp -o build/temp.linux-x86_64-2.7/src/fileType.o | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc/ -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c src/bedFile.cpp -o build/temp.linux-x86_64-2.7/src/bedFile.o | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isrc/ -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c src/gzstream.cpp -o build/temp.linux-x86_64-2.7/src/gzstream.o | |
| cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default] | |
| c++ -pthread -shared build/temp.linux-x86_64-2.7/pybedtools/featurefuncs.o build/temp.linux-x86_64-2.7/pybedtools/cbedtools.o build/temp.linux-x86_64-2.7/src/fileType.o build/temp.linux-x86_64-2.7/src/bedFile.o build/temp.linux-x86_64-2.7/src/gzstream.o -L/usr/local/share/bcbio-nextgen/anaconda/lib -lstdc++ -lz -lpython2.7 -o build/lib.linux-x86_64-2.7/pybedtools/featurefuncs.so | |
| cythoning pybedtools/_Window.pyx to pybedtools/_Window.c | |
| building 'pybedtools._Window' extension | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c pybedtools/_Window.c -o build/temp.linux-x86_64-2.7/pybedtools/_Window.o | |
| gcc -pthread -shared build/temp.linux-x86_64-2.7/pybedtools/_Window.o -L/usr/local/share/bcbio-nextgen/anaconda/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/pybedtools/_Window.so | |
| changing mode of build/scripts-2.7/venn_gchart.py from 664 to 775 | |
| changing mode of build/scripts-2.7/venn_mpl.py from 664 to 775 | |
| changing mode of build/scripts-2.7/annotate.py from 664 to 775 | |
| changing mode of build/scripts-2.7/peak_pie.py from 664 to 775 | |
| changing mode of build/scripts-2.7/intersection_matrix.py from 664 to 775 | |
| changing mode of build/scripts-2.7/intron_exon_reads.py from 664 to 775 | |
| changing mode of build/scripts-2.7/pybedtools_demo.py from 664 to 775 | |
| changing mode of build/scripts-2.7/pbt_plotting_example.py from 664 to 775 | |
| changing mode of build/scripts-2.7/pybedtools from 664 to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/peak_pie.py to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/intersection_matrix.py to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/venn_mpl.py to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/annotate.py to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/pbt_plotting_example.py to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/pybedtools to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/venn_gchart.py to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/pybedtools_demo.py to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/intron_exon_reads.py to 775 | |
| Running setup.py install for sh | |
| Running setup.py install for arvados-python-client | |
| fatal: Not a git repository (or any of the parent directories): .git | |
| changing mode of build/scripts-2.7/arv-get from 664 to 775 | |
| changing mode of build/scripts-2.7/arv-keepdocker from 664 to 775 | |
| changing mode of build/scripts-2.7/arv-ls from 664 to 775 | |
| changing mode of build/scripts-2.7/arv-normalize from 664 to 775 | |
| changing mode of build/scripts-2.7/arv-put from 664 to 775 | |
| changing mode of build/scripts-2.7/arv-ws from 664 to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/arv-ws to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/arv-put to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/arv-ls to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/arv-keepdocker to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/arv-normalize to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/arv-get to 775 | |
| Running setup.py install for bcbio-nextgen | |
| fatal: Not a git repository (or any of the parent directories): .git | |
| changing mode of build/scripts-2.7/bcbio_nextgen.py from 664 to 775 | |
| warning: no files found matching 'config/*.ini' | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py to 775 | |
| Running setup.py install for netifaces | |
| checking for getifaddrs...found. | |
| checking for getnameinfo...found. | |
| checking for optional header files...netash/ash.h netatalk/at.h netax25/ax25.h neteconet/ec.h netipx/ipx.h netpacket/packet.h linux/irda.h linux/atm.h linux/llc.h linux/tipc.h linux/dn.h. | |
| checking whether struct sockaddr has a length field...no. | |
| checking which sockaddr_xxx structs are defined...at ax25 in in6 ipx un ash ec ll atmpvc atmsvc dn irda llc. | |
| checking for routing socket support...no. | |
| checking for sysctl(CTL_NET...) support...no. | |
| checking for netlink support...yes. | |
| will use netlink to read routing table | |
| building 'netifaces' extension | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DNETIFACES_VERSION=0.10.4 -DHAVE_GETIFADDRS=1 -DHAVE_GETNAMEINFO=1 -DHAVE_NETASH_ASH_H=1 -DHAVE_NETATALK_AT_H=1 -DHAVE_NETAX25_AX25_H=1 -DHAVE_NETECONET_EC_H=1 -DHAVE_NETIPX_IPX_H=1 -DHAVE_NETPACKET_PACKET_H=1 -DHAVE_LINUX_IRDA_H=1 -DHAVE_LINUX_ATM_H=1 -DHAVE_LINUX_LLC_H=1 -DHAVE_LINUX_TIPC_H=1 -DHAVE_LINUX_DN_H=1 -DHAVE_SOCKADDR_AT=1 -DHAVE_SOCKADDR_AX25=1 -DHAVE_SOCKADDR_IN=1 -DHAVE_SOCKADDR_IN6=1 -DHAVE_SOCKADDR_IPX=1 -DHAVE_SOCKADDR_UN=1 -DHAVE_SOCKADDR_ASH=1 -DHAVE_SOCKADDR_EC=1 -DHAVE_SOCKADDR_LL=1 -DHAVE_SOCKADDR_ATMPVC=1 -DHAVE_SOCKADDR_ATMSVC=1 -DHAVE_SOCKADDR_DN=1 -DHAVE_SOCKADDR_IRDA=1 -DHAVE_SOCKADDR_LLC=1 -DHAVE_PF_NETLINK=1 -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c netifaces.c -o build/temp.linux-x86_64-2.7/netifaces.o | |
| gcc -pthread -shared build/temp.linux-x86_64-2.7/netifaces.o -L/usr/local/share/bcbio-nextgen/anaconda/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/netifaces.so | |
| Running setup.py install for poster | |
| Running setup.py install for argh | |
| Running setup.py install for argcomplete | |
| changing mode of build/scripts-2.7/python-argcomplete-check-easy-install-script from 664 to 775 | |
| changing mode of build/scripts-2.7/activate-global-python-argcomplete from 664 to 775 | |
| changing mode of build/scripts-2.7/register-python-argcomplete from 664 to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/python-argcomplete-check-easy-install-script to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/activate-global-python-argcomplete to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/register-python-argcomplete to 775 | |
| Running setup.py install for simplejson | |
| building 'simplejson._speedups' extension | |
| gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/usr/local/share/bcbio-nextgen/anaconda/include/python2.7 -c simplejson/_speedups.c -o build/temp.linux-x86_64-2.7/simplejson/_speedups.o | |
| gcc -pthread -shared build/temp.linux-x86_64-2.7/simplejson/_speedups.o -L/usr/local/share/bcbio-nextgen/anaconda/lib -lpython2.7 -o build/lib.linux-x86_64-2.7/simplejson/_speedups.so | |
| Running setup.py install for python-gflags | |
| Running setup.py install for google-api-python-client | |
| warning: no files found matching '*.json' under directory 'apiclient' | |
| Running setup.py install for httplib2 | |
| Running setup.py install for urllib3 | |
| warning: no previously-included files matching '*' found under directory 'docs/_build' | |
| Running setup.py install for ws4py | |
| Running setup.py install for path.py | |
| Running setup.py install for toml | |
| Running setup.py install for distribute | |
| Successfully installed ipython-cluster-helper Logbook bioblend cutadapt gffutils HTSeq joblib openpyxl prettyplotlib psutil pybedtools sh arvados-python-client chanjo bcbio-nextgen netifaces poster argh argcomplete simplejson brewer2mpl python-gflags google-api-python-client httplib2 urllib3 ws4py Click path.py toml distribute | |
| Cleaning up... | |
| Installing data and third party dependencies | |
| Upgrading third party tools to latest versions | |
| Cloning into 'cloudbiolinux'... | |
| remote: Counting objects: 10170, done. | |
| remote: Total 10170 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (10170/10170), 7.33 MiB | 2.65 MiB/s, done. | |
| Resolving deltas: 100% (5541/5541), done. | |
| Checking connectivity... done. | |
| Setting up virtual machine | |
| INFO: <cloudbio.flavor.Flavor instance at 0x7ff1f122cbd8> | |
| INFO: This is a ngs_pipeline_minimal flavor | |
| INFO: Reading default fabricrc.txt | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/fabricrc.txt | |
| INFO: Distribution __auto__ | |
| INFO: Get local environment | |
| [localhost] local: cat /etc/*release | grep DISTRIB_CODENAME | cut -f 2 -d = | |
| INFO: Ubuntu setup | |
| DBG [distribution.py]: Debian-shared setup | |
| DBG [distribution.py]: Source=trusty | |
| DBG [distribution.py]: Checking target distribution ubuntu | |
| [localhost] local: cat /proc/version | |
| [localhost] local: cat /etc/*release | grep DISTRIB_CODENAME | cut -f 2 -d = | |
| DBG [distribution.py]: NixPkgs: Ignored | |
| [localhost] local: echo $HOME | |
| [localhost] local: uname -m | |
| INFO: Now, testing connection to host... | |
| INFO: Connection to host appears to work! | |
| DBG [utils.py]: Expand paths | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml | |
| INFO: Meta-package information from /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml | |
| - Packages: minimal,libraries,perl,python,java,r,ruby,bio_nextgen | |
| - Libraries: r-libs | |
| [localhost] local: echo $HOME | |
| /home/vagrant | |
| DBG [deb.py]: _setup_apt_sources /etc/apt/sources.list.d/cloudbiolinux.list | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "touch /etc/apt/sources.list.d/cloudbiolinux.list" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo '# This file was modified for ngs_pipeline_minimal' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\"" | |
| DBG [deb.py]: Source deb http://us.archive.ubuntu.com/ubuntu/ trusty universe | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo 'deb http://us.archive.ubuntu.com/ubuntu/ trusty universe' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\"" | |
| DBG [deb.py]: Source deb http://us.archive.ubuntu.com/ubuntu/ trusty multiverse | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo 'deb http://us.archive.ubuntu.com/ubuntu/ trusty multiverse' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\"" | |
| DBG [deb.py]: Source deb http://us.archive.ubuntu.com/ubuntu/ trusty-updates universe | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo 'deb http://us.archive.ubuntu.com/ubuntu/ trusty-updates universe' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\"" | |
| DBG [deb.py]: Source deb http://us.archive.ubuntu.com/ubuntu/ trusty-updates multiverse | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo 'deb http://us.archive.ubuntu.com/ubuntu/ trusty-updates multiverse' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\"" | |
| DBG [deb.py]: Source deb http://archive.canonical.com/ubuntu trusty partner | |
| DBG [deb.py]: Source deb http://downloads-distro.mongodb.org/repo/ubuntu-upstart dist 10gen | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo 'deb http://downloads-distro.mongodb.org/repo/ubuntu-upstart dist 10gen' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\"" | |
| DBG [deb.py]: Source deb http://cran.fhcrc.org/bin/linux/ubuntu trusty/ | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo 'deb http://cran.fhcrc.org/bin/linux/ubuntu trusty/' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\"" | |
| DBG [deb.py]: Source deb http://archive.cloudera.com/debian maverick-cdh3 contrib | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo 'deb http://archive.cloudera.com/debian maverick-cdh3 contrib' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\"" | |
| DBG [deb.py]: Source deb http://archive.canonical.com/ubuntu trusty partner | |
| DBG [deb.py]: Source deb http://ppa.launchpad.net/freenx-team/ppa/ubuntu precise main | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo 'deb http://ppa.launchpad.net/freenx-team/ppa/ubuntu precise main' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\"" | |
| DBG [deb.py]: Source deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo 'deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\"" | |
| DBG [deb.py]: Source deb [arch=amd64 trusted=yes] http://research.cs.wisc.edu/htcondor/debian/stable/ squeeze contrib | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo 'deb [arch=amd64 trusted=yes] http://research.cs.wisc.edu/htcondor/debian/stable/ squeeze contrib' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\"" | |
| DBG [deb.py]: Source deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo 'deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\"" | |
| DBG [deb.py]: Source deb http://download.virtualbox.org/virtualbox/debian trusty contrib | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo 'deb http://download.virtualbox.org/virtualbox/debian trusty contrib' >> \"$(echo /etc/apt/sources.list.d/cloudbiolinux.list)\"" | |
| [localhost] local: echo 'export DEBIAN_FRONTEND=noninteractive' >> "$(echo ~/.bashrc)" | |
| [localhost] local: sed -i.bak -r -e 's/^([ ]+\*\) return;;)$/#\1/g' "$(echo ~/.bashrc)" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo \"postfix postfix/not_configured boolean true\" | /usr/bin/debconf-set-selections;echo \"postfix postfix/main_mailer_type select 'No configuration'\" | /usr/bin/debconf-set-selections;echo \"mysql-server-5.1 mysql-server/root_password string '(password omitted)'\" | /usr/bin/debconf-set-selections;echo \"mysql-server-5.1 mysql-server/root_password_again string '(password omitted)'\" | /usr/bin/debconf-set-selections;echo \"mysql-server-5.5 mysql-server/root_password string '(password omitted)'\" | /usr/bin/debconf-set-selections;echo \"mysql-server-5.5 mysql-server/root_password_again string '(password omitted)'\" | /usr/bin/debconf-set-selections;echo \"sun-java6-jdk shared/accepted-sun-dlj-v1-1 select true\" | /usr/bin/debconf-set-selections;echo \"sun-java6-jre shared/accepted-sun-dlj-v1-1 select true\" | /usr/bin/debconf-set-selections;echo \"sun-java6-bin shared/accepted-sun-dlj-v1-1 select true\" | /usr/bin/debconf-set-selections;echo \"grub-pc grub2/linux_cmdline string ''\" | /usr/bin/debconf-set-selections;echo \"grub-pc grub-pc/install_devices_empty boolean true\" | /usr/bin/debconf-set-selections;echo \"acroread acroread/default-viewer boolean false\" | /usr/bin/debconf-set-selections;echo \"rabbitmq-server rabbitmq-server/upgrade_previous note\" | /usr/bin/debconf-set-selections;echo \"condor condor/wantdebconf boolean false\" | /usr/bin/debconf-set-selections;echo \"ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula boolean true\" | /usr/bin/debconf-set-selections;echo \"ttf-mscorefonts-installer msttcorefonts/present-mscorefonts-eula note\" | /usr/bin/debconf-set-selections;echo \"gdm shared/default-x-display-manager select gdm\" | /usr/bin/debconf-set-selections;echo \"lightdm shared/default-x-display-manager select gdm\" | /usr/bin/debconf-set-selections;echo \"postfix postfix/mailname string notusedexample.org\" | /usr/bin/debconf-set-selections;echo \"debconf debconf/priority select critical\" | /usr/bin/debconf-set-selections;" | |
| INFO: Update GPG keys for repositories | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "wget -q -O- http://archive.cloudera.com/debian/archive.key | apt-key add -" | |
| OK | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "wget -q -O- http://download.virtualbox.org/virtualbox/debian/oracle_vbox.asc | apt-key add -" | |
| OK | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-key adv --keyserver keyserver.ubuntu.com --recv 7F0CEB10" | |
| Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --homedir /tmp/tmp.WtzQVBApif --no-auto-check-trustdb --trust-model always --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --keyserver keyserver.ubuntu.com --recv 7F0CEB10 | |
| gpg: requesting key 7F0CEB10 from hkp server keyserver.ubuntu.com | |
| gpg: key 7F0CEB10: public key "Richard Kreuter <richard@10gen.com>" imported | |
| gpg: Total number processed: 1 | |
| gpg: imported: 1 (RSA: 1) | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-key adv --keyserver keyserver.ubuntu.com --recv E084DAB9" | |
| Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --homedir /tmp/tmp.3RU1wRqPba --no-auto-check-trustdb --trust-model always --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --keyserver keyserver.ubuntu.com --recv E084DAB9 | |
| gpg: requesting key E084DAB9 from hkp server keyserver.ubuntu.com | |
| gpg: key E084DAB9: public key "Michael Rutter <marutter@gmail.com>" imported | |
| gpg: Total number processed: 1 | |
| gpg: imported: 1 (RSA: 1) | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-key adv --keyserver subkeys.pgp.net --recv D018A4CE" | |
| Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --homedir /tmp/tmp.oLxTP96i5m --no-auto-check-trustdb --trust-model always --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --keyserver subkeys.pgp.net --recv D018A4CE | |
| gpg: requesting key D018A4CE from hkp server subkeys.pgp.net | |
| gpg: keyserver timed out | |
| gpg: keyserver receive failed: keyserver error | |
| Warning: local() encountered an error (return code 2) while executing 'sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-key adv --keyserver subkeys.pgp.net --recv D018A4CE"' | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-key adv --keyserver keyserver.ubuntu.com --recv D67FC6EAE2A11821" | |
| Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --homedir /tmp/tmp.BvaZziNNHc --no-auto-check-trustdb --trust-model always --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --keyserver keyserver.ubuntu.com --recv D67FC6EAE2A11821 | |
| gpg: requesting key E2A11821 from hkp server keyserver.ubuntu.com | |
| gpg: key E2A11821: public key "Vincent Goulet <vincent.goulet@act.ulaval.ca>" imported | |
| gpg: Total number processed: 1 | |
| gpg: imported: 1 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-get update" | |
| Get:1 http://download.virtualbox.org trusty InRelease [5,637 B] | |
| Ign http://cran.fhcrc.org trusty/ InRelease | |
| Ign http://us.archive.ubuntu.com trusty InRelease | |
| Ign http://archive.ubuntu.com trusty InRelease | |
| Ign http://security.ubuntu.com trusty-security InRelease | |
| Ign http://downloads-distro.mongodb.org dist InRelease | |
| Get:2 http://research.cs.wisc.edu squeeze InRelease [1,469 B] | |
| Get:3 http://cran.fhcrc.org trusty/ Release.gpg [490 B] | |
| Ign http://archive.cloudera.com maverick-cdh3 InRelease | |
| Ign http://research.cs.wisc.edu squeeze InRelease | |
| Ign http://us.archive.ubuntu.com trusty-updates InRelease | |
| Ign http://archive.ubuntu.com trusty-updates InRelease | |
| Get:4 http://security.ubuntu.com trusty-security Release.gpg [933 B] | |
| Get:5 http://cran.fhcrc.org trusty/ Release [3,703 B] | |
| Get:6 http://download.virtualbox.org trusty/contrib amd64 Packages [1,322 B] | |
| Get:7 http://us.archive.ubuntu.com trusty Release.gpg [933 B] | |
| Hit http://archive.ubuntu.com trusty Release.gpg | |
| Ign http://ppa.launchpad.net precise InRelease | |
| Get:8 http://archive.cloudera.com maverick-cdh3 Release.gpg [198 B] | |
| Get:9 http://security.ubuntu.com trusty-security Release [59.7 kB] | |
| Get:10 http://cran.fhcrc.org trusty/ Packages [25.4 kB] | |
| Get:11 http://downloads-distro.mongodb.org dist Release.gpg [490 B] | |
| Get:12 http://archive.ubuntu.com trusty-updates Release.gpg [933 B] | |
| Get:13 http://us.archive.ubuntu.com trusty-updates Release.gpg [933 B] | |
| Ign http://nebc.nerc.ac.uk unstable InRelease | |
| Hit http://archive.ubuntu.com trusty Release | |
| Get:14 http://us.archive.ubuntu.com trusty Release [58.5 kB] | |
| Ign http://ppa.launchpad.net precise InRelease | |
| Get:15 http://archive.ubuntu.com trusty-updates Release [59.7 kB] | |
| Get:16 http://downloads-distro.mongodb.org dist Release [2,032 B] | |
| Get:17 http://ppa.launchpad.net precise Release.gpg [316 B] | |
| Get:18 http://security.ubuntu.com trusty-security/main Sources [46.3 kB] | |
| Ign http://download.virtualbox.org trusty/contrib Translation-en_US | |
| Get:19 http://nebc.nerc.ac.uk unstable Release.gpg [198 B] | |
| Ign http://download.virtualbox.org trusty/contrib Translation-en | |
| Get:20 http://downloads-distro.mongodb.org dist/10gen amd64 Packages [22.4 kB] | |
| Get:21 http://us.archive.ubuntu.com trusty-updates Release [59.7 kB] | |
| Get:22 http://ppa.launchpad.net precise Release.gpg [316 B] | |
| Get:23 http://security.ubuntu.com trusty-security/universe Sources [10.8 kB] | |
| Hit http://archive.ubuntu.com trusty/main Sources | |
| Ign http://cran.fhcrc.org trusty/ Translation-en_US | |
| Get:24 http://archive.cloudera.com maverick-cdh3 Release [2,428 B] | |
| Get:25 http://security.ubuntu.com trusty-security/main amd64 Packages [146 kB] | |
| Ign http://cran.fhcrc.org trusty/ Translation-en | |
| Get:26 http://nebc.nerc.ac.uk unstable Release [2,424 B] | |
| Hit http://archive.ubuntu.com trusty/universe Sources | |
| Ign http://nebc.nerc.ac.uk unstable Release | |
| Get:27 http://us.archive.ubuntu.com trusty/universe amd64 Packages [5,859 kB] | |
| Get:28 http://ppa.launchpad.net precise Release [11.9 kB] | |
| Ign http://ppa.launchpad.net precise Release | |
| Get:29 http://archive.cloudera.com maverick-cdh3/contrib amd64 Packages [14.0 kB] | |
| Hit http://archive.ubuntu.com trusty/main amd64 Packages | |
| Hit http://archive.ubuntu.com trusty/universe amd64 Packages | |
| Get:30 http://ppa.launchpad.net precise Release [11.9 kB] | |
| Ign http://ppa.launchpad.net precise Release | |
| Hit http://archive.ubuntu.com trusty/main Translation-en | |
| Get:31 http://security.ubuntu.com trusty-security/universe amd64 Packages [49.0 kB] | |
| Get:32 http://ppa.launchpad.net precise/main amd64 Packages [5,009 B] | |
| Hit http://archive.ubuntu.com trusty/universe Translation-en | |
| Hit http://security.ubuntu.com trusty-security/main Translation-en | |
| Get:33 http://archive.ubuntu.com trusty-updates/main Sources [125 kB] | |
| Hit http://security.ubuntu.com trusty-security/universe Translation-en | |
| Get:34 http://archive.ubuntu.com trusty-updates/universe Sources [86.2 kB] | |
| Get:35 http://ppa.launchpad.net precise/main amd64 Packages [71.8 kB] | |
| Get:36 http://archive.ubuntu.com trusty-updates/main amd64 Packages [337 kB] | |
| Ign http://archive.cloudera.com maverick-cdh3/contrib Translation-en_US | |
| Ign http://archive.cloudera.com maverick-cdh3/contrib Translation-en | |
| Get:37 http://research.cs.wisc.edu squeeze/contrib amd64 Packages [824 B] | |
| Get:38 http://archive.ubuntu.com trusty-updates/universe amd64 Packages [208 kB] | |
| Ign http://downloads-distro.mongodb.org dist/10gen Translation-en_US | |
| Hit http://archive.ubuntu.com trusty-updates/main Translation-en | |
| Ign http://downloads-distro.mongodb.org dist/10gen Translation-en | |
| Ign http://research.cs.wisc.edu squeeze/contrib Translation-en_US | |
| Hit http://archive.ubuntu.com trusty-updates/universe Translation-en | |
| Ign http://research.cs.wisc.edu squeeze/contrib Translation-en | |
| Get:39 http://nebc.nerc.ac.uk unstable/bio-linux amd64 Packages [46.2 kB] | |
| Ign http://archive.ubuntu.com trusty/main Translation-en_US | |
| Ign http://archive.ubuntu.com trusty/universe Translation-en_US | |
| Ign http://nebc.nerc.ac.uk unstable/bio-linux Translation-en_US | |
| Ign http://ppa.launchpad.net precise/main Translation-en_US | |
| Get:40 http://us.archive.ubuntu.com trusty/multiverse amd64 Packages [132 kB] | |
| Ign http://nebc.nerc.ac.uk unstable/bio-linux Translation-en | |
| Ign http://ppa.launchpad.net precise/main Translation-en | |
| Get:41 http://us.archive.ubuntu.com trusty/multiverse Translation-en [102 kB] | |
| Ign http://ppa.launchpad.net precise/main Translation-en_US | |
| Get:42 http://us.archive.ubuntu.com trusty/universe Translation-en [4,089 kB] | |
| Ign http://ppa.launchpad.net precise/main Translation-en | |
| Get:43 http://us.archive.ubuntu.com trusty-updates/universe amd64 Packages [208 kB] | |
| Get:44 http://us.archive.ubuntu.com trusty-updates/multiverse amd64 Packages [9,366 B] | |
| Get:45 http://us.archive.ubuntu.com trusty-updates/multiverse Translation-en [4,719 B] | |
| Get:46 http://us.archive.ubuntu.com trusty-updates/universe Translation-en [105 kB] | |
| Ign http://us.archive.ubuntu.com trusty/multiverse Translation-en_US | |
| Ign http://us.archive.ubuntu.com trusty/universe Translation-en_US | |
| Fetched 12.0 MB in 13s (868 kB/s) | |
| Reading package lists... Done | |
| W: GPG error: http://research.cs.wisc.edu squeeze InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 973FC7D2670079F6 | |
| W: GPG error: http://nebc.nerc.ac.uk unstable Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY B1A598E8128B92BD | |
| W: GPG error: http://ppa.launchpad.net precise Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 2A8E3034D018A4CE | |
| W: GPG error: http://ppa.launchpad.net precise Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 759A8E0E5BA15160 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "sudo apt-get install -y --force-yes bio-linux-keyring" | |
| Reading package lists... Done | |
| Building dependency tree | |
| Reading state information... Done | |
| The following NEW packages will be installed: | |
| bio-linux-keyring | |
| 0 upgraded, 1 newly installed, 0 to remove and 28 not upgraded. | |
| Need to get 8,990 B of archives. | |
| After this operation, 0 B of additional disk space will be used. | |
| WARNING: The following packages cannot be authenticated! | |
| bio-linux-keyring | |
| Get:1 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux bio-linux-keyring all 6 [8,990 B] | |
| Fetched 8,990 B in 5s (1,639 B/s) | |
| Selecting previously unselected package bio-linux-keyring. | |
| (Reading database ... 62971 files and directories currently installed.) | |
| Preparing to unpack .../bio-linux-keyring_6_all.deb ... | |
| Unpacking bio-linux-keyring (6) ... | |
| Setting up bio-linux-keyring (6) ... | |
| OK | |
| OK | |
| OK | |
| OK | |
| OK | |
| OK | |
| INFO: Update the system | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-get update" | |
| Ign http://archive.cloudera.com maverick-cdh3 InRelease | |
| Hit http://download.virtualbox.org trusty InRelease | |
| Ign http://cran.fhcrc.org trusty/ InRelease | |
| Hit http://download.virtualbox.org trusty/contrib amd64 Packages | |
| Hit http://archive.cloudera.com maverick-cdh3 Release.gpg | |
| Hit http://cran.fhcrc.org trusty/ Release.gpg | |
| Hit http://cran.fhcrc.org trusty/ Release | |
| Ign http://downloads-distro.mongodb.org dist InRelease | |
| Get:1 http://research.cs.wisc.edu squeeze InRelease [1,469 B] | |
| Ign http://research.cs.wisc.edu squeeze InRelease | |
| Hit http://cran.fhcrc.org trusty/ Packages | |
| Hit http://archive.cloudera.com maverick-cdh3 Release | |
| Ign http://archive.ubuntu.com trusty InRelease | |
| Ign http://security.ubuntu.com trusty-security InRelease | |
| Ign http://ppa.launchpad.net precise InRelease | |
| Hit http://archive.cloudera.com maverick-cdh3/contrib amd64 Packages | |
| Hit http://downloads-distro.mongodb.org dist Release.gpg | |
| Ign http://archive.ubuntu.com trusty-updates InRelease | |
| Hit http://security.ubuntu.com trusty-security Release.gpg | |
| Ign http://research.cs.wisc.edu squeeze/contrib amd64 Packages/DiffIndex | |
| Ign http://download.virtualbox.org trusty/contrib Translation-en_US | |
| Ign http://ppa.launchpad.net precise InRelease | |
| Ign http://download.virtualbox.org trusty/contrib Translation-en | |
| Ign http://archive.cloudera.com maverick-cdh3/contrib Translation-en_US | |
| Ign http://archive.cloudera.com maverick-cdh3/contrib Translation-en | |
| Hit http://archive.ubuntu.com trusty Release.gpg | |
| Hit http://security.ubuntu.com trusty-security Release | |
| Hit http://downloads-distro.mongodb.org dist Release | |
| Ign http://nebc.nerc.ac.uk unstable InRelease | |
| Get:2 http://ppa.launchpad.net precise Release.gpg [316 B] | |
| Hit http://archive.ubuntu.com trusty-updates Release.gpg | |
| Ign http://cran.fhcrc.org trusty/ Translation-en_US | |
| Hit http://security.ubuntu.com trusty-security/main Sources | |
| Ign http://cran.fhcrc.org trusty/ Translation-en | |
| Hit http://downloads-distro.mongodb.org dist/10gen amd64 Packages | |
| Get:3 http://ppa.launchpad.net precise Release.gpg [316 B] | |
| Hit http://archive.ubuntu.com trusty Release | |
| Get:4 http://nebc.nerc.ac.uk unstable Release.gpg [198 B] | |
| Hit http://security.ubuntu.com trusty-security/universe Sources | |
| Hit http://archive.ubuntu.com trusty-updates Release | |
| Hit http://ppa.launchpad.net precise Release | |
| Ign http://ppa.launchpad.net precise Release | |
| Hit http://security.ubuntu.com trusty-security/main amd64 Packages | |
| Hit http://nebc.nerc.ac.uk unstable Release | |
| Hit http://archive.ubuntu.com trusty/main Sources | |
| Hit http://security.ubuntu.com trusty-security/universe amd64 Packages | |
| Hit http://ppa.launchpad.net precise Release | |
| Hit http://archive.ubuntu.com trusty/universe Sources | |
| Hit http://security.ubuntu.com trusty-security/main Translation-en | |
| Ign http://ppa.launchpad.net precise/main amd64 Packages/DiffIndex | |
| Hit http://nebc.nerc.ac.uk unstable/bio-linux amd64 Packages | |
| Hit http://archive.ubuntu.com trusty/main amd64 Packages | |
| Hit http://security.ubuntu.com trusty-security/universe Translation-en | |
| Hit http://archive.ubuntu.com trusty/universe amd64 Packages | |
| Ign http://us.archive.ubuntu.com trusty InRelease | |
| Hit http://ppa.launchpad.net precise/main amd64 Packages | |
| Hit http://archive.ubuntu.com trusty/main Translation-en | |
| Hit http://archive.ubuntu.com trusty/universe Translation-en | |
| Hit http://archive.ubuntu.com trusty-updates/main Sources | |
| Hit http://ppa.launchpad.net precise/main amd64 Packages | |
| Ign http://us.archive.ubuntu.com trusty-updates InRelease | |
| Hit http://archive.ubuntu.com trusty-updates/universe Sources | |
| Hit http://us.archive.ubuntu.com trusty Release.gpg | |
| Hit http://archive.ubuntu.com trusty-updates/main amd64 Packages | |
| Hit http://us.archive.ubuntu.com trusty-updates Release.gpg | |
| Ign http://downloads-distro.mongodb.org dist/10gen Translation-en_US | |
| Hit http://us.archive.ubuntu.com trusty Release | |
| Hit http://archive.ubuntu.com trusty-updates/universe amd64 Packages | |
| Hit http://us.archive.ubuntu.com trusty-updates Release | |
| Ign http://downloads-distro.mongodb.org dist/10gen Translation-en | |
| Hit http://archive.ubuntu.com trusty-updates/main Translation-en | |
| Hit http://research.cs.wisc.edu squeeze/contrib amd64 Packages | |
| Hit http://archive.ubuntu.com trusty-updates/universe Translation-en | |
| Hit http://us.archive.ubuntu.com trusty/universe amd64 Packages | |
| Ign http://research.cs.wisc.edu squeeze/contrib Translation-en_US | |
| Ign http://research.cs.wisc.edu squeeze/contrib Translation-en | |
| Ign http://nebc.nerc.ac.uk unstable/bio-linux Translation-en_US | |
| Hit http://us.archive.ubuntu.com trusty/multiverse amd64 Packages | |
| Ign http://nebc.nerc.ac.uk unstable/bio-linux Translation-en | |
| Hit http://us.archive.ubuntu.com trusty/multiverse Translation-en | |
| Hit http://us.archive.ubuntu.com trusty/universe Translation-en | |
| Hit http://us.archive.ubuntu.com trusty-updates/universe amd64 Packages | |
| Ign http://archive.ubuntu.com trusty/main Translation-en_US | |
| Hit http://us.archive.ubuntu.com trusty-updates/multiverse amd64 Packages | |
| Hit http://us.archive.ubuntu.com trusty-updates/multiverse Translation-en | |
| Ign http://archive.ubuntu.com trusty/universe Translation-en_US | |
| Hit http://us.archive.ubuntu.com trusty-updates/universe Translation-en | |
| Ign http://ppa.launchpad.net precise/main Translation-en_US | |
| Ign http://ppa.launchpad.net precise/main Translation-en | |
| Ign http://ppa.launchpad.net precise/main Translation-en_US | |
| Ign http://us.archive.ubuntu.com trusty/multiverse Translation-en_US | |
| Ign http://us.archive.ubuntu.com trusty/universe Translation-en_US | |
| Ign http://ppa.launchpad.net precise/main Translation-en | |
| Fetched 2,299 B in 9s (232 B/s) | |
| Reading package lists... Done | |
| W: GPG error: http://research.cs.wisc.edu squeeze InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 973FC7D2670079F6 | |
| W: GPG error: http://ppa.launchpad.net precise Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 2A8E3034D018A4CE | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/packages.yaml | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-get -y --force-yes upgrade" | |
| Reading package lists... Done | |
| Building dependency tree | |
| Reading state information... Done | |
| Calculating upgrade... Done | |
| The following packages have been kept back: | |
| juju juju-core linux-headers-generic linux-headers-virtual | |
| linux-image-virtual linux-virtual | |
| The following packages will be upgraded: | |
| apport apt apt-transport-https apt-utils bash cloud-init dbus | |
| language-selector-common libapt-inst1.5 libapt-pkg4.12 libdbus-1-3 | |
| libpam-systemd libsystemd-daemon0 libsystemd-login0 libudev1 linux-libc-dev | |
| python-apport python-problem-report python3-apport python3-problem-report | |
| systemd-services udev | |
| 22 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. | |
| Need to get 5,349 kB of archives. | |
| After this operation, 15.4 kB of additional disk space will be used. | |
| Get:1 http://archive.ubuntu.com/ubuntu/ trusty-updates/main bash amd64 4.3-7ubuntu1.4 [576 kB] | |
| Get:2 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libapt-pkg4.12 amd64 1.0.1ubuntu2.4.1 [639 kB] | |
| Get:3 http://archive.ubuntu.com/ubuntu/ trusty-updates/main apt amd64 1.0.1ubuntu2.4.1 [954 kB] | |
| Get:4 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libapt-inst1.5 amd64 1.0.1ubuntu2.4.1 [58.5 kB] | |
| Get:5 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libdbus-1-3 amd64 1.6.18-0ubuntu4.2 [132 kB] | |
| Get:6 http://archive.ubuntu.com/ubuntu/ trusty-updates/main udev amd64 204-5ubuntu20.7 [735 kB] | |
| Get:7 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libudev1 amd64 204-5ubuntu20.7 [33.3 kB] | |
| Get:8 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libsystemd-login0 amd64 204-5ubuntu20.7 [26.8 kB] | |
| Get:9 http://archive.ubuntu.com/ubuntu/ trusty-updates/main dbus amd64 1.6.18-0ubuntu4.2 [230 kB] | |
| Get:10 http://archive.ubuntu.com/ubuntu/ trusty-updates/main language-selector-common all 0.129.3 [204 kB] | |
| Get:11 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libpam-systemd amd64 204-5ubuntu20.7 [25.5 kB] | |
| Get:12 http://archive.ubuntu.com/ubuntu/ trusty-updates/main systemd-services amd64 204-5ubuntu20.7 [197 kB] | |
| Get:13 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libsystemd-daemon0 amd64 204-5ubuntu20.7 [9,738 B] | |
| Get:14 http://archive.ubuntu.com/ubuntu/ trusty-updates/main apt-utils amd64 1.0.1ubuntu2.4.1 [172 kB] | |
| Get:15 http://archive.ubuntu.com/ubuntu/ trusty-updates/main apt-transport-https amd64 1.0.1ubuntu2.4.1 [25.1 kB] | |
| Get:16 http://archive.ubuntu.com/ubuntu/ trusty-updates/main python3-problem-report all 2.14.1-0ubuntu3.5 [9,098 B] | |
| Get:17 http://archive.ubuntu.com/ubuntu/ trusty-updates/main python3-apport all 2.14.1-0ubuntu3.5 [74.9 kB] | |
| Get:18 http://archive.ubuntu.com/ubuntu/ trusty-updates/main apport all 2.14.1-0ubuntu3.5 [179 kB] | |
| Get:19 http://archive.ubuntu.com/ubuntu/ trusty-updates/main linux-libc-dev amd64 3.13.0-36.63 [794 kB] | |
| Get:20 http://archive.ubuntu.com/ubuntu/ trusty-updates/main python-problem-report all 2.14.1-0ubuntu3.5 [9,020 B] | |
| Get:21 http://archive.ubuntu.com/ubuntu/ trusty-updates/main python-apport all 2.14.1-0ubuntu3.5 [74.8 kB] | |
| Get:22 http://archive.ubuntu.com/ubuntu/ trusty-updates/main cloud-init all 0.7.5-0ubuntu1.2 [191 kB] | |
| Fetched 5,349 kB in 14s (379 kB/s) | |
| Preconfiguring packages ... | |
| (Reading database ... 62976 files and directories currently installed.) | |
| Preparing to unpack .../bash_4.3-7ubuntu1.4_amd64.deb ... | |
| Unpacking bash (4.3-7ubuntu1.4) over (4.3-7ubuntu1) ... | |
| Processing triggers for man-db (2.6.7.1-1) ... | |
| Processing triggers for install-info (5.2.0.dfsg.1-2) ... | |
| Setting up bash (4.3-7ubuntu1.4) ... | |
| update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode | |
| (Reading database ... 62976 files and directories currently installed.) | |
| Preparing to unpack .../libapt-pkg4.12_1.0.1ubuntu2.4.1_amd64.deb ... | |
| Unpacking libapt-pkg4.12:amd64 (1.0.1ubuntu2.4.1) over (1.0.1ubuntu2.3) ... | |
| Setting up libapt-pkg4.12:amd64 (1.0.1ubuntu2.4.1) ... | |
| Processing triggers for libc-bin (2.19-0ubuntu6.3) ... | |
| (Reading database ... 62976 files and directories currently installed.) | |
| Preparing to unpack .../apt_1.0.1ubuntu2.4.1_amd64.deb ... | |
| Unpacking apt (1.0.1ubuntu2.4.1) over (1.0.1ubuntu2.3) ... | |
| Processing triggers for man-db (2.6.7.1-1) ... | |
| Setting up apt (1.0.1ubuntu2.4.1) ... | |
| Processing triggers for libc-bin (2.19-0ubuntu6.3) ... | |
| (Reading database ... 62976 files and directories currently installed.) | |
| Preparing to unpack .../libapt-inst1.5_1.0.1ubuntu2.4.1_amd64.deb ... | |
| Unpacking libapt-inst1.5:amd64 (1.0.1ubuntu2.4.1) over (1.0.1ubuntu2.3) ... | |
| Preparing to unpack .../libdbus-1-3_1.6.18-0ubuntu4.2_amd64.deb ... | |
| Unpacking libdbus-1-3:amd64 (1.6.18-0ubuntu4.2) over (1.6.18-0ubuntu4.1) ... | |
| Preparing to unpack .../udev_204-5ubuntu20.7_amd64.deb ... | |
| Adding 'diversion of /bin/udevadm to /bin/udevadm.upgrade by fake-udev' | |
| Unpacking udev (204-5ubuntu20.7) over (204-5ubuntu20.6) ... | |
| Preparing to unpack .../libudev1_204-5ubuntu20.7_amd64.deb ... | |
| Unpacking libudev1:amd64 (204-5ubuntu20.7) over (204-5ubuntu20.6) ... | |
| Preparing to unpack .../libsystemd-login0_204-5ubuntu20.7_amd64.deb ... | |
| Unpacking libsystemd-login0:amd64 (204-5ubuntu20.7) over (204-5ubuntu20.6) ... | |
| Preparing to unpack .../dbus_1.6.18-0ubuntu4.2_amd64.deb ... | |
| Unpacking dbus (1.6.18-0ubuntu4.2) over (1.6.18-0ubuntu4.1) ... | |
| Preparing to unpack .../language-selector-common_0.129.3_all.deb ... | |
| Unpacking language-selector-common (0.129.3) over (0.129.2) ... | |
| Preparing to unpack .../libpam-systemd_204-5ubuntu20.7_amd64.deb ... | |
| systemd-logind stop/waiting | |
| Unpacking libpam-systemd:amd64 (204-5ubuntu20.7) over (204-5ubuntu20.6) ... | |
| Preparing to unpack .../systemd-services_204-5ubuntu20.7_amd64.deb ... | |
| Unpacking systemd-services (204-5ubuntu20.7) over (204-5ubuntu20.6) ... | |
| Preparing to unpack .../libsystemd-daemon0_204-5ubuntu20.7_amd64.deb ... | |
| Unpacking libsystemd-daemon0:amd64 (204-5ubuntu20.7) over (204-5ubuntu20.6) ... | |
| Preparing to unpack .../apt-utils_1.0.1ubuntu2.4.1_amd64.deb ... | |
| Unpacking apt-utils (1.0.1ubuntu2.4.1) over (1.0.1ubuntu2.3) ... | |
| Preparing to unpack .../apt-transport-https_1.0.1ubuntu2.4.1_amd64.deb ... | |
| Unpacking apt-transport-https (1.0.1ubuntu2.4.1) over (1.0.1ubuntu2.3) ... | |
| Preparing to unpack .../python3-problem-report_2.14.1-0ubuntu3.5_all.deb ... | |
| Unpacking python3-problem-report (2.14.1-0ubuntu3.5) over (2.14.1-0ubuntu3.4) ... | |
| Preparing to unpack .../python3-apport_2.14.1-0ubuntu3.5_all.deb ... | |
| Unpacking python3-apport (2.14.1-0ubuntu3.5) over (2.14.1-0ubuntu3.4) ... | |
| Preparing to unpack .../apport_2.14.1-0ubuntu3.5_all.deb ... | |
| apport stop/waiting | |
| Unpacking apport (2.14.1-0ubuntu3.5) over (2.14.1-0ubuntu3.4) ... | |
| Preparing to unpack .../linux-libc-dev_3.13.0-36.63_amd64.deb ... | |
| Unpacking linux-libc-dev:amd64 (3.13.0-36.63) over (3.13.0-35.62) ... | |
| Preparing to unpack .../python-problem-report_2.14.1-0ubuntu3.5_all.deb ... | |
| Unpacking python-problem-report (2.14.1-0ubuntu3.5) over (2.14.1-0ubuntu3.4) ... | |
| Preparing to unpack .../python-apport_2.14.1-0ubuntu3.5_all.deb ... | |
| Unpacking python-apport (2.14.1-0ubuntu3.5) over (2.14.1-0ubuntu3.4) ... | |
| Preparing to unpack .../cloud-init_0.7.5-0ubuntu1.2_all.deb ... | |
| Unpacking cloud-init (0.7.5-0ubuntu1.2) over (0.7.5-0ubuntu1.1) ... | |
| Processing triggers for man-db (2.6.7.1-1) ... | |
| Processing triggers for ureadahead (0.100.0-16) ... | |
| Processing triggers for shared-mime-info (1.2-0ubuntu3) ... | |
| Setting up libapt-inst1.5:amd64 (1.0.1ubuntu2.4.1) ... | |
| Setting up libdbus-1-3:amd64 (1.6.18-0ubuntu4.2) ... | |
| Setting up libudev1:amd64 (204-5ubuntu20.7) ... | |
| Setting up udev (204-5ubuntu20.7) ... | |
| Installing new version of config file /etc/init/udev-fallback-graphics.conf ... | |
| udev stop/waiting | |
| udev start/running, process 8491 | |
| Removing 'diversion of /bin/udevadm to /bin/udevadm.upgrade by fake-udev' | |
| update-initramfs: deferring update (trigger activated) | |
| Setting up libsystemd-login0:amd64 (204-5ubuntu20.7) ... | |
| Setting up dbus (1.6.18-0ubuntu4.2) ... | |
| Installing new version of config file /etc/dbus-1/session.conf ... | |
| Setting up language-selector-common (0.129.3) ... | |
| Installing new version of config file /etc/fonts/conf.avail/69-language-selector-zh-sg.conf ... | |
| Installing new version of config file /etc/fonts/conf.avail/69-language-selector-zh-tw.conf ... | |
| Installing new version of config file /etc/fonts/conf.avail/69-language-selector-zh-mo.conf ... | |
| Installing new version of config file /etc/fonts/conf.avail/69-language-selector-zh-hk.conf ... | |
| Installing new version of config file /etc/fonts/conf.avail/69-language-selector-zh-cn.conf ... | |
| Setting up libsystemd-daemon0:amd64 (204-5ubuntu20.7) ... | |
| Setting up apt-utils (1.0.1ubuntu2.4.1) ... | |
| Setting up apt-transport-https (1.0.1ubuntu2.4.1) ... | |
| Setting up python3-problem-report (2.14.1-0ubuntu3.5) ... | |
| Setting up python3-apport (2.14.1-0ubuntu3.5) ... | |
| Setting up apport (2.14.1-0ubuntu3.5) ... | |
| apport start/running | |
| Setting up linux-libc-dev:amd64 (3.13.0-36.63) ... | |
| Setting up python-problem-report (2.14.1-0ubuntu3.5) ... | |
| Setting up python-apport (2.14.1-0ubuntu3.5) ... | |
| Setting up cloud-init (0.7.5-0ubuntu1.2) ... | |
| Installing new version of config file /etc/init/cloud-init-nonet.conf ... | |
| Installing new version of config file /etc/init/cloud-init-local.conf ... | |
| Leaving 'diversion of /etc/init/ureadahead.conf to /etc/init/ureadahead.conf.disabled by cloud-init' | |
| Processing triggers for ureadahead (0.100.0-16) ... | |
| Setting up systemd-services (204-5ubuntu20.7) ... | |
| Setting up libpam-systemd:amd64 (204-5ubuntu20.7) ... | |
| systemd-logind start/running, process 8748 | |
| Processing triggers for libc-bin (2.19-0ubuntu6.3) ... | |
| Processing triggers for initramfs-tools (0.103ubuntu4.2) ... | |
| update-initramfs: Generating /boot/initrd.img-3.13.0-35-generic | |
| INFO: Reading /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/packages.yaml | |
| DBG [shared.py]: Packages to install: fastx-toolkit,last-align,maq,plink,tabix,openjdk-7-jdk,openjdk-7-jre,gsl-bin,libatlas-base-dev,libblas-dev,libbz2-dev,libc6-dev,libcurl4-openssl-dev,libeigen3-dev,libgsl0-dev,libgsl0ldbl,liblapack-dev,liblzma-dev,libncurses5-dev,libnetcdf-dev,libpcre3-dev,libpng12-dev,libreadline-dev,libssl-dev,libxml2,libxml2-dev,libxslt1-dev,libxslt1.1,libzip-dev,mime-support,uuid,uuid-dev,xz-utils,zlib1g-dev,zlib1g-dev,clang,cmake,g++,gcc,gfortran,libtool,make,patch,pkg-config,vim,htop,sudo,bzr,cvs,git-core,mercurial,subversion,curl,wget,axel,gawk,less,openssh-server,rsync,screen,unzip,cpanminus,libextutils-autoinstall-perl,libperl-dev,parrot,parrot-devel,perl,perl-modules,perl-tk,python,python-dev,python-distutils-extra,python-pip,python-rpy,python-setuptools,python-virtualenv,python3,python3-dev,r-base,r-base-core,r-base-dev,r-base-html,ruby1.9.1,ruby1.9.1-dev | |
| INFO: Installing 84 packages | |
| INFO: Package install progress: 0/84 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-get -y --force-yes install fastx-toolkit last-align maq plink tabix openjdk-7-jdk openjdk-7-jre gsl-bin libatlas-base-dev libblas-dev libbz2-dev libc6-dev libcurl4-openssl-dev libeigen3-dev libgsl0-dev libgsl0ldbl liblapack-dev liblzma-dev libncurses5-dev libnetcdf-dev libpcre3-dev libpng12-dev libreadline-dev libssl-dev libxml2 libxml2-dev libxslt1-dev libxslt1.1 libzip-dev mime-support" | |
| Reading package lists... Done | |
| Building dependency tree | |
| Reading state information... Done | |
| mime-support is already the newest version. | |
| libc6-dev is already the newest version. | |
| libc6-dev set to manually installed. | |
| libxml2 is already the newest version. | |
| The following extra packages will be installed: | |
| acl at-spi2-core ca-certificates-java colord comerr-dev dbus-x11 | |
| dconf-gsettings-backend dconf-service desktop-file-utils fontconfig | |
| fontconfig-config fonts-dejavu-core fonts-dejavu-extra gconf-service | |
| gconf-service-backend gconf2 gconf2-common gvfs gvfs-common gvfs-daemons | |
| gvfs-libs hicolor-icon-theme java-common krb5-multidev libasound2 | |
| libasound2-data libasyncns0 libatasmart4 libatk-bridge2.0-0 | |
| libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data | |
| libatlas-dev libatlas3-base libatspi2.0-0 libavahi-client3 | |
| libavahi-common-data libavahi-common3 libavahi-glib1 libblas3 libbonobo2-0 | |
| libbonobo2-common libcairo-gobject2 libcairo2 libcanberra0 libcf0 libcolord1 | |
| libcolorhug1 libcups2 libdatrie1 libdconf1 libexif12 libflac8 libfontconfig1 | |
| libgconf-2-4 libgconf2-4 libgcrypt11-dev libgd-gd2-perl libgd-graph-perl | |
| libgd-text-perl libgd3 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common | |
| libgfortran3 libgif4 libgnome2-0 libgnome2-bin libgnome2-common | |
| libgnomevfs2-0 libgnomevfs2-common libgnutls-dev libgnutlsxx27 | |
| libgpg-error-dev libgphoto2-6 libgphoto2-l10n libgphoto2-port10 | |
| libgraphite2-3 libgssrpc4 libgtextutils0 libgtk-3-0 libgtk-3-bin | |
| libgtk-3-common libgtk2.0-0 libgtk2.0-bin libgtk2.0-common libgudev-1.0-0 | |
| libgusb2 libharfbuzz0b libhdf5-7 libice-dev libidl-common libidl0 | |
| libidn11-dev libieee1284-3 libjasper1 libjbig0 libjpeg-turbo8 libjpeg8 | |
| libkadm5clnt-mit9 libkadm5srv-mit9 libkdb5-7 libkrb5-dev liblapack3 | |
| liblcms2-2 libldap2-dev libltdl7 libnetcdfc++4 libnetcdfc7 libnetcdff5 | |
| libnspr4 libnss3 libnss3-1d libnss3-nssdb libogg0 liborbit-2-0 liborbit2 | |
| libp11-kit-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 | |
| libpcrecpp0 libpcsclite1 libperlio-gzip-perl libpthread-stubs0-dev libpulse0 | |
| libreadline6-dev librtmp-dev libsane libsane-common libsecret-1-0 | |
| libsecret-common libsm-dev libsndfile1 libssl-doc libtasn1-6-dev libtdb1 | |
| libthai-data libthai0 libtiff5 libtinfo-dev libudisks2-0 libv4l-0 | |
| libv4lconvert0 libvorbis0a libvorbisenc2 libvorbisfile3 libvpx1 | |
| libwayland-client0 libwayland-cursor0 libwebp5 libwebpmux1 libx11-dev | |
| libx11-doc libxau-dev libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb1-dev | |
| libxcursor1 libxdmcp-dev libxft2 libxi6 libxinerama1 libxkbcommon0 libxt-dev | |
| libxtst6 libxv1 libxxf86dga1 libzip2 openjdk-7-jre-headless pkg-config | |
| policykit-1-gnome python-imaging python-pil sound-theme-freedesktop | |
| tzdata-java udisks2 x11-utils x11proto-core-dev x11proto-input-dev | |
| x11proto-kb-dev xorg-sgml-doctools xtrans-dev | |
| Suggested packages: | |
| doc-base gconf-defaults-service gvfs-backends gvfs-backends-goa default-jre | |
| equivs krb5-doc libasound2-plugins alsa-utils libblas-doc liblapack-doc | |
| libbonobo2-bin libcanberra-gtk0 libcanberra-pulse cups-common libcurl4-doc | |
| libcurl3-dbg libeigen3-doc libmrpt-dev libgcrypt11-doc ttf-dustin | |
| libgd-tools desktop-base libgnomevfs2-bin libgnomevfs2-extra gamin fam | |
| gnome-mime-data gnutls26-doc gnutls-bin gphoto2 gtkam gsl-ref-psdoc | |
| gsl-doc-pdf gsl-doc-info gsl-ref-html krb5-user librsvg2-common libice-doc | |
| libjasper-runtime liblcms2-utils liblzma-doc ncurses-doc netcdf-bin | |
| netcdf-doc ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp | |
| ttf-arphic-gkai00mp ttf-arphic-bkai00mp pcscd pulseaudio avahi-daemon hplip | |
| hpoj libsane-extras sane-utils libsm-doc libxcb-doc libxt-doc bwa samtools | |
| openjdk-7-demo openjdk-7-source visualvm icedtea-7-plugin | |
| icedtea-7-jre-jamvm libnss-mdns sun-java6-fonts fonts-ipafont-gothic | |
| fonts-ipafont-mincho ttf-wqy-microhei ttf-wqy-zenhei ttf-indic-fonts-core | |
| ttf-telugu-fonts ttf-oriya-fonts ttf-kannada-fonts ttf-bengali-fonts | |
| python-pil-doc python-pil-dbg xfsprogs reiserfsprogs exfat-utils btrfs-tools | |
| mdadm mesa-utils | |
| The following NEW packages will be installed: | |
| acl at-spi2-core ca-certificates-java colord comerr-dev dbus-x11 | |
| dconf-gsettings-backend dconf-service desktop-file-utils fastx-toolkit | |
| fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-extra | |
| gconf-service gconf-service-backend gconf2 gconf2-common gsl-bin gvfs | |
| gvfs-common gvfs-daemons gvfs-libs hicolor-icon-theme java-common | |
| krb5-multidev last-align libasound2 libasound2-data libasyncns0 libatasmart4 | |
| libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 | |
| libatk1.0-data libatlas-base-dev libatlas-dev libatlas3-base libatspi2.0-0 | |
| libavahi-client3 libavahi-common-data libavahi-common3 libavahi-glib1 | |
| libblas-dev libblas3 libbonobo2-0 libbonobo2-common libbz2-dev | |
| libcairo-gobject2 libcairo2 libcanberra0 libcf0 libcolord1 libcolorhug1 | |
| libcups2 libcurl4-openssl-dev libdatrie1 libdconf1 libeigen3-dev libexif12 | |
| libflac8 libfontconfig1 libgconf-2-4 libgconf2-4 libgcrypt11-dev | |
| libgd-gd2-perl libgd-graph-perl libgd-text-perl libgd3 libgdk-pixbuf2.0-0 | |
| libgdk-pixbuf2.0-common libgfortran3 libgif4 libgnome2-0 libgnome2-bin | |
| libgnome2-common libgnomevfs2-0 libgnomevfs2-common libgnutls-dev | |
| libgnutlsxx27 libgpg-error-dev libgphoto2-6 libgphoto2-l10n | |
| libgphoto2-port10 libgraphite2-3 libgsl0-dev libgsl0ldbl libgssrpc4 | |
| libgtextutils0 libgtk-3-0 libgtk-3-bin libgtk-3-common libgtk2.0-0 | |
| libgtk2.0-bin libgtk2.0-common libgudev-1.0-0 libgusb2 libharfbuzz0b | |
| libhdf5-7 libice-dev libidl-common libidl0 libidn11-dev libieee1284-3 | |
| libjasper1 libjbig0 libjpeg-turbo8 libjpeg8 libkadm5clnt-mit9 | |
| libkadm5srv-mit9 libkdb5-7 libkrb5-dev liblapack-dev liblapack3 liblcms2-2 | |
| libldap2-dev libltdl7 liblzma-dev libncurses5-dev libnetcdf-dev | |
| libnetcdfc++4 libnetcdfc7 libnetcdff5 libnspr4 libnss3 libnss3-1d | |
| libnss3-nssdb libogg0 liborbit-2-0 liborbit2 libp11-kit-dev libpango-1.0-0 | |
| libpangocairo-1.0-0 libpangoft2-1.0-0 libpcre3-dev libpcrecpp0 libpcsclite1 | |
| libperlio-gzip-perl libpng12-dev libpthread-stubs0-dev libpulse0 | |
| libreadline-dev libreadline6-dev librtmp-dev libsane libsane-common | |
| libsecret-1-0 libsecret-common libsm-dev libsndfile1 libssl-dev libssl-doc | |
| libtasn1-6-dev libtdb1 libthai-data libthai0 libtiff5 libtinfo-dev | |
| libudisks2-0 libv4l-0 libv4lconvert0 libvorbis0a libvorbisenc2 | |
| libvorbisfile3 libvpx1 libwayland-client0 libwayland-cursor0 libwebp5 | |
| libwebpmux1 libx11-dev libx11-doc libxau-dev libxcb-render0 libxcb-shape0 | |
| libxcb-shm0 libxcb1-dev libxcursor1 libxdmcp-dev libxft2 libxi6 libxinerama1 | |
| libxkbcommon0 libxml2-dev libxslt1-dev libxslt1.1 libxt-dev libxtst6 libxv1 | |
| libxxf86dga1 libzip-dev libzip2 maq openjdk-7-jdk openjdk-7-jre | |
| openjdk-7-jre-headless pkg-config plink policykit-1-gnome python-imaging | |
| python-pil sound-theme-freedesktop tabix tzdata-java udisks2 x11-utils | |
| x11proto-core-dev x11proto-input-dev x11proto-kb-dev xorg-sgml-doctools | |
| xtrans-dev | |
| 0 upgraded, 211 newly installed, 0 to remove and 6 not upgraded. | |
| Need to get 104 MB of archives. | |
| After this operation, 310 MB of additional disk space will be used. | |
| Get:1 http://archive.ubuntu.com/ubuntu/ trusty/main libasound2-data all 1.0.27.2-3ubuntu7 [26.3 kB] | |
| Get:2 http://archive.ubuntu.com/ubuntu/ trusty/main libasound2 amd64 1.0.27.2-3ubuntu7 [327 kB] | |
| Get:3 http://archive.ubuntu.com/ubuntu/ trusty/main libasyncns0 amd64 0.8-4ubuntu2 [11.9 kB] | |
| Get:4 http://archive.ubuntu.com/ubuntu/ trusty/main libatasmart4 amd64 0.19-3 [27.1 kB] | |
| Get:5 http://archive.ubuntu.com/ubuntu/ trusty/main libatk1.0-data all 2.10.0-2ubuntu2 [13.7 kB] | |
| Get:6 http://archive.ubuntu.com/ubuntu/ trusty/main libatk1.0-0 amd64 2.10.0-2ubuntu2 [50.9 kB] | |
| Get:7 http://archive.ubuntu.com/ubuntu/ trusty/main libatspi2.0-0 amd64 2.10.2.is.2.10.1-0ubuntu1 [53.1 kB] | |
| Get:8 http://archive.ubuntu.com/ubuntu/ trusty/main libatk-bridge2.0-0 amd64 2.10.2-2ubuntu1 [46.8 kB] | |
| Get:9 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgtk2.0-common all 2.24.23-0ubuntu1.1 [121 kB] | |
| Get:10 http://archive.ubuntu.com/ubuntu/ trusty/main fonts-dejavu-core all 2.34-1ubuntu1 [1,024 kB] | |
| Get:11 http://archive.ubuntu.com/ubuntu/ trusty-updates/main fontconfig-config all 2.11.0-0ubuntu4.1 [47.4 kB] | |
| Get:12 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libfontconfig1 amd64 2.11.0-0ubuntu4.1 [123 kB] | |
| Get:13 http://archive.ubuntu.com/ubuntu/ trusty/main libxcb-render0 amd64 1.10-2ubuntu1 [11.0 kB] | |
| Get:14 http://archive.ubuntu.com/ubuntu/ trusty/main libxcb-shm0 amd64 1.10-2ubuntu1 [5,432 B] | |
| Get:15 http://archive.ubuntu.com/ubuntu/ trusty/main libcairo2 amd64 1.13.0~20140204-0ubuntu1 [535 kB] | |
| Get:16 http://archive.ubuntu.com/ubuntu/ trusty/main libavahi-common-data amd64 0.6.31-4ubuntu1 [21.2 kB] | |
| Get:17 http://archive.ubuntu.com/ubuntu/ trusty/main libavahi-common3 amd64 0.6.31-4ubuntu1 [21.7 kB] | |
| Get:18 http://archive.ubuntu.com/ubuntu/ trusty/main libavahi-client3 amd64 0.6.31-4ubuntu1 [25.1 kB] | |
| Get:19 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libcups2 amd64 1.7.2-0ubuntu1.2 [179 kB] | |
| Get:20 http://archive.ubuntu.com/ubuntu/ trusty/main libjpeg-turbo8 amd64 1.3.0-0ubuntu2 [104 kB] | |
| Get:21 http://archive.ubuntu.com/ubuntu/ trusty/main libjpeg8 amd64 8c-2ubuntu8 [2,194 B] | |
| Get:22 http://archive.ubuntu.com/ubuntu/ trusty/main libjasper1 amd64 1.900.1-14ubuntu3 [129 kB] | |
| Get:23 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libjbig0 amd64 2.0-2ubuntu4.1 [26.1 kB] | |
| Get:24 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libtiff5 amd64 4.0.3-7ubuntu0.1 [142 kB] | |
| Get:25 http://archive.ubuntu.com/ubuntu/ trusty/main libgdk-pixbuf2.0-common all 2.30.7-0ubuntu1 [8,610 B] | |
| Get:26 http://archive.ubuntu.com/ubuntu/ trusty/main libgdk-pixbuf2.0-0 amd64 2.30.7-0ubuntu1 [160 kB] | |
| Get:27 http://archive.ubuntu.com/ubuntu/ trusty/main libthai-data all 0.1.20-3 [130 kB] | |
| Get:28 http://archive.ubuntu.com/ubuntu/ trusty/main libdatrie1 amd64 0.2.8-1 [16.7 kB] | |
| Get:29 http://archive.ubuntu.com/ubuntu/ trusty/main libthai0 amd64 0.1.20-3 [16.9 kB] | |
| Get:30 http://archive.ubuntu.com/ubuntu/ trusty-updates/main fontconfig amd64 2.11.0-0ubuntu4.1 [176 kB] | |
| Get:31 http://archive.ubuntu.com/ubuntu/ trusty/main libpango-1.0-0 amd64 1.36.3-1ubuntu1 [149 kB] | |
| Get:32 http://archive.ubuntu.com/ubuntu/ trusty/main libgraphite2-3 amd64 1.2.4-1ubuntu1 [53.8 kB] | |
| Get:33 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libharfbuzz0b amd64 0.9.27-1ubuntu1 [127 kB] | |
| Get:34 http://archive.ubuntu.com/ubuntu/ trusty/main libpangoft2-1.0-0 amd64 1.36.3-1ubuntu1 [32.6 kB] | |
| Get:35 http://archive.ubuntu.com/ubuntu/ trusty/main libpangocairo-1.0-0 amd64 1.36.3-1ubuntu1 [19.9 kB] | |
| Get:36 http://archive.ubuntu.com/ubuntu/ trusty/main libxcursor1 amd64 1:1.1.14-1 [22.8 kB] | |
| Get:37 http://archive.ubuntu.com/ubuntu/ trusty/main libxi6 amd64 2:1.7.1.901-1ubuntu1 [31.9 kB] | |
| Get:38 http://archive.ubuntu.com/ubuntu/ trusty/main libxinerama1 amd64 2:1.1.3-1 [7,908 B] | |
| Get:39 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgtk2.0-0 amd64 2.24.23-0ubuntu1.1 [1,733 kB] | |
| Get:40 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libnspr4 amd64 2:4.10.7-0ubuntu0.14.04.1 [111 kB] | |
| Get:41 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libnss3-nssdb all 2:3.17.1-0ubuntu0.14.04.1 [10.6 kB] | |
| Get:42 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libnss3 amd64 2:3.17.1-0ubuntu0.14.04.1 [1,094 kB] | |
| Get:43 http://archive.ubuntu.com/ubuntu/ trusty/main ca-certificates-java all 20130815ubuntu1 [13.4 kB] | |
| Get:44 http://archive.ubuntu.com/ubuntu/ trusty-updates/main tzdata-java all 2014e-0ubuntu0.14.04 [72.2 kB] | |
| Get:45 http://archive.ubuntu.com/ubuntu/ trusty/main java-common all 0.51 [130 kB] | |
| Get:46 http://archive.ubuntu.com/ubuntu/ trusty/main liblcms2-2 amd64 2.5-0ubuntu4 [132 kB] | |
| Get:47 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libnss3-1d amd64 2:3.17.1-0ubuntu0.14.04.1 [9,308 B] | |
| Get:48 http://archive.ubuntu.com/ubuntu/ trusty/main libpcsclite1 amd64 1.8.10-1ubuntu1 [20.9 kB] | |
| Get:49 http://archive.ubuntu.com/ubuntu/ trusty-updates/main openjdk-7-jre-headless amd64 7u65-2.5.2-3~14.04 [39.5 MB] | |
| Get:50 http://archive.ubuntu.com/ubuntu/ trusty/main libgif4 amd64 4.1.6-11 [28.6 kB] | |
| Get:51 http://archive.ubuntu.com/ubuntu/ trusty/main libogg0 amd64 1.3.1-1ubuntu1 [17.0 kB] | |
| Get:52 http://archive.ubuntu.com/ubuntu/ trusty/main libflac8 amd64 1.3.0-2 [94.5 kB] | |
| Get:53 http://archive.ubuntu.com/ubuntu/ trusty/main libvorbis0a amd64 1.3.2-1.3ubuntu1 [87.2 kB] | |
| Get:54 http://archive.ubuntu.com/ubuntu/ trusty/main libvorbisenc2 amd64 1.3.2-1.3ubuntu1 [84.5 kB] | |
| Get:55 http://archive.ubuntu.com/ubuntu/ trusty/main libsndfile1 amd64 1.0.25-7ubuntu2 [136 kB] | |
| Get:56 http://archive.ubuntu.com/ubuntu/ trusty/main libpulse0 amd64 1:4.0-0ubuntu11 [225 kB] | |
| Get:57 http://archive.ubuntu.com/ubuntu/ trusty/main libxtst6 amd64 2:1.2.2-1 [14.1 kB] | |
| Get:58 http://archive.ubuntu.com/ubuntu/ trusty-updates/main openjdk-7-jre amd64 7u65-2.5.2-3~14.04 [183 kB] | |
| Get:59 http://archive.ubuntu.com/ubuntu/ trusty/main libatk-wrapper-java all 0.30.4-4 [30.2 kB] | |
| Get:60 http://archive.ubuntu.com/ubuntu/ trusty/main libatk-wrapper-java-jni amd64 0.30.4-4 [25.2 kB] | |
| Get:61 http://archive.ubuntu.com/ubuntu/ trusty/main libavahi-glib1 amd64 0.6.31-4ubuntu1 [7,756 B] | |
| Get:62 http://archive.ubuntu.com/ubuntu/ trusty/main libbonobo2-common all 2.32.1-0ubuntu5 [34.2 kB] | |
| Get:63 http://archive.ubuntu.com/ubuntu/ trusty/main libidl-common all 0.8.14-0.2ubuntu4 [8,196 B] | |
| Get:64 http://archive.ubuntu.com/ubuntu/ trusty/main libidl0 amd64 0.8.14-0.2ubuntu4 [65.9 kB] | |
| Get:65 http://archive.ubuntu.com/ubuntu/ trusty/main liborbit-2-0 amd64 1:2.14.19-0.3 [138 kB] | |
| Get:66 http://archive.ubuntu.com/ubuntu/ trusty/main liborbit2 amd64 1:2.14.19-0.3 [14.7 kB] | |
| Get:67 http://archive.ubuntu.com/ubuntu/ trusty/main libbonobo2-0 amd64 2.32.1-0ubuntu5 [214 kB] | |
| Get:68 http://archive.ubuntu.com/ubuntu/ trusty/main libcairo-gobject2 amd64 1.13.0~20140204-0ubuntu1 [17.3 kB] | |
| Get:69 http://archive.ubuntu.com/ubuntu/ trusty/main libltdl7 amd64 2.4.2-1.7ubuntu1 [35.0 kB] | |
| Get:70 http://archive.ubuntu.com/ubuntu/ trusty/main libtdb1 amd64 1.2.12-1 [37.8 kB] | |
| Get:71 http://archive.ubuntu.com/ubuntu/ trusty/main libvorbisfile3 amd64 1.3.2-1.3ubuntu1 [15.8 kB] | |
| Get:72 http://archive.ubuntu.com/ubuntu/ trusty/main sound-theme-freedesktop all 0.8-1 [385 kB] | |
| Get:73 http://archive.ubuntu.com/ubuntu/ trusty/main libcanberra0 amd64 0.30-0ubuntu3 [36.5 kB] | |
| Get:74 http://archive.ubuntu.com/ubuntu/ trusty/main libcolord1 amd64 1.0.6-1 [83.1 kB] | |
| Get:75 http://archive.ubuntu.com/ubuntu/ trusty/main libdconf1 amd64 0.20.0-1 [31.5 kB] | |
| Get:76 http://archive.ubuntu.com/ubuntu/ trusty/main libexif12 amd64 0.6.21-1ubuntu1 [75.5 kB] | |
| Get:77 http://archive.ubuntu.com/ubuntu/ trusty/main gconf2-common all 3.2.6-0ubuntu2 [20.2 kB] | |
| Get:78 http://archive.ubuntu.com/ubuntu/ trusty/main libgconf-2-4 amd64 3.2.6-0ubuntu2 [80.8 kB] | |
| Get:79 http://archive.ubuntu.com/ubuntu/ trusty/main libvpx1 amd64 1.3.0-2 [556 kB] | |
| Get:80 http://archive.ubuntu.com/ubuntu/ trusty/main libgd3 amd64 2.1.0-3 [147 kB] | |
| Get:81 http://archive.ubuntu.com/ubuntu/ trusty/main libgfortran3 amd64 4.8.2-19ubuntu1 [250 kB] | |
| Get:82 http://archive.ubuntu.com/ubuntu/ trusty/main gconf-service-backend amd64 3.2.6-0ubuntu2 [56.3 kB] | |
| Get:83 http://archive.ubuntu.com/ubuntu/ trusty/main gconf-service amd64 3.2.6-0ubuntu2 [2,046 B] | |
| Get:84 http://archive.ubuntu.com/ubuntu/ trusty-updates/main dbus-x11 amd64 1.6.18-0ubuntu4.2 [19.2 kB] | |
| Get:85 http://archive.ubuntu.com/ubuntu/ trusty/main gconf2 amd64 3.2.6-0ubuntu2 [65.5 kB] | |
| Get:86 http://archive.ubuntu.com/ubuntu/ trusty/main libgnomevfs2-common amd64 1:2.24.4-1ubuntu6 [22.8 kB] | |
| Get:87 http://archive.ubuntu.com/ubuntu/ trusty/main libgnomevfs2-0 amd64 1:2.24.4-1ubuntu6 [210 kB] | |
| Get:88 http://archive.ubuntu.com/ubuntu/ trusty/main libgnome2-common all 2.32.1-4ubuntu1 [33.3 kB] | |
| Get:89 http://archive.ubuntu.com/ubuntu/ trusty/main libgnome2-bin amd64 2.32.1-4ubuntu1 [15.0 kB] | |
| Get:90 http://archive.ubuntu.com/ubuntu/ trusty/main libgnome2-0 amd64 2.32.1-4ubuntu1 [43.2 kB] | |
| Get:91 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgphoto2-port10 amd64 2.5.3.1-1ubuntu2.2 [40.8 kB] | |
| Get:92 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgphoto2-6 amd64 2.5.3.1-1ubuntu2.2 [737 kB] | |
| Get:93 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgssrpc4 amd64 1.12+dfsg-2ubuntu4.2 [53.1 kB] | |
| Get:94 http://archive.ubuntu.com/ubuntu/ trusty/main dconf-service amd64 0.20.0-1 [26.9 kB] | |
| Get:95 http://archive.ubuntu.com/ubuntu/ trusty/main dconf-gsettings-backend amd64 0.20.0-1 [19.3 kB] | |
| Get:96 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgtk-3-common all 3.10.8-0ubuntu1.2 [167 kB] | |
| Get:97 http://archive.ubuntu.com/ubuntu/ trusty/main libwayland-client0 amd64 1.4.0-1ubuntu1 [22.1 kB] | |
| Get:98 http://archive.ubuntu.com/ubuntu/ trusty/main libwayland-cursor0 amd64 1.4.0-1ubuntu1 [9,918 B] | |
| Get:99 http://archive.ubuntu.com/ubuntu/ trusty/main libxkbcommon0 amd64 0.4.1-0ubuntu1 [87.9 kB] | |
| Get:100 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgtk-3-0 amd64 3.10.8-0ubuntu1.2 [1,957 kB] | |
| Get:101 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgudev-1.0-0 amd64 1:204-5ubuntu20.7 [14.1 kB] | |
| Get:102 http://archive.ubuntu.com/ubuntu/ trusty/universe libhdf5-7 amd64 1.8.11-5ubuntu7 [1,205 kB] | |
| Get:103 http://archive.ubuntu.com/ubuntu/ trusty/main libieee1284-3 amd64 0.2.11-12 [23.8 kB] | |
| Get:104 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libkadm5clnt-mit9 amd64 1.12+dfsg-2ubuntu4.2 [36.2 kB] | |
| Get:105 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libkdb5-7 amd64 1.12+dfsg-2ubuntu4.2 [36.2 kB] | |
| Get:106 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libkadm5srv-mit9 amd64 1.12+dfsg-2ubuntu4.2 [50.3 kB] | |
| Get:107 http://archive.ubuntu.com/ubuntu/ trusty/main libpcrecpp0 amd64 1:8.31-2ubuntu2 [14.5 kB] | |
| Get:108 http://archive.ubuntu.com/ubuntu/ trusty/main acl amd64 2.2.52-1 [43.8 kB] | |
| Get:109 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libsane-common amd64 1.0.23-3ubuntu3.1 [451 kB] | |
| Get:110 http://archive.ubuntu.com/ubuntu/ trusty/main libv4lconvert0 amd64 1.0.1-1 [74.8 kB] | |
| Get:111 http://archive.ubuntu.com/ubuntu/ trusty/main libv4l-0 amd64 1.0.1-1 [38.8 kB] | |
| Get:112 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libsane amd64 1.0.23-3ubuntu3.1 [1,929 kB] | |
| Get:113 http://archive.ubuntu.com/ubuntu/ trusty/main libsecret-common all 0.16-0ubuntu1 [4,166 B] | |
| Get:114 http://archive.ubuntu.com/ubuntu/ trusty/main libsecret-1-0 amd64 0.16-0ubuntu1 [90.7 kB] | |
| Get:115 http://archive.ubuntu.com/ubuntu/ trusty/main libudisks2-0 amd64 2.1.3-1 [90.7 kB] | |
| Get:116 http://archive.ubuntu.com/ubuntu/ trusty/main libxcb-shape0 amd64 1.10-2ubuntu1 [5,654 B] | |
| Get:117 http://archive.ubuntu.com/ubuntu/ trusty/main libxft2 amd64 2.3.1-2 [36.2 kB] | |
| Get:118 http://archive.ubuntu.com/ubuntu/ trusty/main libxslt1.1 amd64 1.1.28-2build1 [145 kB] | |
| Get:119 http://archive.ubuntu.com/ubuntu/ trusty/main libxv1 amd64 2:1.0.10-1 [10.3 kB] | |
| Get:120 http://archive.ubuntu.com/ubuntu/ trusty/main libxxf86dga1 amd64 2:1.1.4-1 [13.7 kB] | |
| Get:121 http://archive.ubuntu.com/ubuntu/ trusty/main libgusb2 amd64 0.1.6-5 [15.4 kB] | |
| Get:122 http://archive.ubuntu.com/ubuntu/ trusty/main libcolorhug1 amd64 1.0.6-1 [21.7 kB] | |
| Get:123 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgnutlsxx27 amd64 2.12.23-12ubuntu2.1 [17.3 kB] | |
| Get:124 http://archive.ubuntu.com/ubuntu/ trusty/main libwebp5 amd64 0.4.0-4 [146 kB] | |
| Get:125 http://archive.ubuntu.com/ubuntu/ trusty/main libwebpmux1 amd64 0.4.0-4 [13.7 kB] | |
| Get:126 http://archive.ubuntu.com/ubuntu/ trusty/main at-spi2-core amd64 2.10.2.is.2.10.1-0ubuntu1 [43.1 kB] | |
| Get:127 http://archive.ubuntu.com/ubuntu/ trusty/main colord amd64 1.0.6-1 [213 kB] | |
| Get:128 http://archive.ubuntu.com/ubuntu/ trusty/main desktop-file-utils amd64 0.22-1ubuntu1 [43.2 kB] | |
| Get:129 http://archive.ubuntu.com/ubuntu/ trusty/universe libgtextutils0 amd64 0.7-1 [19.1 kB] | |
| Get:130 http://archive.ubuntu.com/ubuntu/ trusty/main libgd-gd2-perl amd64 1:2.46-3.1build1 [181 kB] | |
| Get:131 http://archive.ubuntu.com/ubuntu/ trusty/main libgd-text-perl all 0.86-8 [38.2 kB] | |
| Get:132 http://archive.ubuntu.com/ubuntu/ trusty/main libgd-graph-perl all 1.44-6 [371 kB] | |
| Get:133 http://archive.ubuntu.com/ubuntu/ trusty/main libperlio-gzip-perl amd64 0.18-1build3 [16.0 kB] | |
| Get:134 http://archive.ubuntu.com/ubuntu/ trusty/universe fastx-toolkit amd64 0.0.14-1 [85.8 kB] | |
| Get:135 http://archive.ubuntu.com/ubuntu/ trusty/main fonts-dejavu-extra all 2.34-1ubuntu1 [1,736 kB] | |
| Get:136 http://archive.ubuntu.com/ubuntu/ trusty/main libgsl0ldbl amd64 1.16+dfsg-1ubuntu1 [878 kB] | |
| Get:137 http://archive.ubuntu.com/ubuntu/ trusty/universe gsl-bin amd64 1.16+dfsg-1ubuntu1 [10.7 kB] | |
| Get:138 http://archive.ubuntu.com/ubuntu/ trusty/main x11-utils amd64 7.7+1 [230 kB] | |
| Get:139 http://archive.ubuntu.com/ubuntu/ trusty/main udisks2 amd64 2.1.3-1 [170 kB] | |
| Get:140 http://archive.ubuntu.com/ubuntu/ trusty/main gvfs-common all 1.20.1-1ubuntu1 [42.0 kB] | |
| Get:141 http://archive.ubuntu.com/ubuntu/ trusty/main gvfs-libs amd64 1.20.1-1ubuntu1 [104 kB] | |
| Get:142 http://archive.ubuntu.com/ubuntu/ trusty/main gvfs-daemons amd64 1.20.1-1ubuntu1 [108 kB] | |
| Get:143 http://archive.ubuntu.com/ubuntu/ trusty/main gvfs amd64 1.20.1-1ubuntu1 [89.7 kB] | |
| Get:144 http://archive.ubuntu.com/ubuntu/ trusty/main hicolor-icon-theme all 0.13-1 [7,140 B] | |
| Get:145 http://archive.ubuntu.com/ubuntu/ trusty/main comerr-dev amd64 2.1-1.42.9-3ubuntu1 [38.3 kB] | |
| Get:146 http://archive.ubuntu.com/ubuntu/ trusty-updates/main krb5-multidev amd64 1.12+dfsg-2ubuntu4.2 [111 kB] | |
| Get:147 http://archive.ubuntu.com/ubuntu/ trusty/universe last-align amd64 393-1 [435 kB] | |
| Get:148 http://archive.ubuntu.com/ubuntu/ trusty/universe libatlas3-base amd64 3.10.1-4 [2,677 kB] | |
| Get:149 http://archive.ubuntu.com/ubuntu/ trusty/main libblas3 amd64 1.2.20110419-7 [215 kB] | |
| Get:150 http://archive.ubuntu.com/ubuntu/ trusty/main libblas-dev amd64 1.2.20110419-7 [240 kB] | |
| Get:151 http://archive.ubuntu.com/ubuntu/ trusty/universe libatlas-dev all 3.10.1-4 [22.7 kB] | |
| Get:152 http://archive.ubuntu.com/ubuntu/ trusty/universe libatlas-base-dev amd64 3.10.1-4 [3,348 kB] | |
| Get:153 http://archive.ubuntu.com/ubuntu/ trusty/main libbz2-dev amd64 1.0.6-5 [33.2 kB] | |
| Get:154 http://archive.ubuntu.com/ubuntu/ trusty/universe libcf0 amd64 1:4.1.3-7ubuntu2 [24.2 kB] | |
| Get:155 http://archive.ubuntu.com/ubuntu/ trusty/main pkg-config amd64 0.26-1ubuntu4 [40.9 kB] | |
| Get:156 http://archive.ubuntu.com/ubuntu/ trusty/main libidn11-dev amd64 1.28-1ubuntu2 [517 kB] | |
| Get:157 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libkrb5-dev amd64 1.12+dfsg-2ubuntu4.2 [14.4 kB] | |
| Get:158 http://archive.ubuntu.com/ubuntu/ trusty/main libldap2-dev amd64 2.4.31-1+nmu2ubuntu8 [259 kB] | |
| Get:159 http://archive.ubuntu.com/ubuntu/ trusty/main libgpg-error-dev amd64 1.12-0.2ubuntu1 [20.1 kB] | |
| Get:160 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgcrypt11-dev amd64 1.5.3-2ubuntu4.1 [273 kB] | |
| Get:161 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libtasn1-6-dev amd64 3.4-3ubuntu0.1 [384 kB] | |
| Get:162 http://archive.ubuntu.com/ubuntu/ trusty/main libp11-kit-dev amd64 0.20.2-2ubuntu2 [56.4 kB] | |
| Get:163 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgnutls-dev amd64 2.12.23-12ubuntu2.1 [371 kB] | |
| Get:164 http://archive.ubuntu.com/ubuntu/ trusty/main librtmp-dev amd64 2.4+20121230.gitdf6c518-1 [67.1 kB] | |
| Get:165 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libssl-dev amd64 1.0.1f-1ubuntu2.5 [1,067 kB] | |
| Get:166 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libcurl4-openssl-dev amd64 7.35.0-1ubuntu2.1 [244 kB] | |
| Get:167 http://archive.ubuntu.com/ubuntu/ trusty/main libgconf2-4 amd64 3.2.6-0ubuntu2 [2,042 B] | |
| Get:168 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgphoto2-l10n all 2.5.3.1-1ubuntu2.2 [7,602 B] | |
| Get:169 http://archive.ubuntu.com/ubuntu/ trusty/main libgsl0-dev amd64 1.16+dfsg-1ubuntu1 [982 kB] | |
| Get:170 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgtk-3-bin amd64 3.10.8-0ubuntu1.2 [18.1 kB] | |
| Get:171 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgtk2.0-bin amd64 2.24.23-0ubuntu1.1 [9,738 B] | |
| Get:172 http://archive.ubuntu.com/ubuntu/ trusty/main xorg-sgml-doctools all 1:1.11-1 [12.9 kB] | |
| Get:173 http://archive.ubuntu.com/ubuntu/ trusty/main x11proto-core-dev all 7.0.24-1 [748 kB] | |
| Get:174 http://archive.ubuntu.com/ubuntu/ trusty/main libice-dev amd64 2:1.0.8-2 [57.6 kB] | |
| Get:175 http://archive.ubuntu.com/ubuntu/ trusty/main liblapack3 amd64 3.5.0-2ubuntu1 [1,730 kB] | |
| Get:176 http://archive.ubuntu.com/ubuntu/ trusty/main liblapack-dev amd64 3.5.0-2ubuntu1 [1,740 kB] | |
| Get:177 http://archive.ubuntu.com/ubuntu/ trusty/main libtinfo-dev amd64 5.9+20140118-1ubuntu1 [76.3 kB] | |
| Get:178 http://archive.ubuntu.com/ubuntu/ trusty/main libncurses5-dev amd64 5.9+20140118-1ubuntu1 [170 kB] | |
| Get:179 http://archive.ubuntu.com/ubuntu/ trusty/universe libnetcdfc7 amd64 1:4.1.3-7ubuntu2 [247 kB] | |
| Get:180 http://archive.ubuntu.com/ubuntu/ trusty/universe libnetcdff5 amd64 1:4.1.3-7ubuntu2 [72.5 kB] | |
| Get:181 http://archive.ubuntu.com/ubuntu/ trusty/universe libnetcdfc++4 amd64 1:4.1.3-7ubuntu2 [29.7 kB] | |
| Get:182 http://archive.ubuntu.com/ubuntu/ trusty/universe libnetcdf-dev amd64 1:4.1.3-7ubuntu2 [429 kB] | |
| Get:183 http://archive.ubuntu.com/ubuntu/ trusty/main libpcre3-dev amd64 1:8.31-2ubuntu2 [237 kB] | |
| Get:184 http://archive.ubuntu.com/ubuntu/ trusty/main libpng12-dev amd64 1.2.50-1ubuntu2 [206 kB] | |
| Get:185 http://archive.ubuntu.com/ubuntu/ trusty/main libpthread-stubs0-dev amd64 0.3-4 [4,068 B] | |
| Get:186 http://archive.ubuntu.com/ubuntu/ trusty/main libreadline6-dev amd64 6.3-4ubuntu2 [213 kB] | |
| Get:187 http://archive.ubuntu.com/ubuntu/ trusty/main libreadline-dev amd64 6.3-4ubuntu2 [988 B] | |
| Get:188 http://archive.ubuntu.com/ubuntu/ trusty/main libsm-dev amd64 2:1.2.1-2 [19.9 kB] | |
| Get:189 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libssl-doc all 1.0.1f-1ubuntu2.5 [966 kB] | |
| Get:190 http://archive.ubuntu.com/ubuntu/ trusty/main libxau-dev amd64 1:1.0.8-1 [11.1 kB] | |
| Get:191 http://archive.ubuntu.com/ubuntu/ trusty/main libxdmcp-dev amd64 1:1.1.1-1 [26.9 kB] | |
| Get:192 http://archive.ubuntu.com/ubuntu/ trusty/main x11proto-input-dev all 2.3-1 [139 kB] | |
| Get:193 http://archive.ubuntu.com/ubuntu/ trusty/main x11proto-kb-dev all 1.0.6-2 [269 kB] | |
| Get:194 http://archive.ubuntu.com/ubuntu/ trusty/main xtrans-dev all 1.3.2-1 [69.9 kB] | |
| Get:195 http://archive.ubuntu.com/ubuntu/ trusty/main libxcb1-dev amd64 1.10-2ubuntu1 [76.6 kB] | |
| Get:196 http://archive.ubuntu.com/ubuntu/ trusty/main libx11-dev amd64 2:1.6.2-1ubuntu2 [629 kB] | |
| Get:197 http://archive.ubuntu.com/ubuntu/ trusty/main libx11-doc all 2:1.6.2-1ubuntu2 [1,448 kB] | |
| Get:198 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libxml2-dev amd64 2.9.1+dfsg1-3ubuntu4.3 [630 kB] | |
| Get:199 http://archive.ubuntu.com/ubuntu/ trusty/main libxslt1-dev amd64 1.1.28-2build1 [407 kB] | |
| Get:200 http://archive.ubuntu.com/ubuntu/ trusty/main libxt-dev amd64 1:1.1.4-1 [455 kB] | |
| Get:201 http://archive.ubuntu.com/ubuntu/ trusty/main libzip2 amd64 0.10.1-1.2 [29.0 kB] | |
| Get:202 http://archive.ubuntu.com/ubuntu/ trusty/main libzip-dev amd64 0.10.1-1.2 [112 kB] | |
| Get:203 http://archive.ubuntu.com/ubuntu/ trusty/universe maq amd64 0.7.1-5 [298 kB] | |
| Get:204 http://archive.ubuntu.com/ubuntu/ trusty-updates/main openjdk-7-jdk amd64 7u65-2.5.2-3~14.04 [16.1 MB] | |
| Get:205 http://archive.ubuntu.com/ubuntu/ trusty/universe plink amd64 1.07-3 [1,208 kB] | |
| Get:206 http://archive.ubuntu.com/ubuntu/ trusty/main policykit-1-gnome amd64 0.105-1ubuntu4 [27.8 kB] | |
| Get:207 http://archive.ubuntu.com/ubuntu/ trusty/main python-pil amd64 2.3.0-1ubuntu3 [279 kB] | |
| Get:208 http://archive.ubuntu.com/ubuntu/ trusty/main python-imaging all 2.3.0-1ubuntu3 [4,348 B] | |
| Get:209 http://archive.ubuntu.com/ubuntu/ trusty/universe tabix amd64 0.2.6-2 [43.4 kB] | |
| Get:210 http://archive.ubuntu.com/ubuntu/ trusty/universe libeigen3-dev all 3.2.0-8 [494 kB] | |
| Get:211 http://archive.ubuntu.com/ubuntu/ trusty/main liblzma-dev amd64 5.1.1alpha+20120614-2ubuntu2 [137 kB] | |
| Fetched 104 MB in 49s (2,083 kB/s) | |
| Extracting templates from packages: 100% | |
| Selecting previously unselected package libasound2-data. | |
| (Reading database ... 62976 files and directories currently installed.) | |
| Preparing to unpack .../libasound2-data_1.0.27.2-3ubuntu7_all.deb ... | |
| Unpacking libasound2-data (1.0.27.2-3ubuntu7) ... | |
| Selecting previously unselected package libasound2:amd64. | |
| Preparing to unpack .../libasound2_1.0.27.2-3ubuntu7_amd64.deb ... | |
| Unpacking libasound2:amd64 (1.0.27.2-3ubuntu7) ... | |
| Selecting previously unselected package libasyncns0:amd64. | |
| Preparing to unpack .../libasyncns0_0.8-4ubuntu2_amd64.deb ... | |
| Unpacking libasyncns0:amd64 (0.8-4ubuntu2) ... | |
| Selecting previously unselected package libatasmart4:amd64. | |
| Preparing to unpack .../libatasmart4_0.19-3_amd64.deb ... | |
| Unpacking libatasmart4:amd64 (0.19-3) ... | |
| Selecting previously unselected package libatk1.0-data. | |
| Preparing to unpack .../libatk1.0-data_2.10.0-2ubuntu2_all.deb ... | |
| Unpacking libatk1.0-data (2.10.0-2ubuntu2) ... | |
| Selecting previously unselected package libatk1.0-0:amd64. | |
| Preparing to unpack .../libatk1.0-0_2.10.0-2ubuntu2_amd64.deb ... | |
| Unpacking libatk1.0-0:amd64 (2.10.0-2ubuntu2) ... | |
| Selecting previously unselected package libatspi2.0-0:amd64. | |
| Preparing to unpack .../libatspi2.0-0_2.10.2.is.2.10.1-0ubuntu1_amd64.deb ... | |
| Unpacking libatspi2.0-0:amd64 (2.10.2.is.2.10.1-0ubuntu1) ... | |
| Selecting previously unselected package libatk-bridge2.0-0:amd64. | |
| Preparing to unpack .../libatk-bridge2.0-0_2.10.2-2ubuntu1_amd64.deb ... | |
| Unpacking libatk-bridge2.0-0:amd64 (2.10.2-2ubuntu1) ... | |
| Selecting previously unselected package libgtk2.0-common. | |
| Preparing to unpack .../libgtk2.0-common_2.24.23-0ubuntu1.1_all.deb ... | |
| Unpacking libgtk2.0-common (2.24.23-0ubuntu1.1) ... | |
| Selecting previously unselected package fonts-dejavu-core. | |
| Preparing to unpack .../fonts-dejavu-core_2.34-1ubuntu1_all.deb ... | |
| Unpacking fonts-dejavu-core (2.34-1ubuntu1) ... | |
| Selecting previously unselected package fontconfig-config. | |
| Preparing to unpack .../fontconfig-config_2.11.0-0ubuntu4.1_all.deb ... | |
| Unpacking fontconfig-config (2.11.0-0ubuntu4.1) ... | |
| Selecting previously unselected package libfontconfig1:amd64. | |
| Preparing to unpack .../libfontconfig1_2.11.0-0ubuntu4.1_amd64.deb ... | |
| Unpacking libfontconfig1:amd64 (2.11.0-0ubuntu4.1) ... | |
| Selecting previously unselected package libxcb-render0:amd64. | |
| Preparing to unpack .../libxcb-render0_1.10-2ubuntu1_amd64.deb ... | |
| Unpacking libxcb-render0:amd64 (1.10-2ubuntu1) ... | |
| Selecting previously unselected package libxcb-shm0:amd64. | |
| Preparing to unpack .../libxcb-shm0_1.10-2ubuntu1_amd64.deb ... | |
| Unpacking libxcb-shm0:amd64 (1.10-2ubuntu1) ... | |
| Selecting previously unselected package libcairo2:amd64. | |
| Preparing to unpack .../libcairo2_1.13.0~20140204-0ubuntu1_amd64.deb ... | |
| Unpacking libcairo2:amd64 (1.13.0~20140204-0ubuntu1) ... | |
| Selecting previously unselected package libavahi-common-data:amd64. | |
| Preparing to unpack .../libavahi-common-data_0.6.31-4ubuntu1_amd64.deb ... | |
| Unpacking libavahi-common-data:amd64 (0.6.31-4ubuntu1) ... | |
| Selecting previously unselected package libavahi-common3:amd64. | |
| Preparing to unpack .../libavahi-common3_0.6.31-4ubuntu1_amd64.deb ... | |
| Unpacking libavahi-common3:amd64 (0.6.31-4ubuntu1) ... | |
| Selecting previously unselected package libavahi-client3:amd64. | |
| Preparing to unpack .../libavahi-client3_0.6.31-4ubuntu1_amd64.deb ... | |
| Unpacking libavahi-client3:amd64 (0.6.31-4ubuntu1) ... | |
| Selecting previously unselected package libcups2:amd64. | |
| Preparing to unpack .../libcups2_1.7.2-0ubuntu1.2_amd64.deb ... | |
| Unpacking libcups2:amd64 (1.7.2-0ubuntu1.2) ... | |
| Selecting previously unselected package libjpeg-turbo8:amd64. | |
| Preparing to unpack .../libjpeg-turbo8_1.3.0-0ubuntu2_amd64.deb ... | |
| Unpacking libjpeg-turbo8:amd64 (1.3.0-0ubuntu2) ... | |
| Selecting previously unselected package libjpeg8:amd64. | |
| Preparing to unpack .../libjpeg8_8c-2ubuntu8_amd64.deb ... | |
| Unpacking libjpeg8:amd64 (8c-2ubuntu8) ... | |
| Selecting previously unselected package libjasper1:amd64. | |
| Preparing to unpack .../libjasper1_1.900.1-14ubuntu3_amd64.deb ... | |
| Unpacking libjasper1:amd64 (1.900.1-14ubuntu3) ... | |
| Selecting previously unselected package libjbig0:amd64. | |
| Preparing to unpack .../libjbig0_2.0-2ubuntu4.1_amd64.deb ... | |
| Unpacking libjbig0:amd64 (2.0-2ubuntu4.1) ... | |
| Selecting previously unselected package libtiff5:amd64. | |
| Preparing to unpack .../libtiff5_4.0.3-7ubuntu0.1_amd64.deb ... | |
| Unpacking libtiff5:amd64 (4.0.3-7ubuntu0.1) ... | |
| Selecting previously unselected package libgdk-pixbuf2.0-common. | |
| Preparing to unpack .../libgdk-pixbuf2.0-common_2.30.7-0ubuntu1_all.deb ... | |
| Unpacking libgdk-pixbuf2.0-common (2.30.7-0ubuntu1) ... | |
| Selecting previously unselected package libgdk-pixbuf2.0-0:amd64. | |
| Preparing to unpack .../libgdk-pixbuf2.0-0_2.30.7-0ubuntu1_amd64.deb ... | |
| Unpacking libgdk-pixbuf2.0-0:amd64 (2.30.7-0ubuntu1) ... | |
| Selecting previously unselected package libthai-data. | |
| Preparing to unpack .../libthai-data_0.1.20-3_all.deb ... | |
| Unpacking libthai-data (0.1.20-3) ... | |
| Selecting previously unselected package libdatrie1:amd64. | |
| Preparing to unpack .../libdatrie1_0.2.8-1_amd64.deb ... | |
| Unpacking libdatrie1:amd64 (0.2.8-1) ... | |
| Selecting previously unselected package libthai0:amd64. | |
| Preparing to unpack .../libthai0_0.1.20-3_amd64.deb ... | |
| Unpacking libthai0:amd64 (0.1.20-3) ... | |
| Selecting previously unselected package fontconfig. | |
| Preparing to unpack .../fontconfig_2.11.0-0ubuntu4.1_amd64.deb ... | |
| Unpacking fontconfig (2.11.0-0ubuntu4.1) ... | |
| Selecting previously unselected package libpango-1.0-0:amd64. | |
| Preparing to unpack .../libpango-1.0-0_1.36.3-1ubuntu1_amd64.deb ... | |
| Unpacking libpango-1.0-0:amd64 (1.36.3-1ubuntu1) ... | |
| Selecting previously unselected package libgraphite2-3:amd64. | |
| Preparing to unpack .../libgraphite2-3_1.2.4-1ubuntu1_amd64.deb ... | |
| Unpacking libgraphite2-3:amd64 (1.2.4-1ubuntu1) ... | |
| Selecting previously unselected package libharfbuzz0b:amd64. | |
| Preparing to unpack .../libharfbuzz0b_0.9.27-1ubuntu1_amd64.deb ... | |
| Unpacking libharfbuzz0b:amd64 (0.9.27-1ubuntu1) ... | |
| Selecting previously unselected package libpangoft2-1.0-0:amd64. | |
| Preparing to unpack .../libpangoft2-1.0-0_1.36.3-1ubuntu1_amd64.deb ... | |
| Unpacking libpangoft2-1.0-0:amd64 (1.36.3-1ubuntu1) ... | |
| Selecting previously unselected package libpangocairo-1.0-0:amd64. | |
| Preparing to unpack .../libpangocairo-1.0-0_1.36.3-1ubuntu1_amd64.deb ... | |
| Unpacking libpangocairo-1.0-0:amd64 (1.36.3-1ubuntu1) ... | |
| Selecting previously unselected package libxcursor1:amd64. | |
| Preparing to unpack .../libxcursor1_1%3a1.1.14-1_amd64.deb ... | |
| Unpacking libxcursor1:amd64 (1:1.1.14-1) ... | |
| Selecting previously unselected package libxi6:amd64. | |
| Preparing to unpack .../libxi6_2%3a1.7.1.901-1ubuntu1_amd64.deb ... | |
| Unpacking libxi6:amd64 (2:1.7.1.901-1ubuntu1) ... | |
| Selecting previously unselected package libxinerama1:amd64. | |
| Preparing to unpack .../libxinerama1_2%3a1.1.3-1_amd64.deb ... | |
| Unpacking libxinerama1:amd64 (2:1.1.3-1) ... | |
| Selecting previously unselected package libgtk2.0-0:amd64. | |
| Preparing to unpack .../libgtk2.0-0_2.24.23-0ubuntu1.1_amd64.deb ... | |
| Unpacking libgtk2.0-0:amd64 (2.24.23-0ubuntu1.1) ... | |
| Selecting previously unselected package libnspr4:amd64. | |
| Preparing to unpack .../libnspr4_2%3a4.10.7-0ubuntu0.14.04.1_amd64.deb ... | |
| Unpacking libnspr4:amd64 (2:4.10.7-0ubuntu0.14.04.1) ... | |
| Selecting previously unselected package libnss3-nssdb. | |
| Preparing to unpack .../libnss3-nssdb_2%3a3.17.1-0ubuntu0.14.04.1_all.deb ... | |
| Unpacking libnss3-nssdb (2:3.17.1-0ubuntu0.14.04.1) ... | |
| Selecting previously unselected package libnss3:amd64. | |
| Preparing to unpack .../libnss3_2%3a3.17.1-0ubuntu0.14.04.1_amd64.deb ... | |
| Unpacking libnss3:amd64 (2:3.17.1-0ubuntu0.14.04.1) ... | |
| Selecting previously unselected package ca-certificates-java. | |
| Preparing to unpack .../ca-certificates-java_20130815ubuntu1_all.deb ... | |
| Unpacking ca-certificates-java (20130815ubuntu1) ... | |
| Selecting previously unselected package tzdata-java. | |
| Preparing to unpack .../tzdata-java_2014e-0ubuntu0.14.04_all.deb ... | |
| Unpacking tzdata-java (2014e-0ubuntu0.14.04) ... | |
| Selecting previously unselected package java-common. | |
| Preparing to unpack .../java-common_0.51_all.deb ... | |
| Unpacking java-common (0.51) ... | |
| Selecting previously unselected package liblcms2-2:amd64. | |
| Preparing to unpack .../liblcms2-2_2.5-0ubuntu4_amd64.deb ... | |
| Unpacking liblcms2-2:amd64 (2.5-0ubuntu4) ... | |
| Selecting previously unselected package libnss3-1d:amd64. | |
| Preparing to unpack .../libnss3-1d_2%3a3.17.1-0ubuntu0.14.04.1_amd64.deb ... | |
| Unpacking libnss3-1d:amd64 (2:3.17.1-0ubuntu0.14.04.1) ... | |
| Selecting previously unselected package libpcsclite1:amd64. | |
| Preparing to unpack .../libpcsclite1_1.8.10-1ubuntu1_amd64.deb ... | |
| Unpacking libpcsclite1:amd64 (1.8.10-1ubuntu1) ... | |
| Selecting previously unselected package openjdk-7-jre-headless:amd64. | |
| Preparing to unpack .../openjdk-7-jre-headless_7u65-2.5.2-3~14.04_amd64.deb ... | |
| Unpacking openjdk-7-jre-headless:amd64 (7u65-2.5.2-3~14.04) ... | |
| Selecting previously unselected package libgif4:amd64. | |
| Preparing to unpack .../libgif4_4.1.6-11_amd64.deb ... | |
| Unpacking libgif4:amd64 (4.1.6-11) ... | |
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| Setting up fonts-dejavu-extra (2.34-1ubuntu1) ... | |
| Setting up libgsl0ldbl (1.16+dfsg-1ubuntu1) ... | |
| Setting up gsl-bin (1.16+dfsg-1ubuntu1) ... | |
| Setting up x11-utils (7.7+1) ... | |
| Setting up udisks2 (2.1.3-1) ... | |
| Setting up gvfs-common (1.20.1-1ubuntu1) ... | |
| Setting up gvfs-libs:amd64 (1.20.1-1ubuntu1) ... | |
| Setting up gvfs-daemons (1.20.1-1ubuntu1) ... | |
| Setting up gvfs:amd64 (1.20.1-1ubuntu1) ... | |
| Setting up hicolor-icon-theme (0.13-1) ... | |
| Setting up comerr-dev (2.1-1.42.9-3ubuntu1) ... | |
| Setting up krb5-multidev (1.12+dfsg-2ubuntu4.2) ... | |
| Setting up last-align (393-1) ... | |
| Setting up libatlas3-base (3.10.1-4) ... | |
| update-alternatives: using /usr/lib/atlas-base/atlas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode | |
| update-alternatives: using /usr/lib/atlas-base/atlas/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode | |
| Setting up libblas3 (1.2.20110419-7) ... | |
| Setting up libblas-dev (1.2.20110419-7) ... | |
| update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode | |
| Setting up libatlas-dev (3.10.1-4) ... | |
| Setting up libatlas-base-dev (3.10.1-4) ... | |
| update-alternatives: using /usr/lib/atlas-base/atlas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode | |
| update-alternatives: using /usr/lib/atlas-base/atlas/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode | |
| Setting up libbz2-dev:amd64 (1.0.6-5) ... | |
| Setting up libcf0 (1:4.1.3-7ubuntu2) ... | |
| Setting up pkg-config (0.26-1ubuntu4) ... | |
| Setting up libidn11-dev (1.28-1ubuntu2) ... | |
| Setting up libkrb5-dev (1.12+dfsg-2ubuntu4.2) ... | |
| Setting up libldap2-dev:amd64 (2.4.31-1+nmu2ubuntu8) ... | |
| Setting up libgpg-error-dev (1.12-0.2ubuntu1) ... | |
| Setting up libgcrypt11-dev (1.5.3-2ubuntu4.1) ... | |
| Setting up libtasn1-6-dev (3.4-3ubuntu0.1) ... | |
| Setting up libp11-kit-dev (0.20.2-2ubuntu2) ... | |
| Setting up libgnutls-dev (2.12.23-12ubuntu2.1) ... | |
| Setting up librtmp-dev (2.4+20121230.gitdf6c518-1) ... | |
| Setting up libssl-dev:amd64 (1.0.1f-1ubuntu2.5) ... | |
| Setting up libcurl4-openssl-dev:amd64 (7.35.0-1ubuntu2.1) ... | |
| Setting up libgphoto2-l10n (2.5.3.1-1ubuntu2.2) ... | |
| Setting up libgsl0-dev (1.16+dfsg-1ubuntu1) ... | |
| Setting up libgtk-3-bin (3.10.8-0ubuntu1.2) ... | |
| Setting up libgtk2.0-bin (2.24.23-0ubuntu1.1) ... | |
| Setting up xorg-sgml-doctools (1:1.11-1) ... | |
| Setting up x11proto-core-dev (7.0.24-1) ... | |
| Setting up libice-dev:amd64 (2:1.0.8-2) ... | |
| Setting up liblapack3 (3.5.0-2ubuntu1) ... | |
| update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode | |
| Setting up liblapack-dev (3.5.0-2ubuntu1) ... | |
| update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode | |
| Setting up libtinfo-dev:amd64 (5.9+20140118-1ubuntu1) ... | |
| Setting up libncurses5-dev:amd64 (5.9+20140118-1ubuntu1) ... | |
| Setting up libnetcdfc7 (1:4.1.3-7ubuntu2) ... | |
| Setting up libnetcdff5 (1:4.1.3-7ubuntu2) ... | |
| Setting up libnetcdfc++4 (1:4.1.3-7ubuntu2) ... | |
| Setting up libnetcdf-dev (1:4.1.3-7ubuntu2) ... | |
| Setting up libpcre3-dev:amd64 (1:8.31-2ubuntu2) ... | |
| Setting up libpng12-dev (1.2.50-1ubuntu2) ... | |
| Setting up libpthread-stubs0-dev:amd64 (0.3-4) ... | |
| Setting up libreadline6-dev:amd64 (6.3-4ubuntu2) ... | |
| Setting up libreadline-dev:amd64 (6.3-4ubuntu2) ... | |
| Setting up libsm-dev:amd64 (2:1.2.1-2) ... | |
| Setting up libssl-doc (1.0.1f-1ubuntu2.5) ... | |
| Setting up libxau-dev:amd64 (1:1.0.8-1) ... | |
| Setting up libxdmcp-dev:amd64 (1:1.1.1-1) ... | |
| Setting up x11proto-input-dev (2.3-1) ... | |
| Setting up x11proto-kb-dev (1.0.6-2) ... | |
| Setting up xtrans-dev (1.3.2-1) ... | |
| Setting up libxcb1-dev:amd64 (1.10-2ubuntu1) ... | |
| Setting up libx11-dev:amd64 (2:1.6.2-1ubuntu2) ... | |
| Setting up libx11-doc (2:1.6.2-1ubuntu2) ... | |
| Setting up libxml2-dev:amd64 (2.9.1+dfsg1-3ubuntu4.3) ... | |
| Setting up libxslt1-dev:amd64 (1.1.28-2build1) ... | |
| Setting up libxt-dev:amd64 (1:1.1.4-1) ... | |
| Setting up libzip2 (0.10.1-1.2) ... | |
| Setting up libzip-dev (0.10.1-1.2) ... | |
| Setting up maq (0.7.1-5) ... | |
| Setting up plink (1.07-3) ... | |
| Setting up policykit-1-gnome (0.105-1ubuntu4) ... | |
| Setting up python-pil (2.3.0-1ubuntu3) ... | |
| Setting up python-imaging (2.3.0-1ubuntu3) ... | |
| Setting up tabix (0.2.6-2) ... | |
| Setting up libeigen3-dev (3.2.0-8) ... | |
| Setting up liblzma-dev:amd64 (5.1.1alpha+20120614-2ubuntu2) ... | |
| Setting up gconf-service (3.2.6-0ubuntu2) ... | |
| Setting up libgconf2-4:amd64 (3.2.6-0ubuntu2) ... | |
| Setting up libnss3-nssdb (2:3.17.1-0ubuntu0.14.04.1) ... | |
| Setting up libnss3:amd64 (2:3.17.1-0ubuntu0.14.04.1) ... | |
| Setting up libnss3-1d:amd64 (2:3.17.1-0ubuntu0.14.04.1) ... | |
| Setting up openjdk-7-jre-headless:amd64 (7u65-2.5.2-3~14.04) ... | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java to provide /usr/bin/java (java) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode | |
| Setting up openjdk-7-jre:amd64 (7u65-2.5.2-3~14.04) ... | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode | |
| Setting up libatk-wrapper-java (0.30.4-4) ... | |
| Setting up gconf-service-backend (3.2.6-0ubuntu2) ... | |
| Setting up gconf2 (3.2.6-0ubuntu2) ... | |
| update-alternatives: using /usr/bin/gconftool-2 to provide /usr/bin/gconftool (gconftool) in auto mode | |
| (gconftool-2:23330): GConf-WARNING **: Client failed to connect to the D-BUS daemon: | |
| Unable to autolaunch a dbus-daemon without a $DISPLAY for X11 | |
| Setting up libgnomevfs2-common (1:2.24.4-1ubuntu6) ... | |
| Setting up libgnomevfs2-0:amd64 (1:2.24.4-1ubuntu6) ... | |
| Setting up libgnome2-common (2.32.1-4ubuntu1) ... | |
| Setting up libgnome2-bin (2.32.1-4ubuntu1) ... | |
| Setting up libgnome2-0:amd64 (2.32.1-4ubuntu1) ... | |
| Setting up openjdk-7-jdk:amd64 (7u65-2.5.2-3~14.04) ... | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/appletviewer to provide /usr/bin/appletviewer (appletviewer) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/javah to provide /usr/bin/javah (javah) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode | |
| update-alternatives: using /usr/lib/jvm/java-7-openjdk-amd64/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode | |
| Setting up ca-certificates-java (20130815ubuntu1) ... | |
| Adding debian:Entrust_Root_Certification_Authority.pem | |
| Adding debian:GlobalSign_Root_CA.pem | |
| Adding debian:VeriSign_Universal_Root_Certification_Authority.pem | |
| Adding debian:PSCProcert.pem | |
| Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem | |
| Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem | |
| Adding debian:QuoVadis_Root_CA_3.pem | |
| Adding debian:Certinomis_-_Autorité_Racine.pem | |
| Adding debian:TC_TrustCenter_Class_3_CA_II.pem | |
| Adding debian:Certum_Trusted_Network_CA.pem | |
| Adding debian:Chambers_of_Commerce_Root_-_2008.pem | |
| Adding debian:Entrust.net_Secure_Server_CA.pem | |
| Adding debian:SwissSign_Platinum_CA_-_G2.pem | |
| Adding debian:Secure_Global_CA.pem | |
| Adding debian:certSIGN_ROOT_CA.pem | |
| Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem | |
| Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G2.pem | |
| Adding debian:thawte_Primary_Root_CA_-_G3.pem | |
| Adding debian:QuoVadis_Root_CA.pem | |
| Adding debian:EBG_Elektronik_Sertifika_Hizmet_Sağlayıcısı.pem | |
| Adding debian:Camerfirma_Global_Chambersign_Root.pem | |
| Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G2.pem | |
| Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority.pem | |
| Adding debian:UTN_USERFirst_Email_Root_CA.pem | |
| Adding debian:ePKI_Root_Certification_Authority.pem | |
| Adding debian:EE_Certification_Centre_Root_CA.pem | |
| Adding debian:ComSign_CA.pem | |
| Adding debian:CA_Disig_Root_R1.pem | |
| Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem | |
| Adding debian:XRamp_Global_CA_Root.pem | |
| Adding debian:Comodo_Trusted_Services_root.pem | |
| Adding debian:Visa_eCommerce_Root.pem | |
| Adding debian:Baltimore_CyberTrust_Root.pem | |
| Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem | |
| Adding debian:Cybertrust_Global_Root.pem | |
| Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem | |
| Adding debian:TÜBİTAK_UEKAE_Kök_Sertifika_Hizmet_Sağlayıcısı_-_Sürüm_3.pem | |
| Adding debian:GlobalSign_Root_CA_-_R2.pem | |
| Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_2.pem | |
| Adding debian:AddTrust_Public_Services_Root.pem | |
| Adding debian:Verisign_Class_4_Public_Primary_Certification_Authority_-_G3.pem | |
| Adding debian:Juur-SK.pem | |
| Adding debian:Thawte_Server_CA.pem | |
| Adding debian:Sonera_Class_2_Root_CA.pem | |
| Adding debian:UTN_USERFirst_Hardware_Root_CA.pem | |
| Adding debian:Go_Daddy_Class_2_CA.pem | |
| Adding debian:AffirmTrust_Commercial.pem | |
| Adding debian:Digital_Signature_Trust_Co._Global_CA_3.pem | |
| Adding debian:GeoTrust_Global_CA_2.pem | |
| Adding debian:NetLock_Express_=Class_C=_Root.pem | |
| Adding debian:Comodo_Secure_Services_root.pem | |
| Adding debian:TURKTRUST_Certificate_Services_Provider_Root_1.pem | |
| Adding debian:EC-ACC.pem | |
| Adding debian:Network_Solutions_Certificate_Authority.pem | |
| Adding debian:TDC_Internet_Root_CA.pem | |
| Adding debian:Verisign_Class_2_Public_Primary_Certification_Authority_-_G3.pem | |
| Adding debian:Staat_der_Nederlanden_Root_CA.pem | |
| Adding debian:Swisscom_Root_CA_1.pem | |
| Adding debian:GlobalSign_Root_CA_-_R3.pem | |
| Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem | |
| Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem | |
| Adding debian:GeoTrust_Global_CA.pem | |
| Adding debian:Root_CA_Generalitat_Valenciana.pem | |
| Adding debian:Digital_Signature_Trust_Co._Global_CA_1.pem | |
| Adding debian:Microsec_e-Szigno_Root_CA_2009.pem | |
| Adding debian:thawte_Primary_Root_CA_-_G2.pem | |
| Adding debian:Firmaprofesional_Root_CA.pem | |
| Adding debian:A-Trust-nQual-03.pem | |
| Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem | |
| Adding debian:ValiCert_Class_2_VA.pem | |
| Adding debian:CNNIC_ROOT.pem | |
| Adding debian:UTN_DATACorp_SGC_Root_CA.pem | |
| Adding debian:AddTrust_Low-Value_Services_Root.pem | |
| Adding debian:DST_ACES_CA_X6.pem | |
| Adding debian:Security_Communication_Root_CA.pem | |
| Adding debian:ComSign_Secured_CA.pem | |
| Adding debian:QuoVadis_Root_CA_2.pem | |
| Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem | |
| Adding debian:RSA_Root_Certificate_1.pem | |
| Adding debian:ACEDICOM_Root.pem | |
| Adding debian:WellsSecure_Public_Root_Certificate_Authority.pem | |
| Adding debian:Buypass_Class_3_CA_1.pem | |
| Adding debian:SwissSign_Gold_CA_-_G2.pem | |
| Adding debian:ApplicationCA_-_Japanese_Government.pem | |
| Adding debian:CA_Disig.pem | |
| Adding debian:Equifax_Secure_Global_eBusiness_CA.pem | |
| Adding debian:Deutsche_Telekom_Root_CA_2.pem | |
| Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem | |
| Adding debian:DST_Root_CA_X3.pem | |
| Adding debian:E-Guven_Kok_Elektronik_Sertifika_Hizmet_Saglayicisi.pem | |
| Adding debian:SecureSign_RootCA11.pem | |
| Adding debian:Swisscom_Root_EV_CA_2.pem | |
| Adding debian:StartCom_Certification_Authority_G2.pem | |
| Adding debian:TC_TrustCenter_Universal_CA_I.pem | |
| Adding debian:IGC_A.pem | |
| Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2.pem | |
| Adding debian:Camerfirma_Chambers_of_Commerce_Root.pem | |
| Adding debian:thawte_Primary_Root_CA.pem | |
| Adding debian:T-TeleSec_GlobalRoot_Class_3.pem | |
| Adding debian:Wells_Fargo_Root_CA.pem | |
| Adding debian:AddTrust_External_Root.pem | |
| Adding debian:CA_Disig_Root_R2.pem | |
| Adding debian:Security_Communication_RootCA2.pem | |
| Adding debian:StartCom_Certification_Authority.pem | |
| Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem | |
| Adding debian:Equifax_Secure_eBusiness_CA_1.pem | |
| Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority_-_G3.pem | |
| Adding debian:Comodo_AAA_Services_root.pem | |
| Adding debian:Certplus_Class_2_Primary_CA.pem | |
| Adding debian:AffirmTrust_Premium.pem | |
| Adding debian:SwissSign_Silver_CA_-_G2.pem | |
| Adding debian:DigiCert_Global_Root_CA.pem | |
| Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem | |
| Adding debian:Equifax_Secure_CA.pem | |
| Adding debian:DigiCert_Assured_ID_Root_CA.pem | |
| Adding debian:Buypass_Class_3_Root_CA.pem | |
| Adding debian:NetLock_Notary_=Class_A=_Root.pem | |
| Adding debian:GeoTrust_Universal_CA_2.pem | |
| Adding debian:Sonera_Class_1_Root_CA.pem | |
| Adding debian:NetLock_Qualified_=Class_QA=_Root.pem | |
| Adding debian:Izenpe.com.pem | |
| Adding debian:Buypass_Class_2_CA_1.pem | |
| Adding debian:China_Internet_Network_Information_Center_EV_Certificates_Root.pem | |
| Adding debian:AC_Raíz_Certicámara_S.A..pem | |
| Adding debian:America_Online_Root_Certification_Authority_2.pem | |
| Adding debian:RSA_Security_2048_v3.pem | |
| Adding debian:GTE_CyberTrust_Global_Root.pem | |
| Adding debian:Verisign_Class_1_Public_Primary_Certification_Authority.pem | |
| Adding debian:TC_TrustCenter_Class_2_CA_II.pem | |
| Adding debian:Microsec_e-Szigno_Root_CA.pem | |
| Adding debian:Buypass_Class_2_Root_CA.pem | |
| Adding debian:Certigna.pem | |
| Adding debian:Global_Chambersign_Root_-_2008.pem | |
| Adding debian:COMODO_ECC_Certification_Authority.pem | |
| Adding debian:AddTrust_Qualified_Certificates_Root.pem | |
| Adding debian:Swisscom_Root_CA_2.pem | |
| Adding debian:Trustis_FPS_Root_CA.pem | |
| Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem | |
| Adding debian:Actalis_Authentication_Root_CA.pem | |
| Adding debian:ValiCert_Class_1_VA.pem | |
| Adding debian:Certum_Root_CA.pem | |
| Adding debian:NetLock_Business_=Class_B=_Root.pem | |
| Adding debian:spi-cacert-2008.pem | |
| Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G2.pem | |
| Adding debian:America_Online_Root_Certification_Authority_1.pem | |
| Adding debian:S-TRUST_Authentication_and_Encryption_Root_CA_2005_PN.pem | |
| Adding debian:StartCom_Certification_Authority_2.pem | |
| Adding debian:AffirmTrust_Networking.pem | |
| Adding debian:Thawte_Premium_Server_CA.pem | |
| Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem | |
| Adding debian:Security_Communication_EV_RootCA1.pem | |
| Adding debian:TURKTRUST_Certificate_Services_Provider_Root_2007.pem | |
| Adding debian:AffirmTrust_Premium_ECC.pem | |
| Adding debian:GeoTrust_Universal_CA.pem | |
| Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem | |
| Adding debian:COMODO_Certification_Authority.pem | |
| Adding debian:SecureTrust_CA.pem | |
| Adding debian:TDC_OCES_Root_CA.pem | |
| Adding debian:Hongkong_Post_Root_CA_1.pem | |
| Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem | |
| Adding debian:TWCA_Root_Certification_Authority.pem | |
| Adding debian:Taiwan_GRCA.pem | |
| Adding debian:GeoTrust_Primary_Certification_Authority.pem | |
| Adding debian:Starfield_Class_2_CA.pem | |
| done. | |
| Setting up libatk-wrapper-java-jni:amd64 (0.30.4-4) ... | |
| Processing triggers for libc-bin (2.19-0ubuntu6.3) ... | |
| Processing triggers for ca-certificates (20130906ubuntu2) ... | |
| Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. | |
| Running hooks in /etc/ca-certificates/update.d.... | |
| done. | |
| done. | |
| INFO: Package install progress: 30/84 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-get -y --force-yes install uuid uuid-dev xz-utils zlib1g-dev zlib1g-dev clang cmake g++ gcc gfortran libtool make patch pkg-config vim htop sudo bzr cvs git-core mercurial subversion curl wget axel gawk less openssh-server rsync screen" | |
| Reading package lists... Done | |
| Building dependency tree | |
| Reading state information... Done | |
| g++ is already the newest version. | |
| g++ set to manually installed. | |
| gawk is already the newest version. | |
| gcc is already the newest version. | |
| gcc set to manually installed. | |
| less is already the newest version. | |
| make is already the newest version. | |
| make set to manually installed. | |
| pkg-config is already the newest version. | |
| pkg-config set to manually installed. | |
| screen is already the newest version. | |
| sudo is already the newest version. | |
| vim is already the newest version. | |
| wget is already the newest version. | |
| xz-utils is already the newest version. | |
| zlib1g-dev is already the newest version. | |
| curl is already the newest version. | |
| openssh-server is already the newest version. | |
| patch is already the newest version. | |
| rsync is already the newest version. | |
| The following extra packages will be installed: | |
| autotools-dev binfmt-support clang-3.4 cmake-data gfortran-4.8 libapr1 | |
| libaprutil1 libarchive13 libassuan0 libclang-common-3.4-dev libclang1-3.4 | |
| libffi-dev libgfortran-4.8-dev libgpgme11 libltdl-dev liblzo2-2 libnettle4 | |
| libobjc-4.8-dev libobjc4 libossp-uuid16 libserf-1-1 libsvn1 libtcl8.6 | |
| libtk8.6 libutempter0 libxss1 llvm-3.4 llvm-3.4-dev llvm-3.4-runtime | |
| mercurial-common python-bzrlib python-gpgme python-paramiko tcl tcl8.6 tk | |
| tk8.6 xbitmaps xterm | |
| Suggested packages: | |
| bzr-doc bzrtools python-bzrlib.tests codeblocks eclipse mksh rcs | |
| gfortran-multilib gfortran-doc gfortran-4.8-multilib gfortran-4.8-doc | |
| libgfortran3-dbg lrzip gpgsm libtool-doc autoconf automaken gcj-jdk | |
| llvm-3.4-doc qct kdiff3 kdiff3-qt kompare meld tkcvs mgdiff python-mysqldb | |
| python-pygments python-bzrlib-dbg python-kerberos xdg-utils subversion-tools | |
| db5.3-util tcl-tclreadline xfonts-cyrillic | |
| Recommended packages: | |
| wish | |
| The following NEW packages will be installed: | |
| autotools-dev axel binfmt-support bzr clang clang-3.4 cmake cmake-data cvs | |
| gfortran gfortran-4.8 git-core htop libapr1 libaprutil1 libarchive13 | |
| libassuan0 libclang-common-3.4-dev libclang1-3.4 libffi-dev | |
| libgfortran-4.8-dev libgpgme11 libltdl-dev liblzo2-2 libnettle4 | |
| libobjc-4.8-dev libobjc4 libossp-uuid16 libserf-1-1 libsvn1 libtcl8.6 | |
| libtk8.6 libtool libutempter0 libxss1 llvm-3.4 llvm-3.4-dev llvm-3.4-runtime | |
| mercurial mercurial-common python-bzrlib python-gpgme python-paramiko | |
| subversion tcl tcl8.6 tk tk8.6 uuid uuid-dev xbitmaps xterm | |
| 0 upgraded, 52 newly installed, 0 to remove and 6 not upgraded. | |
| Need to get 43.2 MB of archives. | |
| After this operation, 204 MB of additional disk space will be used. | |
| Get:1 http://archive.ubuntu.com/ubuntu/ trusty/main libapr1 amd64 1.5.0-1 [85.1 kB] | |
| Get:2 http://archive.ubuntu.com/ubuntu/ trusty/main libaprutil1 amd64 1.5.3-1 [76.4 kB] | |
| Get:3 http://archive.ubuntu.com/ubuntu/ trusty-updates/main liblzo2-2 amd64 2.06-1.2ubuntu1.1 [46.1 kB] | |
| Get:4 http://archive.ubuntu.com/ubuntu/ trusty/main libnettle4 amd64 2.7.1-1 [121 kB] | |
| Get:5 http://archive.ubuntu.com/ubuntu/ trusty/main libarchive13 amd64 3.1.2-7ubuntu2 [259 kB] | |
| Get:6 http://archive.ubuntu.com/ubuntu/ trusty/main libassuan0 amd64 2.1.1-1ubuntu1 [29.7 kB] | |
| Get:7 http://archive.ubuntu.com/ubuntu/ trusty/main libobjc4 amd64 4.8.2-19ubuntu1 [111 kB] | |
| Get:8 http://archive.ubuntu.com/ubuntu/ trusty/main libobjc-4.8-dev amd64 4.8.2-19ubuntu1 [378 kB] | |
| Get:9 http://archive.ubuntu.com/ubuntu/ trusty/universe libclang1-3.4 amd64 1:3.4-1ubuntu3 [3,534 kB] | |
| Get:10 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgpgme11 amd64 1.4.3-0.1ubuntu5.1 [96.2 kB] | |
| Get:11 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libserf-1-1 amd64 1.3.3-1ubuntu0.1 [42.2 kB] | |
| Get:12 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libsvn1 amd64 1.8.8-1ubuntu3.1 [917 kB] | |
| Get:13 http://archive.ubuntu.com/ubuntu/ trusty/main libtcl8.6 amd64 8.6.1-4ubuntu1 [841 kB] | |
| Get:14 http://archive.ubuntu.com/ubuntu/ trusty/main libxss1 amd64 1:1.2.2-1 [8,582 B] | |
| Get:15 http://archive.ubuntu.com/ubuntu/ trusty/main libtk8.6 amd64 8.6.1-3ubuntu2 [689 kB] | |
| Get:16 http://archive.ubuntu.com/ubuntu/ trusty/main autotools-dev all 20130810.1 [44.3 kB] | |
| Get:17 http://archive.ubuntu.com/ubuntu/ trusty/universe axel amd64 2.4-1 [51.0 kB] | |
| Get:18 http://archive.ubuntu.com/ubuntu/ trusty/main binfmt-support amd64 2.1.4-1 [49.0 kB] | |
| Get:19 http://archive.ubuntu.com/ubuntu/ trusty-updates/main python-bzrlib amd64 2.6.0+bzr6593-1ubuntu1.1 [1,345 kB] | |
| Get:20 http://archive.ubuntu.com/ubuntu/ trusty-updates/main bzr all 2.6.0+bzr6593-1ubuntu1.1 [37.4 kB] | |
| Get:21 http://archive.ubuntu.com/ubuntu/ trusty/universe libclang-common-3.4-dev amd64 1:3.4-1ubuntu3 [667 kB] | |
| Get:22 http://archive.ubuntu.com/ubuntu/ trusty/universe clang-3.4 amd64 1:3.4-1ubuntu3 [8,922 kB] | |
| Get:23 http://archive.ubuntu.com/ubuntu/ trusty/universe clang amd64 1:3.4-0ubuntu1 [2,476 B] | |
| Get:24 http://archive.ubuntu.com/ubuntu/ trusty/main cmake-data all 2.8.12.2-0ubuntu3 [676 kB] | |
| Get:25 http://archive.ubuntu.com/ubuntu/ trusty/main cmake amd64 2.8.12.2-0ubuntu3 [2,618 kB] | |
| Get:26 http://archive.ubuntu.com/ubuntu/ trusty/main cvs amd64 2:1.12.13+real-12 [2,326 kB] | |
| Get:27 http://archive.ubuntu.com/ubuntu/ trusty/main libgfortran-4.8-dev amd64 4.8.2-19ubuntu1 [269 kB] | |
| Get:28 http://archive.ubuntu.com/ubuntu/ trusty/main gfortran-4.8 amd64 4.8.2-19ubuntu1 [4,728 kB] | |
| Get:29 http://archive.ubuntu.com/ubuntu/ trusty/main gfortran amd64 4:4.8.2-1ubuntu6 [1,252 B] | |
| Get:30 http://archive.ubuntu.com/ubuntu/ trusty/main git-core all 1:1.9.1-1 [1,452 B] | |
| Get:31 http://archive.ubuntu.com/ubuntu/ trusty/universe htop amd64 1.0.2-3 [68.0 kB] | |
| Get:32 http://archive.ubuntu.com/ubuntu/ trusty/main libltdl-dev amd64 2.4.2-1.7ubuntu1 [157 kB] | |
| Get:33 http://archive.ubuntu.com/ubuntu/ trusty/main libossp-uuid16 amd64 1.6.2-1.3ubuntu1 [29.6 kB] | |
| Get:34 http://archive.ubuntu.com/ubuntu/ trusty/main libtool amd64 2.4.2-1.7ubuntu1 [188 kB] | |
| Get:35 http://archive.ubuntu.com/ubuntu/ trusty/main libutempter0 amd64 1.1.5-4build1 [8,366 B] | |
| Get:36 http://archive.ubuntu.com/ubuntu/ trusty/main llvm-3.4-runtime amd64 1:3.4-1ubuntu3 [36.2 kB] | |
| Get:37 http://archive.ubuntu.com/ubuntu/ trusty/main llvm-3.4 amd64 1:3.4-1ubuntu3 [1,078 kB] | |
| Get:38 http://archive.ubuntu.com/ubuntu/ trusty/main libffi-dev amd64 3.1~rc1+r3.0.13-12 [99.8 kB] | |
| Get:39 http://archive.ubuntu.com/ubuntu/ trusty/main llvm-3.4-dev amd64 1:3.4-1ubuntu3 [9,801 kB] | |
| Get:40 http://archive.ubuntu.com/ubuntu/ trusty/universe mercurial-common all 2.8.2-1ubuntu1 [1,517 kB] | |
| Get:41 http://archive.ubuntu.com/ubuntu/ trusty/universe mercurial amd64 2.8.2-1ubuntu1 [40.8 kB] | |
| Get:42 http://archive.ubuntu.com/ubuntu/ trusty/main python-gpgme amd64 0.3-0ubuntu3 [24.0 kB] | |
| Get:43 http://archive.ubuntu.com/ubuntu/ trusty/main python-paramiko all 1.10.1-1git1build1 [106 kB] | |
| Get:44 http://archive.ubuntu.com/ubuntu/ trusty-updates/main subversion amd64 1.8.8-1ubuntu3.1 [280 kB] | |
| Get:45 http://archive.ubuntu.com/ubuntu/ trusty/main tcl8.6 amd64 8.6.1-4ubuntu1 [14.2 kB] | |
| Get:46 http://archive.ubuntu.com/ubuntu/ trusty/main tcl amd64 8.6.0+6ubuntu3 [4,900 B] | |
| Get:47 http://archive.ubuntu.com/ubuntu/ trusty/main tk8.6 amd64 8.6.1-3ubuntu2 [12.1 kB] | |
| Get:48 http://archive.ubuntu.com/ubuntu/ trusty/main tk amd64 8.6.0+6ubuntu3 [3,192 B] | |
| Get:49 http://archive.ubuntu.com/ubuntu/ trusty/universe uuid amd64 1.6.2-1.3ubuntu1 [10.9 kB] | |
| Get:50 http://archive.ubuntu.com/ubuntu/ trusty/main xbitmaps all 1.1.1-2 [28.1 kB] | |
| Get:51 http://archive.ubuntu.com/ubuntu/ trusty/main xterm amd64 297-1ubuntu1 [665 kB] | |
| Get:52 http://archive.ubuntu.com/ubuntu/ trusty-updates/main uuid-dev amd64 2.20.1-5.1ubuntu20.1 [23.7 kB] | |
| Fetched 43.2 MB in 42s (1,022 kB/s) | |
| Extracting templates from packages: 100% | |
| Selecting previously unselected package libapr1:amd64. | |
| (Reading database ... 72029 files and directories currently installed.) | |
| Preparing to unpack .../libapr1_1.5.0-1_amd64.deb ... | |
| Unpacking libapr1:amd64 (1.5.0-1) ... | |
| Selecting previously unselected package libaprutil1:amd64. | |
| Preparing to unpack .../libaprutil1_1.5.3-1_amd64.deb ... | |
| Unpacking libaprutil1:amd64 (1.5.3-1) ... | |
| Selecting previously unselected package liblzo2-2:amd64. | |
| Preparing to unpack .../liblzo2-2_2.06-1.2ubuntu1.1_amd64.deb ... | |
| Unpacking liblzo2-2:amd64 (2.06-1.2ubuntu1.1) ... | |
| Selecting previously unselected package libnettle4:amd64. | |
| Preparing to unpack .../libnettle4_2.7.1-1_amd64.deb ... | |
| Unpacking libnettle4:amd64 (2.7.1-1) ... | |
| Selecting previously unselected package libarchive13:amd64. | |
| Preparing to unpack .../libarchive13_3.1.2-7ubuntu2_amd64.deb ... | |
| Unpacking libarchive13:amd64 (3.1.2-7ubuntu2) ... | |
| Selecting previously unselected package libassuan0:amd64. | |
| Preparing to unpack .../libassuan0_2.1.1-1ubuntu1_amd64.deb ... | |
| Unpacking libassuan0:amd64 (2.1.1-1ubuntu1) ... | |
| Selecting previously unselected package libobjc4:amd64. | |
| Preparing to unpack .../libobjc4_4.8.2-19ubuntu1_amd64.deb ... | |
| Unpacking libobjc4:amd64 (4.8.2-19ubuntu1) ... | |
| Selecting previously unselected package libobjc-4.8-dev:amd64. | |
| Preparing to unpack .../libobjc-4.8-dev_4.8.2-19ubuntu1_amd64.deb ... | |
| Unpacking libobjc-4.8-dev:amd64 (4.8.2-19ubuntu1) ... | |
| Selecting previously unselected package libclang1-3.4:amd64. | |
| Preparing to unpack .../libclang1-3.4_1%3a3.4-1ubuntu3_amd64.deb ... | |
| Unpacking libclang1-3.4:amd64 (1:3.4-1ubuntu3) ... | |
| Selecting previously unselected package libgpgme11:amd64. | |
| Preparing to unpack .../libgpgme11_1.4.3-0.1ubuntu5.1_amd64.deb ... | |
| Unpacking libgpgme11:amd64 (1.4.3-0.1ubuntu5.1) ... | |
| Selecting previously unselected package libserf-1-1:amd64. | |
| Preparing to unpack .../libserf-1-1_1.3.3-1ubuntu0.1_amd64.deb ... | |
| Unpacking libserf-1-1:amd64 (1.3.3-1ubuntu0.1) ... | |
| Selecting previously unselected package libsvn1:amd64. | |
| Preparing to unpack .../libsvn1_1.8.8-1ubuntu3.1_amd64.deb ... | |
| Unpacking libsvn1:amd64 (1.8.8-1ubuntu3.1) ... | |
| Selecting previously unselected package libtcl8.6:amd64. | |
| Preparing to unpack .../libtcl8.6_8.6.1-4ubuntu1_amd64.deb ... | |
| Unpacking libtcl8.6:amd64 (8.6.1-4ubuntu1) ... | |
| Selecting previously unselected package libxss1:amd64. | |
| Preparing to unpack .../libxss1_1%3a1.2.2-1_amd64.deb ... | |
| Unpacking libxss1:amd64 (1:1.2.2-1) ... | |
| Selecting previously unselected package libtk8.6:amd64. | |
| Preparing to unpack .../libtk8.6_8.6.1-3ubuntu2_amd64.deb ... | |
| Unpacking libtk8.6:amd64 (8.6.1-3ubuntu2) ... | |
| Selecting previously unselected package autotools-dev. | |
| Preparing to unpack .../autotools-dev_20130810.1_all.deb ... | |
| Unpacking autotools-dev (20130810.1) ... | |
| Selecting previously unselected package axel. | |
| Preparing to unpack .../archives/axel_2.4-1_amd64.deb ... | |
| Unpacking axel (2.4-1) ... | |
| Selecting previously unselected package binfmt-support. | |
| Preparing to unpack .../binfmt-support_2.1.4-1_amd64.deb ... | |
| Unpacking binfmt-support (2.1.4-1) ... | |
| Selecting previously unselected package python-bzrlib. | |
| Preparing to unpack .../python-bzrlib_2.6.0+bzr6593-1ubuntu1.1_amd64.deb ... | |
| Unpacking python-bzrlib (2.6.0+bzr6593-1ubuntu1.1) ... | |
| Selecting previously unselected package bzr. | |
| Preparing to unpack .../bzr_2.6.0+bzr6593-1ubuntu1.1_all.deb ... | |
| Unpacking bzr (2.6.0+bzr6593-1ubuntu1.1) ... | |
| Selecting previously unselected package libclang-common-3.4-dev. | |
| Preparing to unpack .../libclang-common-3.4-dev_1%3a3.4-1ubuntu3_amd64.deb ... | |
| Unpacking libclang-common-3.4-dev (1:3.4-1ubuntu3) ... | |
| Selecting previously unselected package clang-3.4. | |
| Preparing to unpack .../clang-3.4_1%3a3.4-1ubuntu3_amd64.deb ... | |
| Unpacking clang-3.4 (1:3.4-1ubuntu3) ... | |
| Selecting previously unselected package clang. | |
| Preparing to unpack .../clang_1%3a3.4-0ubuntu1_amd64.deb ... | |
| Unpacking clang (1:3.4-0ubuntu1) ... | |
| Selecting previously unselected package cmake-data. | |
| Preparing to unpack .../cmake-data_2.8.12.2-0ubuntu3_all.deb ... | |
| Unpacking cmake-data (2.8.12.2-0ubuntu3) ... | |
| Selecting previously unselected package cmake. | |
| Preparing to unpack .../cmake_2.8.12.2-0ubuntu3_amd64.deb ... | |
| Unpacking cmake (2.8.12.2-0ubuntu3) ... | |
| Selecting previously unselected package cvs. | |
| Preparing to unpack .../cvs_2%3a1.12.13+real-12_amd64.deb ... | |
| Unpacking cvs (2:1.12.13+real-12) ... | |
| Selecting previously unselected package libgfortran-4.8-dev:amd64. | |
| Preparing to unpack .../libgfortran-4.8-dev_4.8.2-19ubuntu1_amd64.deb ... | |
| Unpacking libgfortran-4.8-dev:amd64 (4.8.2-19ubuntu1) ... | |
| Selecting previously unselected package gfortran-4.8. | |
| Preparing to unpack .../gfortran-4.8_4.8.2-19ubuntu1_amd64.deb ... | |
| Unpacking gfortran-4.8 (4.8.2-19ubuntu1) ... | |
| Selecting previously unselected package gfortran. | |
| Preparing to unpack .../gfortran_4%3a4.8.2-1ubuntu6_amd64.deb ... | |
| Unpacking gfortran (4:4.8.2-1ubuntu6) ... | |
| Selecting previously unselected package git-core. | |
| Preparing to unpack .../git-core_1%3a1.9.1-1_all.deb ... | |
| Unpacking git-core (1:1.9.1-1) ... | |
| Selecting previously unselected package htop. | |
| Preparing to unpack .../htop_1.0.2-3_amd64.deb ... | |
| Unpacking htop (1.0.2-3) ... | |
| Selecting previously unselected package libltdl-dev:amd64. | |
| Preparing to unpack .../libltdl-dev_2.4.2-1.7ubuntu1_amd64.deb ... | |
| Unpacking libltdl-dev:amd64 (2.4.2-1.7ubuntu1) ... | |
| Selecting previously unselected package libossp-uuid16. | |
| Preparing to unpack .../libossp-uuid16_1.6.2-1.3ubuntu1_amd64.deb ... | |
| Unpacking libossp-uuid16 (1.6.2-1.3ubuntu1) ... | |
| Selecting previously unselected package libtool. | |
| Preparing to unpack .../libtool_2.4.2-1.7ubuntu1_amd64.deb ... | |
| Unpacking libtool (2.4.2-1.7ubuntu1) ... | |
| Selecting previously unselected package libutempter0. | |
| Preparing to unpack .../libutempter0_1.1.5-4build1_amd64.deb ... | |
| Unpacking libutempter0 (1.1.5-4build1) ... | |
| Selecting previously unselected package llvm-3.4-runtime. | |
| Preparing to unpack .../llvm-3.4-runtime_1%3a3.4-1ubuntu3_amd64.deb ... | |
| Unpacking llvm-3.4-runtime (1:3.4-1ubuntu3) ... | |
| Selecting previously unselected package llvm-3.4. | |
| Preparing to unpack .../llvm-3.4_1%3a3.4-1ubuntu3_amd64.deb ... | |
| Unpacking llvm-3.4 (1:3.4-1ubuntu3) ... | |
| Selecting previously unselected package libffi-dev:amd64. | |
| Preparing to unpack .../libffi-dev_3.1~rc1+r3.0.13-12_amd64.deb ... | |
| Unpacking libffi-dev:amd64 (3.1~rc1+r3.0.13-12) ... | |
| Selecting previously unselected package llvm-3.4-dev. | |
| Preparing to unpack .../llvm-3.4-dev_1%3a3.4-1ubuntu3_amd64.deb ... | |
| Unpacking llvm-3.4-dev (1:3.4-1ubuntu3) ... | |
| Selecting previously unselected package mercurial-common. | |
| Preparing to unpack .../mercurial-common_2.8.2-1ubuntu1_all.deb ... | |
| Unpacking mercurial-common (2.8.2-1ubuntu1) ... | |
| Selecting previously unselected package mercurial. | |
| Preparing to unpack .../mercurial_2.8.2-1ubuntu1_amd64.deb ... | |
| Unpacking mercurial (2.8.2-1ubuntu1) ... | |
| Selecting previously unselected package python-gpgme. | |
| Preparing to unpack .../python-gpgme_0.3-0ubuntu3_amd64.deb ... | |
| Unpacking python-gpgme (0.3-0ubuntu3) ... | |
| Selecting previously unselected package python-paramiko. | |
| Preparing to unpack .../python-paramiko_1.10.1-1git1build1_all.deb ... | |
| Unpacking python-paramiko (1.10.1-1git1build1) ... | |
| Selecting previously unselected package subversion. | |
| Preparing to unpack .../subversion_1.8.8-1ubuntu3.1_amd64.deb ... | |
| Unpacking subversion (1.8.8-1ubuntu3.1) ... | |
| Selecting previously unselected package tcl8.6. | |
| Preparing to unpack .../tcl8.6_8.6.1-4ubuntu1_amd64.deb ... | |
| Unpacking tcl8.6 (8.6.1-4ubuntu1) ... | |
| Selecting previously unselected package tcl. | |
| Preparing to unpack .../tcl_8.6.0+6ubuntu3_amd64.deb ... | |
| Unpacking tcl (8.6.0+6ubuntu3) ... | |
| Selecting previously unselected package tk8.6. | |
| Preparing to unpack .../tk8.6_8.6.1-3ubuntu2_amd64.deb ... | |
| Unpacking tk8.6 (8.6.1-3ubuntu2) ... | |
| Selecting previously unselected package tk. | |
| Preparing to unpack .../tk_8.6.0+6ubuntu3_amd64.deb ... | |
| Unpacking tk (8.6.0+6ubuntu3) ... | |
| Selecting previously unselected package uuid. | |
| Preparing to unpack .../uuid_1.6.2-1.3ubuntu1_amd64.deb ... | |
| Unpacking uuid (1.6.2-1.3ubuntu1) ... | |
| Selecting previously unselected package xbitmaps. | |
| Preparing to unpack .../xbitmaps_1.1.1-2_all.deb ... | |
| Unpacking xbitmaps (1.1.1-2) ... | |
| Selecting previously unselected package xterm. | |
| Preparing to unpack .../xterm_297-1ubuntu1_amd64.deb ... | |
| Unpacking xterm (297-1ubuntu1) ... | |
| Selecting previously unselected package uuid-dev. | |
| Preparing to unpack .../uuid-dev_2.20.1-5.1ubuntu20.1_amd64.deb ... | |
| Unpacking uuid-dev (2.20.1-5.1ubuntu20.1) ... | |
| Processing triggers for man-db (2.6.7.1-1) ... | |
| Processing triggers for ureadahead (0.100.0-16) ... | |
| Processing triggers for install-info (5.2.0.dfsg.1-2) ... | |
| Processing triggers for desktop-file-utils (0.22-1ubuntu1) ... | |
| Processing triggers for mime-support (3.54ubuntu1) ... | |
| Processing triggers for hicolor-icon-theme (0.13-1) ... | |
| Setting up libapr1:amd64 (1.5.0-1) ... | |
| Setting up libaprutil1:amd64 (1.5.3-1) ... | |
| Setting up liblzo2-2:amd64 (2.06-1.2ubuntu1.1) ... | |
| Setting up libnettle4:amd64 (2.7.1-1) ... | |
| Setting up libarchive13:amd64 (3.1.2-7ubuntu2) ... | |
| Setting up libassuan0:amd64 (2.1.1-1ubuntu1) ... | |
| Setting up libobjc4:amd64 (4.8.2-19ubuntu1) ... | |
| Setting up libobjc-4.8-dev:amd64 (4.8.2-19ubuntu1) ... | |
| Setting up libclang1-3.4:amd64 (1:3.4-1ubuntu3) ... | |
| Setting up libgpgme11:amd64 (1.4.3-0.1ubuntu5.1) ... | |
| Setting up libserf-1-1:amd64 (1.3.3-1ubuntu0.1) ... | |
| Setting up libsvn1:amd64 (1.8.8-1ubuntu3.1) ... | |
| Setting up libtcl8.6:amd64 (8.6.1-4ubuntu1) ... | |
| Setting up libxss1:amd64 (1:1.2.2-1) ... | |
| Setting up libtk8.6:amd64 (8.6.1-3ubuntu2) ... | |
| Setting up autotools-dev (20130810.1) ... | |
| Setting up axel (2.4-1) ... | |
| Setting up binfmt-support (2.1.4-1) ... | |
| binfmt-support start/running | |
| Setting up python-bzrlib (2.6.0+bzr6593-1ubuntu1.1) ... | |
| Setting up bzr (2.6.0+bzr6593-1ubuntu1.1) ... | |
| Setting up libclang-common-3.4-dev (1:3.4-1ubuntu3) ... | |
| Setting up clang-3.4 (1:3.4-1ubuntu3) ... | |
| Setting up clang (1:3.4-0ubuntu1) ... | |
| Setting up cmake-data (2.8.12.2-0ubuntu3) ... | |
| Setting up cmake (2.8.12.2-0ubuntu3) ... | |
| Setting up cvs (2:1.12.13+real-12) ... | |
| Allowing use of questionable username. | |
| Adding group `_cvsadmin' (GID 115) ... | |
| Done. | |
| Setting up libgfortran-4.8-dev:amd64 (4.8.2-19ubuntu1) ... | |
| Setting up gfortran-4.8 (4.8.2-19ubuntu1) ... | |
| Setting up gfortran (4:4.8.2-1ubuntu6) ... | |
| update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode | |
| Setting up git-core (1:1.9.1-1) ... | |
| Setting up htop (1.0.2-3) ... | |
| Setting up libltdl-dev:amd64 (2.4.2-1.7ubuntu1) ... | |
| Setting up libossp-uuid16 (1.6.2-1.3ubuntu1) ... | |
| Setting up libtool (2.4.2-1.7ubuntu1) ... | |
| Setting up libutempter0 (1.1.5-4build1) ... | |
| Creating utempter group... | |
| Setting up libffi-dev:amd64 (3.1~rc1+r3.0.13-12) ... | |
| Setting up mercurial-common (2.8.2-1ubuntu1) ... | |
| Setting up mercurial (2.8.2-1ubuntu1) ... | |
| Creating config file /etc/mercurial/hgrc.d/hgext.rc with new version | |
| Setting up python-gpgme (0.3-0ubuntu3) ... | |
| Setting up python-paramiko (1.10.1-1git1build1) ... | |
| Setting up subversion (1.8.8-1ubuntu3.1) ... | |
| Setting up tcl8.6 (8.6.1-4ubuntu1) ... | |
| Setting up tcl (8.6.0+6ubuntu3) ... | |
| Setting up tk8.6 (8.6.1-3ubuntu2) ... | |
| Setting up tk (8.6.0+6ubuntu3) ... | |
| Setting up uuid (1.6.2-1.3ubuntu1) ... | |
| Setting up xbitmaps (1.1.1-2) ... | |
| Setting up xterm (297-1ubuntu1) ... | |
| update-alternatives: using /usr/bin/xterm to provide /usr/bin/x-terminal-emulator (x-terminal-emulator) in auto mode | |
| update-alternatives: using /usr/bin/lxterm to provide /usr/bin/x-terminal-emulator (x-terminal-emulator) in auto mode | |
| Setting up uuid-dev (2.20.1-5.1ubuntu20.1) ... | |
| Processing triggers for ureadahead (0.100.0-16) ... | |
| Setting up llvm-3.4-runtime (1:3.4-1ubuntu3) ... | |
| Setting up llvm-3.4 (1:3.4-1ubuntu3) ... | |
| Setting up llvm-3.4-dev (1:3.4-1ubuntu3) ... | |
| Processing triggers for libc-bin (2.19-0ubuntu6.3) ... | |
| INFO: Package install progress: 60/84 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-get -y --force-yes install unzip cpanminus libextutils-autoinstall-perl libperl-dev parrot parrot-devel perl perl-modules perl-tk python python-dev python-distutils-extra python-pip python-rpy python-setuptools python-virtualenv python3 python3-dev r-base r-base-core r-base-dev r-base-html ruby1.9.1 ruby1.9.1-dev" | |
| Reading package lists... Done | |
| Building dependency tree | |
| Reading state information... Done | |
| perl is already the newest version. | |
| perl-modules is already the newest version. | |
| python is already the newest version. | |
| python-setuptools is already the newest version. | |
| python3 is already the newest version. | |
| ruby1.9.1 is already the newest version. | |
| ruby1.9.1 set to manually installed. | |
| The following extra packages will be installed: | |
| autoconf automake cdbs debhelper dh-apparmor dh-translations gettext | |
| intltool intltool-debian libaliased-perl libasprintf-dev libauthen-sasl-perl | |
| libcpan-distnameinfo-perl libcpan-meta-check-perl libcpan-meta-perl | |
| libcpan-meta-requirements-perl libcroco3 libencode-locale-perl libexpat1-dev | |
| libfile-basedir-perl libfile-desktopentry-perl libfile-listing-perl | |
| libfile-mimeinfo-perl libfile-pushd-perl libfont-afm-perl libgettextpo-dev | |
| libgettextpo0 libhtml-form-perl libhtml-format-perl libhtml-parser-perl | |
| libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl | |
| libhttp-daemon-perl libhttp-date-perl libhttp-message-perl | |
| libhttp-negotiate-perl libio-html-perl libio-socket-inet6-perl | |
| libio-socket-ssl-perl libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev | |
| liblist-moreutils-perl liblocal-lib-perl liblwp-mediatypes-perl | |
| liblwp-protocol-https-perl libmail-sendmail-perl libmailtools-perl | |
| libmodule-cpanfile-perl libmodule-metadata-perl libnet-http-perl | |
| libnet-smtp-ssl-perl libnet-ssleay-perl libpaper-utils libpaper1 | |
| libparrot-dev libparrot5.9.0 libparse-cpan-meta-perl libperl5.18 | |
| libpython-dev libpython2.7-dev libpython3-dev libpython3.4 libpython3.4-dev | |
| libsocket6-perl libstring-shellquote-perl libsys-hostname-long-perl | |
| libunistring0 liburi-perl libwww-perl libwww-robotrules-perl | |
| libxml-parser-perl m4 parrot-minimal po-debconf python-colorama | |
| python-distlib python-html5lib python-numpy python-scour python2.7-dev | |
| python3.4-dev r-cran-boot r-cran-class r-cran-cluster r-cran-codetools | |
| r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix | |
| r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial | |
| r-cran-survival r-doc-html r-recommended x11-xserver-utils xdg-utils zip | |
| Suggested packages: | |
| autoconf2.13 autoconf-archive gnu-standards autoconf-doc devscripts dh-make | |
| apparmor-easyprof gettext-doc libdigest-hmac-perl libgssapi-perl | |
| libsort-versions-perl libdata-dump-perl libcapture-tiny-perl | |
| libcrypt-ssleay-perl libauthen-ntlm-perl parrot-doc libmail-box-perl | |
| python-lxml python-genshi python-nose python-numpy-dbg python-numpy-doc | |
| python-rpy-docs python-rsvg python-cairo ess r-doc-info r-doc-pdf r-mathlib | |
| texlive-base texlive-latex-base texlive-generic-recommended | |
| texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils | |
| texlive-latex-recommended texlive-latex-extra texinfo nickle cairo-5c | |
| xorg-docs-core gvfs-bin | |
| Recommended packages: | |
| python-dev-all | |
| The following NEW packages will be installed: | |
| autoconf automake cdbs cpanminus debhelper dh-apparmor dh-translations | |
| gettext intltool intltool-debian libaliased-perl libasprintf-dev | |
| libauthen-sasl-perl libcpan-distnameinfo-perl libcpan-meta-check-perl | |
| libcpan-meta-perl libcpan-meta-requirements-perl libcroco3 | |
| libencode-locale-perl libexpat1-dev libextutils-autoinstall-perl | |
| libfile-basedir-perl libfile-desktopentry-perl libfile-listing-perl | |
| libfile-mimeinfo-perl libfile-pushd-perl libfont-afm-perl libgettextpo-dev | |
| libgettextpo0 libhtml-form-perl libhtml-format-perl libhtml-parser-perl | |
| libhtml-tagset-perl libhtml-tree-perl libhttp-cookies-perl | |
| libhttp-daemon-perl libhttp-date-perl libhttp-message-perl | |
| libhttp-negotiate-perl libio-html-perl libio-socket-inet6-perl | |
| libio-socket-ssl-perl libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev | |
| liblist-moreutils-perl liblocal-lib-perl liblwp-mediatypes-perl | |
| liblwp-protocol-https-perl libmail-sendmail-perl libmailtools-perl | |
| libmodule-cpanfile-perl libmodule-metadata-perl libnet-http-perl | |
| libnet-smtp-ssl-perl libnet-ssleay-perl libpaper-utils libpaper1 | |
| libparrot-dev libparrot5.9.0 libparse-cpan-meta-perl libperl-dev libperl5.18 | |
| libpython-dev libpython2.7-dev libpython3-dev libpython3.4 libpython3.4-dev | |
| libsocket6-perl libstring-shellquote-perl libsys-hostname-long-perl | |
| libunistring0 liburi-perl libwww-perl libwww-robotrules-perl | |
| libxml-parser-perl m4 parrot parrot-devel parrot-minimal perl-tk po-debconf | |
| python-colorama python-dev python-distlib python-distutils-extra | |
| python-html5lib python-numpy python-pip python-rpy python-scour | |
| python-virtualenv python2.7-dev python3-dev python3.4-dev r-base r-base-core | |
| r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster | |
| r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass | |
| r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart | |
| r-cran-spatial r-cran-survival r-doc-html r-recommended ruby1.9.1-dev unzip | |
| x11-xserver-utils xdg-utils zip | |
| 0 upgraded, 121 newly installed, 0 to remove and 6 not upgraded. | |
| Need to get 105 MB of archives. | |
| After this operation, 225 MB of additional disk space will be used. | |
| Get:1 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-base-core 3.1.1-1trusty0 [19.7 MB] | |
| Get:2 http://archive.ubuntu.com/ubuntu/ trusty/main libcroco3 amd64 0.6.8-2ubuntu1 [82.4 kB] | |
| Get:3 http://archive.ubuntu.com/ubuntu/ trusty/main libunistring0 amd64 0.9.3-5ubuntu3 [271 kB] | |
| Get:4 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgettextpo0 amd64 0.18.3.1-1ubuntu3 [108 kB] | |
| Get:5 http://archive.ubuntu.com/ubuntu/ trusty/main libpaper1 amd64 1.1.24+nmu2ubuntu3 [13.4 kB] | |
| Get:6 http://archive.ubuntu.com/ubuntu/ trusty/main libexpat1-dev amd64 2.1.0-4ubuntu1 [115 kB] | |
| Get:7 http://archive.ubuntu.com/ubuntu/ trusty/main libpython2.7-dev amd64 2.7.6-8 [22.0 MB] | |
| Get:8 http://archive.ubuntu.com/ubuntu/ trusty/main libpython3.4 amd64 3.4.0-2ubuntu1 [1,303 kB] | |
| Get:9 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ python-rpy 1.0.3-30trusty0 [30.7 kB] | |
| Get:10 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-cran-boot 1.3-13-1trusty0 [568 kB] | |
| Get:11 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-cran-cluster 1.15.3-1trusty0 [474 kB] | |
| Get:12 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-cran-foreign 0.8.61-1trusty0 [213 kB] | |
| Get:13 http://archive.ubuntu.com/ubuntu/ trusty/main libpython3.4-dev amd64 3.4.0-2ubuntu1 [27.0 MB] | |
| Get:14 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-cran-mass 7.3-34-1trusty0 [1,013 kB] | |
| Get:15 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-cran-kernsmooth 2.23-13-1trusty0 [81.0 kB] | |
| Get:16 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-cran-lattice 0.20-29-1trusty0 [712 kB] | |
| Get:17 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-cran-nlme 3.1.117-1trusty0 [2,017 kB] | |
| Get:18 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-cran-matrix 1.1-4-1trusty0 [2,917 kB] | |
| Get:19 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-cran-mgcv 1.8-3-1trusty0 [1,722 kB] | |
| Get:20 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-cran-rpart 4.1-8-1trusty0 [861 kB] | |
| Get:21 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-cran-class 7.3-11-1trusty0 [80.7 kB] | |
| Get:22 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-cran-nnet 7.3-8-1trusty0 [95.7 kB] | |
| Get:23 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-cran-spatial 7.3-7-1trusty0 [120 kB] | |
| Get:24 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-cran-codetools 0.2-9-1trusty0 [45.7 kB] | |
| Get:25 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-recommended 3.1.1-1trusty0 [2,720 B] | |
| Get:26 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-base 3.1.1-1trusty0 [37.6 kB] | |
| Get:27 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-base-dev 3.1.1-1trusty0 [3,930 B] | |
| Get:28 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-doc-html 3.1.1-1trusty0 [529 kB] | |
| Get:29 http://cran.fhcrc.org/bin/linux/ubuntu/ trusty/ r-base-html 3.1.1-1trusty0 [81.3 kB] | |
| Get:30 http://archive.ubuntu.com/ubuntu/ trusty/main m4 amd64 1.4.17-2ubuntu1 [195 kB] | |
| Get:31 http://archive.ubuntu.com/ubuntu/ trusty/main autoconf all 2.69-6 [322 kB] | |
| Get:32 http://archive.ubuntu.com/ubuntu/ trusty/main automake all 1:1.14.1-2ubuntu1 [510 kB] | |
| Get:33 http://archive.ubuntu.com/ubuntu/ trusty-updates/main gettext amd64 0.18.3.1-1ubuntu3 [829 kB] | |
| Get:34 http://archive.ubuntu.com/ubuntu/ trusty/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] | |
| Get:35 http://archive.ubuntu.com/ubuntu/ trusty/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] | |
| Get:36 http://archive.ubuntu.com/ubuntu/ trusty/main dh-apparmor all 2.8.95~2430-0ubuntu5 [11.3 kB] | |
| Get:37 http://archive.ubuntu.com/ubuntu/ trusty/main debhelper all 9.20131227ubuntu1 [604 kB] | |
| Get:38 http://archive.ubuntu.com/ubuntu/ trusty/main liburi-perl all 1.60-1 [89.6 kB] | |
| Get:39 http://archive.ubuntu.com/ubuntu/ trusty/main libencode-locale-perl all 1.03-1 [12.4 kB] | |
| Get:40 http://archive.ubuntu.com/ubuntu/ trusty/main libhttp-date-perl all 6.02-1 [10.4 kB] | |
| Get:41 http://archive.ubuntu.com/ubuntu/ trusty/main libfile-listing-perl all 6.04-1 [9,774 B] | |
| Get:42 http://archive.ubuntu.com/ubuntu/ trusty/main libhtml-tagset-perl all 3.20-2 [13.5 kB] | |
| Get:43 http://archive.ubuntu.com/ubuntu/ trusty/main libhtml-parser-perl amd64 3.71-1build1 [98.2 kB] | |
| Get:44 http://archive.ubuntu.com/ubuntu/ trusty/main libhtml-tree-perl all 5.03-1 [215 kB] | |
| Get:45 http://archive.ubuntu.com/ubuntu/ trusty/main libio-html-perl all 1.00-1 [15.7 kB] | |
| Get:46 http://archive.ubuntu.com/ubuntu/ trusty/main liblwp-mediatypes-perl all 6.02-1 [21.7 kB] | |
| Get:47 http://archive.ubuntu.com/ubuntu/ trusty/main libhttp-message-perl all 6.06-1 [78.7 kB] | |
| Get:48 http://archive.ubuntu.com/ubuntu/ trusty/main libhttp-cookies-perl all 6.00-2 [23.3 kB] | |
| Get:49 http://archive.ubuntu.com/ubuntu/ trusty/main libhttp-negotiate-perl all 6.00-2 [13.4 kB] | |
| Get:50 http://archive.ubuntu.com/ubuntu/ trusty/main libnet-ssleay-perl amd64 1.58-1 [243 kB] | |
| Get:51 http://archive.ubuntu.com/ubuntu/ trusty/main libio-socket-ssl-perl all 1.965-1ubuntu1 [73.7 kB] | |
| Get:52 http://archive.ubuntu.com/ubuntu/ trusty/main libnet-http-perl all 6.06-1 [24.2 kB] | |
| Get:53 http://archive.ubuntu.com/ubuntu/ trusty-updates/main liblwp-protocol-https-perl all 6.04-2ubuntu0.1 [7,644 B] | |
| Get:54 http://archive.ubuntu.com/ubuntu/ trusty/main libwww-robotrules-perl all 6.01-1 [14.1 kB] | |
| Get:55 http://archive.ubuntu.com/ubuntu/ trusty/main libwww-perl all 6.05-2 [146 kB] | |
| Get:56 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-parser-perl amd64 2.41-1build3 [294 kB] | |
| Get:57 http://archive.ubuntu.com/ubuntu/ trusty/main intltool all 0.50.2-2 [52.0 kB] | |
| Get:58 http://archive.ubuntu.com/ubuntu/ trusty/main dh-translations all 121 [21.6 kB] | |
| Get:59 http://archive.ubuntu.com/ubuntu/ trusty/main python-scour all 0.26-3build1 [40.5 kB] | |
| Get:60 http://archive.ubuntu.com/ubuntu/ trusty/main cdbs all 0.4.122ubuntu2 [42.1 kB] | |
| Get:61 http://archive.ubuntu.com/ubuntu/ trusty/universe libaliased-perl all 0.31-1 [11.7 kB] | |
| Get:62 http://archive.ubuntu.com/ubuntu/ trusty/universe libcpan-distnameinfo-perl all 0.12-1 [8,662 B] | |
| Get:63 http://archive.ubuntu.com/ubuntu/ trusty/main liblist-moreutils-perl amd64 0.33-1build3 [48.5 kB] | |
| Get:64 http://archive.ubuntu.com/ubuntu/ trusty/universe libcpan-meta-requirements-perl all 2.125-1 [12.8 kB] | |
| Get:65 http://archive.ubuntu.com/ubuntu/ trusty/universe libparse-cpan-meta-perl all 1.4409-1 [11.3 kB] | |
| Get:66 http://archive.ubuntu.com/ubuntu/ trusty/main libcpan-meta-perl all 2.133380-2 [69.2 kB] | |
| Get:67 http://archive.ubuntu.com/ubuntu/ trusty/main libcpan-meta-check-perl all 0.007-1 [7,716 B] | |
| Get:68 http://archive.ubuntu.com/ubuntu/ trusty/universe libfile-pushd-perl all 1.005-1 [10.6 kB] | |
| Get:69 http://archive.ubuntu.com/ubuntu/ trusty/universe liblocal-lib-perl all 1.008023-1 [46.8 kB] | |
| Get:70 http://archive.ubuntu.com/ubuntu/ trusty/universe libmodule-cpanfile-perl all 1.0002-1 [27.3 kB] | |
| Get:71 http://archive.ubuntu.com/ubuntu/ trusty/universe libmodule-metadata-perl all 1.000019-1 [18.8 kB] | |
| Get:72 http://archive.ubuntu.com/ubuntu/ trusty/universe libstring-shellquote-perl all 1.03-1 [14.0 kB] | |
| Get:73 http://archive.ubuntu.com/ubuntu/ trusty/universe cpanminus all 1.7001-1 [234 kB] | |
| Get:74 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libasprintf-dev amd64 0.18.3.1-1ubuntu3 [4,438 B] | |
| Get:75 http://archive.ubuntu.com/ubuntu/ trusty/universe libextutils-autoinstall-perl all 0.63-2 [22.0 kB] | |
| Get:76 http://archive.ubuntu.com/ubuntu/ trusty/main libfile-basedir-perl all 0.03-1fakesync1 [10.5 kB] | |
| Get:77 http://archive.ubuntu.com/ubuntu/ trusty/main libfile-desktopentry-perl all 0.07-1 [19.4 kB] | |
| Get:78 http://archive.ubuntu.com/ubuntu/ trusty/main libfile-mimeinfo-perl all 0.22-1 [46.6 kB] | |
| Get:79 http://archive.ubuntu.com/ubuntu/ trusty/main libfont-afm-perl all 1.20-1 [14.3 kB] | |
| Get:80 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgettextpo-dev amd64 0.18.3.1-1ubuntu3 [122 kB] | |
| Get:81 http://archive.ubuntu.com/ubuntu/ trusty/main libhtml-form-perl all 6.03-1 [23.5 kB] | |
| Get:82 http://archive.ubuntu.com/ubuntu/ trusty/main libhtml-format-perl all 2.11-1 [44.7 kB] | |
| Get:83 http://archive.ubuntu.com/ubuntu/ trusty/main libhttp-daemon-perl all 6.01-1 [17.0 kB] | |
| Get:84 http://archive.ubuntu.com/ubuntu/ trusty/main libsocket6-perl amd64 0.25-1 [23.5 kB] | |
| Get:85 http://archive.ubuntu.com/ubuntu/ trusty/main libio-socket-inet6-perl all 2.71-1 [14.6 kB] | |
| Get:86 http://archive.ubuntu.com/ubuntu/ trusty/main libjpeg-turbo8-dev amd64 1.3.0-0ubuntu2 [242 kB] | |
| Get:87 http://archive.ubuntu.com/ubuntu/ trusty/main libjpeg8-dev amd64 8c-2ubuntu8 [1,552 B] | |
| Get:88 http://archive.ubuntu.com/ubuntu/ trusty/main libjpeg-dev amd64 8c-2ubuntu8 [1,546 B] | |
| Get:89 http://archive.ubuntu.com/ubuntu/ trusty/main libsys-hostname-long-perl all 1.4-3 [11.3 kB] | |
| Get:90 http://archive.ubuntu.com/ubuntu/ trusty/main libmail-sendmail-perl all 0.79.16-1 [26.5 kB] | |
| Get:91 http://archive.ubuntu.com/ubuntu/ trusty/main libnet-smtp-ssl-perl all 1.01-3 [5,948 B] | |
| Get:92 http://archive.ubuntu.com/ubuntu/ trusty/main libmailtools-perl all 2.12-1 [84.1 kB] | |
| Get:93 http://archive.ubuntu.com/ubuntu/ trusty/main libpaper-utils amd64 1.1.24+nmu2ubuntu3 [8,244 B] | |
| Get:94 http://archive.ubuntu.com/ubuntu/ trusty/universe libparrot5.9.0 amd64 5.9.0-1build1 [521 kB] | |
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| Preparing to unpack .../python-rpy_1.0.3-30trusty0_amd64.deb ... | |
| Unpacking python-rpy (1.0.3-30trusty0) ... | |
| Selecting previously unselected package python-virtualenv. | |
| Preparing to unpack .../python-virtualenv_1.11.4-1_all.deb ... | |
| Unpacking python-virtualenv (1.11.4-1) ... | |
| Selecting previously unselected package python3.4-dev. | |
| Preparing to unpack .../python3.4-dev_3.4.0-2ubuntu1_amd64.deb ... | |
| Unpacking python3.4-dev (3.4.0-2ubuntu1) ... | |
| Selecting previously unselected package python3-dev. | |
| Preparing to unpack .../python3-dev_3.4.0-0ubuntu2_amd64.deb ... | |
| Unpacking python3-dev (3.4.0-0ubuntu2) ... | |
| Selecting previously unselected package r-cran-boot. | |
| Preparing to unpack .../r-cran-boot_1.3-13-1trusty0_all.deb ... | |
| Unpacking r-cran-boot (1.3-13-1trusty0) ... | |
| Selecting previously unselected package r-cran-cluster. | |
| Preparing to unpack .../r-cran-cluster_1.15.3-1trusty0_amd64.deb ... | |
| Unpacking r-cran-cluster (1.15.3-1trusty0) ... | |
| Selecting previously unselected package r-cran-foreign. | |
| Preparing to unpack .../r-cran-foreign_0.8.61-1trusty0_amd64.deb ... | |
| Unpacking r-cran-foreign (0.8.61-1trusty0) ... | |
| Selecting previously unselected package r-cran-mass. | |
| Preparing to unpack .../r-cran-mass_7.3-34-1trusty0_amd64.deb ... | |
| Unpacking r-cran-mass (7.3-34-1trusty0) ... | |
| Selecting previously unselected package r-cran-kernsmooth. | |
| Preparing to unpack .../r-cran-kernsmooth_2.23-13-1trusty0_amd64.deb ... | |
| Unpacking r-cran-kernsmooth (2.23-13-1trusty0) ... | |
| Selecting previously unselected package r-cran-lattice. | |
| Preparing to unpack .../r-cran-lattice_0.20-29-1trusty0_amd64.deb ... | |
| Unpacking r-cran-lattice (0.20-29-1trusty0) ... | |
| Selecting previously unselected package r-cran-nlme. | |
| Preparing to unpack .../r-cran-nlme_3.1.117-1trusty0_amd64.deb ... | |
| Unpacking r-cran-nlme (3.1.117-1trusty0) ... | |
| Selecting previously unselected package r-cran-matrix. | |
| Preparing to unpack .../r-cran-matrix_1.1-4-1trusty0_amd64.deb ... | |
| Unpacking r-cran-matrix (1.1-4-1trusty0) ... | |
| Selecting previously unselected package r-cran-mgcv. | |
| Preparing to unpack .../r-cran-mgcv_1.8-3-1trusty0_amd64.deb ... | |
| Unpacking r-cran-mgcv (1.8-3-1trusty0) ... | |
| Selecting previously unselected package r-cran-survival. | |
| Preparing to unpack .../r-cran-survival_2.37-7-1_amd64.deb ... | |
| Unpacking r-cran-survival (2.37-7-1) ... | |
| Selecting previously unselected package r-cran-rpart. | |
| Preparing to unpack .../r-cran-rpart_4.1-8-1trusty0_amd64.deb ... | |
| Unpacking r-cran-rpart (4.1-8-1trusty0) ... | |
| Selecting previously unselected package r-cran-class. | |
| Preparing to unpack .../r-cran-class_7.3-11-1trusty0_amd64.deb ... | |
| Unpacking r-cran-class (7.3-11-1trusty0) ... | |
| Selecting previously unselected package r-cran-nnet. | |
| Preparing to unpack .../r-cran-nnet_7.3-8-1trusty0_amd64.deb ... | |
| Unpacking r-cran-nnet (7.3-8-1trusty0) ... | |
| Selecting previously unselected package r-cran-spatial. | |
| Preparing to unpack .../r-cran-spatial_7.3-7-1trusty0_amd64.deb ... | |
| Unpacking r-cran-spatial (7.3-7-1trusty0) ... | |
| Selecting previously unselected package r-cran-codetools. | |
| Preparing to unpack .../r-cran-codetools_0.2-9-1trusty0_all.deb ... | |
| Unpacking r-cran-codetools (0.2-9-1trusty0) ... | |
| Selecting previously unselected package r-recommended. | |
| Preparing to unpack .../r-recommended_3.1.1-1trusty0_all.deb ... | |
| Unpacking r-recommended (3.1.1-1trusty0) ... | |
| Selecting previously unselected package r-base. | |
| Preparing to unpack .../r-base_3.1.1-1trusty0_all.deb ... | |
| Unpacking r-base (3.1.1-1trusty0) ... | |
| Selecting previously unselected package r-base-dev. | |
| Preparing to unpack .../r-base-dev_3.1.1-1trusty0_all.deb ... | |
| Unpacking r-base-dev (3.1.1-1trusty0) ... | |
| Selecting previously unselected package r-doc-html. | |
| Preparing to unpack .../r-doc-html_3.1.1-1trusty0_all.deb ... | |
| Unpacking r-doc-html (3.1.1-1trusty0) ... | |
| Selecting previously unselected package ruby1.9.1-dev. | |
| Preparing to unpack .../ruby1.9.1-dev_1.9.3.484-2ubuntu1_amd64.deb ... | |
| Unpacking ruby1.9.1-dev (1.9.3.484-2ubuntu1) ... | |
| Selecting previously unselected package x11-xserver-utils. | |
| Preparing to unpack .../x11-xserver-utils_7.7+2ubuntu1_amd64.deb ... | |
| Unpacking x11-xserver-utils (7.7+2ubuntu1) ... | |
| Selecting previously unselected package libauthen-sasl-perl. | |
| Preparing to unpack .../libauthen-sasl-perl_2.1500-1_all.deb ... | |
| Unpacking libauthen-sasl-perl (2.1500-1) ... | |
| Selecting previously unselected package r-base-html. | |
| Preparing to unpack .../r-base-html_3.1.1-1trusty0_all.deb ... | |
| Unpacking r-base-html (3.1.1-1trusty0) ... | |
| Processing triggers for man-db (2.6.7.1-1) ... | |
| Processing triggers for install-info (5.2.0.dfsg.1-2) ... | |
| Processing triggers for mime-support (3.54ubuntu1) ... | |
| Processing triggers for hicolor-icon-theme (0.13-1) ... | |
| Processing triggers for desktop-file-utils (0.22-1ubuntu1) ... | |
| Setting up libcroco3:amd64 (0.6.8-2ubuntu1) ... | |
| Setting up libunistring0:amd64 (0.9.3-5ubuntu3) ... | |
| Setting up libgettextpo0:amd64 (0.18.3.1-1ubuntu3) ... | |
| Setting up libpaper1:amd64 (1.1.24+nmu2ubuntu3) ... | |
| Creating config file /etc/papersize with new version | |
| Setting up libexpat1-dev:amd64 (2.1.0-4ubuntu1) ... | |
| Setting up libpython2.7-dev:amd64 (2.7.6-8) ... | |
| Setting up libpython3.4:amd64 (3.4.0-2ubuntu1) ... | |
| Setting up libpython3.4-dev:amd64 (3.4.0-2ubuntu1) ... | |
| Setting up m4 (1.4.17-2ubuntu1) ... | |
| Setting up autoconf (2.69-6) ... | |
| Setting up automake (1:1.14.1-2ubuntu1) ... | |
| update-alternatives: using /usr/bin/automake-1.14 to provide /usr/bin/automake (automake) in auto mode | |
| Setting up gettext (0.18.3.1-1ubuntu3) ... | |
| Setting up intltool-debian (0.35.0+20060710.1) ... | |
| Setting up po-debconf (1.0.16+nmu2ubuntu1) ... | |
| Setting up dh-apparmor (2.8.95~2430-0ubuntu5) ... | |
| Setting up debhelper (9.20131227ubuntu1) ... | |
| Setting up liburi-perl (1.60-1) ... | |
| Setting up libencode-locale-perl (1.03-1) ... | |
| Setting up libhttp-date-perl (6.02-1) ... | |
| Setting up libfile-listing-perl (6.04-1) ... | |
| Setting up libhtml-tagset-perl (3.20-2) ... | |
| Setting up libhtml-parser-perl (3.71-1build1) ... | |
| Setting up libhtml-tree-perl (5.03-1) ... | |
| Setting up libio-html-perl (1.00-1) ... | |
| Setting up liblwp-mediatypes-perl (6.02-1) ... | |
| Setting up libhttp-message-perl (6.06-1) ... | |
| Setting up libhttp-cookies-perl (6.00-2) ... | |
| Setting up libhttp-negotiate-perl (6.00-2) ... | |
| Setting up libnet-ssleay-perl (1.58-1) ... | |
| Setting up libio-socket-ssl-perl (1.965-1ubuntu1) ... | |
| Setting up libnet-http-perl (6.06-1) ... | |
| Setting up libwww-robotrules-perl (6.01-1) ... | |
| Setting up python-scour (0.26-3build1) ... | |
| Setting up libaliased-perl (0.31-1) ... | |
| Setting up libcpan-distnameinfo-perl (0.12-1) ... | |
| Setting up liblist-moreutils-perl (0.33-1build3) ... | |
| Setting up libcpan-meta-requirements-perl (2.125-1) ... | |
| Setting up libparse-cpan-meta-perl (1.4409-1) ... | |
| Setting up libcpan-meta-perl (2.133380-2) ... | |
| Setting up libcpan-meta-check-perl (0.007-1) ... | |
| Setting up libfile-pushd-perl (1.005-1) ... | |
| Setting up liblocal-lib-perl (1.008023-1) ... | |
| Setting up libmodule-cpanfile-perl (1.0002-1) ... | |
| Setting up libmodule-metadata-perl (1.000019-1) ... | |
| Setting up libstring-shellquote-perl (1.03-1) ... | |
| Setting up cpanminus (1.7001-1) ... | |
| Setting up libasprintf-dev:amd64 (0.18.3.1-1ubuntu3) ... | |
| Setting up libextutils-autoinstall-perl (0.63-2) ... | |
| Setting up libfile-basedir-perl (0.03-1fakesync1) ... | |
| Setting up libfile-desktopentry-perl (0.07-1) ... | |
| Setting up libfile-mimeinfo-perl (0.22-1) ... | |
| Setting up libfont-afm-perl (1.20-1) ... | |
| Setting up libgettextpo-dev:amd64 (0.18.3.1-1ubuntu3) ... | |
| Setting up libhtml-form-perl (6.03-1) ... | |
| Setting up libhtml-format-perl (2.11-1) ... | |
| Setting up libhttp-daemon-perl (6.01-1) ... | |
| Setting up libsocket6-perl (0.25-1) ... | |
| Setting up libio-socket-inet6-perl (2.71-1) ... | |
| Setting up libjpeg-turbo8-dev:amd64 (1.3.0-0ubuntu2) ... | |
| Setting up libjpeg8-dev:amd64 (8c-2ubuntu8) ... | |
| Setting up libjpeg-dev:amd64 (8c-2ubuntu8) ... | |
| Setting up libsys-hostname-long-perl (1.4-3) ... | |
| Setting up libmail-sendmail-perl (0.79.16-1) ... | |
| Setting up libnet-smtp-ssl-perl (1.01-3) ... | |
| Setting up libmailtools-perl (2.12-1) ... | |
| Setting up libpaper-utils (1.1.24+nmu2ubuntu3) ... | |
| Setting up libparrot5.9.0 (5.9.0-1build1) ... | |
| Setting up parrot-minimal (5.9.0-1build1) ... | |
| Setting up parrot (5.9.0-1build1) ... | |
| Setting up libparrot-dev (5.9.0-1build1) ... | |
| Setting up libperl5.18 (5.18.2-2ubuntu1) ... | |
| Setting up libperl-dev (5.18.2-2ubuntu1) ... | |
| Setting up libpython-dev:amd64 (2.7.5-5ubuntu3) ... | |
| Setting up libpython3-dev:amd64 (3.4.0-0ubuntu2) ... | |
| Setting up parrot-devel (5.9.0-1build1) ... | |
| Setting up perl-tk (1:804.031-1build1) ... | |
| Setting up python-colorama (0.2.5-0.1ubuntu1) ... | |
| Setting up python2.7-dev (2.7.6-8) ... | |
| Setting up python-dev (2.7.5-5ubuntu3) ... | |
| Setting up python-distlib (0.1.8-1) ... | |
| Setting up python-html5lib (0.999-2) ... | |
| Setting up python-numpy (1:1.8.2-0ubuntu0.1) ... | |
| Setting up python-pip (1.5.4-1) ... | |
| Setting up zip (3.0-8) ... | |
| Setting up unzip (6.0-9ubuntu1) ... | |
| Setting up xdg-utils (1.1.0~rc1-2ubuntu7.1) ... | |
| Setting up r-base-core (3.1.1-1trusty0) ... | |
| Creating config file /etc/R/Renviron with new version | |
| Setting up python-rpy (1.0.3-30trusty0) ... | |
| Setting up python-virtualenv (1.11.4-1) ... | |
| Setting up python3.4-dev (3.4.0-2ubuntu1) ... | |
| Setting up python3-dev (3.4.0-0ubuntu2) ... | |
| Setting up r-cran-boot (1.3-13-1trusty0) ... | |
| Setting up r-cran-cluster (1.15.3-1trusty0) ... | |
| Setting up r-cran-foreign (0.8.61-1trusty0) ... | |
| Setting up r-cran-mass (7.3-34-1trusty0) ... | |
| Setting up r-cran-kernsmooth (2.23-13-1trusty0) ... | |
| Setting up r-cran-lattice (0.20-29-1trusty0) ... | |
| Setting up r-cran-nlme (3.1.117-1trusty0) ... | |
| Setting up r-cran-matrix (1.1-4-1trusty0) ... | |
| Setting up r-cran-mgcv (1.8-3-1trusty0) ... | |
| Setting up r-cran-survival (2.37-7-1) ... | |
| Setting up r-cran-rpart (4.1-8-1trusty0) ... | |
| Setting up r-cran-class (7.3-11-1trusty0) ... | |
| Setting up r-cran-nnet (7.3-8-1trusty0) ... | |
| Setting up r-cran-spatial (7.3-7-1trusty0) ... | |
| Setting up r-cran-codetools (0.2-9-1trusty0) ... | |
| Setting up r-recommended (3.1.1-1trusty0) ... | |
| Setting up r-base (3.1.1-1trusty0) ... | |
| Setting up r-doc-html (3.1.1-1trusty0) ... | |
| Setting up ruby1.9.1-dev (1.9.3.484-2ubuntu1) ... | |
| Setting up x11-xserver-utils (7.7+2ubuntu1) ... | |
| Setting up libauthen-sasl-perl (2.1500-1) ... | |
| Setting up r-base-html (3.1.1-1trusty0) ... | |
| Setting up liblwp-protocol-https-perl (6.04-2ubuntu0.1) ... | |
| Setting up libwww-perl (6.05-2) ... | |
| Setting up libxml-parser-perl (2.41-1build3) ... | |
| Setting up intltool (0.50.2-2) ... | |
| Setting up dh-translations (121) ... | |
| Setting up cdbs (0.4.122ubuntu2) ... | |
| Setting up python-distutils-extra (2.38-1build1) ... | |
| Setting up r-base-dev (3.1.1-1trusty0) ... | |
| Processing triggers for libc-bin (2.19-0ubuntu6.3) ... | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-get clean" | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/custom.yaml | |
| INFO: Reading /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/custom.yaml | |
| DBG [shared.py]: Packages to install: ucsc_tools,cufflinks,picard,featurecounts,rnaseqc,bcbio_variation,grabix,mutect,varscan | |
| INFO: Custom install for 'ucsc_tools' start time: 2014-10-02 23:02:02.267302 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_ucsc_tools | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux' | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/aca8c9be-f0ce-3f0d-94ca-cacd559a818b' | |
| [localhost] local: wget --continue --no-check-certificate -O liftOver 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver' | |
| --2014-10-02 23:02:02-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 12588734 (12M) [text/plain] | |
| Saving to: ‘liftOver’ | |
| 100%[========================================================================================================================>] 12,588,734 1.88MB/s in 8.7s | |
| 2014-10-02 23:02:16 (1.38 MB/s) - ‘liftOver’ saved [12588734/12588734] | |
| [localhost] local: mv liftOver /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/aca8c9be-f0ce-3f0d-94ca-cacd559a818b | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f liftOver /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/liftOver" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/487dd22f-5aaf-36fd-82cd-cc62df31de03' | |
| [localhost] local: wget --continue --no-check-certificate -O faToTwoBit 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit' | |
| --2014-10-02 23:02:16-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 994732 (971K) [text/plain] | |
| Saving to: ‘faToTwoBit’ | |
| 100%[========================================================================================================================>] 994,732 1.06MB/s in 0.9s | |
| 2014-10-02 23:02:22 (1.06 MB/s) - ‘faToTwoBit’ saved [994732/994732] | |
| [localhost] local: mv faToTwoBit /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/487dd22f-5aaf-36fd-82cd-cc62df31de03 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f faToTwoBit /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/faToTwoBit" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/5affe66f-958b-34f0-910c-b01e734cf992' | |
| [localhost] local: wget --continue --no-check-certificate -O bedToBigBed 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed' | |
| --2014-10-02 23:02:22-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 1477498 (1.4M) [text/plain] | |
| Saving to: ‘bedToBigBed’ | |
| 100%[========================================================================================================================>] 1,477,498 1.24MB/s in 1.1s | |
| 2014-10-02 23:02:28 (1.24 MB/s) - ‘bedToBigBed’ saved [1477498/1477498] | |
| [localhost] local: mv bedToBigBed /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/5affe66f-958b-34f0-910c-b01e734cf992 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f bedToBigBed /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/bedToBigBed" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/0fbd49dc-1608-34e8-b85e-6bbaff2e4903' | |
| [localhost] local: wget --continue --no-check-certificate -O bigBedInfo 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedInfo' | |
| --2014-10-02 23:02:28-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedInfo | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 1478873 (1.4M) [text/plain] | |
| Saving to: ‘bigBedInfo’ | |
| 100%[========================================================================================================================>] 1,478,873 1.35MB/s in 1.0s | |
| 2014-10-02 23:02:34 (1.35 MB/s) - ‘bigBedInfo’ saved [1478873/1478873] | |
| [localhost] local: mv bigBedInfo /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/0fbd49dc-1608-34e8-b85e-6bbaff2e4903 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f bigBedInfo /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/bigBedInfo" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/251e0c9b-2bdf-36a9-a998-ab922410702e' | |
| [localhost] local: wget --continue --no-check-certificate -O bigBedSummary 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedSummary' | |
| --2014-10-02 23:02:34-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedSummary | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 1479197 (1.4M) [text/plain] | |
| Saving to: ‘bigBedSummary’ | |
| 100%[========================================================================================================================>] 1,479,197 1.59MB/s in 0.9s | |
| 2014-10-02 23:02:40 (1.59 MB/s) - ‘bigBedSummary’ saved [1479197/1479197] | |
| [localhost] local: mv bigBedSummary /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/251e0c9b-2bdf-36a9-a998-ab922410702e | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f bigBedSummary /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/bigBedSummary" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/eed8c20e-175c-3d6a-9fd4-6e46f5313c8a' | |
| [localhost] local: wget --continue --no-check-certificate -O bigBedToBed 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedToBed' | |
| --2014-10-02 23:02:41-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedToBed | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 1477610 (1.4M) [text/plain] | |
| Saving to: ‘bigBedToBed’ | |
| 100%[========================================================================================================================>] 1,477,610 1.41MB/s in 1.0s | |
| 2014-10-02 23:02:47 (1.41 MB/s) - ‘bigBedToBed’ saved [1477610/1477610] | |
| [localhost] local: mv bigBedToBed /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/eed8c20e-175c-3d6a-9fd4-6e46f5313c8a | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f bigBedToBed /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/bigBedToBed" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/ac24bc4e-7c2a-338a-801b-c47abc269ae1' | |
| [localhost] local: wget --continue --no-check-certificate -O bedGraphToBigWig 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig' | |
| --2014-10-02 23:02:47-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 1158245 (1.1M) [text/plain] | |
| Saving to: ‘bedGraphToBigWig’ | |
| 100%[========================================================================================================================>] 1,158,245 1.33MB/s in 0.8s | |
| 2014-10-02 23:02:53 (1.33 MB/s) - ‘bedGraphToBigWig’ saved [1158245/1158245] | |
| [localhost] local: mv bedGraphToBigWig /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/ac24bc4e-7c2a-338a-801b-c47abc269ae1 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f bedGraphToBigWig /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/bedGraphToBigWig" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/1f5f0f48-5520-3c8a-be39-03bc723baa2c' | |
| [localhost] local: wget --continue --no-check-certificate -O bigWigInfo 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo' | |
| --2014-10-02 23:02:53-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 1149449 (1.1M) [text/plain] | |
| Saving to: ‘bigWigInfo’ | |
| 100%[========================================================================================================================>] 1,149,449 1.30MB/s in 0.8s | |
| 2014-10-02 23:02:59 (1.30 MB/s) - ‘bigWigInfo’ saved [1149449/1149449] | |
| [localhost] local: mv bigWigInfo /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/1f5f0f48-5520-3c8a-be39-03bc723baa2c | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f bigWigInfo /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/bigWigInfo" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/aea886eb-a73a-3ecf-b988-ab70ff9c3c59' | |
| [localhost] local: wget --continue --no-check-certificate -O bigWigSummary 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary' | |
| --2014-10-02 23:02:59-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 1159535 (1.1M) [text/plain] | |
| Saving to: ‘bigWigSummary’ | |
| 100%[========================================================================================================================>] 1,159,535 1.27MB/s in 0.9s | |
| 2014-10-02 23:03:05 (1.27 MB/s) - ‘bigWigSummary’ saved [1159535/1159535] | |
| [localhost] local: mv bigWigSummary /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/aea886eb-a73a-3ecf-b988-ab70ff9c3c59 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f bigWigSummary /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/bigWigSummary" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/326a432f-265f-393e-98b6-10c17e801e43' | |
| [localhost] local: wget --continue --no-check-certificate -O bigWigToBedGraph 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph' | |
| --2014-10-02 23:03:05-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 1150243 (1.1M) [text/plain] | |
| Saving to: ‘bigWigToBedGraph’ | |
| 100%[========================================================================================================================>] 1,150,243 1.43MB/s in 0.8s | |
| 2014-10-02 23:03:11 (1.43 MB/s) - ‘bigWigToBedGraph’ saved [1150243/1150243] | |
| [localhost] local: mv bigWigToBedGraph /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/326a432f-265f-393e-98b6-10c17e801e43 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f bigWigToBedGraph /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/bigWigToBedGraph" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/8ac624e8-93ad-34bb-b76b-ffe5ec049a90' | |
| [localhost] local: wget --continue --no-check-certificate -O bigWigToWig 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToWig' | |
| --2014-10-02 23:03:11-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToWig | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 1148977 (1.1M) [text/plain] | |
| Saving to: ‘bigWigToWig’ | |
| 100%[========================================================================================================================>] 1,148,977 1.23MB/s in 0.9s | |
| 2014-10-02 23:03:17 (1.23 MB/s) - ‘bigWigToWig’ saved [1148977/1148977] | |
| [localhost] local: mv bigWigToWig /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/8ac624e8-93ad-34bb-b76b-ffe5ec049a90 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f bigWigToWig /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/bigWigToWig" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/607f7a42-aef5-3fdf-9dca-efb73f7a83fb' | |
| [localhost] local: wget --continue --no-check-certificate -O fetchChromSizes 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes' | |
| --2014-10-02 23:03:17-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/fetchChromSizes | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 2695 (2.6K) [text/plain] | |
| Saving to: ‘fetchChromSizes’ | |
| 100%[========================================================================================================================>] 2,695 --.-K/s in 0s | |
| 2014-10-02 23:03:22 (326 MB/s) - ‘fetchChromSizes’ saved [2695/2695] | |
| [localhost] local: mv fetchChromSizes /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/607f7a42-aef5-3fdf-9dca-efb73f7a83fb | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f fetchChromSizes /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/fetchChromSizes" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/e1688689-179b-3d3e-936e-5949269fb419' | |
| [localhost] local: wget --continue --no-check-certificate -O wigToBigWig 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig' | |
| --2014-10-02 23:03:22-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 1188803 (1.1M) [text/plain] | |
| Saving to: ‘wigToBigWig’ | |
| 100%[========================================================================================================================>] 1,188,803 1.42MB/s in 0.8s | |
| 2014-10-02 23:03:28 (1.42 MB/s) - ‘wigToBigWig’ saved [1188803/1188803] | |
| [localhost] local: mv wigToBigWig /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/e1688689-179b-3d3e-936e-5949269fb419 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f wigToBigWig /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/wigToBigWig" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/ab1f7d79-a7ed-3363-8f03-f9e454cb5b16' | |
| [localhost] local: wget --continue --no-check-certificate -O faSize 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faSize' | |
| --2014-10-02 23:03:28-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faSize | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 933899 (912K) [text/plain] | |
| Saving to: ‘faSize’ | |
| 100%[========================================================================================================================>] 933,899 1.25MB/s in 0.7s | |
| 2014-10-02 23:03:34 (1.25 MB/s) - ‘faSize’ saved [933899/933899] | |
| [localhost] local: mv faSize /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/ab1f7d79-a7ed-3363-8f03-f9e454cb5b16 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f faSize /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/faSize" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/8c2239ad-1ae5-3737-bd9d-17fb071d5cd0' | |
| [localhost] local: wget --continue --no-check-certificate -O twoBitInfo 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitInfo' | |
| --2014-10-02 23:03:34-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitInfo | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 957506 (935K) [text/plain] | |
| Saving to: ‘twoBitInfo’ | |
| 100%[========================================================================================================================>] 957,506 1.34MB/s in 0.7s | |
| 2014-10-02 23:03:40 (1.34 MB/s) - ‘twoBitInfo’ saved [957506/957506] | |
| [localhost] local: mv twoBitInfo /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/8c2239ad-1ae5-3737-bd9d-17fb071d5cd0 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f twoBitInfo /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/twoBitInfo" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/0a1054cd-d071-3ef7-aae0-a959393db03f' | |
| [localhost] local: wget --continue --no-check-certificate -O twoBitToFa 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitToFa' | |
| --2014-10-02 23:03:40-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitToFa | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 1279043 (1.2M) [text/plain] | |
| Saving to: ‘twoBitToFa’ | |
| 100%[========================================================================================================================>] 1,279,043 1.39MB/s in 0.9s | |
| 2014-10-02 23:03:46 (1.39 MB/s) - ‘twoBitToFa’ saved [1279043/1279043] | |
| [localhost] local: mv twoBitToFa /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/0a1054cd-d071-3ef7-aae0-a959393db03f | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f twoBitToFa /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/twoBitToFa" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/24e0d74b-92e0-39fc-a6ba-779c3babc159' | |
| [localhost] local: wget --continue --no-check-certificate -O faCount 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faCount' | |
| --2014-10-02 23:03:46-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faCount | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 930811 (909K) [text/plain] | |
| Saving to: ‘faCount’ | |
| 100%[========================================================================================================================>] 930,811 1.27MB/s in 0.7s | |
| 2014-10-02 23:03:51 (1.27 MB/s) - ‘faCount’ saved [930811/930811] | |
| [localhost] local: mv faCount /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/24e0d74b-92e0-39fc-a6ba-779c3babc159 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f faCount /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/faCount" | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/6ec73f12-8d66-3a57-ba4c-75d1e2db7c18' | |
| [localhost] local: wget --continue --no-check-certificate -O gtfToGenePred 'http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred' | |
| --2014-10-02 23:03:51-- http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred | |
| Resolving hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)... 128.114.119.163 | |
| Connecting to hgdownload.cse.ucsc.edu (hgdownload.cse.ucsc.edu)|128.114.119.163|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 12590758 (12M) [text/plain] | |
| Saving to: ‘gtfToGenePred’ | |
| 100%[========================================================================================================================>] 12,590,758 4.71MB/s in 2.6s | |
| 2014-10-02 23:03:59 (4.71 MB/s) - ‘gtfToGenePred’ saved [12590758/12590758] | |
| [localhost] local: mv gtfToGenePred /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/6ec73f12-8d66-3a57-ba4c-75d1e2db7c18 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -f gtfToGenePred /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chmod uga+rx /usr/local/bin/gtfToGenePred" | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux | |
| INFO: Custom install for 'ucsc_tools' end time: 2014-10-02 23:03:59.683175; duration: 0:01:57.415873 | |
| INFO: Custom install for 'cufflinks' start time: 2014-10-02 23:03:59.684101 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_cufflinks | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux' | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/62430a6e-ecde-37c3-8ddb-4be74a783ba7' | |
| [localhost] local: wget --continue --no-check-certificate -O cufflinks-2.1.1.Linux_x86_64.tar.gz 'http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.1.1.Linux_x86_64.tar.gz' | |
| --2014-10-02 23:03:59-- http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.1.1.Linux_x86_64.tar.gz | |
| Resolving cufflinks.cbcb.umd.edu (cufflinks.cbcb.umd.edu)... 128.8.120.95 | |
| Connecting to cufflinks.cbcb.umd.edu (cufflinks.cbcb.umd.edu)|128.8.120.95|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 18666555 (18M) [application/x-gzip] | |
| Saving to: ‘cufflinks-2.1.1.Linux_x86_64.tar.gz’ | |
| 100%[========================================================================================================================>] 18,666,555 249KB/s in 73s | |
| 2014-10-02 23:05:18 (249 KB/s) - ‘cufflinks-2.1.1.Linux_x86_64.tar.gz’ saved [18666555/18666555] | |
| [localhost] local: mv cufflinks-2.1.1.Linux_x86_64.tar.gz /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/62430a6e-ecde-37c3-8ddb-4be74a783ba7 | |
| [localhost] local: tar -xzpf cufflinks-2.1.1.Linux_x86_64.tar.gz | |
| [localhost] local: find . -perm -100 -type f | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -rf ./cufflinks /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -rf ./cuffcompare /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -rf ./gffread /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -rf ./gtf_to_sam /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -rf ./cuffmerge /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -rf ./cuffdiff /usr/local/bin" | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux | |
| INFO: Custom install for 'cufflinks' end time: 2014-10-02 23:05:18.835871; duration: 0:01:19.151770 | |
| INFO: Custom install for 'picard' start time: 2014-10-02 23:05:18.836403 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_picard | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "mkdir -p /usr/local/share/java/picard-1.96" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "ln -sf picard-1.96 /usr/local/share/java/picard" | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux' | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/389ac4d3-4d4d-3b7e-a9d8-cc02432f2ffe' | |
| [localhost] local: wget --continue --no-check-certificate -O picard-tools-1.96.zip 'http://downloads.sourceforge.net/project/picard/picard-tools/1.96/picard-tools-1.96.zip' | |
| --2014-10-02 23:05:18-- http://downloads.sourceforge.net/project/picard/picard-tools/1.96/picard-tools-1.96.zip | |
| Resolving downloads.sourceforge.net (downloads.sourceforge.net)... 216.34.181.59 | |
| Connecting to downloads.sourceforge.net (downloads.sourceforge.net)|216.34.181.59|:80... connected. | |
| HTTP request sent, awaiting response... 302 Found | |
| Location: http://iweb.dl.sourceforge.net/project/picard/picard-tools/1.96/picard-tools-1.96.zip [following] | |
| --2014-10-02 23:05:24-- http://iweb.dl.sourceforge.net/project/picard/picard-tools/1.96/picard-tools-1.96.zip | |
| Resolving iweb.dl.sourceforge.net (iweb.dl.sourceforge.net)... 70.38.0.134, 2607:f748:10:12::5f:2 | |
| Connecting to iweb.dl.sourceforge.net (iweb.dl.sourceforge.net)|70.38.0.134|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 43330167 (41M) [application/octet-stream] | |
| Saving to: ‘picard-tools-1.96.zip’ | |
| 100%[========================================================================================================================>] 43,330,167 5.20MB/s in 22s | |
| 2014-10-02 23:05:46 (1.88 MB/s) - ‘picard-tools-1.96.zip’ saved [43330167/43330167] | |
| [localhost] local: mv picard-tools-1.96.zip /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/389ac4d3-4d4d-3b7e-a9d8-cc02432f2ffe | |
| [localhost] local: unzip picard-tools-1.96.zip | |
| Archive: picard-tools-1.96.zip | |
| creating: picard-tools-1.96/ | |
| inflating: picard-tools-1.96/AddOrReplaceReadGroups.jar | |
| inflating: picard-tools-1.96/BamIndexStats.jar | |
| inflating: picard-tools-1.96/BamToBfq.jar | |
| inflating: picard-tools-1.96/BuildBamIndex.jar | |
| inflating: picard-tools-1.96/CalculateHsMetrics.jar | |
| inflating: picard-tools-1.96/CheckIlluminaDirectory.jar | |
| inflating: picard-tools-1.96/CleanSam.jar | |
| inflating: picard-tools-1.96/CollectAlignmentSummaryMetrics.jar | |
| inflating: picard-tools-1.96/CollectGcBiasMetrics.jar | |
| inflating: picard-tools-1.96/CollectInsertSizeMetrics.jar | |
| inflating: picard-tools-1.96/CollectMultipleMetrics.jar | |
| inflating: picard-tools-1.96/CollectRnaSeqMetrics.jar | |
| inflating: picard-tools-1.96/CollectTargetedPcrMetrics.jar | |
| inflating: picard-tools-1.96/CompareSAMs.jar | |
| inflating: picard-tools-1.96/CreateSequenceDictionary.jar | |
| inflating: picard-tools-1.96/DownsampleSam.jar | |
| inflating: picard-tools-1.96/EstimateLibraryComplexity.jar | |
| inflating: picard-tools-1.96/ExtractIlluminaBarcodes.jar | |
| inflating: picard-tools-1.96/ExtractSequences.jar | |
| inflating: picard-tools-1.96/FastqToSam.jar | |
| inflating: picard-tools-1.96/FilterSamReads.jar | |
| inflating: picard-tools-1.96/FixMateInformation.jar | |
| inflating: picard-tools-1.96/IlluminaBasecallsToFastq.jar | |
| inflating: picard-tools-1.96/IlluminaBasecallsToSam.jar | |
| inflating: picard-tools-1.96/IntervalListTools.jar | |
| inflating: picard-tools-1.96/MarkDuplicates.jar | |
| inflating: picard-tools-1.96/MeanQualityByCycle.jar | |
| inflating: picard-tools-1.96/MergeBamAlignment.jar | |
| inflating: picard-tools-1.96/MergeSamFiles.jar | |
| inflating: picard-tools-1.96/MergeVcfs.jar | |
| inflating: picard-tools-1.96/NormalizeFasta.jar | |
| inflating: picard-tools-1.96/QualityScoreDistribution.jar | |
| inflating: picard-tools-1.96/ReorderSam.jar | |
| inflating: picard-tools-1.96/ReplaceSamHeader.jar | |
| inflating: picard-tools-1.96/RevertSam.jar | |
| inflating: picard-tools-1.96/SamFormatConverter.jar | |
| inflating: picard-tools-1.96/SamToFastq.jar | |
| inflating: picard-tools-1.96/SortSam.jar | |
| inflating: picard-tools-1.96/SplitVcfs.jar | |
| inflating: picard-tools-1.96/ValidateSamFile.jar | |
| inflating: picard-tools-1.96/VcfFormatConverter.jar | |
| inflating: picard-tools-1.96/ViewSam.jar | |
| inflating: picard-tools-1.96/apache-ant-1.8.2-bzip2.jar | |
| inflating: picard-tools-1.96/commons-jexl-2.1.1.jar | |
| inflating: picard-tools-1.96/commons-logging-1.1.1.jar | |
| inflating: picard-tools-1.96/picard-1.96.jar | |
| inflating: picard-tools-1.96/sam-1.96.jar | |
| inflating: picard-tools-1.96/snappy-java-1.0.3-rc3.jar | |
| inflating: picard-tools-1.96/tribble-1.96.jar | |
| inflating: picard-tools-1.96/variant-1.96.jar | |
| inflating: snappy-java-1.0.3-rc3.jar | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "mv *.jar /usr/local/share/java/picard-1.96" | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux | |
| INFO: Custom install for 'picard' end time: 2014-10-02 23:05:46.681820; duration: 0:00:27.845417 | |
| INFO: Custom install for 'featurecounts' start time: 2014-10-02 23:05:46.682401 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_featurecounts | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux' | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/7c0bb391-9789-3187-85de-428035116327' | |
| [localhost] local: wget --continue --no-check-certificate -O subread-1.4.4-Linux-x86_64.tar.gz 'http://downloads.sourceforge.net/project/subread/subread-1.4.4/subread-1.4.4-Linux-x86_64.tar.gz' | |
| --2014-10-02 23:05:46-- http://downloads.sourceforge.net/project/subread/subread-1.4.4/subread-1.4.4-Linux-x86_64.tar.gz | |
| Resolving downloads.sourceforge.net (downloads.sourceforge.net)... 216.34.181.59 | |
| Connecting to downloads.sourceforge.net (downloads.sourceforge.net)|216.34.181.59|:80... connected. | |
| HTTP request sent, awaiting response... 302 Found | |
| Location: http://softlayer-dal.dl.sourceforge.net/project/subread/subread-1.4.4/subread-1.4.4-Linux-x86_64.tar.gz [following] | |
| --2014-10-02 23:05:51-- http://softlayer-dal.dl.sourceforge.net/project/subread/subread-1.4.4/subread-1.4.4-Linux-x86_64.tar.gz | |
| Resolving softlayer-dal.dl.sourceforge.net (softlayer-dal.dl.sourceforge.net)... 67.228.157.232 | |
| Connecting to softlayer-dal.dl.sourceforge.net (softlayer-dal.dl.sourceforge.net)|67.228.157.232|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 39364030 (38M) [application/x-gzip] | |
| Saving to: ‘subread-1.4.4-Linux-x86_64.tar.gz’ | |
| 100%[========================================================================================================================>] 39,364,030 4.14MB/s in 10s | |
| 2014-10-02 23:06:02 (3.58 MB/s) - ‘subread-1.4.4-Linux-x86_64.tar.gz’ saved [39364030/39364030] | |
| [localhost] local: mv subread-1.4.4-Linux-x86_64.tar.gz /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/7c0bb391-9789-3187-85de-428035116327 | |
| [localhost] local: tar -xzpf subread-1.4.4-Linux-x86_64.tar.gz | |
| [localhost] local: find . -type f -perm -100 -name 'featureCounts' | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -rf ./bin/featureCounts /usr/local/bin" | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux | |
| INFO: Custom install for 'featurecounts' end time: 2014-10-02 23:06:03.418957; duration: 0:00:16.736556 | |
| INFO: Custom install for 'rnaseqc' start time: 2014-10-02 23:06:03.419556 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_rnaseqc | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "mkdir -p /usr/local/share/java/RNA-SeQC-1.1.7" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "ln -sf RNA-SeQC-1.1.7 /usr/local/share/java/RNA-SeQC" | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux' | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/f1e2dd8c-d0fa-3096-8ad0-568cf9b02e9a' | |
| [localhost] local: wget --continue --no-check-certificate -O RNA-SeQC_v1.1.7.jar 'https://github.com/chapmanb/RNA-SeQC/releases/download/v1.1.7/RNA-SeQC_v1.1.7.jar' | |
| --2014-10-02 23:06:03-- https://github.com/chapmanb/RNA-SeQC/releases/download/v1.1.7/RNA-SeQC_v1.1.7.jar | |
| Resolving github.com (github.com)... 192.30.252.131 | |
| Connecting to github.com (github.com)|192.30.252.131|:443... connected. | |
| HTTP request sent, awaiting response... 302 Found | |
| Location: https://s3.amazonaws.com/github-cloud/releases/21035654/186ae230-f86e-11e3-9f17-9dab1fdbf767.jar?response-content-disposition=attachment%3B%20filename%3DRNA-SeQC_v1.1.7.jar&response-content-type=application/octet-stream&AWSAccessKeyId=AKIAISTNZFOVBIJMK3TQ&Expires=1412291228&Signature=vQxfASw%2FMdmHZMJYbaoA63YRJOU%3D [following] | |
| --2014-10-02 23:06:08-- https://s3.amazonaws.com/github-cloud/releases/21035654/186ae230-f86e-11e3-9f17-9dab1fdbf767.jar?response-content-disposition=attachment%3B%20filename%3DRNA-SeQC_v1.1.7.jar&response-content-type=application/octet-stream&AWSAccessKeyId=AKIAISTNZFOVBIJMK3TQ&Expires=1412291228&Signature=vQxfASw%2FMdmHZMJYbaoA63YRJOU%3D | |
| Resolving s3.amazonaws.com (s3.amazonaws.com)... 54.231.1.96 | |
| Connecting to s3.amazonaws.com (s3.amazonaws.com)|54.231.1.96|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 46231841 (44M) [application/octet-stream] | |
| Saving to: ‘RNA-SeQC_v1.1.7.jar’ | |
| 100%[========================================================================================================================>] 46,231,841 5.04MB/s in 9.3s | |
| 2014-10-02 23:06:18 (4.74 MB/s) - ‘RNA-SeQC_v1.1.7.jar’ saved [46231841/46231841] | |
| [localhost] local: mv RNA-SeQC_v1.1.7.jar /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/f1e2dd8c-d0fa-3096-8ad0-568cf9b02e9a | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "mv RNA-SeQC_v1.1.7.jar /usr/local/share/java/RNA-SeQC-1.1.7" | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux | |
| INFO: Custom install for 'rnaseqc' end time: 2014-10-02 23:06:18.598359; duration: 0:00:15.178803 | |
| INFO: Custom install for 'bcbio_variation' start time: 2014-10-02 23:06:18.598807 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_bcbio_variation | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "mkdir -p /usr/local/share/java/bcbio_variation-0.1.7" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "ln -sf bcbio_variation-0.1.7 /usr/local/share/java/bcbio_variation" | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux' | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/9fd6f270-4067-3904-979f-96dc6aee3367' | |
| [localhost] local: wget --continue --no-check-certificate -O bcbio.variation-0.1.7-standalone.jar 'https://github.com/chapmanb/bcbio.variation/releases/download/v0.1.7/bcbio.variation-0.1.7-standalone.jar' | |
| --2014-10-02 23:06:18-- https://github.com/chapmanb/bcbio.variation/releases/download/v0.1.7/bcbio.variation-0.1.7-standalone.jar | |
| Resolving github.com (github.com)... 192.30.252.131 | |
| Connecting to github.com (github.com)|192.30.252.131|:443... connected. | |
| HTTP request sent, awaiting response... 302 Found | |
| Location: https://s3.amazonaws.com/github-cloud/releases/2956280/64b804ea-1283-11e4-880d-050b7ae3342b.jar?response-content-disposition=attachment%3B%20filename%3Dbcbio.variation-0.1.7-standalone.jar&response-content-type=application/octet-stream&AWSAccessKeyId=AKIAISTNZFOVBIJMK3TQ&Expires=1412291243&Signature=IiTR4KId4Hr1mWsVD3tIyuLsuHE%3D [following] | |
| --2014-10-02 23:06:24-- https://s3.amazonaws.com/github-cloud/releases/2956280/64b804ea-1283-11e4-880d-050b7ae3342b.jar?response-content-disposition=attachment%3B%20filename%3Dbcbio.variation-0.1.7-standalone.jar&response-content-type=application/octet-stream&AWSAccessKeyId=AKIAISTNZFOVBIJMK3TQ&Expires=1412291243&Signature=IiTR4KId4Hr1mWsVD3tIyuLsuHE%3D | |
| Resolving s3.amazonaws.com (s3.amazonaws.com)... 54.231.1.96 | |
| Connecting to s3.amazonaws.com (s3.amazonaws.com)|54.231.1.96|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 35435161 (34M) [application/octet-stream] | |
| Saving to: ‘bcbio.variation-0.1.7-standalone.jar’ | |
| 100%[========================================================================================================================>] 35,435,161 5.05MB/s in 8.4s | |
| 2014-10-02 23:06:32 (4.01 MB/s) - ‘bcbio.variation-0.1.7-standalone.jar’ saved [35435161/35435161] | |
| [localhost] local: mv bcbio.variation-0.1.7-standalone.jar /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/9fd6f270-4067-3904-979f-96dc6aee3367 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "mv bcbio.variation-0.1.7-standalone.jar /usr/local/share/java/bcbio_variation-0.1.7" | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux | |
| INFO: Custom install for 'bcbio_variation' end time: 2014-10-02 23:06:32.918697; duration: 0:00:14.319890 | |
| INFO: Custom install for 'grabix' start time: 2014-10-02 23:06:32.919074 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_grabix | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux' | |
| [localhost] local: git clone https://github.com/arq5x/grabix.git | |
| Cloning into 'grabix'... | |
| remote: Counting objects: 82, done. | |
| remote: Total 82 (delta 0), reused 0 (delta 0) | |
| Unpacking objects: 100% (82/82), done. | |
| Checking connectivity... done. | |
| [localhost] local: cd grabix && git checkout a78cbaf488 | |
| Note: checking out 'a78cbaf488'. | |
| You are in 'detached HEAD' state. You can look around, make experimental | |
| changes and commit them, and you can discard any commits you make in this | |
| state without impacting any branches by performing another checkout. | |
| If you want to create a new branch to retain commits you create, you may | |
| do so (now or later) by using -b with the checkout command again. Example: | |
| git checkout -b new_branch_name | |
| HEAD is now at a78cbaf... Merge pull request #12 from chapmanb/master | |
| [localhost] local: make | |
| gcc -Wall -O2 -o grabix grabix.cpp bgzf.c -lstdc++ -lz | |
| bgzf.c: In function ‘bgzf_check_EOF’: | |
| bgzf.c:60:39: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] | |
| #define _bgzf_read(fp, buf, len) fread((buf), 1, (len), (FILE*)(fp)) | |
| ^ | |
| bgzf.c:622:2: note: in expansion of macro ‘_bgzf_read’ | |
| _bgzf_read(fp->fp, buf, 28); | |
| ^ | |
| [localhost] local: ls -1 grabix | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "cp -rf grabix /usr/local/bin" | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux | |
| INFO: Custom install for 'grabix' end time: 2014-10-02 23:06:45.848583; duration: 0:00:12.929509 | |
| INFO: Custom install for 'mutect' start time: 2014-10-02 23:06:45.849135 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_mutect | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "mkdir -p /usr/local/share/java/mutect-1.1.5" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "ln -sf mutect-1.1.5 /usr/local/share/java/mutect" | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux' | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/c8754fd4-a5f2-3221-8796-4383a51ae41f' | |
| [localhost] local: wget --continue --no-check-certificate -O muTect-1.1.5-bin.zip 'https://github.com/broadinstitute/mutect/releases/download/1.1.5/muTect-1.1.5-bin.zip' | |
| --2014-10-02 23:06:45-- https://github.com/broadinstitute/mutect/releases/download/1.1.5/muTect-1.1.5-bin.zip | |
| Resolving github.com (github.com)... 192.30.252.131 | |
| Connecting to github.com (github.com)|192.30.252.131|:443... connected. | |
| HTTP request sent, awaiting response... 302 Found | |
| Location: https://s3.amazonaws.com/github-cloud/releases/7894514/e1943ada-0f2b-11e3-856b-730e2489d072.zip?response-content-disposition=attachment%3B%20filename%3DmuTect-1.1.5-bin.zip&response-content-type=application/octet-stream&AWSAccessKeyId=AKIAISTNZFOVBIJMK3TQ&Expires=1412291271&Signature=zdB5KLpyHAfDH5SU17Z9HQYHRBY%3D [following] | |
| --2014-10-02 23:06:51-- https://s3.amazonaws.com/github-cloud/releases/7894514/e1943ada-0f2b-11e3-856b-730e2489d072.zip?response-content-disposition=attachment%3B%20filename%3DmuTect-1.1.5-bin.zip&response-content-type=application/octet-stream&AWSAccessKeyId=AKIAISTNZFOVBIJMK3TQ&Expires=1412291271&Signature=zdB5KLpyHAfDH5SU17Z9HQYHRBY%3D | |
| Resolving s3.amazonaws.com (s3.amazonaws.com)... 54.231.0.24 | |
| Connecting to s3.amazonaws.com (s3.amazonaws.com)|54.231.0.24|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 9666901 (9.2M) [application/octet-stream] | |
| Saving to: ‘muTect-1.1.5-bin.zip’ | |
| 100%[========================================================================================================================>] 9,666,901 3.81MB/s in 2.4s | |
| 2014-10-02 23:06:54 (3.81 MB/s) - ‘muTect-1.1.5-bin.zip’ saved [9666901/9666901] | |
| [localhost] local: mv muTect-1.1.5-bin.zip /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/c8754fd4-a5f2-3221-8796-4383a51ae41f | |
| [localhost] local: unzip muTect-1.1.5-bin.zip | |
| Archive: muTect-1.1.5-bin.zip | |
| inflating: LICENSE.TXT | |
| inflating: muTect-1.1.5.jar | |
| inflating: version.txt | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "mv *.jar version.txt LICENSE* /usr/local/share/java/mutect-1.1.5" | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux | |
| INFO: Custom install for 'mutect' end time: 2014-10-02 23:06:54.211075; duration: 0:00:08.361940 | |
| INFO: Custom install for 'varscan' start time: 2014-10-02 23:06:54.211626 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_varscan | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "mkdir -p /usr/local/share/java/varscan-2.3.7" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "ln -sf varscan-2.3.7 /usr/local/share/java/varscan" | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux' | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/0a039ad5-5bb8-3251-ac13-362f8cf9e744' | |
| [localhost] local: wget --continue --no-check-certificate -O VarScan.v2.3.7.jar 'http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.7.jar' | |
| --2014-10-02 23:06:54-- http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.7.jar | |
| Resolving downloads.sourceforge.net (downloads.sourceforge.net)... 216.34.181.59 | |
| Connecting to downloads.sourceforge.net (downloads.sourceforge.net)|216.34.181.59|:80... connected. | |
| HTTP request sent, awaiting response... 302 Found | |
| Location: http://iweb.dl.sourceforge.net/project/varscan/VarScan.v2.3.7.jar [following] | |
| --2014-10-02 23:06:59-- http://iweb.dl.sourceforge.net/project/varscan/VarScan.v2.3.7.jar | |
| Resolving iweb.dl.sourceforge.net (iweb.dl.sourceforge.net)... 70.38.0.134, 2607:f748:10:12::5f:2 | |
| Connecting to iweb.dl.sourceforge.net (iweb.dl.sourceforge.net)|70.38.0.134|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 102587 (100K) [application/java-archive] | |
| Saving to: ‘VarScan.v2.3.7.jar’ | |
| 100%[========================================================================================================================>] 102,587 207KB/s in 0.5s | |
| 2014-10-02 23:07:00 (207 KB/s) - ‘VarScan.v2.3.7.jar’ saved [102587/102587] | |
| [localhost] local: mv VarScan.v2.3.7.jar /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/0a039ad5-5bb8-3251-ac13-362f8cf9e744 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "mv VarScan.v2.3.7.jar /usr/local/share/java/varscan-2.3.7" | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux | |
| INFO: Custom install for 'varscan' end time: 2014-10-02 23:07:00.190426; duration: 0:00:05.978800 | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/chef_recipes.yaml | |
| INFO: Reading /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/chef_recipes.yaml | |
| DBG [shared.py]: Packages to install: | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/puppet_classes.yaml | |
| INFO: Reading /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/puppet_classes.yaml | |
| DBG [shared.py]: Packages to install: | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml | |
| INFO: Meta-package information from /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml | |
| - Packages: minimal,libraries,perl,python,java,r,ruby,bio_nextgen | |
| - Libraries: r-libs | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/packages-homebrew.yaml | |
| INFO: Reading /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/packages-homebrew.yaml | |
| DBG [shared.py]: Packages to install: bcftools,htslib,samtools,bamtools,bedtools,biobambam,cramtools,fastqc,kraken,libmaus,oncofuse,qualimap,sambamba,samblaster,seqtk,sickle,speedseq,staden_io_lib,bcbio-variation-recall,delly;--with-binary,freebayes,gatk-framework,glia,hall-lab-sv-tools,lumpy-sv,pindel,platypus-variant,qsignature,rtg-tools,scalpel,snpeff,vardict,vcflib,vep,vt,bowtie2,bwa,novoalign,rna-star,snap-aligner,tophat-binary,cmake,cpanminus | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux' | |
| [localhost] local: git clone https://github.com/Homebrew/linuxbrew.git | |
| Cloning into 'linuxbrew'... | |
| remote: Counting objects: 202714, done. | |
| remote: Compressing objects: 100% (2475/2475), done. | |
| remote: Total 202714 (delta 1722), reused 0 (delta 0) | |
| Receiving objects: 100% (202714/202714), 37.08 MiB | 5.37 MiB/s, done. | |
| Resolving deltas: 100% (149886/149886), done. | |
| Checking connectivity... done. | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chown vagrant /usr/local" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chown vagrant /usr/local/bin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chown vagrant /usr/local/etc" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chown vagrant /usr/local/include" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chown vagrant /usr/local/lib" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chown vagrant /usr/local/sbin" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chown vagrant /usr/local/share" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chown vagrant /usr/local/share/java" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chown vagrant /usr/local/share/man" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "chown vagrant /usr/local/lib/python2.7/site-packages" | |
| [localhost] local: mv Library /usr/local | |
| [localhost] local: mv .git /usr/local | |
| [localhost] local: mkdir -p /usr/local/share/man/man1 | |
| [localhost] local: mv -f share/man/man1/brew.1 /usr/local/share/man/man1 | |
| [localhost] local: mv -f bin/brew /usr/local/bin | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux | |
| [localhost] local: /usr/local/bin/brew tap | |
| [localhost] local: /usr/local/bin/brew update | |
| Already up-to-date. | |
| [localhost] local: /usr/local/bin/brew tap homebrew/science | |
| Cloning into '/usr/local/Library/Taps/homebrew/homebrew-science'... | |
| remote: Counting objects: 6167, done. | |
| remote: Compressing objects: 100% (9/9), done. | |
| remote: Total 6167 (delta 2), reused 0 (delta 0) | |
| Receiving objects: 100% (6167/6167), 1.55 MiB | 1.25 MiB/s, done. | |
| Resolving deltas: 100% (3281/3281), done. | |
| Checking connectivity... done. | |
| Tapped 362 formulae | |
| [localhost] local: /usr/local/bin/brew tap chapmanb/cbl | |
| Cloning into '/usr/local/Library/Taps/chapmanb/homebrew-cbl'... | |
| remote: Counting objects: 366, done. | |
| remote: Compressing objects: 100% (6/6), done. | |
| remote: Total 366 (delta 1), reused 0 (delta 0) | |
| Receiving objects: 100% (366/366), 58.33 KiB | 0 bytes/s, done. | |
| Resolving deltas: 100% (200/200), done. | |
| Checking connectivity... done. | |
| Tapped 28 formulae | |
| [localhost] local: /usr/local/bin/brew tap --repair | |
| Pruned 0 dead formulae | |
| Tapped 390 formulae | |
| [localhost] local: /usr/local/bin/brew outdated | |
| [localhost] local: /usr/local/bin/brew info cmake | |
| [localhost] local: /usr/local/bin/brew --cache | |
| [localhost] local: /usr/local/bin/brew --prefix | |
| [localhost] local: mkdir -p '/home/vagrant/.cache/Homebrew/6359734d-c31b-3a64-b70c-f9b1c9c7d21c' | |
| [localhost] local: wget --continue --no-check-certificate -O cmake-3.0.2.x86_64-linux.bottle.tar.gz 'https://s3.amazonaws.com/cloudbiolinux/brew_bottles/cmake-3.0.2.x86_64-linux.bottle.tar.gz' | |
| --2014-10-02 23:08:12-- https://s3.amazonaws.com/cloudbiolinux/brew_bottles/cmake-3.0.2.x86_64-linux.bottle.tar.gz | |
| Resolving s3.amazonaws.com (s3.amazonaws.com)... 54.231.2.184 | |
| Connecting to s3.amazonaws.com (s3.amazonaws.com)|54.231.2.184|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 9268853 (8.8M) [binary/octet-stream] | |
| Saving to: ‘cmake-3.0.2.x86_64-linux.bottle.tar.gz’ | |
| 100%[========================================================================================================================>] 9,268,853 3.82MB/s in 2.3s | |
| 2014-10-02 23:08:20 (3.82 MB/s) - ‘cmake-3.0.2.x86_64-linux.bottle.tar.gz’ saved [9268853/9268853] | |
| [localhost] local: mv cmake-3.0.2.x86_64-linux.bottle.tar.gz /home/vagrant/.cache/Homebrew | |
| [localhost] local: rm -rf /home/vagrant/.cache/Homebrew/6359734d-c31b-3a64-b70c-f9b1c9c7d21c | |
| [localhost] local: tar -xf /home/vagrant/.cache/Homebrew/cmake-3.0.2.x86_64-linux.bottle.tar.gz | |
| [localhost] local: /usr/local/bin/brew link --overwrite cmake | |
| Linking /usr/local/Cellar/cmake/3.0.2... 7 symlinks created | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit expat | |
| ==> Downloading https://downloads.sourceforge.net/project/expat/expat/2.1.0/expat-2.1.0.tar.gz | |
| ######################################################################## 100.0% | |
| ==> ./configure --prefix=/usr/local/Cellar/expat/2.1.0 --mandir=/usr/local/Cellar/expat/2.1.0/share/man | |
| ==> make install | |
| /usr/local/Cellar/expat/2.1.0: 11 files, 500K, built in 18 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite expat | |
| Warning: Already linked: /usr/local/Cellar/expat/2.1.0 | |
| To relink: brew unlink expat && brew link expat | |
| [localhost] local: /usr/local/bin/brew list samtools | grep -c bctools | |
| Warning: local() encountered an error (return code 1) while executing '/usr/local/bin/brew list samtools | grep -c bctools' | |
| [localhost] local: /usr/local/bin/brew list samtools | grep -c vcfutils.pl | |
| Warning: local() encountered an error (return code 1) while executing '/usr/local/bin/brew list samtools | grep -c vcfutils.pl' | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit samtools | |
| ==> Installing samtools dependency: htslib | |
| ==> Downloading https://github.com/samtools/htslib/archive/1.1.tar.gz | |
| ######################################################################## 100.0% | |
| ==> echo '#define HTS_VERSION "1.1"' > version.h | |
| ==> make | |
| ==> make install prefix=/usr/local/Cellar/htslib/1.1 | |
| /usr/local/Cellar/htslib/1.1: 31 files, 8.5M, built in 33 seconds | |
| ==> Installing samtools | |
| ==> Downloading https://github.com/samtools/samtools/archive/1.1.tar.gz | |
| ######################################################################## 100.0% | |
| ==> make HTSDIR=/usr/local/opt/htslib/include HTSLIB=/usr/local/opt/htslib/lib/libhts.a | |
| /usr/local/Cellar/samtools/1.1: 45 files, 4.0M, built in 27 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite samtools | |
| Warning: Already linked: /usr/local/Cellar/samtools/1.1 | |
| To relink: brew unlink samtools && brew link samtools | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit htslib | |
| Warning: htslib-1.1 already installed | |
| [localhost] local: /usr/local/bin/brew link --overwrite htslib | |
| Warning: Already linked: /usr/local/Cellar/htslib/1.1 | |
| To relink: brew unlink htslib && brew link htslib | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit libmaus | |
| ==> Installing dependencies for libmaus: pkg-config, staden_io_lib | |
| ==> Installing libmaus dependency: pkg-config | |
| ==> Downloading http://pkgconfig.freedesktop.org/releases/pkg-config-0.28.tar.gz | |
| curl: (28) Resolving timed out after 5541 milliseconds | |
| Trying a mirror... | |
| ==> Downloading http://fossies.org/linux/misc/pkg-config-0.28.tar.gz | |
| ######################################################################## 100.0% | |
| ==> ./configure --prefix=/usr/local/Cellar/pkg-config/0.28 --disable-host-tool --with-internal-glib --with-pc-path=/usr/local/lib/pkgconfig:/usr/local/share/pkgco | |
| ==> make | |
| ==> make check | |
| ==> make install | |
| /usr/local/Cellar/pkg-config/0.28: 10 files, 644K, built in 35 seconds | |
| ==> Installing libmaus dependency: staden_io_lib | |
| ==> Downloading http://downloads.sourceforge.net/project/staden/io_lib/1.13.7/io_lib-1.13.7.tar.gz | |
| ######################################################################## 100.0% | |
| ==> ./configure --prefix=/usr/local/Cellar/staden_io_lib/1.13.7 | |
| ==> make | |
| ==> make install | |
| /usr/local/Cellar/staden_io_lib/1.13.7: 115 files, 2.5M, built in 35 seconds | |
| ==> Installing libmaus | |
| ==> Downloading https://github.com/gt1/libmaus/archive/0.0.147-release-20140714102038.tar.gz | |
| ######################################################################## 100.0% | |
| ==> ./configure --prefix=/usr/local/Cellar/libmaus/0.0.147 --with-io-lib=/usr/local/opt/staden_io_lib | |
| ==> make | |
| ==> make install | |
| /usr/local/Cellar/libmaus/0.0.147: 839 files, 12M, built in 6.3 minutes | |
| [localhost] local: /usr/local/bin/brew link --overwrite libmaus | |
| Warning: Already linked: /usr/local/Cellar/libmaus/0.0.147 | |
| To relink: brew unlink libmaus && brew link libmaus | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit cmake | |
| Warning: cmake-3.0.2 already installed | |
| [localhost] local: /usr/local/bin/brew link --overwrite cmake | |
| Warning: Already linked: /usr/local/Cellar/cmake/3.0.2 | |
| To relink: brew unlink cmake && brew link cmake | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit cpanminus | |
| ==> Downloading https://github.com/miyagawa/cpanminus/archive/1.7011.tar.gz | |
| ######################################################################## 100.0% | |
| /usr/local/Cellar/cpanminus/1.7011: 5 files, 388K, built in 12 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite cpanminus | |
| Warning: Already linked: /usr/local/Cellar/cpanminus/1.7011 | |
| To relink: brew unlink cpanminus && brew link cpanminus | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Statistics::Descriptive' | |
| --> Working on Statistics::Descriptive | |
| Fetching http://www.cpan.org/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0607.tar.gz ... OK | |
| Configuring Statistics-Descriptive-3.0607 ... OK | |
| Building Statistics-Descriptive-3.0607 ... OK | |
| Successfully installed Statistics-Descriptive-3.0607 | |
| 1 distribution installed | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Archive::Extract' | |
| --> Working on Archive::Extract | |
| Fetching http://www.cpan.org/authors/id/B/BI/BINGOS/Archive-Extract-0.72.tar.gz ... OK | |
| Configuring Archive-Extract-0.72 ... OK | |
| Building Archive-Extract-0.72 ... OK | |
| Successfully installed Archive-Extract-0.72 (upgraded from 0.70) | |
| 1 distribution installed | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Archive::Zip' | |
| --> Working on Archive::Zip | |
| Fetching http://www.cpan.org/authors/id/P/PH/PHRED/Archive-Zip-1.38.tar.gz ... OK | |
| Configuring Archive-Zip-1.38 ... OK | |
| Building Archive-Zip-1.38 ... OK | |
| Successfully installed Archive-Zip-1.38 | |
| 1 distribution installed | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Archive::Tar' | |
| --> Working on Archive::Tar | |
| Fetching http://www.cpan.org/authors/id/B/BI/BINGOS/Archive-Tar-2.02.tar.gz ... OK | |
| Configuring Archive-Tar-2.02 ... OK | |
| Building Archive-Tar-2.02 ... OK | |
| Successfully installed Archive-Tar-2.02 (upgraded from 1.90) | |
| 1 distribution installed | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'DBI' | |
| --> Working on DBI | |
| Fetching http://www.cpan.org/authors/id/T/TI/TIMB/DBI-1.631.tar.gz ... OK | |
| Configuring DBI-1.631 ... OK | |
| Building DBI-1.631 ... OK | |
| Successfully installed DBI-1.631 | |
| 1 distribution installed | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'LWP::Simple' | |
| LWP::Simple is up to date. (6.00) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'LWP::Protocol::https' | |
| --> Working on LWP::Protocol::https | |
| Fetching http://www.cpan.org/authors/id/M/MS/MSCHILLI/LWP-Protocol-https-6.06.tar.gz ... OK | |
| Configuring LWP-Protocol-https-6.06 ... OK | |
| ==> Found dependencies: LWP::UserAgent, Mozilla::CA | |
| --> Working on LWP::UserAgent | |
| Fetching http://www.cpan.org/authors/id/M/MS/MSCHILLI/libwww-perl-6.08.tar.gz ... OK | |
| Configuring libwww-perl-6.08 ... OK | |
| ==> Found dependencies: Net::HTTP | |
| --> Working on Net::HTTP | |
| Fetching http://www.cpan.org/authors/id/M/MS/MSCHILLI/Net-HTTP-6.07.tar.gz ... OK | |
| Configuring Net-HTTP-6.07 ... OK | |
| Building Net-HTTP-6.07 ... OK | |
| Successfully installed Net-HTTP-6.07 (upgraded from 6.06) | |
| Building libwww-perl-6.08 ... OK | |
| Successfully installed libwww-perl-6.08 (upgraded from 6.05) | |
| --> Working on Mozilla::CA | |
| Fetching http://www.cpan.org/authors/id/A/AB/ABH/Mozilla-CA-20130114.tar.gz ... OK | |
| Configuring Mozilla-CA-20130114 ... OK | |
| Building Mozilla-CA-20130114 ... OK | |
| Successfully installed Mozilla-CA-20130114 | |
| Building LWP-Protocol-https-6.06 ... OK | |
| Successfully installed LWP-Protocol-https-6.06 (upgraded from 6.04) | |
| 4 distributions installed | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Time::HiRes' | |
| --> Working on Time::HiRes | |
| Fetching http://www.cpan.org/authors/id/Z/ZE/ZEFRAM/Time-HiRes-1.9726.tar.gz ... OK | |
| Configuring Time-HiRes-1.9726 ... OK | |
| Building Time-HiRes-1.9726 ... OK | |
| Successfully installed Time-HiRes-1.9726 (upgraded from 1.9725) | |
| 1 distribution installed | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit bcftools | |
| ==> Downloading https://github.com/samtools/bcftools/archive/1.1.tar.gz | |
| ######################################################################## 100.0% | |
| ==> echo '#define BCFTOOLS_VERSION "1.1"' > version.h | |
| ==> make bcftools HTSDIR=/usr/local/opt/htslib/include HTSLIB=/usr/local/opt/htslib/lib/libhts.a | |
| ==> make install prefix=/usr/local/Cellar/bcftools/1.1 HTSDIR=/usr/local/opt/htslib/include HTSLIB=/usr/local/opt/htslib/lib/libhts.a | |
| /usr/local/Cellar/bcftools/1.1: 8 files, 4.0M, built in 21 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite bcftools | |
| Warning: Already linked: /usr/local/Cellar/bcftools/1.1 | |
| To relink: brew unlink bcftools && brew link bcftools | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit htslib | |
| Warning: htslib-1.1 already installed | |
| [localhost] local: /usr/local/bin/brew link --overwrite htslib | |
| Warning: Already linked: /usr/local/Cellar/htslib/1.1 | |
| To relink: brew unlink htslib && brew link htslib | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit samtools | |
| Warning: samtools-1.1 already installed | |
| [localhost] local: /usr/local/bin/brew link --overwrite samtools | |
| Warning: Already linked: /usr/local/Cellar/samtools/1.1 | |
| To relink: brew unlink samtools && brew link samtools | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit bamtools | |
| ==> Downloading https://github.com/pezmaster31/bamtools/archive/v2.3.0.tar.gz | |
| ######################################################################## 100.0% | |
| ==> Downloading https://github.com/sjackman/bamtools/commit/3b6b89d.diff | |
| ######################################################################## 100.0% | |
| ==> Patching | |
| patching file src/api/CMakeLists.txt | |
| ==> cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/bamtools/2.3.0 -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERBOSE_MAKEFILE=ON -Wno-dev | |
| ==> make install | |
| /usr/local/Cellar/bamtools/2.3.0: 26 files, 2.8M, built in 58 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite bamtools | |
| Warning: Already linked: /usr/local/Cellar/bamtools/2.3.0 | |
| To relink: brew unlink bamtools && brew link bamtools | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit bedtools | |
| ==> Downloading https://github.com/arq5x/bedtools2/releases/download/v2.21.0/bedtools-2.21.0.tar.gz | |
| ######################################################################## 100.0% | |
| ==> make | |
| /usr/local/Cellar/bedtools/2.21.0: 41 files, 2.3M, built in 82 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite bedtools | |
| Warning: Already linked: /usr/local/Cellar/bedtools/2.21.0 | |
| To relink: brew unlink bedtools && brew link bedtools | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit biobambam | |
| ==> Downloading https://github.com/gt1/biobambam/archive/0.0.154-release-20140709001615.tar.gz | |
| ######################################################################## 100.0% | |
| ==> export PKG_CONFIG=$(export PATH=/usr/local/bin:$PATH && which pkg-config) | |
| ==> ./configure --prefix=/usr/local/Cellar/biobambam/0.0.154 | |
| ==> make | |
| ==> make install | |
| /usr/local/Cellar/biobambam/0.0.154: 86 files, 15M, built in 6.6 minutes | |
| [localhost] local: /usr/local/bin/brew link --overwrite biobambam | |
| Warning: Already linked: /usr/local/Cellar/biobambam/0.0.154 | |
| To relink: brew unlink biobambam && brew link biobambam | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit cramtools | |
| ==> Downloading https://github.com/enasequence/cramtools/raw/master/cramtools-2.1.jar | |
| ######################################################################## 100.0% | |
| /usr/local/Cellar/cramtools/2.1-b237: 3 files, 5.6M, built in 16 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite cramtools | |
| Warning: Already linked: /usr/local/Cellar/cramtools/2.1-b237 | |
| To relink: brew unlink cramtools && brew link cramtools | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit fastqc | |
| ==> Downloading http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.2.zip | |
| ######################################################################## 100.0% | |
| /usr/local/Cellar/fastqc/0.11.2: 209 files, 2.4M, built in 14 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite fastqc | |
| Warning: Already linked: /usr/local/Cellar/fastqc/0.11.2 | |
| To relink: brew unlink fastqc && brew link fastqc | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit kraken | |
| ==> Downloading http://ccb.jhu.edu/software/kraken/dl/kraken-0.10.3-beta.tgz | |
| ######################################################################## 100.0% | |
| ==> ./install_kraken.sh /usr/local/Cellar/kraken/0.10.3-beta/libexec | |
| /usr/local/Cellar/kraken/0.10.3-beta: 20 files, 384K, built in 8 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite kraken | |
| Warning: Already linked: /usr/local/Cellar/kraken/0.10.3-beta | |
| To relink: brew unlink kraken && brew link kraken | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit libmaus | |
| Warning: libmaus-0.0.147 already installed | |
| [localhost] local: /usr/local/bin/brew link --overwrite libmaus | |
| Warning: Already linked: /usr/local/Cellar/libmaus/0.0.147 | |
| To relink: brew unlink libmaus && brew link libmaus | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit oncofuse | |
| ==> Downloading https://github.com/mikessh/oncofuse/releases/download/v1.0.7/oncofuse-v1.0.7.zip | |
| ######################################################################## 100.0% | |
| /usr/local/Cellar/oncofuse/1.0.7: 32 files, 59M, built in 17 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite oncofuse | |
| Warning: Already linked: /usr/local/Cellar/oncofuse/1.0.7 | |
| To relink: brew unlink oncofuse && brew link oncofuse | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit qualimap | |
| ==> Downloading http://qualimap.bioinfo.cipf.es/release/qualimap_v0.7.1.zip | |
| ######################################################################## 100.0% | |
| /usr/local/Cellar/qualimap/0.7.1: 62 files, 36M, built in 42 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite qualimap | |
| Warning: Already linked: /usr/local/Cellar/qualimap/0.7.1 | |
| To relink: brew unlink qualimap && brew link qualimap | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit sambamba | |
| ==> Downloading https://github.com/lomereiter/sambamba/releases/download/v0.4.7/sambamba_v0.4.7_centos5.tar.bz2 | |
| ######################################################################## 100.0% | |
| /usr/local/Cellar/sambamba/0.4.7: 2 files, 7.1M, built in 12 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite sambamba | |
| Warning: Already linked: /usr/local/Cellar/sambamba/0.4.7 | |
| To relink: brew unlink sambamba && brew link sambamba | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit samblaster | |
| ==> Downloading https://github.com/GregoryFaust/samblaster/releases/download/v.0.1.20/samblaster-v.0.1.20.tar.gz | |
| ######################################################################## 100.0% | |
| ==> make | |
| /usr/local/Cellar/samblaster/0.1.20: 4 files, 72K, built in 12 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite samblaster | |
| Warning: Already linked: /usr/local/Cellar/samblaster/0.1.20 | |
| To relink: brew unlink samblaster && brew link samblaster | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit seqtk | |
| ==> Downloading https://github.com/lh3/seqtk/archive/73866e7.tar.gz | |
| ######################################################################## 100.0% | |
| ==> make | |
| /usr/local/Cellar/seqtk/1.0-r68: 3 files, 208K, built in 13 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite seqtk | |
| Warning: Already linked: /usr/local/Cellar/seqtk/1.0-r68 | |
| To relink: brew unlink seqtk && brew link seqtk | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit sickle | |
| ==> Downloading https://github.com/najoshi/sickle/archive/v1.33.tar.gz | |
| ######################################################################## 100.0% | |
| ==> make | |
| /usr/local/Cellar/sickle/1.33: 4 files, 60K, built in 13 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite sickle | |
| Warning: Already linked: /usr/local/Cellar/sickle/1.33 | |
| To relink: brew unlink sickle && brew link sickle | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit speedseq | |
| ==> Installing speedseq dependency: lumpy-sv | |
| ==> Downloading https://github.com/arq5x/lumpy-sv/releases/download/0.2.7/lumpy-sv-0.2.7.tar.gz | |
| ######################################################################## 100.0% | |
| ==> make | |
| /usr/local/Cellar/lumpy-sv/0.2.7: 13 files, 12M, built in 71 seconds | |
| ==> Installing speedseq | |
| ==> Cloning https://github.com/cc2qe/speedseq.git | |
| Cloning into '/home/vagrant/.cache/Homebrew/speedseq--git'... | |
| remote: Counting objects: 1503, done. | |
| remote: Compressing objects: 100% (9/9), done. | |
| remote: Total 1503 (delta 1), reused 0 (delta 0) | |
| Receiving objects: 100% (1503/1503), 1.50 MiB | 1.31 MiB/s, done. | |
| Resolving deltas: 100% (634/634), done. | |
| Checking connectivity... done. | |
| /usr/local/Cellar/speedseq/2014-08-22: 4 files, 92K, built in 12 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite speedseq | |
| Warning: Already linked: /usr/local/Cellar/speedseq/2014-08-22 | |
| To relink: brew unlink speedseq && brew link speedseq | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit staden_io_lib | |
| Warning: staden_io_lib-1.13.7 already installed | |
| [localhost] local: /usr/local/bin/brew link --overwrite staden_io_lib | |
| Warning: Already linked: /usr/local/Cellar/staden_io_lib/1.13.7 | |
| To relink: brew unlink staden_io_lib && brew link staden_io_lib | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit bcbio-variation-recall | |
| ==> Downloading https://github.com/chapmanb/bcbio.variation.recall/releases/download/v0.0.2/bcbio-variation-recall | |
| ######################################################################## 100.0% | |
| /usr/local/Cellar/bcbio-variation-recall/0.0.2: 2 files, 8.5M, built in 17 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite bcbio-variation-recall | |
| Warning: Already linked: /usr/local/Cellar/bcbio-variation-recall/0.0.2 | |
| To relink: brew unlink bcbio-variation-recall && brew link bcbio-variation-recall | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit --with-binary delly | |
| ==> Downloading https://github.com/tobiasrausch/delly/archive/v0.5.6.tar.gz | |
| ######################################################################## 100.0% | |
| ==> Downloading https://github.com/tobiasrausch/delly/releases/download/v0.5.6/delly_v0.5.6_CentOS5.4_x86_64bit | |
| ######################################################################## 100.0% | |
| /usr/local/Cellar/delly/0.5.6: 6 files, 3.4M, built in 25 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite delly | |
| Warning: Already linked: /usr/local/Cellar/delly/0.5.6 | |
| To relink: brew unlink delly && brew link delly | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit freebayes | |
| ==> Cloning https://github.com/ekg/freebayes.git | |
| Cloning into '/home/vagrant/.cache/Homebrew/freebayes--git'... | |
| remote: Counting objects: 4139, done. | |
| remote: Total 4139 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (4139/4139), 6.31 MiB | 2.10 MiB/s, done. | |
| Resolving deltas: 100% (2666/2666), done. | |
| Checking connectivity... done. | |
| Submodule 'bamtools' (https://github.com/pezmaster31/bamtools.git) registered for path 'bamtools' | |
| Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'intervaltree' | |
| Submodule 'vcflib' (https://github.com/ekg/vcflib.git) registered for path 'vcflib' | |
| Cloning into 'bamtools'... | |
| remote: Counting objects: 4012, done. | |
| remote: Total 4012 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (4012/4012), 2.84 MiB | 1.61 MiB/s, done. | |
| Resolving deltas: 100% (2437/2437), done. | |
| Checking connectivity... done. | |
| Submodule path 'bamtools': checked out 'b307a397f7d818d0fa064b91229e312707e43951' | |
| Cloning into 'intervaltree'... | |
| remote: Counting objects: 70, done. | |
| remote: Total 70 (delta 0), reused 0 (delta 0) | |
| Unpacking objects: 100% (70/70), done. | |
| Checking connectivity... done. | |
| Submodule path 'intervaltree': checked out 'd151b487804861dc9f932e9f1fe4f8c499673cec' | |
| Cloning into 'vcflib'... | |
| remote: Counting objects: 1513, done. | |
| remote: Compressing objects: 100% (17/17), done. | |
| remote: Total 1513 (delta 7), reused 0 (delta 0) | |
| Receiving objects: 100% (1513/1513), 1.06 MiB | 830.00 KiB/s, done. | |
| Resolving deltas: 100% (857/857), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib': checked out '1e2c464f4d07053a306ee5023d91bf133b3016da' | |
| Submodule 'fastahack' (https://github.com/ekg/fastahack.git) registered for path 'fastahack' | |
| Submodule 'filevercmp' (https://github.com/ekg/filevercmp.git) registered for path 'filevercmp' | |
| Submodule 'fsom' (https://github.com/ekg/fsom.git) registered for path 'fsom' | |
| Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'intervaltree' | |
| Submodule 'multichoose' (https://github.com/ekg/multichoose.git) registered for path 'multichoose' | |
| Submodule 'smithwaterman' (https://github.com/ekg/smithwaterman.git) registered for path 'smithwaterman' | |
| Submodule 'tabixpp' (https://github.com/ekg/tabixpp.git) registered for path 'tabixpp' | |
| Cloning into 'fastahack'... | |
| remote: Counting objects: 181, done. | |
| remote: Total 181 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (181/181), 42.33 KiB | 0 bytes/s, done. | |
| Resolving deltas: 100% (106/106), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib/fastahack': checked out 'c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd' | |
| Cloning into 'filevercmp'... | |
| remote: Counting objects: 18, done. | |
| remote: Compressing objects: 100% (10/10), done. | |
| remote: Total 18 (delta 8), reused 18 (delta 8) | |
| Unpacking objects: 100% (18/18), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib/filevercmp': checked out '378bae779b897f1506043c1b647a5e5f8031ea4b' | |
| Cloning into 'fsom'... | |
| remote: Counting objects: 35, done. | |
| remote: Compressing objects: 100% (22/22), done. | |
| remote: Total 35 (delta 12), reused 35 (delta 12) | |
| Unpacking objects: 100% (35/35), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib/fsom': checked out 'f688ef24bbe230ec46c7be3de8bf5e67fdbc1b4d' | |
| Cloning into 'intervaltree'... | |
| remote: Counting objects: 70, done. | |
| remote: Total 70 (delta 0), reused 0 (delta 0) | |
| Unpacking objects: 100% (70/70), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib/intervaltree': checked out '1290744283cef8076bb8a2968d4899b7228435f4' | |
| Cloning into 'multichoose'... | |
| remote: Counting objects: 70, done. | |
| remote: Total 70 (delta 0), reused 0 (delta 0) | |
| Unpacking objects: 100% (70/70), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib/multichoose': checked out '73d35daa18bf35729b9ba758041a9247a72484a5' | |
| Cloning into 'smithwaterman'... | |
| remote: Counting objects: 278, done. | |
| remote: Total 278 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (278/278), 83.93 KiB | 0 bytes/s, done. | |
| Resolving deltas: 100% (180/180), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib/smithwaterman': checked out 'd9724f156c07cf16d00d251bebc20c6383eb6bde' | |
| Cloning into 'tabixpp'... | |
| remote: Counting objects: 67, done. | |
| remote: Total 67 (delta 0), reused 0 (delta 0) | |
| Unpacking objects: 100% (67/67), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib/tabixpp': checked out 'c2d6c12eb827805fb13db4bab20f74b212b8b6d0' | |
| ==> cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/Cellar/freebayes/0.9.14-15 -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_VERBOSE_MAKEFILE=ON -Wno-dev | |
| ==> make | |
| ==> make | |
| ==> make | |
| ==> make autoversion | |
| ==> make | |
| /usr/local/Cellar/freebayes/0.9.14-15: 5 files, 3.0M, built in 4.4 minutes | |
| [localhost] local: /usr/local/bin/brew link --overwrite freebayes | |
| Warning: Already linked: /usr/local/Cellar/freebayes/0.9.14-15 | |
| To relink: brew unlink freebayes && brew link freebayes | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit gatk-framework | |
| ==> Downloading https://github.com/chapmanb/gatk/releases/download/v3.2-4-framework/gatk-framework-3.2-4.tar.gz | |
| ######################################################################## 100.0% | |
| /usr/local/Cellar/gatk-framework/3.2-4: 3 files, 11M, built in 14 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite gatk-framework | |
| Warning: Already linked: /usr/local/Cellar/gatk-framework/3.2-4 | |
| To relink: brew unlink gatk-framework && brew link gatk-framework | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit glia | |
| ==> Cloning https://github.com/ekg/glia.git | |
| Cloning into '/home/vagrant/.cache/Homebrew/glia--git'... | |
| remote: Counting objects: 788, done. | |
| remote: Total 788 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (788/788), 2.74 MiB | 1.44 MiB/s, done. | |
| Resolving deltas: 100% (441/441), done. | |
| Checking connectivity... done. | |
| Submodule 'bamtools' (git://github.com/pezmaster31/bamtools.git) registered for path 'bamtools' | |
| Submodule 'fastahack' (git://github.com/ekg/fastahack.git) registered for path 'fastahack' | |
| Submodule 'gssw' (https://github.com/ekg/gssw.git) registered for path 'gssw' | |
| Submodule 'rapidjson' (https://github.com/kennytm/rapidjson.git) registered for path 'rapidjson' | |
| Submodule 'vcflib' (git://github.com/ekg/vcflib.git) registered for path 'vcflib' | |
| Cloning into 'bamtools'... | |
| remote: Counting objects: 4012, done. | |
| remote: Total 4012 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (4012/4012), 2.84 MiB | 1.62 MiB/s, done. | |
| Resolving deltas: 100% (2437/2437), done. | |
| Checking connectivity... done. | |
| Submodule path 'bamtools': checked out '2d7685d2aeedd11c46ad3bd67886d9ed65c30f3e' | |
| Cloning into 'fastahack'... | |
| remote: Counting objects: 181, done. | |
| remote: Total 181 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (181/181), 42.33 KiB | 0 bytes/s, done. | |
| Resolving deltas: 100% (106/106), done. | |
| Checking connectivity... done. | |
| Submodule path 'fastahack': checked out 'c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd' | |
| Cloning into 'gssw'... | |
| remote: Counting objects: 1283, done. | |
| remote: Total 1283 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (1283/1283), 6.22 MiB | 2.42 MiB/s, done. | |
| Resolving deltas: 100% (844/844), done. | |
| Checking connectivity... done. | |
| Submodule path 'gssw': checked out '5cd667de259db836f98466f376cec9b33da219dd' | |
| Cloning into 'rapidjson'... | |
| remote: Counting objects: 500, done. | |
| remote: Total 500 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (500/500), 651.31 KiB | 841.00 KiB/s, done. | |
| Resolving deltas: 100% (204/204), done. | |
| Checking connectivity... done. | |
| Submodule path 'rapidjson': checked out '52d4fc5f074d6b0525d9eb117f69c00b320ca8b0' | |
| Cloning into 'vcflib'... | |
| remote: Counting objects: 1513, done. | |
| remote: Compressing objects: 100% (17/17), done. | |
| remote: Total 1513 (delta 7), reused 0 (delta 0) | |
| Receiving objects: 100% (1513/1513), 1.06 MiB | 894.00 KiB/s, done. | |
| Resolving deltas: 100% (857/857), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib': checked out '1e2c464f4d07053a306ee5023d91bf133b3016da' | |
| Submodule 'fastahack' (https://github.com/ekg/fastahack.git) registered for path 'fastahack' | |
| Submodule 'filevercmp' (https://github.com/ekg/filevercmp.git) registered for path 'filevercmp' | |
| Submodule 'fsom' (https://github.com/ekg/fsom.git) registered for path 'fsom' | |
| Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'intervaltree' | |
| Submodule 'multichoose' (https://github.com/ekg/multichoose.git) registered for path 'multichoose' | |
| Submodule 'smithwaterman' (https://github.com/ekg/smithwaterman.git) registered for path 'smithwaterman' | |
| Submodule 'tabixpp' (https://github.com/ekg/tabixpp.git) registered for path 'tabixpp' | |
| Cloning into 'fastahack'... | |
| remote: Counting objects: 181, done. | |
| remote: Total 181 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (181/181), 42.33 KiB | 0 bytes/s, done. | |
| Resolving deltas: 100% (106/106), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib/fastahack': checked out 'c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd' | |
| Cloning into 'filevercmp'... | |
| remote: Counting objects: 18, done. | |
| remote: Compressing objects: 100% (10/10), done. | |
| remote: Total 18 (delta 8), reused 18 (delta 8) | |
| Unpacking objects: 100% (18/18), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib/filevercmp': checked out '378bae779b897f1506043c1b647a5e5f8031ea4b' | |
| Cloning into 'fsom'... | |
| remote: Counting objects: 35, done. | |
| remote: Compressing objects: 100% (22/22), done. | |
| remote: Total 35 (delta 12), reused 35 (delta 12) | |
| Unpacking objects: 100% (35/35), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib/fsom': checked out 'f688ef24bbe230ec46c7be3de8bf5e67fdbc1b4d' | |
| Cloning into 'intervaltree'... | |
| remote: Counting objects: 70, done. | |
| remote: Total 70 (delta 0), reused 0 (delta 0) | |
| Unpacking objects: 100% (70/70), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib/intervaltree': checked out '1290744283cef8076bb8a2968d4899b7228435f4' | |
| Cloning into 'multichoose'... | |
| remote: Counting objects: 70, done. | |
| remote: Total 70 (delta 0), reused 0 (delta 0) | |
| Unpacking objects: 100% (70/70), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib/multichoose': checked out '73d35daa18bf35729b9ba758041a9247a72484a5' | |
| Cloning into 'smithwaterman'... | |
| remote: Counting objects: 278, done. | |
| remote: Total 278 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (278/278), 83.93 KiB | 0 bytes/s, done. | |
| Resolving deltas: 100% (180/180), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib/smithwaterman': checked out 'd9724f156c07cf16d00d251bebc20c6383eb6bde' | |
| Cloning into 'tabixpp'... | |
| remote: Counting objects: 67, done. | |
| remote: Total 67 (delta 0), reused 0 (delta 0) | |
| Unpacking objects: 100% (67/67), done. | |
| Checking connectivity... done. | |
| Submodule path 'vcflib/tabixpp': checked out 'c2d6c12eb827805fb13db4bab20f74b212b8b6d0' | |
| warning: unable to rmdir gssw: Directory not empty | |
| ==> make | |
| /usr/local/Cellar/glia/2013-12-29: 3 files, 1.1M, built in 4.4 minutes | |
| [localhost] local: /usr/local/bin/brew link --overwrite glia | |
| Warning: Already linked: /usr/local/Cellar/glia/2013-12-29 | |
| To relink: brew unlink glia && brew link glia | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit hall-lab-sv-tools | |
| ==> Cloning https://github.com/hall-lab/sv-tools.git | |
| Cloning into '/home/vagrant/.cache/Homebrew/hall-lab-sv-tools--git'... | |
| remote: Counting objects: 76, done. | |
| remote: Compressing objects: 100% (15/15), done. | |
| remote: Total 76 (delta 7), reused 0 (delta 0) | |
| Unpacking objects: 100% (76/76), done. | |
| Checking connectivity... done. | |
| ==> Checking out revision 85438625 | |
| /usr/local/Cellar/hall-lab-sv-tools/2014-08-16: 7 files, 84K, built in 11 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite hall-lab-sv-tools | |
| Warning: Already linked: /usr/local/Cellar/hall-lab-sv-tools/2014-08-16 | |
| To relink: brew unlink hall-lab-sv-tools && brew link hall-lab-sv-tools | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit lumpy-sv | |
| Warning: lumpy-sv-0.2.7 already installed | |
| [localhost] local: /usr/local/bin/brew link --overwrite lumpy-sv | |
| Warning: Already linked: /usr/local/Cellar/lumpy-sv/0.2.7 | |
| To relink: brew unlink lumpy-sv && brew link lumpy-sv | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit pindel | |
| ==> Downloading https://github.com/genome/pindel/archive/bcbio.tar.gz | |
| ######################################################################## 100.0% | |
| ==> Downloading https://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2 | |
| ######################################################################## 100.0% | |
| ==> make | |
| ==> echo 'SAMTOOLS=/usr/local/Cellar/pindel/0.2.5a7/samtools' > Makefile.local | |
| ==> ./INSTALL /usr/local/Cellar/pindel/0.2.5a7/samtools | |
| /usr/local/Cellar/pindel/0.2.5a7: 207 files, 23M, built in 75 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite pindel | |
| Warning: Already linked: /usr/local/Cellar/pindel/0.2.5a7 | |
| To relink: brew unlink pindel && brew link pindel | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit platypus-variant | |
| ==> Downloading https://github.com/chapmanb/Platypus/releases/download/v0.7.9.2/Platypus_0.7.9.2.tgz | |
| ######################################################################## 100.0% | |
| ==> ./buildPlatypus.sh | |
| /usr/local/Cellar/platypus-variant/0.7.9.2: 209 files, 33M, built in 43 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite platypus-variant | |
| Warning: Already linked: /usr/local/Cellar/platypus-variant/0.7.9.2 | |
| To relink: brew unlink platypus-variant && brew link platypus-variant | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit qsignature | |
| ==> Downloading http://downloads.sourceforge.net/project/adamajava/qsignature.tar.bz2 | |
| ######################################################################## 100.0% | |
| /usr/local/Cellar/qsignature/0.1pre: 10 files, 4.5M, built in 24 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite qsignature | |
| Warning: Already linked: /usr/local/Cellar/qsignature/0.1pre | |
| To relink: brew unlink qsignature && brew link qsignature | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit rtg-tools | |
| ==> Downloading ftp://ftp-trace.ncbi.nih.gov/giab/ftp/tools/RTG/rtg-tools-1.0.0-nojre.zip | |
| ######################################################################## 100.0% | |
| /usr/local/Cellar/rtg-tools/1.0.0: 7 files, 3.9M, built in 10 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite rtg-tools | |
| Warning: Already linked: /usr/local/Cellar/rtg-tools/1.0.0 | |
| To relink: brew unlink rtg-tools && brew link rtg-tools | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit scalpel | |
| ==> Downloading http://downloads.sourceforge.net/project/scalpel/scalpel-0.2.1.tar.gz | |
| ######################################################################## 100.0% | |
| Warning: Cannot verify integrity of scalpel-0.2.1.tar.gz | |
| A checksum was not provided for this resource | |
| For your reference the SHA1 is: 6ac6bd9b073307cfd28a14660d91e0af3bee1312 | |
| ==> Downloading https://gist.githubusercontent.com/chapmanb/9248ab8409a473249a07/raw/61af40ea24ad8dedf00efb19003bc44dd7436baa/samtools_index.patch | |
| ######################################################################## 100.0% | |
| ==> Patching | |
| patching file FindSomatic.pl | |
| Hunk #1 succeeded at 488 (offset 2 lines). | |
| patching file FindVariants.pl | |
| Hunk #1 succeeded at 87 (offset 1 line). | |
| Hunk #2 succeeded at 213 (offset 7 lines). | |
| Hunk #3 succeeded at 450 (offset -5 lines). | |
| Hunk #4 succeeded at 464 (offset -5 lines). | |
| ==> make bamtools | |
| ==> make Microassembler | |
| ==> make | |
| /usr/local/Cellar/scalpel/0.2.1: 487 files, 100M, built in 82 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite scalpel | |
| Warning: Already linked: /usr/local/Cellar/scalpel/0.2.1 | |
| To relink: brew unlink scalpel && brew link scalpel | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit snpeff | |
| ==> Downloading https://downloads.sourceforge.net/project/snpeff/snpEff_v3_6_core.zip | |
| ######################################################################## 100.0% | |
| ==> Caveats | |
| Download the human database using the command | |
| snpEff download -v GRCh37.75 | |
| The databases will be installed in /usr/local/Cellar/snpeff/3.6c/share/data | |
| ==> Summary | |
| /usr/local/Cellar/snpeff/3.6c: 64 files, 56M, built in 30 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite snpeff | |
| Warning: Already linked: /usr/local/Cellar/snpeff/3.6c | |
| To relink: brew unlink snpeff && brew link snpeff | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit vardict | |
| ==> Cloning https://github.com/AstraZeneca-NGS/VarDict.git | |
| Cloning into '/home/vagrant/.cache/Homebrew/vardict--git'... | |
| remote: Counting objects: 216, done. | |
| remote: Total 216 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (216/216), 805.73 KiB | 923.00 KiB/s, done. | |
| Resolving deltas: 100% (137/137), done. | |
| Checking connectivity... done. | |
| ==> Checking out revision a68faeb1c | |
| /usr/local/Cellar/vardict/2014-10-02: 20 files, 4.4M, built in 12 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite vardict | |
| Warning: Already linked: /usr/local/Cellar/vardict/2014-10-02 | |
| To relink: brew unlink vardict && brew link vardict | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit vcflib | |
| ==> Cloning https://github.com/ekg/vcflib.git | |
| Cloning into '/home/vagrant/.cache/Homebrew/vcflib--git'... | |
| remote: Counting objects: 1513, done. | |
| remote: Compressing objects: 100% (17/17), done. | |
| remote: Total 1513 (delta 7), reused 0 (delta 0) | |
| Receiving objects: 100% (1513/1513), 1.06 MiB | 933.00 KiB/s, done. | |
| Resolving deltas: 100% (857/857), done. | |
| Checking connectivity... done. | |
| Submodule 'fastahack' (https://github.com/ekg/fastahack.git) registered for path 'fastahack' | |
| Submodule 'filevercmp' (https://github.com/ekg/filevercmp.git) registered for path 'filevercmp' | |
| Submodule 'fsom' (https://github.com/ekg/fsom.git) registered for path 'fsom' | |
| Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) registered for path 'intervaltree' | |
| Submodule 'multichoose' (https://github.com/ekg/multichoose.git) registered for path 'multichoose' | |
| Submodule 'smithwaterman' (https://github.com/ekg/smithwaterman.git) registered for path 'smithwaterman' | |
| Submodule 'tabixpp' (https://github.com/ekg/tabixpp.git) registered for path 'tabixpp' | |
| Cloning into 'fastahack'... | |
| remote: Counting objects: 181, done. | |
| remote: Total 181 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (181/181), 42.33 KiB | 0 bytes/s, done. | |
| Resolving deltas: 100% (106/106), done. | |
| Checking connectivity... done. | |
| Submodule path 'fastahack': checked out 'c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd' | |
| Cloning into 'filevercmp'... | |
| remote: Counting objects: 18, done. | |
| remote: Compressing objects: 100% (10/10), done. | |
| remote: Total 18 (delta 8), reused 18 (delta 8) | |
| Unpacking objects: 100% (18/18), done. | |
| Checking connectivity... done. | |
| Submodule path 'filevercmp': checked out '378bae779b897f1506043c1b647a5e5f8031ea4b' | |
| Cloning into 'fsom'... | |
| remote: Counting objects: 35, done. | |
| remote: Compressing objects: 100% (22/22), done. | |
| remote: Total 35 (delta 12), reused 35 (delta 12) | |
| Unpacking objects: 100% (35/35), done. | |
| Checking connectivity... done. | |
| Submodule path 'fsom': checked out 'f688ef24bbe230ec46c7be3de8bf5e67fdbc1b4d' | |
| Cloning into 'intervaltree'... | |
| remote: Counting objects: 70, done. | |
| remote: Total 70 (delta 0), reused 0 (delta 0) | |
| Unpacking objects: 100% (70/70), done. | |
| Checking connectivity... done. | |
| Submodule path 'intervaltree': checked out '1290744283cef8076bb8a2968d4899b7228435f4' | |
| Cloning into 'multichoose'... | |
| remote: Counting objects: 70, done. | |
| remote: Total 70 (delta 0), reused 0 (delta 0) | |
| Unpacking objects: 100% (70/70), done. | |
| Checking connectivity... done. | |
| Submodule path 'multichoose': checked out '73d35daa18bf35729b9ba758041a9247a72484a5' | |
| Cloning into 'smithwaterman'... | |
| remote: Counting objects: 278, done. | |
| remote: Total 278 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (278/278), 83.93 KiB | 0 bytes/s, done. | |
| Resolving deltas: 100% (180/180), done. | |
| Checking connectivity... done. | |
| Submodule path 'smithwaterman': checked out 'd9724f156c07cf16d00d251bebc20c6383eb6bde' | |
| Cloning into 'tabixpp'... | |
| remote: Counting objects: 67, done. | |
| remote: Total 67 (delta 0), reused 0 (delta 0) | |
| Unpacking objects: 100% (67/67), done. | |
| Checking connectivity... done. | |
| Submodule path 'tabixpp': checked out 'c2d6c12eb827805fb13db4bab20f74b212b8b6d0' | |
| ==> make | |
| /usr/local/Cellar/vcflib/2014-08-13: 98 files, 35M, built in 2.6 minutes | |
| [localhost] local: /usr/local/bin/brew link --overwrite vcflib | |
| Warning: Already linked: /usr/local/Cellar/vcflib/2014-08-13 | |
| To relink: brew unlink vcflib && brew link vcflib | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit vep | |
| ==> Downloading https://github.com/Ensembl/ensembl-tools/archive/771dfa1016c357145be7016c91e1155ae7c021f2.zip | |
| ######################################################################## 100.0% | |
| ==> export FTP_PASSIVE=1 && /usr/local/Cellar/vep/75_2014-06-12/INSTALL.pl -a a -d /usr/local/Cellar/vep/75_2014-06-12/lib -c /usr/local/Cellar/vep/75_2014-06-12/ | |
| ==> Downloading https://github.com/ensembl-variation/VEP_plugins/archive/2c123faff2deef07ee094984fc44e19c48975af4.zip | |
| ######################################################################## 100.0% | |
| ==> Downloading https://github.com/konradjk/loftee/archive/545cf9ac5f25b6a6872984dd1a3197a7e7caf000.zip | |
| ######################################################################## 100.0% | |
| ==> Caveats | |
| To install cached genome databases in /usr/local/Cellar/vep/75_2014-06-12/share/data: | |
| vep_install.pl -a c -s homo_sapiens | |
| or install data in a different location: | |
| vep_install.pl -a c -s homo_sapiens -c /path/to/data | |
| ==> Summary | |
| /usr/local/Cellar/vep/75_2014-06-12: 1417 files, 22M, built in 62 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite vep | |
| Warning: Already linked: /usr/local/Cellar/vep/75_2014-06-12 | |
| To relink: brew unlink vep && brew link vep | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit vt | |
| ==> Cloning https://github.com/atks/vt.git | |
| Cloning into '/home/vagrant/.cache/Homebrew/vt--git'... | |
| remote: Counting objects: 3627, done. | |
| remote: Compressing objects: 100% (1024/1024), done. | |
| remote: Total 3627 (delta 2533), reused 3123 (delta 2533) | |
| Receiving objects: 100% (3627/3627), 3.01 MiB | 1.55 MiB/s, done. | |
| Resolving deltas: 100% (2533/2533), done. | |
| Checking connectivity... done. | |
| ==> Checking out revision e33fc00b3b | |
| ==> make | |
| /usr/local/Cellar/vt/2014-08-16: 4 files, 45M, built in 2.6 minutes | |
| [localhost] local: /usr/local/bin/brew link --overwrite vt | |
| Warning: Already linked: /usr/local/Cellar/vt/2014-08-16 | |
| To relink: brew unlink vt && brew link vt | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit bowtie2 | |
| ==> Downloading https://github.com/BenLangmead/bowtie2/archive/v2.2.3.tar.gz | |
| ######################################################################## 100.0% | |
| ==> make | |
| /usr/local/Cellar/bowtie2/2.2.3: 73 files, 51M, built in 2.5 minutes | |
| [localhost] local: /usr/local/bin/brew link --overwrite bowtie2 | |
| Warning: Already linked: /usr/local/Cellar/bowtie2/2.2.3 | |
| To relink: brew unlink bowtie2 && brew link bowtie2 | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit bwa | |
| ==> Downloading https://downloads.sf.net/project/bio-bwa/bwa-0.7.10.tar.bz2 | |
| ######################################################################## 100.0% | |
| ==> make CC=/usr/bin/gcc CFLAGS=-Os -w -pipe | |
| /usr/local/Cellar/bwa/0.7.10: 7 files, 524K, built in 16 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite bwa | |
| Warning: Already linked: /usr/local/Cellar/bwa/0.7.10 | |
| To relink: brew unlink bwa && brew link bwa | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit novoalign | |
| ==> Downloading http://www.novocraft.com/homebrew/novocraftV3.02.02.Linux2.6.tar.gz | |
| ######################################################################## 100.0% | |
| /usr/local/Cellar/novoalign/3.02.02: 22 files, 28M, built in 8 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite novoalign | |
| Warning: Already linked: /usr/local/Cellar/novoalign/3.02.02 | |
| To relink: brew unlink novoalign && brew link novoalign | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit rna-star | |
| ==> Downloading https://github.com/alexdobin/STAR/archive/STAR_2.4.0c.tar.gz | |
| ######################################################################## 100.0% | |
| /usr/local/Cellar/rna-star/2.4.0c: 5 files, 3.5M, built in 13 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite rna-star | |
| Warning: Already linked: /usr/local/Cellar/rna-star/2.4.0c | |
| To relink: brew unlink rna-star && brew link rna-star | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit snap-aligner | |
| ==> Cloning https://github.com/amplab/snap.git | |
| Cloning into '/home/vagrant/.cache/Homebrew/snap-aligner--git'... | |
| remote: Counting objects: 243, done. | |
| remote: Compressing objects: 100% (208/208), done. | |
| remote: Total 243 (delta 41), reused 129 (delta 31) | |
| Receiving objects: 100% (243/243), 5.09 MiB | 1.30 MiB/s, done. | |
| Resolving deltas: 100% (41/41), done. | |
| Checking connectivity... done. | |
| ==> Checking out branch dev | |
| ==> make | |
| /usr/local/Cellar/snap-aligner/1.0dev.40: 7 files, 6.7M, built in 32 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite snap-aligner | |
| Warning: Already linked: /usr/local/Cellar/snap-aligner/1.0dev.40 | |
| To relink: brew unlink snap-aligner && brew link snap-aligner | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit tophat-binary | |
| ==> Downloading http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.12.Linux_x86_64.tar.gz | |
| ######################################################################## 100.0% | |
| ==> Downloading https://gist.githubusercontent.com/chapmanb/b04cccddfe1e18c2b542/raw/a2d5626109454a83c7b0431860b33934d5d29b32/tophat_samtools_10.diff | |
| ######################################################################## 100.0% | |
| ==> Patching | |
| patching file tophat | |
| /usr/local/Cellar/tophat-binary/2.0.12.1: 22 files, 42M, built in 16 seconds | |
| [localhost] local: /usr/local/bin/brew link --overwrite tophat-binary | |
| Warning: Already linked: /usr/local/Cellar/tophat-binary/2.0.12.1 | |
| To relink: brew unlink tophat-binary && brew link tophat-binary | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit cmake | |
| Warning: cmake-3.0.2 already installed | |
| [localhost] local: /usr/local/bin/brew link --overwrite cmake | |
| Warning: Already linked: /usr/local/Cellar/cmake/3.0.2 | |
| To relink: brew unlink cmake && brew link cmake | |
| [localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit cpanminus | |
| Warning: cpanminus-1.7011 already installed | |
| [localhost] local: /usr/local/bin/brew link --overwrite cpanminus | |
| Warning: Already linked: /usr/local/Cellar/cpanminus/1.7011 | |
| To relink: brew unlink cpanminus && brew link cpanminus | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/r-libs.yaml | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux' | |
| [localhost] local: touch /home/vagrant/tmp/cloudbiolinux/install_packages.R | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "mkdir -p /usr/local/lib/R/site-library" | |
| [localhost] local: echo ' | |
| .libPaths(c("/usr/local/lib/R/site-library")) | |
| library(methods) | |
| cran.repos <- getOption("repos") | |
| cran.repos["CRAN" ] <- "http://cran.fhcrc.org/" | |
| options(repos=cran.repos) | |
| source("http://bioconductor.org/biocLite.R") | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: echo ' | |
| repo.installer <- function(repos, install.fn) { | |
| update.packages(lib.loc="/usr/local/lib/R/site-library", repos=repos, ask=FALSE) | |
| maybe.install <- function(pname) { | |
| if (!(pname %in% installed.packages())) | |
| install.fn(pname) | |
| } | |
| } | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: echo ' | |
| std.pkgs <- c("cghFLasso", "ggplot2", "gsalib", "matrixStats", "snow") | |
| std.installer = repo.installer(cran.repos, install.packages) | |
| lapply(std.pkgs, std.installer) | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: echo ' | |
| bioc.pkgs <- c("cn.mops", "rtracklayer", "DEXSeq", "DNAcopy") | |
| bioc.installer = repo.installer(biocinstallRepos(), biocLite) | |
| lapply(bioc.pkgs, bioc.installer) | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: echo ' | |
| std2.pkgs <- c("PSCBS") | |
| lapply(std2.pkgs, std.installer) | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "Rscript /home/vagrant/tmp/cloudbiolinux/install_packages.R" | |
| Installing package into ‘/usr/local/lib/R/site-library’ | |
| (as ‘lib’ is unspecified) | |
| trying URL 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/BiocInstaller_1.14.2.tar.gz' | |
| Content type 'application/x-gzip' length 14053 bytes (13 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 13 Kb | |
| * installing *source* package ‘BiocInstaller’ ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help | |
| * DONE (BiocInstaller) | |
| The downloaded source packages are in | |
| ‘/tmp/RtmpHRfdWL/downloaded_packages’ | |
| Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help | |
| Installing package into ‘/usr/local/lib/R/site-library’ | |
| (as ‘lib’ is unspecified) | |
| trying URL 'http://cran.fhcrc.org/src/contrib/cghFLasso_0.2-1.tar.gz' | |
| Content type 'application/x-gzip' length 129919 bytes (126 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 126 Kb | |
| * installing *source* package ‘cghFLasso’ ... | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c L2L1VitExact.c -o L2L1VitExact.o | |
| gfortran -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -c smooth.f90 -o smooth.o | |
| gfortran -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o cghFLasso.so L2L1VitExact.o smooth.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/cghFLasso/libs | |
| ** R | |
| ** data | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (cghFLasso) | |
| The downloaded source packages are in | |
| ‘/tmp/RtmpHRfdWL/downloaded_packages’ | |
| Installing package into ‘/usr/local/lib/R/site-library’ | |
| (as ‘lib’ is unspecified) | |
| also installing the dependencies ‘colorspace’, ‘Rcpp’, ‘stringr’, ‘RColorBrewer’, ‘dichromat’, ‘munsell’, ‘labeling’, ‘plyr’, ‘digest’, ‘gtable’, ‘reshape2’, ‘scales’, ‘proto’ | |
| trying URL 'http://cran.fhcrc.org/src/contrib/colorspace_1.2-4.tar.gz' | |
| Content type 'application/x-gzip' length 242791 bytes (237 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 237 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/Rcpp_0.11.3.tar.gz' | |
| Content type 'application/x-gzip' length 2169583 bytes (2.1 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 2.1 Mb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/stringr_0.6.2.tar.gz' | |
| Content type 'application/x-gzip' length 20636 bytes (20 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 20 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/RColorBrewer_1.0-5.tar.gz' | |
| Content type 'application/x-gzip' length 10656 bytes (10 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 10 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/dichromat_2.0-0.tar.gz' | |
| Content type 'application/x-gzip' length 84320 bytes (82 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 82 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/munsell_0.4.2.tar.gz' | |
| Content type 'application/x-gzip' length 91026 bytes (88 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 88 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/labeling_0.3.tar.gz' | |
| Content type 'application/x-gzip' length 10722 bytes (10 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 10 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/plyr_1.8.1.tar.gz' | |
| Content type 'application/x-gzip' length 393233 bytes (384 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 384 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/digest_0.6.4.tar.gz' | |
| Content type 'application/x-gzip' length 79309 bytes (77 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 77 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/gtable_0.1.2.tar.gz' | |
| Content type 'application/x-gzip' length 19667 bytes (19 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 19 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/reshape2_1.4.tar.gz' | |
| Content type 'application/x-gzip' length 34121 bytes (33 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 33 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/scales_0.2.4.tar.gz' | |
| Content type 'application/x-gzip' length 40093 bytes (39 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 39 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/proto_0.3-10.tar.gz' | |
| Content type 'application/x-gzip' length 530758 bytes (518 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 518 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/ggplot2_1.0.0.tar.gz' | |
| Content type 'application/x-gzip' length 2351447 bytes (2.2 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 2.2 Mb | |
| * installing *source* package ‘colorspace’ ... | |
| ** package ‘colorspace’ successfully unpacked and MD5 sums checked | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c colorspace.c -o colorspace.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o colorspace.so colorspace.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/colorspace/libs | |
| ** R | |
| ** data | |
| *** moving datasets to lazyload DB | |
| ** inst | |
| ** preparing package for lazy loading | |
| Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘colorspace’ | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (colorspace) | |
| * installing *source* package ‘Rcpp’ ... | |
| ** package ‘Rcpp’ successfully unpacked and MD5 sums checked | |
| ** libs | |
| g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o | |
| g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Module.cpp -o Module.o | |
| g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Rcpp_init.cpp -o Rcpp_init.o | |
| g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c api.cpp -o api.o | |
| g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c attributes.cpp -o attributes.o | |
| g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c barrier.cpp -o barrier.o | |
| g++ -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/Rcpp/libs | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (Rcpp) | |
| * installing *source* package ‘stringr’ ... | |
| ** package ‘stringr’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (stringr) | |
| * installing *source* package ‘RColorBrewer’ ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (RColorBrewer) | |
| * installing *source* package ‘dichromat’ ... | |
| ** package ‘dichromat’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** data | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (dichromat) | |
| * installing *source* package ‘labeling’ ... | |
| ** package ‘labeling’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (labeling) | |
| * installing *source* package ‘digest’ ... | |
| ** package ‘digest’ successfully unpacked and MD5 sums checked | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c aes.c -o aes.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c crc32.c -o crc32.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c digest.c -o digest.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c md5.c -o md5.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c raes.c -o raes.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sha1.c -o sha1.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sha2.c -o sha2.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sha256.c -o sha256.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o digest.so aes.o crc32.o digest.o md5.o raes.o sha1.o sha2.o sha256.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/digest/libs | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (digest) | |
| * installing *source* package ‘gtable’ ... | |
| ** package ‘gtable’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (gtable) | |
| * installing *source* package ‘proto’ ... | |
| ** package ‘proto’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** demo | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ‘proto.Rnw’ | |
| ‘protoref.Rnw’ | |
| ** testing if installed package can be loaded | |
| * DONE (proto) | |
| * installing *source* package ‘munsell’ ... | |
| ** package ‘munsell’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (munsell) | |
| * installing *source* package ‘plyr’ ... | |
| ** package ‘plyr’ successfully unpacked and MD5 sums checked | |
| ** libs | |
| g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o | |
| g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c loop-apply.cpp -o loop-apply.o | |
| g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c split-numeric.cpp -o split-numeric.o | |
| g++ -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o plyr.so RcppExports.o loop-apply.o split-numeric.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/plyr/libs | |
| ** R | |
| ** data | |
| *** moving datasets to lazyload DB | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (plyr) | |
| * installing *source* package ‘reshape2’ ... | |
| ** package ‘reshape2’ successfully unpacked and MD5 sums checked | |
| ** libs | |
| g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o | |
| g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c melt.cpp -o melt.o | |
| g++ -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o reshape2.so RcppExports.o melt.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/reshape2/libs | |
| ** R | |
| ** data | |
| *** moving datasets to lazyload DB | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (reshape2) | |
| * installing *source* package ‘scales’ ... | |
| ** package ‘scales’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (scales) | |
| * installing *source* package ‘ggplot2’ ... | |
| ** package ‘ggplot2’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** data | |
| *** moving datasets to lazyload DB | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (ggplot2) | |
| The downloaded source packages are in | |
| ‘/tmp/RtmpHRfdWL/downloaded_packages’ | |
| Installing package into ‘/usr/local/lib/R/site-library’ | |
| (as ‘lib’ is unspecified) | |
| trying URL 'http://cran.fhcrc.org/src/contrib/gsalib_2.0.tar.gz' | |
| Content type 'application/x-gzip' length 4424 bytes | |
| opened URL | |
| ================================================== | |
| downloaded 4424 bytes | |
| * installing *source* package ‘gsalib’ ... | |
| ** package ‘gsalib’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (gsalib) | |
| The downloaded source packages are in | |
| ‘/tmp/RtmpHRfdWL/downloaded_packages’ | |
| Installing package into ‘/usr/local/lib/R/site-library’ | |
| (as ‘lib’ is unspecified) | |
| also installing the dependency ‘R.methodsS3’ | |
| trying URL 'http://cran.fhcrc.org/src/contrib/R.methodsS3_1.6.1.tar.gz' | |
| Content type 'application/x-gzip' length 23156 bytes (22 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 22 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/matrixStats_0.10.0.tar.gz' | |
| Content type 'application/x-gzip' length 78876 bytes (77 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 77 Kb | |
| * installing *source* package ‘R.methodsS3’ ... | |
| ** package ‘R.methodsS3’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (R.methodsS3) | |
| * installing *source* package ‘matrixStats’ ... | |
| ** package ‘matrixStats’ successfully unpacked and MD5 sums checked | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c anyMissing.c -o anyMissing.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c binCounts.c -o binCounts.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c binMeans.c -o binMeans.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c logSumExp.c -o logSumExp.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c productExpSumLog.c -o productExpSumLog.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c psortKM.c -o psortKM.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rowCounts.c -o rowCounts.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rowMedians.c -o rowMedians.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rowOrderStats.c -o rowOrderStats.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rowRanks.c -o rowRanks.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rowRanks_Integer.c -o rowRanks_Integer.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rowRanks_Real.c -o rowRanks_Real.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rowRanks_TYPE_TIES.c -o rowRanks_TYPE_TIES.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c signTabulate.c -o signTabulate.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o matrixStats.so anyMissing.o binCounts.o binMeans.o logSumExp.o productExpSumLog.o psortKM.o rowCounts.o rowMedians.o rowOrderStats.o rowRanks.o rowRanks_Integer.o rowRanks_Real.o rowRanks_TYPE_TIES.o signTabulate.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/matrixStats/libs | |
| ** R | |
| ** inst | |
| ** byte-compile and prepare package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (matrixStats) | |
| The downloaded source packages are in | |
| ‘/tmp/RtmpHRfdWL/downloaded_packages’ | |
| Installing package into ‘/usr/local/lib/R/site-library’ | |
| (as ‘lib’ is unspecified) | |
| trying URL 'http://cran.fhcrc.org/src/contrib/snow_0.3-13.tar.gz' | |
| Content type 'application/x-gzip' length 22741 bytes (22 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 22 Kb | |
| * installing *source* package ‘snow’ ... | |
| ** package ‘snow’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (snow) | |
| The downloaded source packages are in | |
| ‘/tmp/RtmpHRfdWL/downloaded_packages’ | |
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| BioC_mirror: http://bioconductor.org | |
| Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version | |
| 3.1.1. | |
| Installing package(s) 'cn.mops' | |
| also installing the dependencies ‘GenomeInfoDb’, ‘XVector’, ‘Biostrings’, ‘zlibbioc’, ‘bitops’, ‘BiocGenerics’, ‘Biobase’, ‘IRanges’, ‘GenomicRanges’, ‘Rsamtools’ | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomeInfoDb_1.0.2.tar.gz' | |
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| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/XVector_0.4.0.tar.gz' | |
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| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/zlibbioc_1.10.0.tar.gz' | |
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| trying URL 'http://cran.fhcrc.org/src/contrib/bitops_1.0-6.tar.gz' | |
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| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/BiocGenerics_0.10.0.tar.gz' | |
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| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/IRanges_1.22.10.tar.gz' | |
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| downloaded 664 Kb | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicRanges_1.16.4.tar.gz' | |
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| downloaded 563 Kb | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/Rsamtools_1.16.1.tar.gz' | |
| Content type 'application/x-gzip' length 2937488 bytes (2.8 Mb) | |
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| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/cn.mops_1.10.1.tar.gz' | |
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| * installing *source* package ‘GenomeInfoDb’ ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (GenomeInfoDb) | |
| * installing *source* package ‘zlibbioc’ ... | |
| configure: creating ./config.status | |
| config.status: creating src/Makevars | |
| ** libs | |
| mkdir -p "/usr/local/lib/R/site-library/zlibbioc/include" | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_zlibbioc.c -o R_init_zlibbioc.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o zlibbioc.so R_init_zlibbioc.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/zlibbioc/libs | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (zlibbioc) | |
| * installing *source* package ‘bitops’ ... | |
| ** package ‘bitops’ successfully unpacked and MD5 sums checked | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bit-ops.c -o bit-ops.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c cksum.c -o cksum.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o bitops.so bit-ops.o cksum.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/bitops/libs | |
| ** R | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (bitops) | |
| * installing *source* package ‘BiocGenerics’ ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| Creating a new generic function for ‘append’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘as.vector’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘eval’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘Find’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘Map’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘Position’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘get’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘mget’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘match’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘order’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘paste’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘rank’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘rep.int’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘union’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘sort’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘table’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘unique’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘unlist’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘clusterCall’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘clusterApply’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘clusterApplyLB’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘clusterEvalQ’ in package ‘BiocGenerics’ | |
| Warning in getPackageName(environment(fdef)) : | |
| Created a package name, ‘2014-10-02 23:57:01’, when none found | |
| Creating a new generic function for ‘clusterExport’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘clusterMap’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘parLapply’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘parSapply’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘parApply’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘parRapply’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘parCapply’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘parLapplyLB’ in package ‘BiocGenerics’ | |
| Creating a new generic function for ‘parSapplyLB’ in package ‘BiocGenerics’ | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (BiocGenerics) | |
| * installing *source* package ‘Biobase’ ... | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Rinit.c -o Rinit.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c anyMissing.c -o anyMissing.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c envir.c -o envir.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c matchpt.c -o matchpt.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rowMedians.c -o rowMedians.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sublist_extract.c -o sublist_extract.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/Biobase/libs | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (Biobase) | |
| * installing *source* package ‘IRanges’ ... | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c AEbufs.c -o AEbufs.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c CompressedList_class.c -o CompressedList_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c DataFrame_class.c -o DataFrame_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c GappedRanges_class.c -o GappedRanges_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Grouping_class.c -o Grouping_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Hits_class.c -o Hits_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c IRanges_class.c -o IRanges_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c IRanges_constructor.c -o IRanges_constructor.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c IntervalTree.c -o IntervalTree.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_IRanges.c -o R_init_IRanges.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RangedData_class.c -o RangedData_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Ranges_class.c -o Ranges_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Ranges_comparison.c -o Ranges_comparison.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RleViews_utils.c -o RleViews_utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Rle_class.c -o Rle_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Rle_utils.c -o Rle_utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c SEXP_utils.c -o SEXP_utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c SimpleList_class.c -o SimpleList_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c SimpleRangesList_class.c -o SimpleRangesList_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Vector_class.c -o Vector_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c anyMissing.c -o anyMissing.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c common.c -o common.o | |
| common.c: In function ‘firstWordInFile’: | |
| common.c:1787:6: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] | |
| fgets(wordBuf, wordBufSize, f); | |
| ^ | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c compact_bitvector.c -o compact_bitvector.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c coverage_methods.c -o coverage_methods.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dlist.c -o dlist.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c errabort.c -o errabort.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c hash_utils.c -o hash_utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c int_utils.c -o int_utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c inter_range_methods.c -o inter_range_methods.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c localmem.c -o localmem.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c memalloc.c -o memalloc.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rbTree.c -o rbTree.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c safe_arithm.c -o safe_arithm.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sort_utils.c -o sort_utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c str_utils.c -o str_utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc_handlers.c -o ucsc_handlers.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o IRanges.so AEbufs.o CompressedIRangesList_class.o CompressedList_class.o DataFrame_class.o GappedRanges_class.o Grouping_class.o Hits_class.o IRanges_class.o IRanges_constructor.o IntervalTree.o R_init_IRanges.o RangedData_class.o Ranges_class.o Ranges_comparison.o RleViews_utils.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o SimpleRangesList_class.o Vector_class.o anyMissing.o common.o compact_bitvector.o coverage_methods.o dlist.o errabort.o hash_utils.o int_utils.o inter_range_methods.o localmem.o memalloc.o rbTree.o safe_arithm.o sort_utils.o str_utils.o ucsc_handlers.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/IRanges/libs | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| Creating a generic function for ‘head’ from package ‘utils’ in package ‘IRanges’ | |
| Creating a generic function for ‘tail’ from package ‘utils’ in package ‘IRanges’ | |
| Creating a generic function for ‘window’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘window<-’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘rev’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘subset’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘with’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘aggregate’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘%in%’ from package ‘base’ in package ‘IRanges’ | |
| Creating a new generic function for ‘findMatches’ in package ‘IRanges’ | |
| Creating a generic function for ‘as.list’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘stack’ from package ‘utils’ in package ‘IRanges’ | |
| Creating a generic function for ‘within’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘start’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘end’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘as.matrix’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘na.omit’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘na.exclude’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘merge’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘by’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘mean’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘which.max’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘which.min’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘which’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘ifelse’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘diff’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘var’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘cov’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘cor’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘sd’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘median’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘mad’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘IQR’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘nchar’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘substr’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘substring’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘levels’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘droplevels’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘split’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘unsplit’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘split<-’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘quantile’ from package ‘stats’ in package ‘IRanges’ | |
| Creating a generic function for ‘rownames<-’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘colnames<-’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘as.table’ from package ‘base’ in package ‘IRanges’ | |
| Creating a generic function for ‘t’ from package ‘base’ in package ‘IRanges’ | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (IRanges) | |
| * installing *source* package ‘XVector’ ... | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_XVector.c -o R_init_XVector.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c SharedDouble_class.c -o SharedDouble_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c SharedInteger_class.c -o SharedInteger_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c SharedRaw_class.c -o SharedRaw_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c SharedVector_class.c -o SharedVector_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c XRawList_comparison.c -o XRawList_comparison.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c XVectorList_class.c -o XVectorList_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c XVector_class.c -o XVector_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c slice_methods.c -o slice_methods.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c vector_copy.c -o vector_copy.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c view_summarization_methods.c -o view_summarization_methods.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o R_init_XVector.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XRawList_comparison.o XVectorList_class.o XVector_class.o slice_methods.o vector_copy.o view_summarization_methods.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/XVector/libs | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| Creating a generic function for ‘toString’ from package ‘base’ in package ‘XVector’ | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (XVector) | |
| * installing *source* package ‘Biostrings’ ... | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c BAB_class.c -o BAB_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c BitMatrix.c -o BitMatrix.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c MIndex_class.c -o MIndex_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c PreprocessedTB_class.c -o PreprocessedTB_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_Biostrings.c -o R_init_Biostrings.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RoSeqs_utils.c -o RoSeqs_utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c SparseList_utils.c -o SparseList_utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c XStringSetList_class.c -o XStringSetList_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c XStringSet_class.c -o XStringSet_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c XStringSet_io.c -o XStringSet_io.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c XString_class.c -o XString_class.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c align_needwunsQS.c -o align_needwunsQS.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c align_utils.c -o align_utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c find_palindromes.c -o find_palindromes.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c gtestsim.c -o gtestsim.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c inject_code.c -o inject_code.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c io_utils.c -o io_utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c letter_frequency.c -o letter_frequency.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c lowlevel_matching.c -o lowlevel_matching.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c match_BOC.c -o match_BOC.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c match_BOC2.c -o match_BOC2.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c match_PWM.c -o match_PWM.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c match_pattern.c -o match_pattern.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c match_pattern_indels.c -o match_pattern_indels.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c match_pattern_shiftor.c -o match_pattern_shiftor.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c match_pdict.c -o match_pdict.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c match_pdict_Twobit.c -o match_pdict_Twobit.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c match_pdict_utils.c -o match_pdict_utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c match_reporting.c -o match_reporting.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c matchprobes.c -o matchprobes.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c pmatchPattern.c -o pmatchPattern.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c replace_letter_at.c -o replace_letter_at.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c strutils.c -o strutils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c translate.c -o translate.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c unstrsplit_methods.c -o unstrsplit_methods.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c xscat.c -o xscat.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XStringSet_io.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o io_utils.o letter_frequency.o lowlevel_matching.o match_BOC.o match_BOC2.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -lz -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/Biostrings/libs | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| Creating a generic function for ‘setequal’ from package ‘base’ in package ‘Biostrings’ | |
| Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’ | |
| Creating a new generic function for ‘offset’ in package ‘Biostrings’ | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (Biostrings) | |
| * installing *source* package ‘GenomicRanges’ ... | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c transcript_utils.c -o transcript_utils.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o XVector_stubs.o transcript_utils.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/GenomicRanges/libs | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (GenomicRanges) | |
| * installing *source* package ‘Rsamtools’ ... | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Biostrings_stubs.c -o Biostrings_stubs.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_Rsamtools.c -o R_init_Rsamtools.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c as_bam.c -o as_bam.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bam_data.c -o bam_data.o | |
| g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bam_mate_iter.cpp -o bam_mate_iter.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bambuffer.c -o bambuffer.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bamfile.c -o bamfile.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bcffile.c -o bcffile.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c encode.c -o encode.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fafile.c -o fafile.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c io_sam.c -o io_sam.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c pileupbam.c -o pileupbam.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools_patch.c -o samtools_patch.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scan_bam_data.c -o scan_bam_data.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c tabixfile.c -o tabixfile.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c utilities.c -o utilities.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c zip_compression.c -o zip_compression.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bgzf.c -o samtools/bgzf.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/kstring.c -o samtools/kstring.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_aux.c -o samtools/bam_aux.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam.c -o samtools/bam.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_import.c -o samtools/bam_import.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/sam.c -o samtools/sam.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_index.c -o samtools/bam_index.o | |
| samtools/bam_index.c: In function ‘bam_index_load_core’: | |
| samtools/bam_index.c:335:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] | |
| fread(magic, 1, 4, fp); | |
| ^ | |
| samtools/bam_index.c:342:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] | |
| fread(&idx->n, 4, 1, fp); | |
| ^ | |
| samtools/bam_index.c:355:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] | |
| fread(&size, 4, 1, fp); | |
| ^ | |
| samtools/bam_index.c:358:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] | |
| fread(&key, 4, 1, fp); | |
| ^ | |
| samtools/bam_index.c:362:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] | |
| fread(&p->n, 4, 1, fp); | |
| ^ | |
| samtools/bam_index.c:366:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] | |
| fread(p->list, 16, p->n, fp); | |
| ^ | |
| samtools/bam_index.c:376:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] | |
| fread(&index2->n, 4, 1, fp); | |
| ^ | |
| samtools/bam_index.c:380:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] | |
| fread(index2->offset, index2->n, 8, fp); | |
| ^ | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_pileup.c -o samtools/bam_pileup.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_md.c -o samtools/bam_md.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/razf.c -o samtools/razf.o | |
| samtools/razf.c: In function ‘razf_flush’: | |
| samtools/razf.c:221:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] | |
| write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | |
| ^ | |
| samtools/razf.c:234:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] | |
| write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | |
| ^ | |
| samtools/razf.c: In function ‘_razf_write’: | |
| samtools/razf.c:201:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] | |
| write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | |
| ^ | |
| samtools/razf.c: In function ‘razf_close’: | |
| samtools/razf.c:810:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] | |
| write(rz->x.fpw, &rz->in, sizeof(int64_t)); | |
| ^ | |
| samtools/razf.c:811:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] | |
| write(rz->x.fpw, &rz->out, sizeof(int64_t)); | |
| ^ | |
| samtools/razf.c:814:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] | |
| write(rz->x.fpw, &v64, sizeof(int64_t)); | |
| ^ | |
| samtools/razf.c:816:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] | |
| write(rz->x.fpw, &v64, sizeof(int64_t)); | |
| ^ | |
| samtools/razf.c: In function ‘razf_end_flush’: | |
| samtools/razf.c:258:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] | |
| write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | |
| ^ | |
| samtools/razf.c: In function ‘save_zindex’: | |
| samtools/razf.c:96:17: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] | |
| if(is_be) write(fd, &rz->index->size, sizeof(int)); | |
| ^ | |
| samtools/razf.c:99:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] | |
| write(fd, &v32, sizeof(uint32_t)); | |
| ^ | |
| samtools/razf.c:106:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] | |
| write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); | |
| ^ | |
| samtools/razf.c:107:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] | |
| write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | |
| ^ | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/faidx.c -o samtools/faidx.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/knetfile.c -o samtools/knetfile.o | |
| In file included from samtools/knetfile.c:49:0: | |
| samtools/knetfile.c: In function ‘kftp_send_cmd’: | |
| samtools/knetfile.h:9:37: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] | |
| #define netwrite(fd, ptr, len) write(fd, ptr, len) | |
| ^ | |
| samtools/knetfile.c:239:2: note: in expansion of macro ‘netwrite’ | |
| netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | |
| ^ | |
| samtools/knetfile.c: In function ‘khttp_connect_file’: | |
| samtools/knetfile.h:9:37: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] | |
| #define netwrite(fd, ptr, len) write(fd, ptr, len) | |
| ^ | |
| samtools/knetfile.c:418:2: note: in expansion of macro ‘netwrite’ | |
| netwrite(fp->fd, buf, l); | |
| ^ | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_sort.c -o samtools/bam_sort.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/sam_header.c -o samtools/sam_header.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bam_reheader.c -o samtools/bam_reheader.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/kprobaln.c -o samtools/kprobaln.o | |
| ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/index.c -o samtools/bcftools/index.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o | |
| ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c tabix/index.c -o tabix/index.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c tabix/bedidx.c -o tabix/bedidx.o | |
| ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o | |
| mkdir -p "/usr/local/lib/R/site-library/Rsamtools/usretc" | |
| cp ../Rsamtools.mk "/usr/local/lib/R/site-library/Rsamtools/usretc" | |
| mkdir -p "/usr/local/lib/R/site-library/Rsamtools/include/samtools/bcftools" | |
| mkdir -p "/usr/local/lib/R/site-library/Rsamtools/include/tabix" | |
| cp samtools/*.h "/usr/local/lib/R/site-library/Rsamtools/include/samtools/" | |
| cp samtools/bcftools/*h "/usr/local/lib/R/site-library/Rsamtools/include/samtools/bcftools/" | |
| cp tabix/*h "/usr/local/lib/R/site-library/Rsamtools/include/tabix/" | |
| cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \ | |
| "/usr/local/lib/R/site-library/Rsamtools/include/tabix/" | |
| mkdir -p "/usr/local/lib/R/site-library/Rsamtools/usrlib" | |
| cp libbam.a libbcf.a libtabix.a "/usr/local/lib/R/site-library/Rsamtools/usrlib" | |
| g++ -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o io_sam.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o utilities.o zip_compression.o -pthread -fopenmp /usr/local/lib/R/site-library/Rsamtools/usrlib/libbam.a /usr/local/lib/R/site-library/Rsamtools/usrlib/libbcf.a /usr/local/lib/R/site-library/Rsamtools/usrlib/libtabix.a -lz -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/Rsamtools/libs | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (Rsamtools) | |
| * installing *source* package ‘cn.mops’ ... | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_cnmops.c -o R_init_cnmops.o | |
| g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c cnmops.cpp -o cnmops.o | |
| g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c segment.cpp -o segment.o | |
| g++ -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/cn.mops/libs | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘cn.mops’ | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (cn.mops) | |
| The downloaded source packages are in | |
| ‘/tmp/RtmpHRfdWL/downloaded_packages’ | |
| Old packages: 'MASS', 'spatial' | |
| BioC_mirror: http://bioconductor.org | |
| Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version | |
| 3.1.1. | |
| Installing package(s) 'rtracklayer' | |
| also installing the dependencies ‘base64enc’, ‘iterators’, ‘checkmate’, ‘DBI’, ‘RSQLite’, ‘sendmailR’, ‘brew’, ‘fail’, ‘foreach’, ‘BatchJobs’, ‘BBmisc’, ‘BiocParallel’, ‘XML’, ‘BSgenome’, ‘RCurl’, ‘GenomicAlignments’ | |
| trying URL 'http://cran.fhcrc.org/src/contrib/base64enc_0.1-2.tar.gz' | |
| Content type 'application/x-gzip' length 6407 bytes | |
| opened URL | |
| ================================================== | |
| downloaded 6407 bytes | |
| trying URL 'http://cran.fhcrc.org/src/contrib/iterators_1.0.7.tar.gz' | |
| Content type 'application/x-gzip' length 289453 bytes (282 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 282 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/checkmate_1.4.tar.gz' | |
| Content type 'application/x-gzip' length 46961 bytes (45 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 45 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/DBI_0.3.1.tar.gz' | |
| Content type 'application/x-gzip' length 30106 bytes (29 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 29 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/RSQLite_0.11.4.tar.gz' | |
| Content type 'application/x-gzip' length 1599919 bytes (1.5 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 1.5 Mb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/sendmailR_1.2-1.tar.gz' | |
| Content type 'application/x-gzip' length 7367 bytes | |
| opened URL | |
| ================================================== | |
| downloaded 7367 bytes | |
| trying URL 'http://cran.fhcrc.org/src/contrib/brew_1.0-6.tar.gz' | |
| Content type 'application/x-gzip' length 83315 bytes (81 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 81 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/fail_1.2.tar.gz' | |
| Content type 'application/x-gzip' length 10599 bytes (10 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 10 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/foreach_1.4.2.tar.gz' | |
| Content type 'application/x-gzip' length 359739 bytes (351 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 351 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/BatchJobs_1.4.tar.gz' | |
| Content type 'application/x-gzip' length 105861 bytes (103 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 103 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/BBmisc_1.7.tar.gz' | |
| Content type 'application/x-gzip' length 74502 bytes (72 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 72 Kb | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/BiocParallel_0.6.1.tar.gz' | |
| Content type 'application/x-gzip' length 296525 bytes (289 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 289 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/XML_3.98-1.1.tar.gz' | |
| Content type 'application/x-gzip' length 1582216 bytes (1.5 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 1.5 Mb | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/BSgenome_1.32.0.tar.gz' | |
| Content type 'application/x-gzip' length 539752 bytes (527 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 527 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/RCurl_1.95-4.3.tar.gz' | |
| Content type 'application/x-gzip' length 879143 bytes (858 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 858 Kb | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/GenomicAlignments_1.0.6.tar.gz' | |
| Content type 'application/x-gzip' length 1936108 bytes (1.8 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 1.8 Mb | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/rtracklayer_1.24.2.tar.gz' | |
| Content type 'application/x-gzip' length 1337492 bytes (1.3 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 1.3 Mb | |
| * installing *source* package ‘base64enc’ ... | |
| ** package ‘base64enc’ successfully unpacked and MD5 sums checked | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c uriencode.c -o uriencode.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o base64enc.so base64.o uriencode.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/base64enc/libs | |
| ** R | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (base64enc) | |
| * installing *source* package ‘iterators’ ... | |
| ** package ‘iterators’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (iterators) | |
| * installing *source* package ‘checkmate’ ... | |
| ** package ‘checkmate’ successfully unpacked and MD5 sums checked | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c all_missing.c -o all_missing.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c all_nchar.c -o all_nchar.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c any_missing.c -o any_missing.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c assertions.c -o assertions.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bounds.c -o bounds.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c checks.c -o checks.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c cmessages.c -o cmessages.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c comps.c -o comps.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c helper.c -o helper.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c is_integerish.c -o is_integerish.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c qassert.c -o qassert.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c qtest.c -o qtest.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rules.c -o rules.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c which_first.c -o which_first.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o checkmate.so all_missing.o all_nchar.o any_missing.o assertions.o bounds.o checks.o cmessages.o comps.o helper.o is_integerish.o qassert.o qtest.o rules.o which_first.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/checkmate/libs | |
| ** R | |
| ** byte-compile and prepare package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (checkmate) | |
| * installing *source* package ‘DBI’ ... | |
| ** package ‘DBI’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (DBI) | |
| * installing *source* package ‘brew’ ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (brew) | |
| * installing *source* package ‘XML’ ... | |
| ** package ‘XML’ successfully unpacked and MD5 sums checked | |
| checking for gcc... gcc | |
| checking for C compiler default output file name... rm: cannot remove 'a.out.dSYM': Is a directory | |
| a.out | |
| checking whether the C compiler works... yes | |
| checking whether we are cross compiling... no | |
| checking for suffix of executables... | |
| checking for suffix of object files... o | |
| checking whether we are using the GNU C compiler... yes | |
| checking whether gcc accepts -g... yes | |
| checking for gcc option to accept ISO C89... none needed | |
| checking how to run the C preprocessor... gcc -E | |
| checking for sed... /bin/sed | |
| checking for pkg-config... /usr/local/bin/pkg-config | |
| checking for xml2-config... /usr/bin/xml2-config | |
| USE_XML2 = yes | |
| SED_EXTENDED_ARG: -E | |
| Minor 9, Patch 1 for 2.9.1 | |
| Located parser file -I/usr/include/libxml2/parser.h | |
| Checking for 1.8: -I/usr/include/libxml2 | |
| Using libxml2.* | |
| checking for gzopen in -lz... yes | |
| checking for xmlParseFile in -lxml2... yes | |
| checking for xmlHashSize in -lxml2... yes | |
| Using built-in xmlHashSize | |
| Checking DTD parsing (presence of externalSubset)... | |
| checking for xmlHashSize in -lxml2... yes | |
| Found xmlHashSize | |
| checking for xmlOutputBufferCreateBuffer in -lxml2... yes | |
| have xmlOutputBufferCreateBuffer() | |
| checking for xmlDocDumpFormatMemoryEnc in -lxml2... yes | |
| checking libxml/xmlversion.h usability... yes | |
| checking libxml/xmlversion.h presence... yes | |
| checking for libxml/xmlversion.h... yes | |
| Expat: FALSE | |
| Checking for return type of xmlHashScan element routine. | |
| No return value for xmlHashScan | |
| xmlNs has a context field | |
| Checking for cetype_t enumeration | |
| No cetype_t enumeration defined in R headers. | |
| checking for xmlsec1-config... no | |
| nodegc default | |
| xml-debug default | |
| Version has XML_WITH_ZLIB | |
| Version has xmlHasFeature() | |
| **************************************** | |
| Configuration information: | |
| Libxml settings | |
| libxml include directory: -I/usr/include/libxml2 | |
| libxml library directory: -lxml2 -lz -lxml2 | |
| libxml 2: -DLIBXML2=1 | |
| Compilation flags: -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 | |
| Link flags: -lxml2 -lz -lxml2 | |
| **************************************** | |
| configure: creating ./config.status | |
| config.status: creating src/Makevars | |
| config.status: creating R/supports.R | |
| config.status: creating inst/scripts/RSXML.csh | |
| config.status: creating inst/scripts/RSXML.bsh | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c DocParse.c -o DocParse.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c EventParse.c -o EventParse.o | |
| EventParse.c: In function ‘RS_XML_textHandler’: | |
| EventParse.c:419:37: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| if(s == (XML_Char*)NULL || s[0] == (XML_Char)NULL || len == 0 | |
| ^ | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ExpatParse.c -o ExpatParse.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c HTMLParse.c -o HTMLParse.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c NodeGC.c -o NodeGC.o | |
| In file included from NodeGC.c:31:0: | |
| NodeGC.c: In function ‘R_xmlFreeDoc’: | |
| NodeGC.h:14:151: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| #define IS_NOT_OUR_DOC_TO_TOUCH(doc) (doc->_private == NULL || (doc->_private && doc->_private == &R_XML_NoMemoryMgmt) || ((int*)doc->_private)[1] != (int) R_MEMORY_MANAGER_MARKER) | |
| ^ | |
| NodeGC.c:40:14: note: in expansion of macro ‘IS_NOT_OUR_DOC_TO_TOUCH’ | |
| if(doc && !IS_NOT_OUR_DOC_TO_TOUCH(doc)) { | |
| ^ | |
| NodeGC.c: In function ‘initDocRefCounter’: | |
| NodeGC.c:178:12: warning: assignment makes integer from pointer without a cast [enabled by default] | |
| val[1] = R_MEMORY_MANAGER_MARKER; | |
| ^ | |
| In file included from NodeGC.c:31:0: | |
| NodeGC.c: In function ‘incrementDocRefBy’: | |
| NodeGC.h:14:151: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| #define IS_NOT_OUR_DOC_TO_TOUCH(doc) (doc->_private == NULL || (doc->_private && doc->_private == &R_XML_NoMemoryMgmt) || ((int*)doc->_private)[1] != (int) R_MEMORY_MANAGER_MARKER) | |
| ^ | |
| NodeGC.c:185:16: note: in expansion of macro ‘IS_NOT_OUR_DOC_TO_TOUCH’ | |
| if(!doc || IS_NOT_OUR_DOC_TO_TOUCH(doc)) | |
| ^ | |
| NodeGC.c: In function ‘getNodeCount’: | |
| NodeGC.h:15:182: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| #define IS_NOT_OUR_NODE_TO_TOUCH(node) ((node->_private == NULL) || (node->doc && node->doc->_private && node->doc->_private == &R_XML_NoMemoryMgmt) || ((int*)node->_private)[1] != (int) R_MEMORY_MANAGER_MARKER) | |
| ^ | |
| NodeGC.c:213:15: note: in expansion of macro ‘IS_NOT_OUR_NODE_TO_TOUCH’ | |
| if(!node || IS_NOT_OUR_NODE_TO_TOUCH(node)) | |
| ^ | |
| NodeGC.c: In function ‘internal_incrementNodeRefCount’: | |
| NodeGC.h:15:182: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| #define IS_NOT_OUR_NODE_TO_TOUCH(node) ((node->_private == NULL) || (node->doc && node->doc->_private && node->doc->_private == &R_XML_NoMemoryMgmt) || ((int*)node->_private)[1] != (int) R_MEMORY_MANAGER_MARKER) | |
| ^ | |
| NodeGC.c:229:17: note: in expansion of macro ‘IS_NOT_OUR_NODE_TO_TOUCH’ | |
| if(!node || IS_NOT_OUR_NODE_TO_TOUCH(node) || !node->_private) | |
| ^ | |
| NodeGC.c: In function ‘R_getXMLRefCount’: | |
| NodeGC.h:15:182: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| #define IS_NOT_OUR_NODE_TO_TOUCH(node) ((node->_private == NULL) || (node->doc && node->doc->_private && node->doc->_private == &R_XML_NoMemoryMgmt) || ((int*)node->_private)[1] != (int) R_MEMORY_MANAGER_MARKER) | |
| ^ | |
| NodeGC.c:240:17: note: in expansion of macro ‘IS_NOT_OUR_NODE_TO_TOUCH’ | |
| if(!node || IS_NOT_OUR_NODE_TO_TOUCH(node) || !node->_private) | |
| ^ | |
| NodeGC.c: In function ‘checkDescendantsInR’: | |
| NodeGC.h:15:182: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| #define IS_NOT_OUR_NODE_TO_TOUCH(node) ((node->_private == NULL) || (node->doc && node->doc->_private && node->doc->_private == &R_XML_NoMemoryMgmt) || ((int*)node->_private)[1] != (int) R_MEMORY_MANAGER_MARKER) | |
| ^ | |
| NodeGC.c:249:29: note: in expansion of macro ‘IS_NOT_OUR_NODE_TO_TOUCH’ | |
| if(!node && (process || IS_NOT_OUR_NODE_TO_TOUCH(node))) | |
| ^ | |
| NodeGC.c: In function ‘internal_decrementNodeRefCount’: | |
| NodeGC.h:15:182: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| #define IS_NOT_OUR_NODE_TO_TOUCH(node) ((node->_private == NULL) || (node->doc && node->doc->_private && node->doc->_private == &R_XML_NoMemoryMgmt) || ((int*)node->_private)[1] != (int) R_MEMORY_MANAGER_MARKER) | |
| ^ | |
| NodeGC.c:269:17: note: in expansion of macro ‘IS_NOT_OUR_NODE_TO_TOUCH’ | |
| if(!node || IS_NOT_OUR_NODE_TO_TOUCH(node)) | |
| ^ | |
| NodeGC.h:14:151: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| #define IS_NOT_OUR_DOC_TO_TOUCH(doc) (doc->_private == NULL || (doc->_private && doc->_private == &R_XML_NoMemoryMgmt) || ((int*)doc->_private)[1] != (int) R_MEMORY_MANAGER_MARKER) | |
| ^ | |
| NodeGC.c:307:19: note: in expansion of macro ‘IS_NOT_OUR_DOC_TO_TOUCH’ | |
| if(node->doc && !IS_NOT_OUR_DOC_TO_TOUCH(node->doc)) { | |
| ^ | |
| NodeGC.c: In function ‘clearNodeMemoryManagement’: | |
| NodeGC.c:385:99: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| int isOurs = (a = node->_private != &R_XML_NoMemoryMgmt) && (b = ((int *)(node->_private))[1] == (int) &R_XML_MemoryMgrMarker); | |
| ^ | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RSDTD.c -o RSDTD.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RUtils.c -o RUtils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Rcatalog.c -o Rcatalog.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Utils.c -o Utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c XMLEventParse.c -o XMLEventParse.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c XMLHashTree.c -o XMLHashTree.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c XMLTree.c -o XMLTree.o | |
| In file included from XMLTree.c:42:0: | |
| XMLTree.c: In function ‘R_createXMLNodeRefDirect’: | |
| NodeGC.h:15:182: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| #define IS_NOT_OUR_NODE_TO_TOUCH(node) ((node->_private == NULL) || (node->doc && node->doc->_private && node->doc->_private == &R_XML_NoMemoryMgmt) || ((int*)node->_private)[1] != (int) R_MEMORY_MANAGER_MARKER) | |
| ^ | |
| XMLTree.c:1057:48: note: in expansion of macro ‘IS_NOT_OUR_NODE_TO_TOUCH’ | |
| if(addFinalizer > 0 || (addFinalizer < 0 && !IS_NOT_OUR_NODE_TO_TOUCH(node))) { | |
| ^ | |
| XMLTree.c: In function ‘R_createXMLNodeRef’: | |
| XMLTree.c:1098:71: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| if(addFinalizer && ((node->_private && ((int*)node->_private)[1] == (int) R_MEMORY_MANAGER_MARKER) | |
| ^ | |
| In file included from XMLTree.c:42:0: | |
| NodeGC.h:14:151: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] | |
| #define IS_NOT_OUR_DOC_TO_TOUCH(doc) (doc->_private == NULL || (doc->_private && doc->_private == &R_XML_NoMemoryMgmt) || ((int*)doc->_private)[1] != (int) R_MEMORY_MANAGER_MARKER) | |
| ^ | |
| XMLTree.c:1099:29: note: in expansion of macro ‘IS_NOT_OUR_DOC_TO_TOUCH’ | |
| || !node->doc || (!(IS_NOT_OUR_DOC_TO_TOUCH(node->doc))))) { | |
| ^ | |
| XMLTree.c:1103:9: warning: assignment makes integer from pointer without a cast [enabled by default] | |
| val[1] = R_MEMORY_MANAGER_MARKER; | |
| ^ | |
| XMLTree.c: In function ‘R_xmlSearchNs’: | |
| XMLTree.c:1695:39: warning: comparison of distinct pointer types lacks a cast [enabled by default] | |
| xmlDocPtr doc = (xmlDocPtr) r_doc == NULL_USER_OBJECT ? NULL : R_ExternalPtrAddr(r_doc); | |
| ^ | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fixNS.c -o fixNS.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c libxmlFeatures.c -o libxmlFeatures.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c schema.c -o schema.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c xmlsecurity.c -o xmlsecurity.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DLIBXML -I/usr/include/libxml2 -DUSE_EXTERNAL_SUBSET=1 -DROOT_HAS_DTD_NODE=1 -DDUMP_WITH_ENCODING=1 -DUSE_XML_VERSION_H=1 -DXML_ELEMENT_ETYPE=1 -DXML_ATTRIBUTE_ATYPE=1 -DNO_XML_HASH_SCANNER_RETURN=1 -DLIBXML_NAMESPACE_HAS_CONTEXT=1 -DHAVE_XML_WITH_ZLIB=1 -DHAVE_XML_HAS_FEATURE=1 -DUSE_R=1 -D_R_=1 -DHAVE_VALIDITY=1 -DXML_REF_COUNT_NODES=1 -I. -DLIBXML2=1 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c xpath.c -o xpath.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o XML.so DocParse.o EventParse.o ExpatParse.o HTMLParse.o NodeGC.o RSDTD.o RUtils.o Rcatalog.o Utils.o XMLEventParse.o XMLHashTree.o XMLTree.o fixNS.o libxmlFeatures.o schema.o xmlsecurity.o xpath.o -lxml2 -lz -lxml2 -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/XML/libs | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| Creating a generic function for ‘source’ from package ‘base’ in package ‘XML’ | |
| in method for ‘xmlAttrsToDataFrame’ with signature ‘"AsIs"’: no definition for class “AsIs” | |
| in method for ‘readKeyValueDB’ with signature ‘"AsIs"’: no definition for class “AsIs” | |
| in method for ‘readSolrDoc’ with signature ‘"AsIs"’: no definition for class “AsIs” | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (XML) | |
| * installing *source* package ‘BSgenome’ ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (BSgenome) | |
| * installing *source* package ‘RCurl’ ... | |
| ** package ‘RCurl’ successfully unpacked and MD5 sums checked | |
| checking for curl-config... /usr/bin/curl-config | |
| checking for gcc... gcc | |
| checking whether the C compiler works... yes | |
| checking for C compiler default output file name... a.out | |
| checking for suffix of executables... | |
| checking whether we are cross compiling... no | |
| checking for suffix of object files... o | |
| checking whether we are using the GNU C compiler... yes | |
| checking whether gcc accepts -g... yes | |
| checking for gcc option to accept ISO C89... none needed | |
| checking how to run the C preprocessor... gcc -E | |
| Version has a libidn field | |
| Version has CURLOPT_URL | |
| Version has CURLINFO_EFFECTIVE_URL | |
| Version has CURLINFO_RESPONSE_CODE | |
| Version has CURLINFO_TOTAL_TIME | |
| Version has CURLINFO_NAMELOOKUP_TIME | |
| Version has CURLINFO_CONNECT_TIME | |
| Version has CURLINFO_PRETRANSFER_TIME | |
| Version has CURLINFO_SIZE_UPLOAD | |
| Version has CURLINFO_SIZE_DOWNLOAD | |
| Version has CURLINFO_SPEED_DOWNLOAD | |
| Version has CURLINFO_SPEED_UPLOAD | |
| Version has CURLINFO_HEADER_SIZE | |
| Version has CURLINFO_REQUEST_SIZE | |
| Version has CURLINFO_SSL_VERIFYRESULT | |
| Version has CURLINFO_FILETIME | |
| Version has CURLINFO_CONTENT_LENGTH_DOWNLOAD | |
| Version has CURLINFO_CONTENT_LENGTH_UPLOAD | |
| Version has CURLINFO_STARTTRANSFER_TIME | |
| Version has CURLINFO_CONTENT_TYPE | |
| Version has CURLINFO_REDIRECT_TIME | |
| Version has CURLINFO_REDIRECT_COUNT | |
| Version has CURLINFO_PRIVATE | |
| Version has CURLINFO_HTTP_CONNECTCODE | |
| Version has CURLINFO_HTTPAUTH_AVAIL | |
| Version has CURLINFO_PROXYAUTH_AVAIL | |
| Version has CURLINFO_OS_ERRNO | |
| Version has CURLINFO_NUM_CONNECTS | |
| Version has CURLINFO_SSL_ENGINES | |
| Version has CURLINFO_COOKIELIST | |
| Version has CURLINFO_LASTSOCKET | |
| Version has CURLINFO_FTP_ENTRY_PATH | |
| Version has CURLINFO_REDIRECT_URL | |
| Version has CURLINFO_PRIMARY_IP | |
| Version has CURLINFO_APPCONNECT_TIME | |
| Version has CURLINFO_CERTINFO | |
| Version has CURLINFO_CONDITION_UNMET | |
| Version has CURLOPT_WRITEDATA | |
| Version has CURLOPT_KEYPASSWD | |
| Version has CURLOPT_DIRLISTONLY | |
| Version has CURLOPT_APPEND | |
| Version has CURLOPT_KRBLEVEL | |
| Version has CURLOPT_USE_SSL | |
| Version has CURLOPT_TIMEOUT_MS | |
| Version has CURLOPT_CONNECTTIMEOUT_MS | |
| Version has CURLOPT_HTTP_TRANSFER_DECODING | |
| Version has CURLOPT_HTTP_CONTENT_DECODING | |
| Version has CURLOPT_NEW_FILE_PERMS | |
| Version has CURLOPT_NEW_DIRECTORY_PERMS | |
| Version has CURLOPT_POSTREDIR | |
| Version has CURLOPT_OPENSOCKETFUNCTION | |
| Version has CURLOPT_OPENSOCKETDATA | |
| Version has CURLOPT_COPYPOSTFIELDS | |
| Version has CURLOPT_PROXY_TRANSFER_MODE | |
| Version has CURLOPT_SEEKFUNCTION | |
| Version has CURLOPT_SEEKDATA | |
| Version has CURLOPT_CRLFILE | |
| Version has CURLOPT_ISSUERCERT | |
| Version has CURLOPT_ADDRESS_SCOPE | |
| Version has CURLOPT_CERTINFO | |
| Version has CURLOPT_USERNAME | |
| Version has CURLOPT_PASSWORD | |
| Version has CURLOPT_PROXYUSERNAME | |
| Version has CURLOPT_PROXYPASSWORD | |
| Version has CURLOPT_SSH_HOST_PUBLIC_KEY_MD5 | |
| Version has CURLOPT_NOPROXY | |
| Version has CURLOPT_TFTP_BLKSIZE | |
| Version has CURLOPT_SOCKS5_GSSAPI_SERVICE | |
| Version has CURLOPT_SOCKS5_GSSAPI_NEC | |
| Version has CURLOPT_PROTOCOLS | |
| Version has CURLOPT_REDIR_PROTOCOLS | |
| Version has CURLOPT_SSH_AUTH_TYPES | |
| Version has CURLOPT_SSH_PUBLIC_KEYFILE | |
| Version has CURLOPT_SSH_PRIVATE_KEYFILE | |
| Version has CURLOPT_FTP_SSL_CCC | |
| Version has CURLOPT_COOKIELIST | |
| Version has CURLOPT_IGNORE_CONTENT_LENGTH | |
| Version has CURLOPT_FTP_SKIP_PASV_IP | |
| Version has CURLOPT_FTP_FILEMETHOD | |
| Version has CURLOPT_LOCALPORT | |
| Version has CURLOPT_LOCALPORTRANGE | |
| Version has CURLOPT_CONNECT_ONLY | |
| Version has CURLOPT_CONV_FROM_NETWORK_FUNCTION | |
| Version has CURLOPT_CONV_TO_NETWORK_FUNCTION | |
| Version has CURLOPT_CONV_FROM_UTF8_FUNCTION | |
| Version has CURLOPT_MAX_SEND_SPEED_LARGE | |
| Version has CURLOPT_MAX_RECV_SPEED_LARGE | |
| Version has CURLOPT_FTP_ALTERNATIVE_TO_USER | |
| Version has CURLOPT_SOCKOPTFUNCTION | |
| Version has CURLOPT_SOCKOPTDATA | |
| Version has CURLOPT_SSL_SESSIONID_CACHE | |
| libcurl version: libcurl 7.35.0 | |
| configure: creating ./config.status | |
| config.status: creating src/Makevars | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c curl.c -o curl.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c curlInit.c -o curlInit.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c curl_base64.c -o curl_base64.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c enums.c -o enums.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c json.c -o json.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c memoryManagement.c -o memoryManagement.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c myUTF8.c -o myUTF8.o | |
| myUTF8.c: In function ‘StringValue’: | |
| myUTF8.c:284:5: warning: passing argument 1 of ‘Rf_mkCharLenCE’ from incompatible pointer type [enabled by default] | |
| yylval = mkCharLenCE(wcs, wcnt, CE_UTF8); /* include terminator */ | |
| ^ | |
| In file included from /usr/share/R/include/Rdefines.h:29:0, | |
| from myUTF8.c:3: | |
| /usr/share/R/include/Rinternals.h:841:6: note: expected ‘const char *’ but argument is of type ‘ucs_t *’ | |
| SEXP Rf_mkCharLenCE(const char *, int, cetype_t); | |
| ^ | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o RCurl.so base64.o curl.o curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -L/usr/lib/x86_64-linux-gnu -lcurl -lxml2 -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/RCurl/libs | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| Creating a generic function for ‘close’ from package ‘base’ in package ‘RCurl’ | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (RCurl) | |
| * installing *source* package ‘RSQLite’ ... | |
| ** package ‘RSQLite’ successfully unpacked and MD5 sums checked | |
| checking for gcc... gcc -std=gnu99 | |
| checking for C compiler default output file name... a.out | |
| checking whether the C compiler works... yes | |
| checking whether we are cross compiling... no | |
| checking for suffix of executables... | |
| checking for suffix of object files... o | |
| checking whether we are using the GNU C compiler... yes | |
| checking whether gcc -std=gnu99 accepts -g... yes | |
| checking for gcc -std=gnu99 option to accept ISO C89... none needed | |
| checking how to run the C preprocessor... gcc -std=gnu99 -E | |
| checking for gcc... (cached) gcc -std=gnu99 | |
| checking whether we are using the GNU C compiler... (cached) yes | |
| checking whether gcc -std=gnu99 accepts -g... (cached) yes | |
| checking for gcc -std=gnu99 option to accept ISO C89... (cached) none needed | |
| checking for library containing fdatasync... none required | |
| configure: creating ./config.status | |
| config.status: creating src/Makevars | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_SOUNDEX -DSQLITE_MAX_VARIABLE_NUMBER=40000 -DSQLITE_MAX_COLUMN=30000 -DTHREADSAFE=0 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RS-DBI.c -o RS-DBI.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_SOUNDEX -DSQLITE_MAX_VARIABLE_NUMBER=40000 -DSQLITE_MAX_COLUMN=30000 -DTHREADSAFE=0 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RS-SQLite.c -o RS-SQLite.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_SOUNDEX -DSQLITE_MAX_VARIABLE_NUMBER=40000 -DSQLITE_MAX_COLUMN=30000 -DTHREADSAFE=0 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c param_binding.c -o param_binding.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_SOUNDEX -DSQLITE_MAX_VARIABLE_NUMBER=40000 -DSQLITE_MAX_COLUMN=30000 -DTHREADSAFE=0 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sqlite-all.c -o sqlite-all.o | |
| sqlite-all.c:1:35: warning: extra tokens at end of #ifdef directive [enabled by default] | |
| #ifdef RSQLITE_USE_BUNDLED_SQLITE || WIN32 | |
| ^ | |
| mkdir -p ../inst/include | |
| cp sqlite/sqlite3.h ../inst/include | |
| cp sqlite/sqlite3ext.h ../inst/include | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o RSQLite.so RS-DBI.o RS-SQLite.o param_binding.o sqlite-all.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/RSQLite/libs | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| Creating a generic function for ‘summary’ from package ‘base’ in package ‘RSQLite’ | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (RSQLite) | |
| * installing *source* package ‘sendmailR’ ... | |
| ** package ‘sendmailR’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (sendmailR) | |
| * installing *source* package ‘foreach’ ... | |
| ** package ‘foreach’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** demo | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (foreach) | |
| * installing *source* package ‘BBmisc’ ... | |
| ** package ‘BBmisc’ successfully unpacked and MD5 sums checked | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c getMaxColRowIndex.c -o getMaxColRowIndex.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c getMaxIndex.c -o getMaxIndex.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c which_first.c -o which_first.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o BBmisc.so getMaxColRowIndex.o getMaxIndex.o which_first.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/BBmisc/libs | |
| ** R | |
| ** byte-compile and prepare package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (BBmisc) | |
| * installing *source* package ‘fail’ ... | |
| ** package ‘fail’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** inst | |
| ** byte-compile and prepare package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (fail) | |
| * installing *source* package ‘BatchJobs’ ... | |
| ** package ‘BatchJobs’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** inst | |
| ** byte-compile and prepare package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (BatchJobs) | |
| * installing *source* package ‘BiocParallel’ ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (BiocParallel) | |
| * installing *source* package ‘GenomicAlignments’ ... | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c cigar_utils.c -o cigar_utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/IRanges/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o cigar_utils.o encodeOverlaps_methods.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/GenomicAlignments/libs | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (GenomicAlignments) | |
| * installing *source* package ‘rtracklayer’ ... | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c R_init_rtracklayer.c -o R_init_rtracklayer.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c bigWig.c -o bigWig.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c chain_io.c -o chain_io.o | |
| chain_io.c: In function ‘read_chain_file’: | |
| chain_io.c:119:14: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] | |
| fgets(linebuf, LINEBUF_SIZE, stream); /* skip empty line */ | |
| ^ | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c twoBit.c -o twoBit.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c handlers.c -o handlers.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/bbiRead.c -o ucsc/bbiRead.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/cirTree.c -o ucsc/cirTree.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/common.c -o ucsc/common.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/dnaseq.c -o ucsc/dnaseq.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/dnautil.c -o ucsc/dnautil.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/errabort.c -o ucsc/errabort.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/hash.c -o ucsc/hash.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/linefile.c -o ucsc/linefile.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/localmem.c -o ucsc/localmem.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/sqlNum.c -o ucsc/sqlNum.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/zlibFace.c -o ucsc/zlibFace.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/dystring.c -o ucsc/dystring.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/hmmstats.c -o ucsc/hmmstats.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/obscure.c -o ucsc/obscure.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/pipeline.c -o ucsc/pipeline.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/rangeTree.c -o ucsc/rangeTree.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/rbTree.c -o ucsc/rbTree.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/memalloc.c -o ucsc/memalloc.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/dlist.c -o ucsc/dlist.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/udc.c -o ucsc/udc.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/net.c -o ucsc/net.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/bits.c -o ucsc/bits.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/twoBit.c -o ucsc/twoBit.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/internet.c -o ucsc/internet.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/https.c -o ucsc/https.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/base64.c -o ucsc/base64.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/verbose.c -o ucsc/verbose.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/os.c -o ucsc/os.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/wildcmp.c -o ucsc/wildcmp.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -g -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ucsc/_portimpl.c -o ucsc/_portimpl.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o rtracklayer.so IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o bigWig.o chain_io.o twoBit.o handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errabort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/rtracklayer/libs | |
| ** R | |
| ** data | |
| ** demo | |
| ** inst | |
| ** preparing package for lazy loading | |
| Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’ | |
| Creating a generic function from function ‘uri’ in package ‘rtracklayer’ | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| 'BiocParallel' did not register default BiocParallelParams | |
| Warning: system call failed: Cannot allocate memory | |
| * DONE (rtracklayer) | |
| The downloaded source packages are in | |
| ‘/tmp/RtmpHRfdWL/downloaded_packages’ | |
| Old packages: 'MASS', 'spatial' | |
| BioC_mirror: http://bioconductor.org | |
| Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version | |
| 3.1.1. | |
| Installing package(s) 'DEXSeq' | |
| also installing the dependencies ‘xtable’, ‘RcppArmadillo’, ‘locfit’, ‘AnnotationDbi’, ‘annotate’, ‘DESeq2’, ‘biomaRt’, ‘hwriter’, ‘statmod’, ‘geneplotter’, ‘genefilter’ | |
| trying URL 'http://cran.fhcrc.org/src/contrib/xtable_1.7-4.tar.gz' | |
| Content type 'application/x-gzip' length 350204 bytes (341 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 341 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/RcppArmadillo_0.4.450.1.0.tar.gz' | |
| Content type 'application/x-gzip' length 931597 bytes (909 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 909 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/locfit_1.5-9.1.tar.gz' | |
| Content type 'application/x-gzip' length 196560 bytes (191 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 191 Kb | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/AnnotationDbi_1.26.1.tar.gz' | |
| Content type 'application/x-gzip' length 4253685 bytes (4.1 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 4.1 Mb | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/annotate_1.42.1.tar.gz' | |
| Content type 'application/x-gzip' length 1859389 bytes (1.8 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 1.8 Mb | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/DESeq2_1.4.5.tar.gz' | |
| Content type 'application/x-gzip' length 1190439 bytes (1.1 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 1.1 Mb | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/biomaRt_2.20.0.tar.gz' | |
| Content type 'application/x-gzip' length 276933 bytes (270 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 270 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/hwriter_1.3.2.tar.gz' | |
| Content type 'application/x-gzip' length 114012 bytes (111 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 111 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/statmod_1.4.20.tar.gz' | |
| Content type 'application/x-gzip' length 55377 bytes (54 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 54 Kb | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/geneplotter_1.42.0.tar.gz' | |
| Content type 'application/x-gzip' length 1396054 bytes (1.3 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 1.3 Mb | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/genefilter_1.46.1.tar.gz' | |
| Content type 'application/x-gzip' length 1156622 bytes (1.1 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 1.1 Mb | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/DEXSeq_1.10.8.tar.gz' | |
| Content type 'application/x-gzip' length 376168 bytes (367 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 367 Kb | |
| * installing *source* package ‘xtable’ ... | |
| ** package ‘xtable’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (xtable) | |
| * installing *source* package ‘RcppArmadillo’ ... | |
| ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked | |
| * checking LAPACK_LIBS: divide-and-conquer complex SVD available via system LAPACK | |
| ** libs | |
| g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppArmadillo.cpp -o RcppArmadillo.o | |
| g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o | |
| g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I../inst/include -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fastLm.cpp -o fastLm.o | |
| g++ -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/RcppArmadillo/libs | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (RcppArmadillo) | |
| * installing *source* package ‘locfit’ ... | |
| ** package ‘locfit’ successfully unpacked and MD5 sums checked | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c S_enter.c -o S_enter.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c band.c -o band.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dbinom.c -o dbinom.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dens_haz.c -o dens_haz.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dens_int.c -o dens_int.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c dens_odi.c -o dens_odi.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c density.c -o density.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ev_atree.c -o ev_atree.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ev_interp.c -o ev_interp.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ev_kdtre.c -o ev_kdtre.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ev_main.c -o ev_main.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ev_sphere.c -o ev_sphere.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c ev_trian.c -o ev_trian.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c family.c -o family.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fitted.c -o fitted.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c frend.c -o frend.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c lf_adap.c -o lf_adap.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c lf_dercor.c -o lf_dercor.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c lf_fitfun.c -o lf_fitfun.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c lf_nbhd.c -o lf_nbhd.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c lf_robust.c -o lf_robust.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c lf_vari.c -o lf_vari.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c lf_wdiag.c -o lf_wdiag.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c lfstr.c -o lfstr.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c locfit.c -o locfit.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c m_chol.c -o m_chol.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c m_eigen.c -o m_eigen.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c m_icirc.c -o m_icirc.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c m_imont.c -o m_imont.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c m_isimp.c -o m_isimp.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c m_isphr.c -o m_isphr.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c m_jacob.c -o m_jacob.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c m_max.c -o m_max.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c m_qr.c -o m_qr.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c m_solve.c -o m_solve.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c m_svd.c -o m_svd.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c m_vector.c -o m_vector.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c math.c -o math.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c minmax.c -o minmax.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c pcomp.c -o pcomp.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c preplot.c -o preplot.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c prob.c -o prob.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c procv.c -o procv.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scb.c -o scb.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scb_cons.c -o scb_cons.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scb_crit.c -o scb_crit.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c scb_iface.c -o scb_iface.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c simul.c -o simul.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c smisc.c -o smisc.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c startlf.c -o startlf.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c weight.c -o weight.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o locfit.so S_enter.o band.o dbinom.o dens_haz.o dens_int.o dens_odi.o density.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_sphere.o ev_trian.o family.o fitted.o frend.o lf_adap.o lf_dercor.o lf_fitfun.o lf_nbhd.o lf_robust.o lf_vari.o lf_wdiag.o lfstr.o locfit.o m_chol.o m_eigen.o m_icirc.o m_imont.o m_isimp.o m_isphr.o m_jacob.o m_max.o m_qr.o m_solve.o m_svd.o m_vector.o math.o minmax.o pcomp.o preplot.o prob.o procv.o scb.o scb_cons.o scb_crit.o scb_iface.o simul.o smisc.o startlf.o weight.o -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/locfit/libs | |
| ** R | |
| ** data | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (locfit) | |
| * installing *source* package ‘AnnotationDbi’ ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’ | |
| Creating a generic function for ‘toString’ from package ‘base’ in package ‘AnnotationDbi’ | |
| Creating a generic function for ‘rev’ from package ‘base’ in package ‘AnnotationDbi’ | |
| Creating a generic function for ‘subset’ from package ‘base’ in package ‘AnnotationDbi’ | |
| Creating a generic function for ‘head’ from package ‘utils’ in package ‘AnnotationDbi’ | |
| Creating a generic function for ‘tail’ from package ‘utils’ in package ‘AnnotationDbi’ | |
| Creating a generic function for ‘as.list’ from package ‘base’ in package ‘AnnotationDbi’ | |
| Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’ | |
| Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’ | |
| Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’ | |
| Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’ | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (AnnotationDbi) | |
| * installing *source* package ‘hwriter’ ... | |
| ** package ‘hwriter’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (hwriter) | |
| * installing *source* package ‘statmod’ ... | |
| ** package ‘statmod’ successfully unpacked and MD5 sums checked | |
| ** libs | |
| gfortran -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -c gaussq.f -o gaussq.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o statmod.so gaussq.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/statmod/libs | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (statmod) | |
| * installing *source* package ‘annotate’ ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (annotate) | |
| * installing *source* package ‘biomaRt’ ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (biomaRt) | |
| * installing *source* package ‘geneplotter’ ... | |
| ** R | |
| ** data | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (geneplotter) | |
| * installing *source* package ‘genefilter’ ... | |
| ** libs | |
| g++ -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c half_range_mode.cpp -o half_range_mode.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c nd.c -o nd.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c pAUC.c -o pAUC.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rowPAUCs.c -o rowPAUCs.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rowttests.c -o rowttests.o | |
| gfortran -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -c ttest.f -o ttest.o | |
| g++ -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/genefilter/libs | |
| ** R | |
| ** data | |
| *** moving datasets to lazyload DB | |
| ** inst | |
| ** preparing package for lazy loading | |
| Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘genefilter’ | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (genefilter) | |
| * installing *source* package ‘DESeq2’ ... | |
| ** libs | |
| g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c DESeq2.cpp -o DESeq2.o | |
| virtual memory exhausted: Cannot allocate memory | |
| make: *** [DESeq2.o] Error 1 | |
| ERROR: compilation failed for package ‘DESeq2’ | |
| * removing ‘/usr/local/lib/R/site-library/DESeq2’ | |
| ERROR: dependency ‘DESeq2’ is not available for package ‘DEXSeq’ | |
| * removing ‘/usr/local/lib/R/site-library/DEXSeq’ | |
| The downloaded source packages are in | |
| ‘/tmp/RtmpHRfdWL/downloaded_packages’ | |
| Old packages: 'MASS', 'spatial' | |
| BioC_mirror: http://bioconductor.org | |
| Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version | |
| 3.1.1. | |
| Installing package(s) 'DNAcopy' | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/DNAcopy_1.38.1.tar.gz' | |
| Content type 'application/x-gzip' length 335138 bytes (327 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 327 Kb | |
| * installing *source* package ‘DNAcopy’ ... | |
| ** libs | |
| gfortran -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -c cbsWtstats.f -o cbsWtstats.o | |
| gfortran -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -c cbststats.f -o cbststats.o | |
| gfortran -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -c changepoints-wtd.f -o changepoints-wtd.o | |
| gfortran -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -c changepoints.f -o changepoints.o | |
| gfortran -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -c esegment.f -o esegment.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c flchoose.c -o flchoose.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fphyper.c -o fphyper.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fpnorm.c -o fpnorm.o | |
| gfortran -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -c getbdry.f -o getbdry.o | |
| gfortran -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -c prune.f -o prune.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rshared.c -o rshared.o | |
| gfortran -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -c segmentp.f -o segmentp.o | |
| gfortran -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -c smoothCNA.f -o smoothCNA.o | |
| gfortran -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -c tailprobs.f -o tailprobs.o | |
| gcc -std=gnu99 -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/DNAcopy/libs | |
| ** R | |
| ** data | |
| *** moving datasets to lazyload DB | |
| ** demo | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (DNAcopy) | |
| The downloaded source packages are in | |
| ‘/tmp/RtmpHRfdWL/downloaded_packages’ | |
| Old packages: 'MASS', 'spatial' | |
| [[1]] | |
| [1] "cn.mops" | |
| [[2]] | |
| [1] "rtracklayer" | |
| [[3]] | |
| [1] "DEXSeq" | |
| [[4]] | |
| [1] "DNAcopy" | |
| Warning messages: | |
| 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : | |
| installation of package ‘DESeq2’ had non-zero exit status | |
| 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : | |
| installation of package ‘DEXSeq’ had non-zero exit status | |
| Installing package into ‘/usr/local/lib/R/site-library’ | |
| (as ‘lib’ is unspecified) | |
| also installing the dependencies ‘R.oo’, ‘R.utils’, ‘R.cache’ | |
| trying URL 'http://cran.fhcrc.org/src/contrib/R.oo_1.18.0.tar.gz' | |
| Content type 'application/x-gzip' length 394545 bytes (385 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 385 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/R.utils_1.33.0.tar.gz' | |
| Content type 'application/x-gzip' length 344332 bytes (336 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 336 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/R.cache_0.10.0.tar.gz' | |
| Content type 'application/x-gzip' length 28588 bytes (27 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 27 Kb | |
| trying URL 'http://cran.fhcrc.org/src/contrib/PSCBS_0.43.0.tar.gz' | |
| Content type 'application/x-gzip' length 3529512 bytes (3.4 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 3.4 Mb | |
| * installing *source* package ‘R.oo’ ... | |
| ** package ‘R.oo’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (R.oo) | |
| * installing *source* package ‘R.utils’ ... | |
| ** package ‘R.utils’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : | |
| Renamed the preexisting function warnings to warnings.default, which was defined in environment base. | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (R.utils) | |
| * installing *source* package ‘R.cache’ ... | |
| ** package ‘R.cache’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (R.cache) | |
| * installing *source* package ‘PSCBS’ ... | |
| ** package ‘PSCBS’ successfully unpacked and MD5 sums checked | |
| ** R | |
| ** inst | |
| ** byte-compile and prepare package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (PSCBS) | |
| The downloaded source packages are in | |
| ‘/tmp/RtmpHRfdWL/downloaded_packages’ | |
| [[1]] | |
| NULL | |
| [localhost] local: rm -f /home/vagrant/tmp/cloudbiolinux/install_packages.R | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux | |
| INFO: Cleaning up space from package builds | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "rm -rf .cpanm" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "rm -f /var/crash/*" | |
| [localhost] local: rm -f ~/*.dot | |
| [localhost] local: rm -f ~/*.log | |
| Creating manifest of installed packages in /usr/local/share/bcbio-nextgen/manifest | |
| Installing additional tools | |
| Third party tools upgrade complete. | |
| Upgrading bcbio-nextgen data files | |
| Cloning into 'cloudbiolinux'... | |
| remote: Counting objects: 10170, done. | |
| remote: Total 10170 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (10170/10170), 7.33 MiB | 2.66 MiB/s, done. | |
| Resolving deltas: 100% (5541/5541), done. | |
| Checking connectivity... done. | |
| Setting up virtual machine | |
| INFO: <cloudbio.flavor.Flavor instance at 0x7ff1f0e1c7e8> | |
| INFO: <cloudbio.flavor.Flavor instance at 0x7ff1f0e1c7e8> | |
| INFO: This is a ngs_pipeline_minimal flavor | |
| INFO: This is a ngs_pipeline_minimal flavor | |
| INFO: Distribution __auto__ | |
| INFO: Distribution __auto__ | |
| INFO: Get local environment | |
| INFO: Get local environment | |
| [localhost] local: cat /etc/*release | grep DISTRIB_CODENAME | cut -f 2 -d = | |
| INFO: Ubuntu setup | |
| INFO: Ubuntu setup | |
| DBG [distribution.py]: Debian-shared setup | |
| DBG [distribution.py]: Debian-shared setup | |
| DBG [distribution.py]: Source=trusty | |
| DBG [distribution.py]: Source=trusty | |
| DBG [distribution.py]: Checking target distribution ubuntu | |
| DBG [distribution.py]: Checking target distribution ubuntu | |
| [localhost] local: cat /proc/version | |
| [localhost] local: cat /etc/*release | grep DISTRIB_CODENAME | cut -f 2 -d = | |
| DBG [distribution.py]: NixPkgs: Ignored | |
| DBG [distribution.py]: NixPkgs: Ignored | |
| [localhost] local: echo $HOME | |
| [localhost] local: uname -m | |
| INFO: Now, testing connection to host... | |
| INFO: Now, testing connection to host... | |
| INFO: Connection to host appears to work! | |
| INFO: Connection to host appears to work! | |
| DBG [utils.py]: Expand paths | |
| DBG [utils.py]: Expand paths | |
| INFO: List of genomes to get (from the config file at '{'install_liftover': False, 'genome_indexes': ['bwa'], 'genomes': [{'rnaseq': True, 'dbsnp': True, 'name': 'Human (hg19)', 'dbkey': 'hg19'}], 'install_uniref': False}'): Human (hg19) | |
| INFO: List of genomes to get (from the config file at '{'install_liftover': False, 'genome_indexes': ['bwa'], 'genomes': [{'rnaseq': True, 'dbsnp': True, 'name': 'Human (hg19)', 'dbkey': 'hg19'}], 'install_uniref': False}'): Human (hg19) | |
| [localhost] local: mkdir -p /usr/local/share/bcbio-nextgen/genomes | |
| [localhost] local: mkdir -p /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19 | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/3ecf9675-fc2a-3b4f-b095-c4b33b0d7c5e' | |
| [localhost] local: wget --continue --no-check-certificate -O hg19-rnaseq-2014-07-17.tar.xz 'https://s3.amazonaws.com/biodata/annotation/hg19-rnaseq-2014-07-17.tar.xz' | |
| --2014-10-03 00:01:05-- https://s3.amazonaws.com/biodata/annotation/hg19-rnaseq-2014-07-17.tar.xz | |
| Resolving s3.amazonaws.com (s3.amazonaws.com)... 54.231.2.232 | |
| Connecting to s3.amazonaws.com (s3.amazonaws.com)|54.231.2.232|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 544817560 (520M) [binary/octet-stream] | |
| Saving to: ‘hg19-rnaseq-2014-07-17.tar.xz’ | |
| 100%[========================================================================================================================>] 544,817,560 5.16MB/s in 1m 53s | |
| 2014-10-03 00:03:03 (4.61 MB/s) - ‘hg19-rnaseq-2014-07-17.tar.xz’ saved [544817560/544817560] | |
| [localhost] local: mv hg19-rnaseq-2014-07-17.tar.xz /usr/local/share/bcbio-nextgen/genomes/Hsapiens | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/3ecf9675-fc2a-3b4f-b095-c4b33b0d7c5e | |
| INFO: Extracting RNA-seq references: hg19-rnaseq-2014-07-17.tar.xz | |
| INFO: Extracting RNA-seq references: hg19-rnaseq-2014-07-17.tar.xz | |
| [localhost] local: xz -dc hg19-rnaseq-2014-07-17.tar.xz | tar -xpf - | |
| [localhost] local: rm -f hg19-rnaseq-2014-07-17.tar.xz | |
| [localhost] local: ln -sf rnaseq-2014-07-17 rnaseq | |
| INFO: Downloading genome from s3: hg19 bwa | |
| INFO: Downloading genome from s3: hg19 bwa | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/7e48759a-2d65-3745-ba64-85402829593e' | |
| [localhost] local: wget --continue --no-check-certificate -O hg19-bwa.tar.xz 'https://s3.amazonaws.com/biodata/genomes/hg19-bwa.tar.xz' | |
| --2014-10-03 00:04:34-- https://s3.amazonaws.com/biodata/genomes/hg19-bwa.tar.xz | |
| Resolving s3.amazonaws.com (s3.amazonaws.com)... 54.231.16.168 | |
| Connecting to s3.amazonaws.com (s3.amazonaws.com)|54.231.16.168|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 2989323712 (2.8G) [binary/octet-stream] | |
| Saving to: ‘hg19-bwa.tar.xz’ | |
| 100%[======================================================================================================================>] 2,989,323,712 4.98MB/s in 10m 28s | |
| 2014-10-03 00:15:07 (4.54 MB/s) - ‘hg19-bwa.tar.xz’ saved [2989323712/2989323712] | |
| [localhost] local: mv hg19-bwa.tar.xz /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19 | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/7e48759a-2d65-3745-ba64-85402829593e | |
| [localhost] local: xz -dc hg19-bwa.tar.xz | tar -xvpf - | |
| bwa/ | |
| bwa/hg19.fa.pac | |
| bwa/hg19.fa.amb | |
| bwa/hg19.fa.sa | |
| bwa/hg19.fa.ann | |
| bwa/hg19.fa.bwt | |
| [localhost] local: rm -f hg19-bwa.tar.xz | |
| INFO: Downloading genome from s3: hg19 seq | |
| INFO: Downloading genome from s3: hg19 seq | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/43e0e524-6595-3cea-abee-df9d934f5388' | |
| [localhost] local: wget --continue --no-check-certificate -O hg19-seq.tar.xz 'https://s3.amazonaws.com/biodata/genomes/hg19-seq.tar.xz' | |
| --2014-10-03 00:19:10-- https://s3.amazonaws.com/biodata/genomes/hg19-seq.tar.xz | |
| Resolving s3.amazonaws.com (s3.amazonaws.com)... 54.231.8.232 | |
| Connecting to s3.amazonaws.com (s3.amazonaws.com)|54.231.8.232|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 756626880 (722M) [binary/octet-stream] | |
| Saving to: ‘hg19-seq.tar.xz’ | |
| 100%[========================================================================================================================>] 756,626,880 3.70MB/s in 3m 29s | |
| 2014-10-03 00:22:44 (3.46 MB/s) - ‘hg19-seq.tar.xz’ saved [756626880/756626880] | |
| [localhost] local: mv hg19-seq.tar.xz /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19 | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/43e0e524-6595-3cea-abee-df9d934f5388 | |
| [localhost] local: xz -dc hg19-seq.tar.xz | tar -xvpf - | |
| seq/ | |
| seq/hg19.fa | |
| seq/hg19.fa.fai | |
| [localhost] local: rm -f hg19-seq.tar.xz | |
| [localhost] local: java -Xms500m -Xmx1g -jar /usr/local/share/java/picard/CreateSequenceDictionary.jar REFERENCE=/usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa OUTPUT=/usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.dict | |
| [Fri Oct 03 00:23:56 UTC 2014] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa OUTPUT=/usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.dict TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false | |
| [Fri Oct 03 00:23:56 UTC 2014] Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_65-b32; Picard version: 1.96(1510) | |
| [Fri Oct 03 00:24:12 UTC 2014] net.sf.picard.sam.CreateSequenceDictionary done. Elapsed time: 0.27 minutes. | |
| Runtime.totalMemory()=506986496 | |
| [localhost] local: mkdir -p /usr/local/share/bcbio-nextgen/galaxy/tool-data | |
| [localhost] local: touch sam_fa_indices.loc | |
| [localhost] local: echo 'index hg19 /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa' >> "$(echo sam_fa_indices.loc)" | |
| [localhost] local: touch picard_index.loc | |
| [localhost] local: echo 'hg19 hg19 Human (hg19) /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa' >> "$(echo picard_index.loc)" | |
| [localhost] local: touch gatk_sorted_picard_index.loc | |
| [localhost] local: echo 'hg19 hg19 Human (hg19) /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa' >> "$(echo gatk_sorted_picard_index.loc)" | |
| [localhost] local: touch bwa_index.loc | |
| [localhost] local: echo 'hg19 hg19 Human (hg19) /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/bwa/hg19.fa' >> "$(echo bwa_index.loc)" | |
| [localhost] local: mkdir -p /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/ec00997c-1bc9-3ad3-b927-c1e98b64f8cc' | |
| [localhost] local: wget --continue --no-check-certificate -O dbsnp_138.hg19.vcf.gz 'ftp://gsapubftp-anonymous:@ftp.broadinstitute.org/bundle/2.8/hg19/dbsnp_138.hg19.vcf.gz' | |
| --2014-10-03 00:24:12-- ftp://gsapubftp-anonymous:*password*@ftp.broadinstitute.org/bundle/2.8/hg19/dbsnp_138.hg19.vcf.gz | |
| => ‘dbsnp_138.hg19.vcf.gz’ | |
| Resolving ftp.broadinstitute.org (ftp.broadinstitute.org)... 69.173.80.251 | |
| Connecting to ftp.broadinstitute.org (ftp.broadinstitute.org)|69.173.80.251|:21... connected. | |
| Logging in as gsapubftp-anonymous ... Logged in! | |
| ==> SYST ... done. ==> PWD ... done. | |
| ==> TYPE I ... done. ==> CWD (1) /bundle/2.8/hg19 ... done. | |
| ==> SIZE dbsnp_138.hg19.vcf.gz ... 1470262409 | |
| ==> PASV ... done. ==> RETR dbsnp_138.hg19.vcf.gz ... done. | |
| Length: 1470262409 (1.4G) (unauthoritative) | |
| 100%[======================================================================================================================>] 1,470,262,409 3.08MB/s in 6m 31s | |
| 2014-10-03 00:30:49 (3.59 MB/s) - ‘dbsnp_138.hg19.vcf.gz’ saved [1470262409] | |
| [localhost] local: mv dbsnp_138.hg19.vcf.gz /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/ec00997c-1bc9-3ad3-b927-c1e98b64f8cc | |
| [localhost] local: gunzip -c dbsnp_138.hg19.vcf.gz | bgzip -c > dbsnp_138.vcf.gz | |
| [localhost] local: tabix -f -p vcf dbsnp_138.vcf.gz | |
| [localhost] local: rm -f dbsnp_138.hg19.vcf.gz | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/137d5535-400d-32de-a360-ecf8d707317c' | |
| [localhost] local: wget --continue --no-check-certificate -O hapmap_3.3.hg19.sites.vcf.gz 'ftp://gsapubftp-anonymous:@ftp.broadinstitute.org/bundle/2.8/hg19/hapmap_3.3.hg19.sites.vcf.gz' | |
| --2014-10-03 00:35:52-- ftp://gsapubftp-anonymous:*password*@ftp.broadinstitute.org/bundle/2.8/hg19/hapmap_3.3.hg19.sites.vcf.gz | |
| => ‘hapmap_3.3.hg19.sites.vcf.gz’ | |
| Resolving ftp.broadinstitute.org (ftp.broadinstitute.org)... 69.173.80.251 | |
| Connecting to ftp.broadinstitute.org (ftp.broadinstitute.org)|69.173.80.251|:21... connected. | |
| Logging in as gsapubftp-anonymous ... Logged in! | |
| ==> SYST ... done. ==> PWD ... done. | |
| ==> TYPE I ... done. ==> CWD (1) /bundle/2.8/hg19 ... done. | |
| ==> SIZE hapmap_3.3.hg19.sites.vcf.gz ... 60780530 | |
| ==> PASV ... done. ==> RETR hapmap_3.3.hg19.sites.vcf.gz ... done. | |
| Length: 60780530 (58M) (unauthoritative) | |
| 100%[========================================================================================================================>] 60,780,530 3.85MB/s in 18s | |
| 2014-10-03 00:36:16 (3.23 MB/s) - ‘hapmap_3.3.hg19.sites.vcf.gz’ saved [60780530] | |
| [localhost] local: mv hapmap_3.3.hg19.sites.vcf.gz /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/137d5535-400d-32de-a360-ecf8d707317c | |
| [localhost] local: gunzip -c hapmap_3.3.hg19.sites.vcf.gz | bgzip -c > hapmap_3.3.vcf.gz | |
| [localhost] local: tabix -f -p vcf hapmap_3.3.vcf.gz | |
| [localhost] local: rm -f hapmap_3.3.hg19.sites.vcf.gz | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/8fdafb8a-09a8-3e58-bbbf-19c70f391939' | |
| [localhost] local: wget --continue --no-check-certificate -O 1000G_omni2.5.hg19.sites.vcf.gz 'ftp://gsapubftp-anonymous:@ftp.broadinstitute.org/bundle/2.8/hg19/1000G_omni2.5.hg19.sites.vcf.gz' | |
| --2014-10-03 00:36:27-- ftp://gsapubftp-anonymous:*password*@ftp.broadinstitute.org/bundle/2.8/hg19/1000G_omni2.5.hg19.sites.vcf.gz | |
| => ‘1000G_omni2.5.hg19.sites.vcf.gz’ | |
| Resolving ftp.broadinstitute.org (ftp.broadinstitute.org)... 69.173.80.251 | |
| Connecting to ftp.broadinstitute.org (ftp.broadinstitute.org)|69.173.80.251|:21... connected. | |
| Logging in as gsapubftp-anonymous ... Logged in! | |
| ==> SYST ... done. ==> PWD ... done. | |
| ==> TYPE I ... done. ==> CWD (1) /bundle/2.8/hg19 ... done. | |
| ==> SIZE 1000G_omni2.5.hg19.sites.vcf.gz ... 51811347 | |
| ==> PASV ... done. ==> RETR 1000G_omni2.5.hg19.sites.vcf.gz ... done. | |
| Length: 51811347 (49M) (unauthoritative) | |
| 100%[========================================================================================================================>] 51,811,347 3.89MB/s in 15s | |
| 2014-10-03 00:36:49 (3.20 MB/s) - ‘1000G_omni2.5.hg19.sites.vcf.gz’ saved [51811347] | |
| [localhost] local: mv 1000G_omni2.5.hg19.sites.vcf.gz /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/8fdafb8a-09a8-3e58-bbbf-19c70f391939 | |
| [localhost] local: gunzip -c 1000G_omni2.5.hg19.sites.vcf.gz | bgzip -c > 1000G_omni2.5.vcf.gz | |
| [localhost] local: tabix -f -p vcf 1000G_omni2.5.vcf.gz | |
| [localhost] local: rm -f 1000G_omni2.5.hg19.sites.vcf.gz | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/b232aa9f-fe69-38c9-9dac-d8f85942176d' | |
| [localhost] local: wget --continue --no-check-certificate -O 1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz 'ftp://gsapubftp-anonymous:@ftp.broadinstitute.org/bundle/2.8/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz' | |
| --2014-10-03 00:36:56-- ftp://gsapubftp-anonymous:*password*@ftp.broadinstitute.org/bundle/2.8/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz | |
| => ‘1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz’ | |
| Resolving ftp.broadinstitute.org (ftp.broadinstitute.org)... 69.173.80.251 | |
| Connecting to ftp.broadinstitute.org (ftp.broadinstitute.org)|69.173.80.251|:21... connected. | |
| Logging in as gsapubftp-anonymous ... Logged in! | |
| ==> SYST ... done. ==> PWD ... done. | |
| ==> TYPE I ... done. ==> CWD (1) /bundle/2.8/hg19 ... done. | |
| ==> SIZE 1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz ... 1801561307 | |
| ==> PASV ... done. ==> RETR 1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz ... done. | |
| Length: 1801561307 (1.7G) (unauthoritative) | |
| 100%[======================================================================================================================>] 1,801,561,307 3.66MB/s in 7m 52s | |
| 2014-10-03 00:44:55 (3.64 MB/s) - ‘1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz’ saved [1801561307] | |
| [localhost] local: mv 1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/b232aa9f-fe69-38c9-9dac-d8f85942176d | |
| [localhost] local: gunzip -c 1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz | bgzip -c > 1000G_phase1.snps.high_confidence.vcf.gz | |
| [localhost] local: tabix -f -p vcf 1000G_phase1.snps.high_confidence.vcf.gz | |
| [localhost] local: rm -f 1000G_phase1.snps.high_confidence.hg19.sites.vcf.gz | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/b0b5bf74-7ae8-32e5-823f-a5c5cf5f54dc' | |
| [localhost] local: wget --continue --no-check-certificate -O Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz 'ftp://gsapubftp-anonymous:@ftp.broadinstitute.org/bundle/2.8/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz' | |
| --2014-10-03 00:49:55-- ftp://gsapubftp-anonymous:*password*@ftp.broadinstitute.org/bundle/2.8/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz | |
| => ‘Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz’ | |
| Resolving ftp.broadinstitute.org (ftp.broadinstitute.org)... 69.173.80.251 | |
| Connecting to ftp.broadinstitute.org (ftp.broadinstitute.org)|69.173.80.251|:21... connected. | |
| Logging in as gsapubftp-anonymous ... Logged in! | |
| ==> SYST ... done. ==> PWD ... done. | |
| ==> TYPE I ... done. ==> CWD (1) /bundle/2.8/hg19 ... done. | |
| ==> SIZE Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz ... 19980713 | |
| ==> PASV ... done. ==> RETR Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz ... done. | |
| Length: 19980713 (19M) (unauthoritative) | |
| 100%[========================================================================================================================>] 19,980,713 3.63MB/s in 7.8s | |
| 2014-10-03 00:50:09 (2.44 MB/s) - ‘Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz’ saved [19980713] | |
| [localhost] local: mv Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/b0b5bf74-7ae8-32e5-823f-a5c5cf5f54dc | |
| [localhost] local: gunzip -c Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz | bgzip -c > Mills_and_1000G_gold_standard.indels.vcf.gz | |
| [localhost] local: tabix -f -p vcf Mills_and_1000G_gold_standard.indels.vcf.gz | |
| [localhost] local: rm -f Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/9a2bacf5-59c7-3326-bff8-06d2ab033419' | |
| [localhost] local: wget --continue --no-check-certificate -O cosmic-v68-hg19.vcf.gz 'https://s3.amazonaws.com/biodata/variants/cosmic-v68-hg19.vcf.gz' | |
| --2014-10-03 00:50:12-- https://s3.amazonaws.com/biodata/variants/cosmic-v68-hg19.vcf.gz | |
| Resolving s3.amazonaws.com (s3.amazonaws.com)... 205.251.243.139 | |
| Connecting to s3.amazonaws.com (s3.amazonaws.com)|205.251.243.139|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 20540355 (20M) [text/x-vcard] | |
| Saving to: ‘cosmic-v68-hg19.vcf.gz’ | |
| 100%[========================================================================================================================>] 20,540,355 4.81MB/s in 6.3s | |
| 2014-10-03 00:50:25 (3.11 MB/s) - ‘cosmic-v68-hg19.vcf.gz’ saved [20540355/20540355] | |
| [localhost] local: mv cosmic-v68-hg19.vcf.gz /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/9a2bacf5-59c7-3326-bff8-06d2ab033419 | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/d7a7c551-a73b-30c2-8f73-84c6af13461b' | |
| [localhost] local: wget --continue --no-check-certificate -O cosmic-v68-hg19.vcf.gz.tbi 'https://s3.amazonaws.com/biodata/variants/cosmic-v68-hg19.vcf.gz.tbi' | |
| --2014-10-03 00:50:25-- https://s3.amazonaws.com/biodata/variants/cosmic-v68-hg19.vcf.gz.tbi | |
| Resolving s3.amazonaws.com (s3.amazonaws.com)... 205.251.243.139 | |
| Connecting to s3.amazonaws.com (s3.amazonaws.com)|205.251.243.139|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 913645 (892K) [application/octet-stream] | |
| Saving to: ‘cosmic-v68-hg19.vcf.gz.tbi’ | |
| 100%[========================================================================================================================>] 913,645 475KB/s in 1.9s | |
| 2014-10-03 00:50:32 (475 KB/s) - ‘cosmic-v68-hg19.vcf.gz.tbi’ saved [913645/913645] | |
| [localhost] local: mv cosmic-v68-hg19.vcf.gz.tbi /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/d7a7c551-a73b-30c2-8f73-84c6af13461b | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/ec2dffc4-ed2c-3a47-8c7f-c224d21f2850' | |
| [localhost] local: wget --continue --no-check-certificate -O human.hg19.excl.tsv 'https://raw.githubusercontent.com/chapmanb/delly/master/human.hg19.excl.tsv' | |
| --2014-10-03 00:50:32-- https://raw.githubusercontent.com/chapmanb/delly/master/human.hg19.excl.tsv | |
| Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 23.235.47.133 | |
| Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|23.235.47.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 7518 (7.3K) [text/plain] | |
| Saving to: ‘human.hg19.excl.tsv’ | |
| 100%[========================================================================================================================>] 7,518 --.-K/s in 0s | |
| 2014-10-03 00:50:37 (90.3 MB/s) - ‘human.hg19.excl.tsv’ saved [7518/7518] | |
| [localhost] local: grep ^chr human.hg19.excl.tsv > sv_repeat_telomere_centromere.bed | |
| [localhost] local: mv sv_repeat_telomere_centromere.bed /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/ec2dffc4-ed2c-3a47-8c7f-c224d21f2850 | |
| [localhost] local: pwd | |
| [localhost] local: echo $HOME | |
| [localhost] local: mkdir -p '/home/vagrant/tmp/cloudbiolinux/9edd9dd6-2dc0-34e2-9e1a-466458c9e75b' | |
| [localhost] local: wget --continue --no-check-certificate -O LCR-hs37d5.bed.gz 'https://github.com/lh3/varcmp/raw/master/scripts/LCR-hs37d5.bed.gz' | |
| --2014-10-03 00:50:37-- https://github.com/lh3/varcmp/raw/master/scripts/LCR-hs37d5.bed.gz | |
| Resolving github.com (github.com)... 192.30.252.129 | |
| Connecting to github.com (github.com)|192.30.252.129|:443... connected. | |
| HTTP request sent, awaiting response... 302 Found | |
| Location: https://raw.githubusercontent.com/lh3/varcmp/master/scripts/LCR-hs37d5.bed.gz [following] | |
| --2014-10-03 00:50:43-- https://raw.githubusercontent.com/lh3/varcmp/master/scripts/LCR-hs37d5.bed.gz | |
| Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 23.235.47.133 | |
| Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|23.235.47.133|:443... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 9915051 (9.5M) [application/octet-stream] | |
| Saving to: ‘LCR-hs37d5.bed.gz’ | |
| 100%[========================================================================================================================>] 9,915,051 2.96MB/s in 3.5s | |
| 2014-10-03 00:50:51 (2.73 MB/s) - ‘LCR-hs37d5.bed.gz’ saved [9915051/9915051] | |
| [localhost] local: zcat LCR-hs37d5.bed.gz | grep -v ^GL | grep -v ^NC | grep -v ^hs | sed 's/^/chr/' | bgzip -c > LCR.bed.gz | |
| [localhost] local: mv LCR.bed.gz /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/variation | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux/9edd9dd6-2dc0-34e2-9e1a-466458c9e75b | |
| [localhost] local: tabix -p vcf -f LCR.bed.gz | |
| [localhost] local: ln -sf ../../GRCh37/variation/human_ancestor.fa.rz human_ancestor.fa.rz | |
| [localhost] local: ln -sf ../../GRCh37/variation/human_ancestor.fa.rz.fai human_ancestor.fa.rz.fai | |
| [localhost] local: ln -sf ../../GRCh37/variation/qsignature.tar.bz2 qsignature.tar.bz2 | |
| Updating hg19 genome resources configuration | |
| Installing snpEff database hg19 in /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/snpeff | |
| --2014-10-03 00:51:00-- http://downloads.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_hg19.zip | |
| Resolving downloads.sourceforge.net (downloads.sourceforge.net)... 216.34.181.59 | |
| Connecting to downloads.sourceforge.net (downloads.sourceforge.net)|216.34.181.59|:80... connected. | |
| HTTP request sent, awaiting response... 302 Found | |
| Location: http://hivelocity.dl.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_hg19.zip [following] | |
| --2014-10-03 00:51:06-- http://hivelocity.dl.sourceforge.net/project/snpeff/databases/v3_6/snpEff_v3_6_hg19.zip | |
| Resolving hivelocity.dl.sourceforge.net (hivelocity.dl.sourceforge.net)... 74.50.101.106 | |
| Connecting to hivelocity.dl.sourceforge.net (hivelocity.dl.sourceforge.net)|74.50.101.106|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 41438372 (40M) [application/octet-stream] | |
| Saving to: ‘snpEff_v3_6_hg19.zip’ | |
| 100%[========================================================================================================================>] 41,438,372 2.87MB/s in 16s | |
| 2014-10-03 00:51:22 (2.49 MB/s) - ‘snpEff_v3_6_hg19.zip’ saved [41438372/41438372] | |
| Archive: snpEff_v3_6_hg19.zip | |
| inflating: data/hg19/snpEffectPredictor.bin | |
| UNIVERSAL->import is deprecated and will be removed in a future perl at /usr/local/Cellar/vep/75_2014-06-12/lib/Bio/Tree/TreeFunctionsI.pm line 94. | |
| bcbio-nextgen data upgrade complete. | |
| Upgrade completed successfully. | |
| Finished: bcbio-nextgen, tools and data installed | |
| Genome data installed in: | |
| /usr/local/share/bcbio-nextgen | |
| Tools installed in: | |
| /usr/local | |
| Ready to use system configuration at: | |
| /usr/local/share/bcbio-nextgen/galaxy/bcbio_system.yaml | |
| Edit configuration file as needed to match your machine or cluster | |
| vagrant@vagrant-ubuntu-trusty-64:~/tmp$ bcbio_nextgen.py upgrade -u development | |
| Fetching package metadata: .. | |
| Solving package specifications: . | |
| Package plan for installation in environment /usr/local/share/bcbio-nextgen/anaconda: | |
| The following packages will be UPDATED: | |
| numpy: 1.8.2-py27_0 --> 1.9.0-py27_0 | |
| Unlinking packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Linking packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Fetching package metadata: ... | |
| Solving package specifications: ............... | |
| Package plan for installation in environment /usr/local/share/bcbio-nextgen/anaconda: | |
| The following packages will be downloaded: | |
| package | build | |
| ---------------------------|----------------- | |
| ipython-2.3.0 | py27_0 2.8 MB | |
| The following packages will be UPDATED: | |
| ipython: 2.2.0-py27_0 --> 2.3.0-py27_0 | |
| The following packages will be DOWNGRADED: | |
| numpy: 1.9.0-py27_0 --> 1.8.2-py27_0 | |
| Fetching packages ... | |
| ipython-2.3.0- 100% |##################################################################################################################| Time: 0:00:03 860.24 kB/s | |
| Extracting packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Unlinking packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Linking packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Upgrading bcbio-nextgen to latest development version | |
| Requirement already satisfied (use --upgrade to upgrade): bcbio-nextgen from git+git://github.com/chapmanb/bcbio-nextgen.git in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages | |
| Requirement already satisfied (use --upgrade to upgrade): biopython>=1.61 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): boto>=2.9.6 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): Cython>=0.19 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): ipython>=2.0.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): ipython-cluster-helper>=0.3.3 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): Logbook>=0.6.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): lxml>=3.3.5 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): nose>=1.3.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): pysam>=0.7.7 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): pyzmq>=2.2.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): PyYAML>=3.10 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): toolz>=0.6.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): tornado>=3.1.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): bioblend>=0.4.3 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): cutadapt==1.4.2 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): fabric>=1.7.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): gffutils>=0.8.1 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): HTSeq>=0.5.4p5 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): joblib>=0.7.0d in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): openpyxl>=1.6.1,<2.0.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): prettyplotlib>=0.1.7 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): psutil>=1.2.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): pybedtools>=0.6.2 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): PyVCF>=0.6.7 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): sh>=1.07 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): arvados-python-client>=0.1.1405019228.4a7ca04 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): chanjo>=2.0.2 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): msgpack-python>=0.4.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): netifaces>=0.10.3 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from ipython-cluster-helper>=0.3.3->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): requests>=1.1.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bioblend>=0.4.3->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): poster in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bioblend>=0.4.3->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): paramiko>=1.10 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from fabric>=1.7.0->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): six in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from gffutils>=0.8.1->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): argh in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from gffutils>=0.8.1->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): argcomplete in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from gffutils>=0.8.1->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): simplejson in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from gffutils>=0.8.1->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): matplotlib>=1.2.1 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from prettyplotlib>=0.1.7->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): brewer2mpl>=1.3.1 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from prettyplotlib>=0.1.7->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): distribute in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from PyVCF>=0.6.7->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): python-gflags in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from arvados-python-client>=0.1.1405019228.4a7ca04->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): google-api-python-client in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from arvados-python-client>=0.1.1405019228.4a7ca04->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): httplib2 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from arvados-python-client>=0.1.1405019228.4a7ca04->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): urllib3 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from arvados-python-client>=0.1.1405019228.4a7ca04->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): ws4py in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from arvados-python-client>=0.1.1405019228.4a7ca04->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): setuptools>=0.7 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/setuptools-5.8-py2.7.egg (from distribute->PyVCF>=0.6.7->bcbio-nextgen) | |
| Cleaning up... | |
| Downloading/unpacking bcbio-nextgen from git+git://github.com/chapmanb/bcbio-nextgen.git | |
| Cloning git://github.com/chapmanb/bcbio-nextgen.git to /tmp/pip_build_vagrant/bcbio-nextgen | |
| Running setup.py (path:/tmp/pip_build_vagrant/bcbio-nextgen/setup.py) egg_info for package bcbio-nextgen | |
| warning: no files found matching 'config/*.ini' | |
| Installing collected packages: bcbio-nextgen | |
| Found existing installation: bcbio-nextgen 0.8.2 | |
| Uninstalling bcbio-nextgen: | |
| Successfully uninstalled bcbio-nextgen | |
| Running setup.py install for bcbio-nextgen | |
| changing mode of build/scripts-2.7/bcbio_nextgen.py from 664 to 775 | |
| warning: no files found matching 'config/*.ini' | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/bcbio_setup_genome.py to 775 | |
| Successfully installed bcbio-nextgen | |
| Cleaning up... | |
| Upgrade of bcbio-nextgen development code complete. | |
| Upgrading third party tools to latest versions | |
| Cloning into 'cloudbiolinux'... | |
| remote: Counting objects: 10170, done. | |
| remote: Total 10170 (delta 0), reused 0 (delta 0) | |
| Receiving objects: 100% (10170/10170), 7.33 MiB | 2.24 MiB/s, done. | |
| Resolving deltas: 100% (5541/5541), done. | |
| Checking connectivity... done. | |
| Setting up virtual machine | |
| INFO: <cloudbio.flavor.Flavor instance at 0x7fae2dc4d680> | |
| INFO: This is a ngs_pipeline_minimal flavor | |
| INFO: Reading default fabricrc.txt | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/fabricrc.txt | |
| INFO: Distribution __auto__ | |
| INFO: Get local environment | |
| [localhost] local: cat /etc/*release | grep DISTRIB_CODENAME | cut -f 2 -d = | |
| INFO: Ubuntu setup | |
| DBG [distribution.py]: Debian-shared setup | |
| DBG [distribution.py]: Source=trusty | |
| DBG [distribution.py]: Checking target distribution ubuntu | |
| [localhost] local: cat /proc/version | |
| [localhost] local: cat /etc/*release | grep DISTRIB_CODENAME | cut -f 2 -d = | |
| DBG [distribution.py]: NixPkgs: Ignored | |
| [localhost] local: echo $HOME | |
| [localhost] local: uname -m | |
| INFO: Now, testing connection to host... | |
| INFO: Connection to host appears to work! | |
| DBG [utils.py]: Expand paths | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml | |
| INFO: Meta-package information from /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml | |
| - Packages: minimal,libraries,perl,python,java,r,ruby,bio_nextgen | |
| - Libraries: r-libs | |
| [localhost] local: whoami | |
| [localhost] local: echo $PATH | |
| [localhost] local: echo ' | |
| # CloudBioLinux PATH updates' >> "$(echo ~/.bashrc)" | |
| [localhost] local: echo 'export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH' >> "$(echo ~/.bashrc)" | |
| [localhost] local: echo 'export PERL5LIB=/usr/local/lib/perl5:/usr/local/lib/perl5/site_perl:${PERL5LIB}' >> "$(echo ~/.bashrc)" | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/custom.yaml | |
| INFO: Reading /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/custom.yaml | |
| DBG [shared.py]: Packages to install: ucsc_tools,cufflinks,picard,featurecounts,rnaseqc,bcbio_variation,grabix,mutect,varscan | |
| INFO: Custom install for 'ucsc_tools' start time: 2014-10-03 01:14:58.854882 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_ucsc_tools | |
| INFO: Custom install for 'ucsc_tools' end time: 2014-10-03 01:14:58.871996; duration: 0:00:00.017114 | |
| INFO: Custom install for 'cufflinks' start time: 2014-10-03 01:14:58.872445 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_cufflinks | |
| INFO: Custom install for 'cufflinks' end time: 2014-10-03 01:14:58.881054; duration: 0:00:00.008609 | |
| INFO: Custom install for 'picard' start time: 2014-10-03 01:14:58.881507 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_picard | |
| [localhost] local: ls /usr/local/share/java/picard-1.96 | |
| INFO: Custom install for 'picard' end time: 2014-10-03 01:14:58.902741; duration: 0:00:00.021234 | |
| INFO: Custom install for 'featurecounts' start time: 2014-10-03 01:14:58.903206 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_featurecounts | |
| INFO: Custom install for 'featurecounts' end time: 2014-10-03 01:14:58.953625; duration: 0:00:00.050419 | |
| INFO: Custom install for 'rnaseqc' start time: 2014-10-03 01:14:58.953866 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_rnaseqc | |
| [localhost] local: ls /usr/local/share/java/RNA-SeQC-1.1.7 | |
| INFO: Custom install for 'rnaseqc' end time: 2014-10-03 01:14:58.965748; duration: 0:00:00.011882 | |
| INFO: Custom install for 'bcbio_variation' start time: 2014-10-03 01:14:58.966011 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_bcbio_variation | |
| [localhost] local: ls /usr/local/share/java/bcbio_variation-0.1.7 | |
| INFO: Custom install for 'bcbio_variation' end time: 2014-10-03 01:14:58.978054; duration: 0:00:00.012043 | |
| INFO: Custom install for 'grabix' start time: 2014-10-03 01:14:58.978491 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_grabix | |
| INFO: Custom install for 'grabix' end time: 2014-10-03 01:14:59.000783; duration: 0:00:00.022292 | |
| INFO: Custom install for 'mutect' start time: 2014-10-03 01:14:59.001183 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_mutect | |
| [localhost] local: ls /usr/local/share/java/mutect-1.1.5 | |
| INFO: Custom install for 'mutect' end time: 2014-10-03 01:14:59.020745; duration: 0:00:00.019562 | |
| INFO: Custom install for 'varscan' start time: 2014-10-03 01:14:59.021181 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_varscan | |
| [localhost] local: ls /usr/local/share/java/varscan-2.3.7 | |
| INFO: Custom install for 'varscan' end time: 2014-10-03 01:14:59.031659; duration: 0:00:00.010478 | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/chef_recipes.yaml | |
| INFO: Reading /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/chef_recipes.yaml | |
| DBG [shared.py]: Packages to install: | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/puppet_classes.yaml | |
| INFO: Reading /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/puppet_classes.yaml | |
| DBG [shared.py]: Packages to install: | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml | |
| INFO: Meta-package information from /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml | |
| - Packages: minimal,libraries,perl,python,java,r,ruby,bio_nextgen | |
| - Libraries: r-libs | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/packages-homebrew.yaml | |
| INFO: Reading /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/packages-homebrew.yaml | |
| DBG [shared.py]: Packages to install: bcftools,htslib,samtools,bamtools,bedtools,biobambam,cramtools,fastqc,kraken,libmaus,oncofuse,qualimap,sambamba,samblaster,seqtk,sickle,speedseq,staden_io_lib,bcbio-variation-recall,delly;--with-binary,freebayes,gatk-framework,glia,hall-lab-sv-tools,lumpy-sv,pindel,platypus-variant,qsignature,rtg-tools,scalpel,snpeff,vardict,vcflib,vep,vt,bowtie2,bwa,novoalign,rna-star,snap-aligner,tophat-binary,cmake,cpanminus | |
| [localhost] local: /usr/local/bin/brew tap | |
| [localhost] local: /usr/local/bin/brew update | |
| Already up-to-date. | |
| [localhost] local: /usr/local/bin/brew tap --repair | |
| Pruned 0 dead formulae | |
| Tapped 390 formulae | |
| [localhost] local: /usr/local/bin/brew outdated | |
| [localhost] local: /usr/local/bin/brew info cmake | |
| [localhost] local: /usr/local/bin/brew info expat | |
| [localhost] local: /usr/local/bin/brew list samtools | grep -c bctools | |
| Warning: local() encountered an error (return code 1) while executing '/usr/local/bin/brew list samtools | grep -c bctools' | |
| [localhost] local: /usr/local/bin/brew list samtools | grep -c vcfutils.pl | |
| Warning: local() encountered an error (return code 1) while executing '/usr/local/bin/brew list samtools | grep -c vcfutils.pl' | |
| [localhost] local: /usr/local/bin/brew info samtools | |
| [localhost] local: /usr/local/bin/brew info cpanminus | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Statistics::Descriptive' | |
| Statistics::Descriptive is up to date. (3.0607) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Archive::Extract' | |
| Archive::Extract is up to date. (0.72) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Archive::Zip' | |
| Archive::Zip is up to date. (1.38) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Archive::Tar' | |
| Archive::Tar is up to date. (2.02) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'DBI' | |
| DBI is up to date. (1.631) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'LWP::Simple' | |
| LWP::Simple is up to date. (6.00) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'LWP::Protocol::https' | |
| LWP::Protocol::https is up to date. (6.06) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Time::HiRes' | |
| Time::HiRes is up to date. (1.9726) | |
| [localhost] local: /usr/local/bin/brew info bcftools | |
| [localhost] local: /usr/local/bin/brew info htslib | |
| [localhost] local: /usr/local/bin/brew info samtools | |
| [localhost] local: /usr/local/bin/brew info bamtools | |
| [localhost] local: /usr/local/bin/brew info bedtools | |
| [localhost] local: /usr/local/bin/brew info biobambam | |
| [localhost] local: /usr/local/bin/brew info cramtools | |
| [localhost] local: /usr/local/bin/brew info fastqc | |
| [localhost] local: /usr/local/bin/brew info kraken | |
| [localhost] local: /usr/local/bin/brew info libmaus | |
| [localhost] local: /usr/local/bin/brew info oncofuse | |
| [localhost] local: /usr/local/bin/brew info qualimap | |
| [localhost] local: /usr/local/bin/brew info sambamba | |
| [localhost] local: /usr/local/bin/brew info samblaster | |
| [localhost] local: /usr/local/bin/brew info seqtk | |
| [localhost] local: /usr/local/bin/brew info sickle | |
| [localhost] local: /usr/local/bin/brew info speedseq | |
| [localhost] local: /usr/local/bin/brew info staden_io_lib | |
| [localhost] local: /usr/local/bin/brew info bcbio-variation-recall | |
| [localhost] local: /usr/local/bin/brew info delly | |
| [localhost] local: /usr/local/bin/brew info freebayes | |
| [localhost] local: /usr/local/bin/brew info gatk-framework | |
| [localhost] local: /usr/local/bin/brew info glia | |
| [localhost] local: /usr/local/bin/brew info hall-lab-sv-tools | |
| [localhost] local: /usr/local/bin/brew info lumpy-sv | |
| [localhost] local: /usr/local/bin/brew info pindel | |
| [localhost] local: /usr/local/bin/brew info platypus-variant | |
| [localhost] local: /usr/local/bin/brew info qsignature | |
| [localhost] local: /usr/local/bin/brew info rtg-tools | |
| [localhost] local: /usr/local/bin/brew info scalpel | |
| [localhost] local: /usr/local/bin/brew info snpeff | |
| [localhost] local: /usr/local/bin/brew info vardict | |
| [localhost] local: /usr/local/bin/brew info vcflib | |
| [localhost] local: /usr/local/bin/brew info vep | |
| [localhost] local: /usr/local/bin/brew info vt | |
| [localhost] local: /usr/local/bin/brew info bowtie2 | |
| [localhost] local: /usr/local/bin/brew info bwa | |
| [localhost] local: /usr/local/bin/brew info novoalign | |
| [localhost] local: /usr/local/bin/brew info rna-star | |
| [localhost] local: /usr/local/bin/brew info snap-aligner | |
| [localhost] local: /usr/local/bin/brew info tophat-binary | |
| [localhost] local: /usr/local/bin/brew info cmake | |
| [localhost] local: /usr/local/bin/brew info cpanminus | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/r-libs.yaml | |
| [localhost] local: echo $HOME | |
| [localhost] local: touch /home/vagrant/tmp/cloudbiolinux/install_packages.R | |
| [localhost] local: mkdir -p /usr/local/lib/R/site-library | |
| [localhost] local: echo ' | |
| .libPaths(c("/usr/local/lib/R/site-library")) | |
| library(methods) | |
| cran.repos <- getOption("repos") | |
| cran.repos["CRAN" ] <- "http://cran.fhcrc.org/" | |
| options(repos=cran.repos) | |
| source("http://bioconductor.org/biocLite.R") | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: echo ' | |
| repo.installer <- function(repos, install.fn) { | |
| update.packages(lib.loc="/usr/local/lib/R/site-library", repos=repos, ask=FALSE) | |
| maybe.install <- function(pname) { | |
| if (!(pname %in% installed.packages())) | |
| install.fn(pname) | |
| } | |
| } | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: echo ' | |
| std.pkgs <- c("cghFLasso", "ggplot2", "gsalib", "matrixStats", "snow") | |
| std.installer = repo.installer(cran.repos, install.packages) | |
| lapply(std.pkgs, std.installer) | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: echo ' | |
| bioc.pkgs <- c("cn.mops", "rtracklayer", "DEXSeq", "DNAcopy") | |
| bioc.installer = repo.installer(biocinstallRepos(), biocLite) | |
| lapply(bioc.pkgs, bioc.installer) | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: echo ' | |
| std2.pkgs <- c("PSCBS") | |
| lapply(std2.pkgs, std.installer) | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: Rscript /home/vagrant/tmp/cloudbiolinux/install_packages.R | |
| Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help | |
| [[1]] | |
| NULL | |
| [[2]] | |
| NULL | |
| [[3]] | |
| NULL | |
| [[4]] | |
| NULL | |
| [[5]] | |
| NULL | |
| BioC_mirror: http://bioconductor.org | |
| Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version | |
| 3.1.1. | |
| Installing package(s) 'DEXSeq' | |
| Warning in install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : | |
| 'lib = "/usr/local/lib/R/site-library"' is not writable | |
| Error in install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : | |
| unable to install packages | |
| Calls: lapply ... FUN -> install.fn -> biocLiteInstall -> install.packages | |
| Execution halted | |
| Fatal error: local() encountered an error (return code 1) while executing 'Rscript /home/vagrant/tmp/cloudbiolinux/install_packages.R' | |
| Aborting. | |
| vagrant@vagrant-ubuntu-trusty-64:~/tmp$ bcbio_nextgen.py upgrade -u development --sudo | |
| Fetching package metadata: .. | |
| Solving package specifications: . | |
| Package plan for installation in environment /usr/local/share/bcbio-nextgen/anaconda: | |
| The following packages will be UPDATED: | |
| numpy: 1.8.2-py27_0 --> 1.9.0-py27_0 | |
| Unlinking packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Linking packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Fetching package metadata: ... | |
| Solving package specifications: ............... | |
| Package plan for installation in environment /usr/local/share/bcbio-nextgen/anaconda: | |
| The following packages will be DOWNGRADED: | |
| numpy: 1.9.0-py27_0 --> 1.8.2-py27_0 | |
| Unlinking packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Linking packages ... | |
| [ COMPLETE ] |####################################################################################################################################| 100% | |
| Upgrading bcbio-nextgen to latest development version | |
| Requirement already satisfied (use --upgrade to upgrade): bcbio-nextgen from git+git://github.com/chapmanb/bcbio-nextgen.git in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages | |
| Requirement already satisfied (use --upgrade to upgrade): biopython>=1.61 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): boto>=2.9.6 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): Cython>=0.19 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): ipython>=2.0.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): ipython-cluster-helper>=0.3.3 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): Logbook>=0.6.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): lxml>=3.3.5 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): nose>=1.3.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): pysam>=0.7.7 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): pyzmq>=2.2.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): PyYAML>=3.10 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): toolz>=0.6.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): tornado>=3.1.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): bioblend>=0.4.3 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): cutadapt==1.4.2 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): fabric>=1.7.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): gffutils>=0.8.1 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): HTSeq>=0.5.4p5 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): joblib>=0.7.0d in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): openpyxl>=1.6.1,<2.0.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): prettyplotlib>=0.1.7 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): psutil>=1.2.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): pybedtools>=0.6.2 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): PyVCF>=0.6.7 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): sh>=1.07 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): arvados-python-client>=0.1.1405019228.4a7ca04 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): chanjo>=2.0.2 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): msgpack-python>=0.4.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): netifaces>=0.10.3 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from ipython-cluster-helper>=0.3.3->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): requests>=1.1.0 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bioblend>=0.4.3->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): poster in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from bioblend>=0.4.3->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): paramiko>=1.10 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from fabric>=1.7.0->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): six in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from gffutils>=0.8.1->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): argh in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from gffutils>=0.8.1->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): argcomplete in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from gffutils>=0.8.1->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): simplejson in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from gffutils>=0.8.1->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): matplotlib>=1.2.1 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from prettyplotlib>=0.1.7->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): brewer2mpl>=1.3.1 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from prettyplotlib>=0.1.7->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): distribute in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from PyVCF>=0.6.7->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): python-gflags in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from arvados-python-client>=0.1.1405019228.4a7ca04->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): google-api-python-client in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from arvados-python-client>=0.1.1405019228.4a7ca04->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): httplib2 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from arvados-python-client>=0.1.1405019228.4a7ca04->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): urllib3 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from arvados-python-client>=0.1.1405019228.4a7ca04->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): ws4py in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages (from arvados-python-client>=0.1.1405019228.4a7ca04->bcbio-nextgen) | |
| Requirement already satisfied (use --upgrade to upgrade): setuptools>=0.7 in /usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/setuptools-5.8-py2.7.egg (from distribute->PyVCF>=0.6.7->bcbio-nextgen) | |
| Cleaning up... | |
| Downloading/unpacking bcbio-nextgen from git+git://github.com/chapmanb/bcbio-nextgen.git | |
| Cloning git://github.com/chapmanb/bcbio-nextgen.git to /tmp/pip_build_vagrant/bcbio-nextgen | |
| Running setup.py (path:/tmp/pip_build_vagrant/bcbio-nextgen/setup.py) egg_info for package bcbio-nextgen | |
| warning: no files found matching 'config/*.ini' | |
| Installing collected packages: bcbio-nextgen | |
| Found existing installation: bcbio-nextgen 0.8.3a | |
| Uninstalling bcbio-nextgen: | |
| Successfully uninstalled bcbio-nextgen | |
| Running setup.py install for bcbio-nextgen | |
| changing mode of build/scripts-2.7/bcbio_nextgen.py from 664 to 775 | |
| warning: no files found matching 'config/*.ini' | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/bcbio_nextgen.py to 775 | |
| changing mode of /usr/local/share/bcbio-nextgen/anaconda/bin/bcbio_setup_genome.py to 775 | |
| Successfully installed bcbio-nextgen | |
| Cleaning up... | |
| Upgrade of bcbio-nextgen development code complete. | |
| Upgrading third party tools to latest versions | |
| Setting up virtual machine | |
| INFO: <cloudbio.flavor.Flavor instance at 0x7fa4f1def248> | |
| INFO: This is a ngs_pipeline_minimal flavor | |
| INFO: Reading default fabricrc.txt | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/fabricrc.txt | |
| INFO: Distribution __auto__ | |
| INFO: Get local environment | |
| [localhost] local: cat /etc/*release | grep DISTRIB_CODENAME | cut -f 2 -d = | |
| INFO: Ubuntu setup | |
| DBG [distribution.py]: Debian-shared setup | |
| DBG [distribution.py]: Source=trusty | |
| DBG [distribution.py]: Checking target distribution ubuntu | |
| [localhost] local: cat /proc/version | |
| [localhost] local: cat /etc/*release | grep DISTRIB_CODENAME | cut -f 2 -d = | |
| DBG [distribution.py]: NixPkgs: Ignored | |
| [localhost] local: echo $HOME | |
| [localhost] local: uname -m | |
| INFO: Now, testing connection to host... | |
| INFO: Connection to host appears to work! | |
| DBG [utils.py]: Expand paths | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml | |
| INFO: Meta-package information from /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml | |
| - Packages: minimal,libraries,perl,python,java,r,ruby,bio_nextgen | |
| - Libraries: r-libs | |
| [localhost] local: echo $HOME | |
| /home/vagrant | |
| DBG [deb.py]: _setup_apt_sources /etc/apt/sources.list.d/cloudbiolinux.list | |
| DBG [deb.py]: Source deb http://us.archive.ubuntu.com/ubuntu/ trusty universe | |
| DBG [deb.py]: Source deb http://us.archive.ubuntu.com/ubuntu/ trusty multiverse | |
| DBG [deb.py]: Source deb http://us.archive.ubuntu.com/ubuntu/ trusty-updates universe | |
| DBG [deb.py]: Source deb http://us.archive.ubuntu.com/ubuntu/ trusty-updates multiverse | |
| DBG [deb.py]: Source deb http://archive.canonical.com/ubuntu trusty partner | |
| DBG [deb.py]: Source deb http://downloads-distro.mongodb.org/repo/ubuntu-upstart dist 10gen | |
| DBG [deb.py]: Source deb http://cran.fhcrc.org/bin/linux/ubuntu trusty/ | |
| DBG [deb.py]: Source deb http://archive.cloudera.com/debian maverick-cdh3 contrib | |
| DBG [deb.py]: Source deb http://archive.canonical.com/ubuntu trusty partner | |
| DBG [deb.py]: Source deb http://ppa.launchpad.net/freenx-team/ppa/ubuntu precise main | |
| DBG [deb.py]: Source deb http://ppa.launchpad.net/nebc/bio-linux/ubuntu precise main | |
| DBG [deb.py]: Source deb [arch=amd64 trusted=yes] http://research.cs.wisc.edu/htcondor/debian/stable/ squeeze contrib | |
| DBG [deb.py]: Source deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux | |
| DBG [deb.py]: Source deb http://download.virtualbox.org/virtualbox/debian trusty contrib | |
| [localhost] local: sed -i.bak -r -e 's/^([ ]+\*\) return;;)$/#\1/g' "$(echo ~/.bashrc)" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "echo \"postfix postfix/not_configured boolean true\" | /usr/bin/debconf-set-selections;echo \"postfix postfix/main_mailer_type select 'No configuration'\" | /usr/bin/debconf-set-selections;echo \"mysql-server-5.1 mysql-server/root_password string '(password omitted)'\" | /usr/bin/debconf-set-selections;echo \"mysql-server-5.1 mysql-server/root_password_again string '(password omitted)'\" | /usr/bin/debconf-set-selections;echo \"mysql-server-5.5 mysql-server/root_password string '(password omitted)'\" | /usr/bin/debconf-set-selections;echo \"mysql-server-5.5 mysql-server/root_password_again string '(password omitted)'\" | /usr/bin/debconf-set-selections;echo \"sun-java6-jdk shared/accepted-sun-dlj-v1-1 select true\" | /usr/bin/debconf-set-selections;echo \"sun-java6-jre shared/accepted-sun-dlj-v1-1 select true\" | /usr/bin/debconf-set-selections;echo \"sun-java6-bin shared/accepted-sun-dlj-v1-1 select true\" | /usr/bin/debconf-set-selections;echo \"grub-pc grub2/linux_cmdline string ''\" | /usr/bin/debconf-set-selections;echo \"grub-pc grub-pc/install_devices_empty boolean true\" | /usr/bin/debconf-set-selections;echo \"acroread acroread/default-viewer boolean false\" | /usr/bin/debconf-set-selections;echo \"rabbitmq-server rabbitmq-server/upgrade_previous note\" | /usr/bin/debconf-set-selections;echo \"condor condor/wantdebconf boolean false\" | /usr/bin/debconf-set-selections;echo \"ttf-mscorefonts-installer msttcorefonts/accepted-mscorefonts-eula boolean true\" | /usr/bin/debconf-set-selections;echo \"ttf-mscorefonts-installer msttcorefonts/present-mscorefonts-eula note\" | /usr/bin/debconf-set-selections;echo \"gdm shared/default-x-display-manager select gdm\" | /usr/bin/debconf-set-selections;echo \"lightdm shared/default-x-display-manager select gdm\" | /usr/bin/debconf-set-selections;echo \"postfix postfix/mailname string notusedexample.org\" | /usr/bin/debconf-set-selections;echo \"debconf debconf/priority select critical\" | /usr/bin/debconf-set-selections;" | |
| INFO: Update GPG keys for repositories | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "wget -q -O- http://archive.cloudera.com/debian/archive.key | apt-key add -" | |
| OK | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "wget -q -O- http://download.virtualbox.org/virtualbox/debian/oracle_vbox.asc | apt-key add -" | |
| OK | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-key adv --keyserver keyserver.ubuntu.com --recv 7F0CEB10" | |
| Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --homedir /tmp/tmp.h3J9KG894d --no-auto-check-trustdb --trust-model always --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --keyserver keyserver.ubuntu.com --recv 7F0CEB10 | |
| gpg: requesting key 7F0CEB10 from hkp server keyserver.ubuntu.com | |
| gpg: key 7F0CEB10: "Richard Kreuter <richard@10gen.com>" not changed | |
| gpg: Total number processed: 1 | |
| gpg: unchanged: 1 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-key adv --keyserver keyserver.ubuntu.com --recv E084DAB9" | |
| Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --homedir /tmp/tmp.06aGS0IfeH --no-auto-check-trustdb --trust-model always --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --keyserver keyserver.ubuntu.com --recv E084DAB9 | |
| gpg: requesting key E084DAB9 from hkp server keyserver.ubuntu.com | |
| gpg: key E084DAB9: "Michael Rutter <marutter@gmail.com>" not changed | |
| gpg: Total number processed: 1 | |
| gpg: unchanged: 1 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-key adv --keyserver subkeys.pgp.net --recv D018A4CE" | |
| Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --homedir /tmp/tmp.oPYpEOjCqH --no-auto-check-trustdb --trust-model always --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --keyserver subkeys.pgp.net --recv D018A4CE | |
| gpg: requesting key D018A4CE from hkp server subkeys.pgp.net | |
| gpg: key D018A4CE: public key "Launchpad PPA for FreeNX Team" imported | |
| gpg: Total number processed: 1 | |
| gpg: imported: 1 (RSA: 1) | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-key adv --keyserver keyserver.ubuntu.com --recv D67FC6EAE2A11821" | |
| Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --homedir /tmp/tmp.Rl1iuNoBG9 --no-auto-check-trustdb --trust-model always --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --keyserver keyserver.ubuntu.com --recv D67FC6EAE2A11821 | |
| gpg: requesting key E2A11821 from hkp server keyserver.ubuntu.com | |
| gpg: key E2A11821: "Vincent Goulet <vincent.goulet@act.ulaval.ca>" not changed | |
| gpg: Total number processed: 1 | |
| gpg: unchanged: 1 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-get update" | |
| Hit http://download.virtualbox.org trusty InRelease | |
| Ign http://cran.fhcrc.org trusty/ InRelease | |
| Ign http://archive.cloudera.com maverick-cdh3 InRelease | |
| Hit http://cran.fhcrc.org trusty/ Release.gpg | |
| Hit http://download.virtualbox.org trusty/contrib amd64 Packages | |
| Hit http://cran.fhcrc.org trusty/ Release | |
| Ign http://downloads-distro.mongodb.org dist InRelease | |
| Ign http://us.archive.ubuntu.com trusty InRelease | |
| Get:1 http://research.cs.wisc.edu squeeze InRelease [1,469 B] | |
| Ign http://research.cs.wisc.edu squeeze InRelease | |
| Hit http://cran.fhcrc.org trusty/ Packages | |
| Ign http://archive.ubuntu.com trusty InRelease | |
| Ign http://security.ubuntu.com trusty-security InRelease | |
| Ign http://us.archive.ubuntu.com trusty-updates InRelease | |
| Ign http://ppa.launchpad.net precise InRelease | |
| Hit http://us.archive.ubuntu.com trusty Release.gpg | |
| Hit http://downloads-distro.mongodb.org dist Release.gpg | |
| Ign http://archive.ubuntu.com trusty-updates InRelease | |
| Get:2 http://security.ubuntu.com trusty-security Release.gpg [933 B] | |
| Ign http://research.cs.wisc.edu squeeze/contrib amd64 Packages/DiffIndex | |
| Get:3 http://us.archive.ubuntu.com trusty-updates Release.gpg [933 B] | |
| Ign http://ppa.launchpad.net precise InRelease | |
| Ign http://nebc.nerc.ac.uk unstable InRelease | |
| Ign http://download.virtualbox.org trusty/contrib Translation-en_US | |
| Ign http://download.virtualbox.org trusty/contrib Translation-en | |
| Hit http://us.archive.ubuntu.com trusty Release | |
| Hit http://archive.ubuntu.com trusty Release.gpg | |
| Get:4 http://security.ubuntu.com trusty-security Release [59.7 kB] | |
| Hit http://downloads-distro.mongodb.org dist Release | |
| Get:5 http://ppa.launchpad.net precise Release.gpg [316 B] | |
| Ign http://cran.fhcrc.org trusty/ Translation-en_US | |
| Get:6 http://archive.ubuntu.com trusty-updates Release.gpg [933 B] | |
| Hit http://nebc.nerc.ac.uk unstable Release.gpg | |
| Ign http://cran.fhcrc.org trusty/ Translation-en | |
| Hit http://downloads-distro.mongodb.org dist/10gen amd64 Packages | |
| Hit http://ppa.launchpad.net precise Release.gpg | |
| Hit http://archive.cloudera.com maverick-cdh3 Release.gpg | |
| Hit http://archive.ubuntu.com trusty Release | |
| Hit http://ppa.launchpad.net precise Release | |
| Hit http://nebc.nerc.ac.uk unstable Release | |
| Get:7 http://archive.ubuntu.com trusty-updates Release [59.7 kB] | |
| Get:8 http://security.ubuntu.com trusty-security/main Sources [46.3 kB] | |
| Get:9 http://us.archive.ubuntu.com trusty-updates Release [59.7 kB] | |
| Hit http://archive.cloudera.com maverick-cdh3 Release | |
| Hit http://ppa.launchpad.net precise Release | |
| Hit http://archive.cloudera.com maverick-cdh3/contrib amd64 Packages | |
| Hit http://nebc.nerc.ac.uk unstable/bio-linux amd64 Packages | |
| Hit http://ppa.launchpad.net precise/main amd64 Packages | |
| Get:10 http://security.ubuntu.com trusty-security/universe Sources [10.8 kB] | |
| Hit http://us.archive.ubuntu.com trusty/universe amd64 Packages | |
| Hit http://archive.ubuntu.com trusty/main Sources | |
| Get:11 http://security.ubuntu.com trusty-security/main amd64 Packages [146 kB] | |
| Hit http://us.archive.ubuntu.com trusty/multiverse amd64 Packages | |
| Hit http://archive.ubuntu.com trusty/universe Sources | |
| Hit http://ppa.launchpad.net precise/main amd64 Packages | |
| Hit http://us.archive.ubuntu.com trusty/multiverse Translation-en | |
| Hit http://archive.ubuntu.com trusty/main amd64 Packages | |
| Hit http://archive.ubuntu.com trusty/universe amd64 Packages | |
| Get:12 http://security.ubuntu.com trusty-security/universe amd64 Packages [49.1 kB] | |
| Hit http://us.archive.ubuntu.com trusty/universe Translation-en | |
| Get:13 http://us.archive.ubuntu.com trusty-updates/universe amd64 Packages [209 kB] | |
| Hit http://security.ubuntu.com trusty-security/main Translation-en | |
| Hit http://archive.ubuntu.com trusty/main Translation-en | |
| Ign http://archive.cloudera.com maverick-cdh3/contrib Translation-en_US | |
| Hit http://security.ubuntu.com trusty-security/universe Translation-en | |
| Ign http://archive.cloudera.com maverick-cdh3/contrib Translation-en | |
| Hit http://archive.ubuntu.com trusty/universe Translation-en | |
| Ign http://downloads-distro.mongodb.org dist/10gen Translation-en_US | |
| Get:14 http://archive.ubuntu.com trusty-updates/main Sources [125 kB] | |
| Ign http://downloads-distro.mongodb.org dist/10gen Translation-en | |
| Get:15 http://us.archive.ubuntu.com trusty-updates/multiverse amd64 Packages [9,366 B] | |
| Get:16 http://archive.ubuntu.com trusty-updates/universe Sources [86.2 kB] | |
| Hit http://us.archive.ubuntu.com trusty-updates/multiverse Translation-en | |
| Hit http://research.cs.wisc.edu squeeze/contrib amd64 Packages | |
| Hit http://us.archive.ubuntu.com trusty-updates/universe Translation-en | |
| Ign http://research.cs.wisc.edu squeeze/contrib Translation-en_US | |
| Get:17 http://archive.ubuntu.com trusty-updates/main amd64 Packages [337 kB] | |
| Ign http://nebc.nerc.ac.uk unstable/bio-linux Translation-en_US | |
| Ign http://research.cs.wisc.edu squeeze/contrib Translation-en | |
| Ign http://nebc.nerc.ac.uk unstable/bio-linux Translation-en | |
| Get:18 http://archive.ubuntu.com trusty-updates/universe amd64 Packages [209 kB] | |
| Ign http://us.archive.ubuntu.com trusty/multiverse Translation-en_US | |
| Ign http://us.archive.ubuntu.com trusty/universe Translation-en_US | |
| Hit http://archive.ubuntu.com trusty-updates/main Translation-en | |
| Ign http://ppa.launchpad.net precise/main Translation-en_US | |
| Ign http://ppa.launchpad.net precise/main Translation-en | |
| Hit http://archive.ubuntu.com trusty-updates/universe Translation-en | |
| Ign http://ppa.launchpad.net precise/main Translation-en_US | |
| Ign http://ppa.launchpad.net precise/main Translation-en | |
| Ign http://archive.ubuntu.com trusty/main Translation-en_US | |
| Ign http://archive.ubuntu.com trusty/universe Translation-en_US | |
| Fetched 1,410 kB in 10s (135 kB/s) | |
| Reading package lists... Done | |
| W: GPG error: http://research.cs.wisc.edu squeeze InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 973FC7D2670079F6 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "sudo apt-get install -y --force-yes bio-linux-keyring" | |
| Reading package lists... Done | |
| Building dependency tree | |
| Reading state information... Done | |
| bio-linux-keyring is already the newest version. | |
| 0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded. | |
| INFO: Update the system | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-get update" | |
| Ign http://archive.cloudera.com maverick-cdh3 InRelease | |
| Hit http://download.virtualbox.org trusty InRelease | |
| Ign http://cran.fhcrc.org trusty/ InRelease | |
| Hit http://download.virtualbox.org trusty/contrib amd64 Packages | |
| Hit http://cran.fhcrc.org trusty/ Release.gpg | |
| Hit http://archive.cloudera.com maverick-cdh3 Release.gpg | |
| Ign http://us.archive.ubuntu.com trusty InRelease | |
| Hit http://cran.fhcrc.org trusty/ Release | |
| Ign http://downloads-distro.mongodb.org dist InRelease | |
| Get:1 http://research.cs.wisc.edu squeeze InRelease [1,469 B] | |
| Ign http://research.cs.wisc.edu squeeze InRelease | |
| Hit http://cran.fhcrc.org trusty/ Packages | |
| Ign http://us.archive.ubuntu.com trusty-updates InRelease | |
| Ign http://security.ubuntu.com trusty-security InRelease | |
| Ign http://archive.ubuntu.com trusty InRelease | |
| Ign http://ppa.launchpad.net precise InRelease | |
| Hit http://us.archive.ubuntu.com trusty Release.gpg | |
| Hit http://archive.cloudera.com maverick-cdh3 Release | |
| Hit http://downloads-distro.mongodb.org dist Release.gpg | |
| Get:2 http://us.archive.ubuntu.com trusty-updates Release.gpg [933 B] | |
| Hit http://security.ubuntu.com trusty-security Release.gpg | |
| Ign http://archive.ubuntu.com trusty-updates InRelease | |
| Hit http://archive.cloudera.com maverick-cdh3/contrib amd64 Packages | |
| Ign http://download.virtualbox.org trusty/contrib Translation-en_US | |
| Ign http://ppa.launchpad.net precise InRelease | |
| Ign http://nebc.nerc.ac.uk unstable InRelease | |
| Hit http://us.archive.ubuntu.com trusty Release | |
| Ign http://research.cs.wisc.edu squeeze/contrib amd64 Packages/DiffIndex | |
| Ign http://download.virtualbox.org trusty/contrib Translation-en | |
| Hit http://security.ubuntu.com trusty-security Release | |
| Get:3 http://us.archive.ubuntu.com trusty-updates Release [59.7 kB] | |
| Hit http://archive.ubuntu.com trusty Release.gpg | |
| Hit http://downloads-distro.mongodb.org dist Release | |
| Ign http://archive.cloudera.com maverick-cdh3/contrib Translation-en_US | |
| Ign http://archive.cloudera.com maverick-cdh3/contrib Translation-en | |
| Hit http://ppa.launchpad.net precise Release.gpg | |
| Ign http://cran.fhcrc.org trusty/ Translation-en_US | |
| Hit http://security.ubuntu.com trusty-security/main Sources | |
| Hit http://archive.ubuntu.com trusty-updates Release.gpg | |
| Hit http://nebc.nerc.ac.uk unstable Release.gpg | |
| Ign http://cran.fhcrc.org trusty/ Translation-en | |
| Hit http://downloads-distro.mongodb.org dist/10gen amd64 Packages | |
| Hit http://ppa.launchpad.net precise Release.gpg | |
| Hit http://security.ubuntu.com trusty-security/universe Sources | |
| Hit http://archive.ubuntu.com trusty Release | |
| Hit http://us.archive.ubuntu.com trusty/universe amd64 Packages | |
| Hit http://ppa.launchpad.net precise Release | |
| Hit http://nebc.nerc.ac.uk unstable Release | |
| Hit http://us.archive.ubuntu.com trusty/multiverse amd64 Packages | |
| Hit http://security.ubuntu.com trusty-security/main amd64 Packages | |
| Hit http://archive.ubuntu.com trusty-updates Release | |
| Hit http://ppa.launchpad.net precise Release | |
| Hit http://security.ubuntu.com trusty-security/universe amd64 Packages | |
| Hit http://us.archive.ubuntu.com trusty/multiverse Translation-en | |
| Hit http://archive.ubuntu.com trusty/main Sources | |
| Hit http://nebc.nerc.ac.uk unstable/bio-linux amd64 Packages | |
| Hit http://security.ubuntu.com trusty-security/main Translation-en | |
| Hit http://archive.ubuntu.com trusty/universe Sources | |
| Hit http://ppa.launchpad.net precise/main amd64 Packages | |
| Hit http://us.archive.ubuntu.com trusty/universe Translation-en | |
| Get:4 http://us.archive.ubuntu.com trusty-updates/universe amd64 Packages [209 kB] | |
| Hit http://security.ubuntu.com trusty-security/universe Translation-en | |
| Hit http://archive.ubuntu.com trusty/main amd64 Packages | |
| Hit http://archive.ubuntu.com trusty/universe amd64 Packages | |
| Hit http://ppa.launchpad.net precise/main amd64 Packages | |
| Hit http://archive.ubuntu.com trusty/main Translation-en | |
| Get:5 http://us.archive.ubuntu.com trusty-updates/multiverse amd64 Packages [9,366 B] | |
| Hit http://us.archive.ubuntu.com trusty-updates/multiverse Translation-en | |
| Hit http://us.archive.ubuntu.com trusty-updates/universe Translation-en | |
| Hit http://archive.ubuntu.com trusty/universe Translation-en | |
| Hit http://archive.ubuntu.com trusty-updates/main Sources | |
| Hit http://archive.ubuntu.com trusty-updates/universe Sources | |
| Ign http://downloads-distro.mongodb.org dist/10gen Translation-en_US | |
| Hit http://archive.ubuntu.com trusty-updates/main amd64 Packages | |
| Hit http://archive.ubuntu.com trusty-updates/universe amd64 Packages | |
| Ign http://downloads-distro.mongodb.org dist/10gen Translation-en | |
| Ign http://us.archive.ubuntu.com trusty/multiverse Translation-en_US | |
| Hit http://archive.ubuntu.com trusty-updates/main Translation-en | |
| Ign http://us.archive.ubuntu.com trusty/universe Translation-en_US | |
| Hit http://research.cs.wisc.edu squeeze/contrib amd64 Packages | |
| Hit http://archive.ubuntu.com trusty-updates/universe Translation-en | |
| Ign http://research.cs.wisc.edu squeeze/contrib Translation-en_US | |
| Ign http://nebc.nerc.ac.uk unstable/bio-linux Translation-en_US | |
| Ign http://nebc.nerc.ac.uk unstable/bio-linux Translation-en | |
| Ign http://research.cs.wisc.edu squeeze/contrib Translation-en | |
| Ign http://archive.ubuntu.com trusty/main Translation-en_US | |
| Ign http://archive.ubuntu.com trusty/universe Translation-en_US | |
| Ign http://ppa.launchpad.net precise/main Translation-en_US | |
| Ign http://ppa.launchpad.net precise/main Translation-en | |
| Ign http://ppa.launchpad.net precise/main Translation-en_US | |
| Ign http://ppa.launchpad.net precise/main Translation-en | |
| Fetched 280 kB in 9s (29.2 kB/s) | |
| Reading package lists... Done | |
| W: GPG error: http://research.cs.wisc.edu squeeze InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 973FC7D2670079F6 | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/packages.yaml | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-get -y --force-yes upgrade" | |
| Reading package lists... Done | |
| Building dependency tree | |
| Reading state information... Done | |
| Calculating upgrade... Done | |
| The following packages have been kept back: | |
| juju juju-core linux-headers-generic linux-headers-virtual | |
| linux-image-virtual linux-virtual | |
| The following packages will be upgraded: | |
| file libmagic1 | |
| 2 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. | |
| Need to get 203 kB of archives. | |
| After this operation, 0 B of additional disk space will be used. | |
| Get:1 http://security.ubuntu.com/ubuntu/ trusty-security/main file amd64 1:5.14-2ubuntu3.2 [18.8 kB] | |
| Get:2 http://security.ubuntu.com/ubuntu/ trusty-security/main libmagic1 amd64 1:5.14-2ubuntu3.2 [184 kB] | |
| Fetched 203 kB in 5s (35.2 kB/s) | |
| (Reading database ... 82046 files and directories currently installed.) | |
| Preparing to unpack .../file_1%3a5.14-2ubuntu3.2_amd64.deb ... | |
| Unpacking file (1:5.14-2ubuntu3.2) over (1:5.14-2ubuntu3.1) ... | |
| Preparing to unpack .../libmagic1_1%3a5.14-2ubuntu3.2_amd64.deb ... | |
| Unpacking libmagic1:amd64 (1:5.14-2ubuntu3.2) over (1:5.14-2ubuntu3.1) ... | |
| Processing triggers for man-db (2.6.7.1-1) ... | |
| Setting up libmagic1:amd64 (1:5.14-2ubuntu3.2) ... | |
| Setting up file (1:5.14-2ubuntu3.2) ... | |
| Processing triggers for libc-bin (2.19-0ubuntu6.3) ... | |
| INFO: Reading /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/packages.yaml | |
| DBG [shared.py]: Packages to install: fastx-toolkit,last-align,maq,plink,tabix,openjdk-7-jdk,openjdk-7-jre,gsl-bin,libatlas-base-dev,libblas-dev,libbz2-dev,libc6-dev,libcurl4-openssl-dev,libeigen3-dev,libgsl0-dev,libgsl0ldbl,liblapack-dev,liblzma-dev,libncurses5-dev,libnetcdf-dev,libpcre3-dev,libpng12-dev,libreadline-dev,libssl-dev,libxml2,libxml2-dev,libxslt1-dev,libxslt1.1,libzip-dev,mime-support,uuid,uuid-dev,xz-utils,zlib1g-dev,zlib1g-dev,clang,cmake,g++,gcc,gfortran,libtool,make,patch,pkg-config,vim,htop,sudo,bzr,cvs,git-core,mercurial,subversion,curl,wget,axel,gawk,less,openssh-server,rsync,screen,unzip,cpanminus,libextutils-autoinstall-perl,libperl-dev,parrot,parrot-devel,perl,perl-modules,perl-tk,python,python-dev,python-distutils-extra,python-pip,python-rpy,python-setuptools,python-virtualenv,python3,python3-dev,r-base,r-base-core,r-base-dev,r-base-html,ruby1.9.1,ruby1.9.1-dev | |
| INFO: Installing 84 packages | |
| INFO: Package install progress: 0/84 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-get -y --force-yes install fastx-toolkit last-align maq plink tabix openjdk-7-jdk openjdk-7-jre gsl-bin libatlas-base-dev libblas-dev libbz2-dev libc6-dev libcurl4-openssl-dev libeigen3-dev libgsl0-dev libgsl0ldbl liblapack-dev liblzma-dev libncurses5-dev libnetcdf-dev libpcre3-dev libpng12-dev libreadline-dev libssl-dev libxml2 libxml2-dev libxslt1-dev libxslt1.1 libzip-dev mime-support" | |
| Reading package lists... Done | |
| Building dependency tree | |
| Reading state information... Done | |
| libblas-dev is already the newest version. | |
| libbz2-dev is already the newest version. | |
| libgsl0-dev is already the newest version. | |
| libgsl0ldbl is already the newest version. | |
| liblapack-dev is already the newest version. | |
| liblzma-dev is already the newest version. | |
| libncurses5-dev is already the newest version. | |
| libpcre3-dev is already the newest version. | |
| libpng12-dev is already the newest version. | |
| libreadline-dev is already the newest version. | |
| libxslt1-dev is already the newest version. | |
| libxslt1.1 is already the newest version. | |
| libzip-dev is already the newest version. | |
| mime-support is already the newest version. | |
| fastx-toolkit is already the newest version. | |
| gsl-bin is already the newest version. | |
| last-align is already the newest version. | |
| libatlas-base-dev is already the newest version. | |
| libeigen3-dev is already the newest version. | |
| libnetcdf-dev is already the newest version. | |
| maq is already the newest version. | |
| plink is already the newest version. | |
| tabix is already the newest version. | |
| libc6-dev is already the newest version. | |
| libcurl4-openssl-dev is already the newest version. | |
| libssl-dev is already the newest version. | |
| libxml2 is already the newest version. | |
| libxml2-dev is already the newest version. | |
| openjdk-7-jdk is already the newest version. | |
| openjdk-7-jre is already the newest version. | |
| 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. | |
| INFO: Package install progress: 30/84 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-get -y --force-yes install uuid uuid-dev xz-utils zlib1g-dev zlib1g-dev clang cmake g++ gcc gfortran libtool make patch pkg-config vim htop sudo bzr cvs git-core mercurial subversion curl wget axel gawk less openssh-server rsync screen" | |
| Reading package lists... Done | |
| Building dependency tree | |
| Reading state information... Done | |
| cmake is already the newest version. | |
| cvs is already the newest version. | |
| g++ is already the newest version. | |
| gawk is already the newest version. | |
| gcc is already the newest version. | |
| gfortran is already the newest version. | |
| git-core is already the newest version. | |
| less is already the newest version. | |
| libtool is already the newest version. | |
| make is already the newest version. | |
| pkg-config is already the newest version. | |
| screen is already the newest version. | |
| sudo is already the newest version. | |
| vim is already the newest version. | |
| wget is already the newest version. | |
| xz-utils is already the newest version. | |
| zlib1g-dev is already the newest version. | |
| axel is already the newest version. | |
| clang is already the newest version. | |
| htop is already the newest version. | |
| mercurial is already the newest version. | |
| uuid is already the newest version. | |
| bzr is already the newest version. | |
| curl is already the newest version. | |
| openssh-server is already the newest version. | |
| patch is already the newest version. | |
| rsync is already the newest version. | |
| subversion is already the newest version. | |
| uuid-dev is already the newest version. | |
| 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. | |
| INFO: Package install progress: 60/84 | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-get -y --force-yes install unzip cpanminus libextutils-autoinstall-perl libperl-dev parrot parrot-devel perl perl-modules perl-tk python python-dev python-distutils-extra python-pip python-rpy python-setuptools python-virtualenv python3 python3-dev r-base r-base-core r-base-dev r-base-html ruby1.9.1 ruby1.9.1-dev" | |
| Reading package lists... Done | |
| Building dependency tree | |
| Reading state information... Done | |
| libperl-dev is already the newest version. | |
| perl is already the newest version. | |
| perl-modules is already the newest version. | |
| python is already the newest version. | |
| python-dev is already the newest version. | |
| python-distutils-extra is already the newest version. | |
| python-setuptools is already the newest version. | |
| python3 is already the newest version. | |
| python3-dev is already the newest version. | |
| ruby1.9.1 is already the newest version. | |
| ruby1.9.1-dev is already the newest version. | |
| unzip is already the newest version. | |
| cpanminus is already the newest version. | |
| libextutils-autoinstall-perl is already the newest version. | |
| parrot is already the newest version. | |
| parrot-devel is already the newest version. | |
| perl-tk is already the newest version. | |
| python-pip is already the newest version. | |
| python-virtualenv is already the newest version. | |
| r-base-dev is already the newest version. | |
| r-base-core is already the newest version. | |
| r-base-html is already the newest version. | |
| r-base is already the newest version. | |
| python-rpy is already the newest version. | |
| 0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded. | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "apt-get clean" | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/custom.yaml | |
| INFO: Reading /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/custom.yaml | |
| DBG [shared.py]: Packages to install: ucsc_tools,cufflinks,picard,featurecounts,rnaseqc,bcbio_variation,grabix,mutect,varscan | |
| INFO: Custom install for 'ucsc_tools' start time: 2014-10-03 01:20:03.187830 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_ucsc_tools | |
| INFO: Custom install for 'ucsc_tools' end time: 2014-10-03 01:20:03.194333; duration: 0:00:00.006503 | |
| INFO: Custom install for 'cufflinks' start time: 2014-10-03 01:20:03.194805 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_cufflinks | |
| INFO: Custom install for 'cufflinks' end time: 2014-10-03 01:20:03.200635; duration: 0:00:00.005830 | |
| INFO: Custom install for 'picard' start time: 2014-10-03 01:20:03.201132 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_picard | |
| [localhost] local: ls /usr/local/share/java/picard-1.96 | |
| INFO: Custom install for 'picard' end time: 2014-10-03 01:20:03.213684; duration: 0:00:00.012552 | |
| INFO: Custom install for 'featurecounts' start time: 2014-10-03 01:20:03.214041 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_featurecounts | |
| INFO: Custom install for 'featurecounts' end time: 2014-10-03 01:20:03.222761; duration: 0:00:00.008720 | |
| INFO: Custom install for 'rnaseqc' start time: 2014-10-03 01:20:03.223492 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_rnaseqc | |
| [localhost] local: ls /usr/local/share/java/RNA-SeQC-1.1.7 | |
| INFO: Custom install for 'rnaseqc' end time: 2014-10-03 01:20:03.236141; duration: 0:00:00.012649 | |
| INFO: Custom install for 'bcbio_variation' start time: 2014-10-03 01:20:03.237059 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_bcbio_variation | |
| [localhost] local: ls /usr/local/share/java/bcbio_variation-0.1.7 | |
| INFO: Custom install for 'bcbio_variation' end time: 2014-10-03 01:20:03.251731; duration: 0:00:00.014672 | |
| INFO: Custom install for 'grabix' start time: 2014-10-03 01:20:03.252166 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_grabix | |
| INFO: Custom install for 'grabix' end time: 2014-10-03 01:20:03.262116; duration: 0:00:00.009950 | |
| INFO: Custom install for 'mutect' start time: 2014-10-03 01:20:03.262869 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_mutect | |
| [localhost] local: ls /usr/local/share/java/mutect-1.1.5 | |
| INFO: Custom install for 'mutect' end time: 2014-10-03 01:20:03.275017; duration: 0:00:00.012148 | |
| INFO: Custom install for 'varscan' start time: 2014-10-03 01:20:03.275581 | |
| DBG [fabfile.py]: Importing module cloudbio.custom.bio_nextgen | |
| DBG [fabfile.py]: Looking for custom install function cloudbio.custom.bio_nextgen.install_varscan | |
| [localhost] local: ls /usr/local/share/java/varscan-2.3.7 | |
| INFO: Custom install for 'varscan' end time: 2014-10-03 01:20:03.289709; duration: 0:00:00.014128 | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/chef_recipes.yaml | |
| INFO: Reading /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/chef_recipes.yaml | |
| DBG [shared.py]: Packages to install: | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/puppet_classes.yaml | |
| INFO: Reading /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../config/puppet_classes.yaml | |
| DBG [shared.py]: Packages to install: | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml | |
| INFO: Meta-package information from /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/main.yaml | |
| - Packages: minimal,libraries,perl,python,java,r,ruby,bio_nextgen | |
| - Libraries: r-libs | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/packages-homebrew.yaml | |
| INFO: Reading /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/packages-homebrew.yaml | |
| DBG [shared.py]: Packages to install: bcftools,htslib,samtools,bamtools,bedtools,biobambam,cramtools,fastqc,kraken,libmaus,oncofuse,qualimap,sambamba,samblaster,seqtk,sickle,speedseq,staden_io_lib,bcbio-variation-recall,delly;--with-binary,freebayes,gatk-framework,glia,hall-lab-sv-tools,lumpy-sv,pindel,platypus-variant,qsignature,rtg-tools,scalpel,snpeff,vardict,vcflib,vep,vt,bowtie2,bwa,novoalign,rna-star,snap-aligner,tophat-binary,cmake,cpanminus | |
| [localhost] local: /usr/local/bin/brew tap | |
| [localhost] local: /usr/local/bin/brew update | |
| Already up-to-date. | |
| [localhost] local: /usr/local/bin/brew tap --repair | |
| Pruned 0 dead formulae | |
| Tapped 390 formulae | |
| [localhost] local: /usr/local/bin/brew outdated | |
| [localhost] local: /usr/local/bin/brew info cmake | |
| [localhost] local: /usr/local/bin/brew info expat | |
| [localhost] local: /usr/local/bin/brew list samtools | grep -c bctools | |
| Warning: local() encountered an error (return code 1) while executing '/usr/local/bin/brew list samtools | grep -c bctools' | |
| [localhost] local: /usr/local/bin/brew list samtools | grep -c vcfutils.pl | |
| Warning: local() encountered an error (return code 1) while executing '/usr/local/bin/brew list samtools | grep -c vcfutils.pl' | |
| [localhost] local: /usr/local/bin/brew info samtools | |
| [localhost] local: /usr/local/bin/brew info cpanminus | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Statistics::Descriptive' | |
| Statistics::Descriptive is up to date. (3.0607) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Archive::Extract' | |
| Archive::Extract is up to date. (0.72) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Archive::Zip' | |
| Archive::Zip is up to date. (1.38) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Archive::Tar' | |
| Archive::Tar is up to date. (2.02) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'DBI' | |
| DBI is up to date. (1.631) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'LWP::Simple' | |
| LWP::Simple is up to date. (6.00) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'LWP::Protocol::https' | |
| LWP::Protocol::https is up to date. (6.06) | |
| [localhost] local: /usr/local/bin/cpanm -i --notest --local-lib=/usr/local 'Time::HiRes' | |
| Time::HiRes is up to date. (1.9726) | |
| [localhost] local: /usr/local/bin/brew info bcftools | |
| [localhost] local: /usr/local/bin/brew info htslib | |
| [localhost] local: /usr/local/bin/brew info samtools | |
| [localhost] local: /usr/local/bin/brew info bamtools | |
| [localhost] local: /usr/local/bin/brew info bedtools | |
| [localhost] local: /usr/local/bin/brew info biobambam | |
| [localhost] local: /usr/local/bin/brew info cramtools | |
| [localhost] local: /usr/local/bin/brew info fastqc | |
| [localhost] local: /usr/local/bin/brew info kraken | |
| [localhost] local: /usr/local/bin/brew info libmaus | |
| [localhost] local: /usr/local/bin/brew info oncofuse | |
| [localhost] local: /usr/local/bin/brew info qualimap | |
| [localhost] local: /usr/local/bin/brew info sambamba | |
| [localhost] local: /usr/local/bin/brew info samblaster | |
| [localhost] local: /usr/local/bin/brew info seqtk | |
| [localhost] local: /usr/local/bin/brew info sickle | |
| [localhost] local: /usr/local/bin/brew info speedseq | |
| [localhost] local: /usr/local/bin/brew info staden_io_lib | |
| [localhost] local: /usr/local/bin/brew info bcbio-variation-recall | |
| [localhost] local: /usr/local/bin/brew info delly | |
| [localhost] local: /usr/local/bin/brew info freebayes | |
| [localhost] local: /usr/local/bin/brew info gatk-framework | |
| [localhost] local: /usr/local/bin/brew info glia | |
| [localhost] local: /usr/local/bin/brew info hall-lab-sv-tools | |
| [localhost] local: /usr/local/bin/brew info lumpy-sv | |
| [localhost] local: /usr/local/bin/brew info pindel | |
| [localhost] local: /usr/local/bin/brew info platypus-variant | |
| [localhost] local: /usr/local/bin/brew info qsignature | |
| [localhost] local: /usr/local/bin/brew info rtg-tools | |
| [localhost] local: /usr/local/bin/brew info scalpel | |
| [localhost] local: /usr/local/bin/brew info snpeff | |
| [localhost] local: /usr/local/bin/brew info vardict | |
| [localhost] local: /usr/local/bin/brew info vcflib | |
| [localhost] local: /usr/local/bin/brew info vep | |
| [localhost] local: /usr/local/bin/brew info vt | |
| [localhost] local: /usr/local/bin/brew info bowtie2 | |
| [localhost] local: /usr/local/bin/brew info bwa | |
| [localhost] local: /usr/local/bin/brew info novoalign | |
| [localhost] local: /usr/local/bin/brew info rna-star | |
| [localhost] local: /usr/local/bin/brew info snap-aligner | |
| [localhost] local: /usr/local/bin/brew info tophat-binary | |
| [localhost] local: /usr/local/bin/brew info cmake | |
| [localhost] local: /usr/local/bin/brew info cpanminus | |
| DBG [config.py]: Using config file /home/vagrant/tmp/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline_minimal/r-libs.yaml | |
| [localhost] local: echo $HOME | |
| [localhost] local: rm -f /home/vagrant/tmp/cloudbiolinux/install_packages.R | |
| [localhost] local: touch /home/vagrant/tmp/cloudbiolinux/install_packages.R | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "mkdir -p /usr/local/lib/R/site-library" | |
| [localhost] local: echo ' | |
| .libPaths(c("/usr/local/lib/R/site-library")) | |
| library(methods) | |
| cran.repos <- getOption("repos") | |
| cran.repos["CRAN" ] <- "http://cran.fhcrc.org/" | |
| options(repos=cran.repos) | |
| source("http://bioconductor.org/biocLite.R") | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: echo ' | |
| repo.installer <- function(repos, install.fn) { | |
| update.packages(lib.loc="/usr/local/lib/R/site-library", repos=repos, ask=FALSE) | |
| maybe.install <- function(pname) { | |
| if (!(pname %in% installed.packages())) | |
| install.fn(pname) | |
| } | |
| } | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: echo ' | |
| std.pkgs <- c("cghFLasso", "ggplot2", "gsalib", "matrixStats", "snow") | |
| std.installer = repo.installer(cran.repos, install.packages) | |
| lapply(std.pkgs, std.installer) | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: echo ' | |
| bioc.pkgs <- c("cn.mops", "rtracklayer", "DEXSeq", "DNAcopy") | |
| bioc.installer = repo.installer(biocinstallRepos(), biocLite) | |
| lapply(bioc.pkgs, bioc.installer) | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: echo ' | |
| std2.pkgs <- c("PSCBS") | |
| lapply(std2.pkgs, std.installer) | |
| ' >> "$(echo /home/vagrant/tmp/cloudbiolinux/install_packages.R)" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "Rscript /home/vagrant/tmp/cloudbiolinux/install_packages.R" | |
| Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help | |
| [[1]] | |
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| BioC_mirror: http://bioconductor.org | |
| Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version | |
| 3.1.1. | |
| Installing package(s) 'DEXSeq' | |
| also installing the dependency ‘DESeq2’ | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/DESeq2_1.4.5.tar.gz' | |
| Content type 'application/x-gzip' length 1190439 bytes (1.1 Mb) | |
| opened URL | |
| ================================================== | |
| downloaded 1.1 Mb | |
| trying URL 'http://bioconductor.org/packages/2.14/bioc/src/contrib/DEXSeq_1.10.8.tar.gz' | |
| Content type 'application/x-gzip' length 376168 bytes (367 Kb) | |
| opened URL | |
| ================================================== | |
| downloaded 367 Kb | |
| * installing *source* package ‘DESeq2’ ... | |
| ** libs | |
| g++ -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c DESeq2.cpp -o DESeq2.o | |
| g++ -shared -Wl,-Bsymbolic-functions -Wl,-z,relro -o DESeq2.so DESeq2.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR | |
| installing to /usr/local/lib/R/site-library/DESeq2/libs | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| * DONE (DESeq2) | |
| * installing *source* package ‘DEXSeq’ ... | |
| ** R | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** installing vignettes | |
| ** testing if installed package can be loaded | |
| Warning: system call failed: Cannot allocate memory | |
| * DONE (DEXSeq) | |
| The downloaded source packages are in | |
| ‘/tmp/RtmpSalGqL/downloaded_packages’ | |
| Old packages: 'MASS', 'spatial' | |
| [[1]] | |
| NULL | |
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| [[3]] | |
| [1] "DEXSeq" | |
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| [localhost] local: rm -f /home/vagrant/tmp/cloudbiolinux/install_packages.R | |
| [localhost] local: rm -rf /home/vagrant/tmp/cloudbiolinux | |
| INFO: Cleaning up space from package builds | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "rm -rf .cpanm" | |
| [localhost] local: sudo http_proxy=$http_proxy https_proxy=$https_proxy bash -c "rm -f /var/crash/*" | |
| [localhost] local: rm -f ~/*.dot | |
| [localhost] local: rm -f ~/*.log | |
| Creating manifest of installed packages in /usr/local/share/bcbio-nextgen/manifest | |
| Installing additional tools | |
| Third party tools upgrade complete. | |
| Upgrade completed successfully. | |
| vagrant@vagrant-ubuntu-trusty-64:~/tmp$ cd ~ | |
| vagrant@vagrant-ubuntu-trusty-64:~$ $ git clone https://github.com/chapmanb/bcbio-nextgen.git | |
| $: command not found | |
| vagrant@vagrant-ubuntu-trusty-64:~$ git clone https://github.com/chapmanb/bcbio-nextgen.git | |
| Cloning into 'bcbio-nextgen'... | |
| remote: Counting objects: 18944, done. | |
| remote: Compressing objects: 100% (24/24), done. | |
| remote: Total 18944 (delta 8), reused 1 (delta 0) | |
| Receiving objects: 100% (18944/18944), 16.82 MiB | 3.55 MiB/s, done. | |
| Resolving deltas: 100% (12505/12505), done. | |
| Checking connectivity... done. | |
| vagrant@vagrant-ubuntu-trusty-64:~$ cd bcbio-nextgen/tests | |
| vagrant@vagrant-ubuntu-trusty-64:~/bcbio-nextgen/tests$ ./run_tests.sh | |
| Check for the presence of runs in an Illumina SampleSheet. ... ok | |
| Convert CSV Illumina SampleSheet to YAML. ... ok | |
| Test variant calling with GATK pipeline. ... /home/vagrant/bcbio-nextgen/tests/data/automated/../110106_FC70BUKAAXX | |
| --2014-10-03 01:40:19-- http://chapmanb.s3.amazonaws.com/110106_FC70BUKAAXX.tar.gz | |
| Resolving chapmanb.s3.amazonaws.com (chapmanb.s3.amazonaws.com)... 54.231.0.57 | |
| Connecting to chapmanb.s3.amazonaws.com (chapmanb.s3.amazonaws.com)|54.231.0.57|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 2778555 (2.6M) [application/x-tar] | |
| Saving to: ‘110106_FC70BUKAAXX.tar.gz’ | |
| 100%[========================================================================================================================>] 2,778,555 2.37MB/s in 1.1s | |
| 2014-10-03 01:40:25 (2.37 MB/s) - ‘110106_FC70BUKAAXX.tar.gz’ saved [2778555/2778555] | |
| 110106_FC70BUKAAXX/ | |
| 110106_FC70BUKAAXX/1_110106_FC70BUKAAXX_1_fastq.txt | |
| 110106_FC70BUKAAXX/1_110106_FC70BUKAAXX_2_fastq.txt | |
| 110106_FC70BUKAAXX/2_110106_FC70BUKAAXX_1_fastq.txt | |
| 110106_FC70BUKAAXX/2_110106_FC70BUKAAXX_2_fastq.txt | |
| 110106_FC70BUKAAXX/3_110106_FC70BUKAAXX_fastq.txt | |
| /home/vagrant/bcbio-nextgen/tests/data/automated/../genomes | |
| --2014-10-03 01:40:25-- http://chapmanb.s3.amazonaws.com/genomes_automated_test.tar.gz | |
| Resolving chapmanb.s3.amazonaws.com (chapmanb.s3.amazonaws.com)... 54.231.0.57 | |
| Connecting to chapmanb.s3.amazonaws.com (chapmanb.s3.amazonaws.com)|54.231.0.57|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 22520455 (21M) [binary/octet-stream] | |
| Saving to: ‘genomes_automated_test.tar.gz’ | |
| 100%[========================================================================================================================>] 22,520,455 4.80MB/s in 5.7s | |
| 2014-10-03 01:40:36 (3.80 MB/s) - ‘genomes_automated_test.tar.gz’ saved [22520455/22520455] | |
| genomes/ | |
| genomes/mm9/ | |
| genomes/mm9/star/ | |
| genomes/mm9/star/SA | |
| genomes/mm9/star/chrLength.txt | |
| genomes/mm9/star/SAindex | |
| genomes/mm9/star/chrName.txt | |
| genomes/mm9/star/genomeParameters.txt | |
| genomes/mm9/star/chrStart.txt | |
| genomes/mm9/star/chrNameLength.txt | |
| genomes/mm9/star/Genome | |
| genomes/mm9/star/old/ | |
| genomes/mm9/Log.out | |
| genomes/mm9/rnaseq/ | |
| genomes/mm9/rnaseq/ref-transcripts-mask.gtf | |
| genomes/mm9/rnaseq/ref-transcripts.gtf | |
| genomes/mm9/rnaseq/ref-transcripts.gtf.db | |
| genomes/mm9/rnaseq/ref-transcripts.refFlat | |
| genomes/mm9/seq/ | |
| genomes/mm9/seq/mm9.dict | |
| genomes/mm9/seq/mm9-resources.yaml | |
| genomes/mm9/seq/mm9.fa | |
| genomes/mm9/seq/mm9.fa.fai | |
| genomes/mm9/Log.progress.out | |
| genomes/mm9/bowtie/ | |
| genomes/mm9/bowtie/mm9.1.ebwt | |
| genomes/mm9/bowtie/mm9.2.ebwt | |
| genomes/mm9/bowtie/mm9.3.ebwt | |
| genomes/mm9/bowtie/mm9.rev.2.ebwt | |
| genomes/mm9/bowtie/mm9.4.ebwt | |
| genomes/mm9/bowtie/mm9.rev.1.ebwt | |
| genomes/mm9/bowtie2/ | |
| genomes/mm9/bowtie2/mm9.rev.2.bt2 | |
| genomes/mm9/bowtie2/mm9.1.bt2 | |
| genomes/mm9/bowtie2/mm9.rev.1.bt2 | |
| genomes/mm9/bowtie2/mm9.3.bt2 | |
| genomes/mm9/bowtie2/mm9.2.bt2 | |
| genomes/mm9/bowtie2/mm9.4.bt2 | |
| genomes/mm9/bwa/ | |
| genomes/mm9/bwa/mm9.fa.bwt | |
| genomes/mm9/bwa/mm9.fa.pac | |
| genomes/mm9/bwa/mm9.fa.sa | |
| genomes/mm9/bwa/mm9.fa.amb | |
| genomes/mm9/bwa/mm9.fa.ann | |
| genomes/mm9/_tmp/ | |
| genomes/mm9/Aligned.out.sam | |
| genomes/mm9/snpeff/ | |
| genomes/hg19/ | |
| genomes/hg19/star/ | |
| genomes/hg19/star/sjdbList.out.tab | |
| genomes/hg19/star/Log.out | |
| genomes/hg19/star/SA | |
| genomes/hg19/star/chrLength.txt | |
| genomes/hg19/star/SAindex | |
| genomes/hg19/star/chrName.txt | |
| genomes/hg19/star/genomeParameters.txt | |
| genomes/hg19/star/chrStart.txt | |
| genomes/hg19/star/chrNameLength.txt | |
| genomes/hg19/star/Genome | |
| genomes/hg19/rnaseq/ | |
| genomes/hg19/rnaseq/ref-transcripts.refflat | |
| genomes/hg19/rnaseq/ref-transcripts-mask.gtf | |
| genomes/hg19/rnaseq/ref-transcripts.gtf | |
| genomes/hg19/seq/ | |
| genomes/hg19/seq/hg19.dict | |
| genomes/hg19/seq/hg19-resources.yaml | |
| genomes/hg19/seq/hg19.fa.fai | |
| genomes/hg19/seq/tx/ | |
| genomes/hg19/seq/hg19.fa | |
| genomes/hg19/snap/ | |
| genomes/hg19/snap/GenomeIndexHash | |
| genomes/hg19/snap/GenomeIndex | |
| genomes/hg19/snap/OverflowTable | |
| genomes/hg19/snap/Genome | |
| genomes/hg19/bowtie/ | |
| genomes/hg19/bowtie/hg19.4.ebwt | |
| genomes/hg19/bowtie/hg19.rev.2.ebwt | |
| genomes/hg19/bowtie/hg19.2.ebwt | |
| genomes/hg19/bowtie/hg19.3.ebwt | |
| genomes/hg19/bowtie/hg19.rev.1.ebwt | |
| genomes/hg19/bowtie/hg19.1.ebwt | |
| genomes/hg19/bowtie2/ | |
| genomes/hg19/bowtie2/hg19.1.bt2 | |
| genomes/hg19/bowtie2/hg19.3.bt2 | |
| genomes/hg19/bowtie2/hg19.rev.2.bt2 | |
| genomes/hg19/bowtie2/hg19.2.bt2 | |
| genomes/hg19/bowtie2/hg19.rev.1.bt2 | |
| genomes/hg19/bowtie2/hg19.4.bt2 | |
| genomes/hg19/mosaik/ | |
| genomes/hg19/mosaik/hg19_keys.jmp | |
| genomes/hg19/mosaik/hg19.dat | |
| genomes/hg19/mosaik/hg19_meta.jmp | |
| genomes/hg19/mosaik/hg19_positions.jmp | |
| genomes/hg19/novoalign/ | |
| genomes/hg19/novoalign/hg19 | |
| genomes/hg19/vep/ | |
| genomes/hg19/vep/homo_sapiens/ | |
| genomes/hg19/vep/homo_sapiens/75/ | |
| genomes/hg19/vep/homo_sapiens/75/info.txt | |
| genomes/hg19/vep/homo_sapiens/75/MT/ | |
| genomes/hg19/vep/homo_sapiens/75/MT/1-1000000_reg.gz | |
| genomes/hg19/vep/homo_sapiens/75/MT/all_vars.gz | |
| genomes/hg19/vep/homo_sapiens/75/MT/1-1000000_var.gz | |
| genomes/hg19/vep/homo_sapiens/75/MT/all_vars.gz.tbi | |
| genomes/hg19/vep/homo_sapiens/75/MT/1-1000000.gz | |
| genomes/hg19/vep/homo_sapiens/75/22/ | |
| genomes/hg19/vep/homo_sapiens/75/22/1-1000000_reg.gz | |
| genomes/hg19/vep/homo_sapiens/75/22/all_vars.gz | |
| genomes/hg19/vep/homo_sapiens/75/22/1-1000000_var.gz | |
| genomes/hg19/vep/homo_sapiens/75/22/all_vars.gz.tbi | |
| genomes/hg19/vep/homo_sapiens/75/22/convert_num.py | |
| genomes/hg19/vep/homo_sapiens/75/22/1-1000000.gz | |
| genomes/hg19/ucsc/ | |
| genomes/hg19/ucsc/hg19.2bit | |
| genomes/hg19/variation/ | |
| genomes/hg19/variation/1000G_phase1.snps.high_confidence.vcf.gz | |
| genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz.tbi | |
| genomes/hg19/variation/human_ancestor.fa.fai | |
| genomes/hg19/variation/dbNSFP_v2.5.gz.tbi | |
| genomes/hg19/variation/dbsnp_132.vcf.gz | |
| genomes/hg19/variation/1000G_omni2.5.vcf.gz | |
| genomes/hg19/variation/Mills_Devine_2hit.indels.vcf.gz | |
| genomes/hg19/variation/1000G_phase1.snps.high_confidence.vcf.gz.tbi | |
| genomes/hg19/variation/cosmic-v68-hg19.vcf.gz | |
| genomes/hg19/variation/dbNSFP_v2.5.gz | |
| genomes/hg19/variation/human_ancestor.fa | |
| genomes/hg19/variation/hapmap_3.3.vcf.gz.tbi | |
| genomes/hg19/variation/hapmap_3.3.vcf.gz | |
| genomes/hg19/variation/1000G_omni2.5.vcf.gz.tbi | |
| genomes/hg19/variation/convert_num.py | |
| genomes/hg19/variation/cosmic-v68-hg19.vcf.gz.tbi | |
| genomes/hg19/variation/dbsnp_132.vcf.gz.tbi | |
| genomes/hg19/bwa/ | |
| genomes/hg19/bwa/hg19.fa.bwt | |
| genomes/hg19/bwa/hg19.fa.amb | |
| genomes/hg19/bwa/hg19.fa.sa | |
| genomes/hg19/bwa/hg19.fa.ann | |
| genomes/hg19/bwa/hg19.fa.pac | |
| genomes/hg19/snpeff/ | |
| genomes/hg19/snpeff/hg19/ | |
| genomes/hg19/snpeff/hg19/snpEffectPredictor.bin | |
| genomes/VERSION | |
| /home/vagrant/bcbio-nextgen/tests/data/automated/../110907_ERP000591 | |
| --2014-10-03 01:41:30-- http://chapmanb.s3.amazonaws.com/110907_ERP000591.tar.gz | |
| Resolving chapmanb.s3.amazonaws.com (chapmanb.s3.amazonaws.com)... 54.231.1.233 | |
| Connecting to chapmanb.s3.amazonaws.com (chapmanb.s3.amazonaws.com)|54.231.1.233|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 2371567 (2.3M) [application/x-gzip] | |
| Saving to: ‘110907_ERP000591.tar.gz’ | |
| 100%[========================================================================================================================>] 2,371,567 624KB/s in 4.4s | |
| 2014-10-03 01:41:40 (530 KB/s) - ‘110907_ERP000591.tar.gz’ saved [2371567/2371567] | |
| 110907_ERP000591/ | |
| 110907_ERP000591/1_110907_ERP000591_2_fastq.txt | |
| 110907_ERP000591/1_110907_ERP000591_1_fastq.txt | |
| /home/vagrant/bcbio-nextgen/tests/data/automated/../100326_FC6107FAAXX | |
| --2014-10-03 01:41:40-- http://chapmanb.s3.amazonaws.com/100326_FC6107FAAXX.tar.gz | |
| Resolving chapmanb.s3.amazonaws.com (chapmanb.s3.amazonaws.com)... 54.231.1.233 | |
| Connecting to chapmanb.s3.amazonaws.com (chapmanb.s3.amazonaws.com)|54.231.1.233|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 7748032 (7.4M) [binary/octet-stream] | |
| Saving to: ‘100326_FC6107FAAXX.tar.gz’ | |
| 100%[========================================================================================================================>] 7,748,032 1.30MB/s in 7.1s | |
| 2014-10-03 01:41:52 (1.04 MB/s) - ‘100326_FC6107FAAXX.tar.gz’ saved [7748032/7748032] | |
| 100326_FC6107FAAXX/ | |
| 100326_FC6107FAAXX/7_100326_FC6107FAAXX.cram | |
| 100326_FC6107FAAXX/7_100326_FC6107FAAXX.cram.crai | |
| 100326_FC6107FAAXX/test.bed | |
| 100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam | |
| 100326_FC6107FAAXX/7_100326_FC6107FAAXX_1_fastq.txt | |
| 100326_FC6107FAAXX/7_100326_FC6107FAAXX_2_fastq.txt | |
| 100326_FC6107FAAXX/8_100326_FC6107FAAXX.bam | |
| 100326_FC6107FAAXX/VERSION | |
| 100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam.bai | |
| 100326_FC6107FAAXX/100326.csv | |
| 100326_FC6107FAAXX/run_summary.tsv | |
| /home/vagrant/bcbio-nextgen/tests/data/automated/../tcga_benchmark | |
| --2014-10-03 01:41:53-- http://chapmanb.s3.amazonaws.com/tcga_benchmark.tar.gz | |
| Resolving chapmanb.s3.amazonaws.com (chapmanb.s3.amazonaws.com)... 54.231.1.233 | |
| Connecting to chapmanb.s3.amazonaws.com (chapmanb.s3.amazonaws.com)|54.231.1.233|:80... connected. | |
| HTTP request sent, awaiting response... 200 OK | |
| Length: 1925985 (1.8M) [binary/octet-stream] | |
| Saving to: ‘tcga_benchmark.tar.gz’ | |
| 100%[========================================================================================================================>] 1,925,985 1.75MB/s in 1.1s | |
| 2014-10-03 01:41:59 (1.75 MB/s) - ‘tcga_benchmark.tar.gz’ saved [1925985/1925985] | |
| tcga_benchmark/ | |
| tcga_benchmark/README.txt | |
| tcga_benchmark/icgc_syn3_tumor.fq.gz | |
| tcga_benchmark/VERSION | |
| tcga_benchmark/icgc_syn3_normal.fq.gz | |
| [2014-10-03 01:42] Using input YAML configuration: /home/vagrant/bcbio-nextgen/tests/data/automated/run_info-variantcall.yaml | |
| [2014-10-03 01:42] Checking sample YAML configuration: /home/vagrant/bcbio-nextgen/tests/data/automated/run_info-variantcall.yaml | |
| [2014-10-03 01:42] Testing minimum versions of installed programs | |
| [2014-10-03 01:42] Resource requests: novoalign, sambamba, samtools; memory: 2.0, 2.0; cores: 16, 1, 16 | |
| [2014-10-03 01:42] Configuring 1 jobs to run, using 1 cores each with 2.2g of memory reserved for each job | |
| [2014-10-03 01:42] Timing: alignment preparation | |
| [2014-10-03 01:42] multiprocessing: prep_align_inputs | |
| [2014-10-03 01:42] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 01:42] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 01:42] bgzip input file | |
| [2014-10-03 01:42] bgzip input file | |
| [2014-10-03 01:42] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 01:42] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 01:42] Index input with grabix: 7_100326_FC6107FAAXX_1_fastq.txt.gz | |
| [2014-10-03 01:42] Index input with grabix: 7_100326_FC6107FAAXX_2_fastq.txt.gz | |
| [2014-10-03 01:42] Timing: alignment | |
| [2014-10-03 01:42] multiprocessing: process_alignment | |
| [2014-10-03 01:42] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 01:42] Novoalign: Test1 | |
| [2014-10-03 01:42] samblaster: Version 0.1.20 | |
| [2014-10-03 01:42] samblaster: Inputting from stdin | |
| [2014-10-03 01:42] samblaster: Outputting to stdout | |
| [2014-10-03 01:42] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 01:42] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 01:42] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 01:42] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 01:42] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 01:42] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 01:42] # License file not found. | |
| [2014-10-03 01:42] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 01:42] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] # Starting at Fri Oct 3 01:42:12 2014 | |
| [2014-10-03 01:42] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 01:42] # Index Build Version: 2.7 | |
| [2014-10-03 01:42] # Hash length: 6 | |
| [2014-10-03 01:42] # Step size: 1 | |
| [2014-10-03 01:42] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 01:42] # Paired Reads: 9000 | |
| [2014-10-03 01:42] # Pairs Aligned: 8889 | |
| [2014-10-03 01:42] # Read Sequences: 18000 | |
| [2014-10-03 01:42] # Aligned: 17874 | |
| [2014-10-03 01:42] # Unique Alignment: 17874 | |
| [2014-10-03 01:42] # Gapped Alignment: 67 | |
| [2014-10-03 01:42] # Quality Filter: 126 | |
| [2014-10-03 01:42] # Homopolymer Filter: 0 | |
| [2014-10-03 01:42] # Elapsed Time: 2.645 (secs.) | |
| [2014-10-03 01:42] # CPU Time: 2.49 (secs.) | |
| [2014-10-03 01:42] # Fragment Length Distribution | |
| [2014-10-03 01:42] # From To Count | |
| [2014-10-03 01:42] # 60 74 9 | |
| [2014-10-03 01:42] # 75 89 197 | |
| [2014-10-03 01:42] # 90 104 300 | |
| [2014-10-03 01:42] # 105 119 628 | |
| [2014-10-03 01:42] # 120 134 1584 | |
| [2014-10-03 01:42] # 135 149 1604 | |
| [2014-10-03 01:42] # 150 164 1419 | |
| [2014-10-03 01:42] # 165 179 1258 | |
| [2014-10-03 01:42] # 180 194 967 | |
| [2014-10-03 01:42] # 195 209 677 | |
| [2014-10-03 01:42] # 210 224 223 | |
| [2014-10-03 01:42] # 225 239 21 | |
| [2014-10-03 01:42] # 240 254 2 | |
| [2014-10-03 01:42] # Mean 153, Std Dev 31.1 | |
| [2014-10-03 01:42] # Done at Fri Oct 3 01:42:15 2014 | |
| [2014-10-03 01:42] samblaster: Output 0 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 01:42] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 01:42] samblaster: Marked 97 of 9000 (1.08%) read ids as duplicates using 1332k memory in 0.041S CPU seconds and 3S wall time. | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-1_36000.bam | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-1_36000-sr.bam | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-1_36000-disc.bam | |
| [2014-10-03 01:42] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 01:42] Novoalign: Test1 | |
| [2014-10-03 01:42] samblaster: Version 0.1.20 | |
| [2014-10-03 01:42] samblaster: Inputting from stdin | |
| [2014-10-03 01:42] samblaster: Outputting to stdout | |
| [2014-10-03 01:42] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 01:42] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 01:42] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 01:42] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 01:42] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 01:42] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 01:42] # License file not found. | |
| [2014-10-03 01:42] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 01:42] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] # Starting at Fri Oct 3 01:42:15 2014 | |
| [2014-10-03 01:42] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 01:42] # Index Build Version: 2.7 | |
| [2014-10-03 01:42] # Hash length: 6 | |
| [2014-10-03 01:42] # Step size: 1 | |
| [2014-10-03 01:42] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 01:42] # Paired Reads: 9000 | |
| [2014-10-03 01:42] # Pairs Aligned: 8899 | |
| [2014-10-03 01:42] # Read Sequences: 18000 | |
| [2014-10-03 01:42] # Aligned: 17888 | |
| [2014-10-03 01:42] # Unique Alignment: 17888 | |
| [2014-10-03 01:42] # Gapped Alignment: 48 | |
| [2014-10-03 01:42] # Quality Filter: 112 | |
| [2014-10-03 01:42] # Homopolymer Filter: 0 | |
| [2014-10-03 01:42] # Elapsed Time: 2.628 (secs.) | |
| [2014-10-03 01:42] # CPU Time: 2.48 (secs.) | |
| [2014-10-03 01:42] # Fragment Length Distribution | |
| [2014-10-03 01:42] # From To Count | |
| [2014-10-03 01:42] # 60 74 5 | |
| [2014-10-03 01:42] # 75 89 195 | |
| [2014-10-03 01:42] # 90 104 308 | |
| [2014-10-03 01:42] # 105 119 669 | |
| [2014-10-03 01:42] # 120 134 1511 | |
| [2014-10-03 01:42] # 135 149 1656 | |
| [2014-10-03 01:42] # 150 164 1379 | |
| [2014-10-03 01:42] # 165 179 1207 | |
| [2014-10-03 01:42] # 180 194 1020 | |
| [2014-10-03 01:42] # 195 209 692 | |
| [2014-10-03 01:42] # 210 224 231 | |
| [2014-10-03 01:42] # 225 239 19 | |
| [2014-10-03 01:42] # 240 254 4 | |
| [2014-10-03 01:42] # 255 269 2 | |
| [2014-10-03 01:42] # 270 284 1 | |
| [2014-10-03 01:42] # Mean 153, Std Dev 31.4 | |
| [2014-10-03 01:42] # Done at Fri Oct 3 01:42:18 2014 | |
| [2014-10-03 01:42] samblaster: Output 1 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 01:42] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 01:42] samblaster: Marked 105 of 9000 (1.17%) read ids as duplicates using 1328k memory in 0.032S CPU seconds and 3S wall time. | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-36000_71999.bam | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-36000_71999-sr.bam | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-36000_71999-disc.bam | |
| [2014-10-03 01:42] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 01:42] Novoalign: Test1 | |
| [2014-10-03 01:42] samblaster: Version 0.1.20 | |
| [2014-10-03 01:42] samblaster: Inputting from stdin | |
| [2014-10-03 01:42] samblaster: Outputting to stdout | |
| [2014-10-03 01:42] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 01:42] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 01:42] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 01:42] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 01:42] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 01:42] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 01:42] # License file not found. | |
| [2014-10-03 01:42] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 01:42] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] # Starting at Fri Oct 3 01:42:18 2014 | |
| [2014-10-03 01:42] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 01:42] # Index Build Version: 2.7 | |
| [2014-10-03 01:42] # Hash length: 6 | |
| [2014-10-03 01:42] # Step size: 1 | |
| [2014-10-03 01:42] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 01:42] # Paired Reads: 9000 | |
| [2014-10-03 01:42] # Pairs Aligned: 8881 | |
| [2014-10-03 01:42] # Read Sequences: 18000 | |
| [2014-10-03 01:42] # Aligned: 17872 | |
| [2014-10-03 01:42] # Unique Alignment: 17872 | |
| [2014-10-03 01:42] # Gapped Alignment: 53 | |
| [2014-10-03 01:42] # Quality Filter: 128 | |
| [2014-10-03 01:42] # Homopolymer Filter: 0 | |
| [2014-10-03 01:42] # Elapsed Time: 2.656 (secs.) | |
| [2014-10-03 01:42] # CPU Time: 2.52 (secs.) | |
| [2014-10-03 01:42] # Fragment Length Distribution | |
| [2014-10-03 01:42] # From To Count | |
| [2014-10-03 01:42] # 60 74 5 | |
| [2014-10-03 01:42] # 75 89 194 | |
| [2014-10-03 01:42] # 90 104 304 | |
| [2014-10-03 01:42] # 105 119 695 | |
| [2014-10-03 01:42] # 120 134 1547 | |
| [2014-10-03 01:42] # 135 149 1598 | |
| [2014-10-03 01:42] # 150 164 1399 | |
| [2014-10-03 01:42] # 165 179 1229 | |
| [2014-10-03 01:42] # 180 194 1010 | |
| [2014-10-03 01:42] # 195 209 669 | |
| [2014-10-03 01:42] # 210 224 202 | |
| [2014-10-03 01:42] # 225 239 24 | |
| [2014-10-03 01:42] # 240 254 2 | |
| [2014-10-03 01:42] # 255 269 2 | |
| [2014-10-03 01:42] # 270 284 1 | |
| [2014-10-03 01:42] # Mean 152, Std Dev 31.2 | |
| [2014-10-03 01:42] # Done at Fri Oct 3 01:42:21 2014 | |
| [2014-10-03 01:42] samblaster: Output 0 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 01:42] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 01:42] samblaster: Marked 105 of 9000 (1.17%) read ids as duplicates using 1332k memory in 0.000S CPU seconds and 3S wall time. | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-72000_107999.bam | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-72000_107999-sr.bam | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-72000_107999-disc.bam | |
| [2014-10-03 01:42] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 01:42] Novoalign: Test1 | |
| [2014-10-03 01:42] samblaster: Version 0.1.20 | |
| [2014-10-03 01:42] samblaster: Inputting from stdin | |
| [2014-10-03 01:42] samblaster: Outputting to stdout | |
| [2014-10-03 01:42] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 01:42] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 01:42] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 01:42] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 01:42] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 01:42] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 01:42] # License file not found. | |
| [2014-10-03 01:42] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 01:42] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] # Starting at Fri Oct 3 01:42:21 2014 | |
| [2014-10-03 01:42] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 01:42] # Index Build Version: 2.7 | |
| [2014-10-03 01:42] # Hash length: 6 | |
| [2014-10-03 01:42] # Step size: 1 | |
| [2014-10-03 01:42] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 01:42] # Paired Reads: 9000 | |
| [2014-10-03 01:42] # Pairs Aligned: 8907 | |
| [2014-10-03 01:42] # Read Sequences: 18000 | |
| [2014-10-03 01:42] # Aligned: 17899 | |
| [2014-10-03 01:42] # Unique Alignment: 17899 | |
| [2014-10-03 01:42] # Gapped Alignment: 58 | |
| [2014-10-03 01:42] # Quality Filter: 101 | |
| [2014-10-03 01:42] # Homopolymer Filter: 0 | |
| [2014-10-03 01:42] # Elapsed Time: 2.697 (secs.) | |
| [2014-10-03 01:42] # CPU Time: 2.55 (secs.) | |
| [2014-10-03 01:42] # Fragment Length Distribution | |
| [2014-10-03 01:42] # From To Count | |
| [2014-10-03 01:42] # 60 74 5 | |
| [2014-10-03 01:42] # 75 89 203 | |
| [2014-10-03 01:42] # 90 104 351 | |
| [2014-10-03 01:42] # 105 119 680 | |
| [2014-10-03 01:42] # 120 134 1579 | |
| [2014-10-03 01:42] # 135 149 1551 | |
| [2014-10-03 01:42] # 150 164 1378 | |
| [2014-10-03 01:42] # 165 179 1255 | |
| [2014-10-03 01:42] # 180 194 984 | |
| [2014-10-03 01:42] # 195 209 684 | |
| [2014-10-03 01:42] # 210 224 203 | |
| [2014-10-03 01:42] # 225 239 27 | |
| [2014-10-03 01:42] # 240 254 6 | |
| [2014-10-03 01:42] # 255 269 1 | |
| [2014-10-03 01:42] # Mean 152, Std Dev 31.6 | |
| [2014-10-03 01:42] # Done at Fri Oct 3 01:42:24 2014 | |
| [2014-10-03 01:42] samblaster: Output 0 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 01:42] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 01:42] samblaster: Marked 106 of 9000 (1.18%) read ids as duplicates using 1332k memory in 0.042S CPU seconds and 3S wall time. | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-108000_143999.bam | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-108000_143999-sr.bam | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-108000_143999-disc.bam | |
| [2014-10-03 01:42] Aligning lane 7_100326_FC6107FAAXX with novoalign aligner | |
| [2014-10-03 01:42] Novoalign: Test1 | |
| [2014-10-03 01:42] Command line argument ignored: -c option is only available in licensed versions. at '-c' | |
| [2014-10-03 01:42] samblaster: Version 0.1.20 | |
| [2014-10-03 01:42] samblaster: Inputting from stdin | |
| [2014-10-03 01:42] samblaster: Outputting to stdout | |
| [2014-10-03 01:42] samblaster: Opening /dev/fd/62 for write. | |
| [2014-10-03 01:42] samblaster: Opening /dev/fd/63 for write. | |
| [2014-10-03 01:42] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] Command line argument ignored: -k option is only available in licensed versions. at '-k' | |
| [2014-10-03 01:42] /usr/local/bin/novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] # novoalign (V3.02.02 - Build Feb 4 2014 @ 15:23:48 - A short read aligner with qualities. | |
| [2014-10-03 01:42] # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. | |
| [2014-10-03 01:42] # License file not found. | |
| [2014-10-03 01:42] # Licensed for evaluation, educational, and not-for-profit use only. | |
| [2014-10-03 01:42] # novoalign -o SAM @RG\tID:7\tPL:illumina\tPU:7_100326_FC6107FAAXX\tSM:Test1 -d /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/novoalign/hg19 -f /dev/fd/63 /dev/fd/62 -c 1 -F STDFQ -r None -o FullNW -k | |
| [2014-10-03 01:42] # Starting at Fri Oct 3 01:42:24 2014 | |
| [2014-10-03 01:42] # Interpreting input files as Sanger FASTQ. | |
| [2014-10-03 01:42] # Index Build Version: 2.7 | |
| [2014-10-03 01:42] # Hash length: 6 | |
| [2014-10-03 01:42] # Step size: 1 | |
| [2014-10-03 01:42] samblaster: Loaded 2 header sequence entries. | |
| [2014-10-03 01:42] # Paired Reads: 4164 | |
| [2014-10-03 01:42] # Pairs Aligned: 4099 | |
| [2014-10-03 01:42] # Read Sequences: 8328 | |
| [2014-10-03 01:42] # Aligned: 8231 | |
| [2014-10-03 01:42] # Unique Alignment: 8231 | |
| [2014-10-03 01:42] # Gapped Alignment: 57 | |
| [2014-10-03 01:42] # Quality Filter: 28 | |
| [2014-10-03 01:42] # Homopolymer Filter: 0 | |
| [2014-10-03 01:42] # Elapsed Time: 1.279 (secs.) | |
| [2014-10-03 01:42] # CPU Time: 1.21 (secs.) | |
| [2014-10-03 01:42] # Fragment Length Distribution | |
| [2014-10-03 01:42] # From To Count | |
| [2014-10-03 01:42] # 60 74 2 | |
| [2014-10-03 01:42] # 75 89 84 | |
| [2014-10-03 01:42] # 90 104 151 | |
| [2014-10-03 01:42] # 105 119 311 | |
| [2014-10-03 01:42] # 120 134 693 | |
| [2014-10-03 01:42] # 135 149 757 | |
| [2014-10-03 01:42] # 150 164 667 | |
| [2014-10-03 01:42] # 165 179 544 | |
| [2014-10-03 01:42] # 180 194 426 | |
| [2014-10-03 01:42] # 195 209 310 | |
| [2014-10-03 01:42] # 210 224 112 | |
| [2014-10-03 01:42] # 225 239 16 | |
| [2014-10-03 01:42] # 240 254 14 | |
| [2014-10-03 01:42] # 255 269 1 | |
| [2014-10-03 01:42] # 270 284 1 | |
| [2014-10-03 01:42] # 285 299 1 | |
| [2014-10-03 01:42] # 300 314 3 | |
| [2014-10-03 01:42] # 315 329 0 | |
| [2014-10-03 01:42] # 330 344 1 | |
| [2014-10-03 01:42] # 345 359 0 | |
| [2014-10-03 01:42] # 360 374 0 | |
| [2014-10-03 01:42] # 375 389 1 | |
| [2014-10-03 01:42] # 390 404 0 | |
| [2014-10-03 01:42] # 405 419 0 | |
| [2014-10-03 01:42] # 420 434 0 | |
| [2014-10-03 01:42] # 435 449 0 | |
| [2014-10-03 01:42] # 450 464 0 | |
| [2014-10-03 01:42] # 465 479 0 | |
| [2014-10-03 01:42] # 480 494 0 | |
| [2014-10-03 01:42] # 495 509 1 | |
| [2014-10-03 01:42] # Mean 153, Std Dev 32.9 | |
| [2014-10-03 01:42] # Done at Fri Oct 3 01:42:25 2014 | |
| [2014-10-03 01:42] samblaster: Output 3 discordant read pairs to /dev/fd/62 | |
| [2014-10-03 01:42] samblaster: Output 0 split reads to /dev/fd/63 | |
| [2014-10-03 01:42] samblaster: Marked 31 of 4164 (0.74%) read ids as duplicates using 1332k memory in 0.032S CPU seconds and 1S wall time. | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-144000_160655.bam | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-144000_160655-sr.bam | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-144000_160655-disc.bam | |
| [2014-10-03 01:42] multiprocessing: delayed_bam_merge | |
| [2014-10-03 01:42] Merge bam files to 7_100326_FC6107FAAXX-sort-sr.bam | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-sr.bam | |
| [2014-10-03 01:42] Merge bam files to 7_100326_FC6107FAAXX-sort-disc.bam | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort-disc.bam | |
| [2014-10-03 01:42] Merge bam files to 7_100326_FC6107FAAXX-sort.bam | |
| [2014-10-03 01:42] Index BAM file: 7_100326_FC6107FAAXX-sort.bam | |
| [2014-10-03 01:42] Timing: callable regions | |
| [2014-10-03 01:42] multiprocessing: prep_samples | |
| [2014-10-03 01:42] Prepare cleaned BED file : Test1 | |
| [2014-10-03 01:42] bgzip variant_regions-variantcall.bed | |
| [2014-10-03 01:42] tabix index variant_regions-variantcall.bed.gz | |
| [2014-10-03 01:42] Prepare merged BED file : Test1 | |
| [2014-10-03 01:42] bgzip variant_regions-variantcall-merged.bed | |
| [2014-10-03 01:42] tabix index variant_regions-variantcall-merged.bed.gz | |
| [2014-10-03 01:42] multiprocessing: postprocess_alignment | |
| [2014-10-03 01:42] Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 01:42] Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 01:42] multiprocessing: calc_callable_loci | |
| [2014-10-03 01:42] bedtools genomecov: chrM : 7_100326_FC6107FAAXX-sort.bam | |
| [2014-10-03 01:42] bedtools genomecov: chr22 : 7_100326_FC6107FAAXX-sort.bam | |
| [2014-10-03 01:42] multiprocessing: combine_bed | |
| [2014-10-03 01:42] Recalibrating ['', 'Test1'] with GATK | |
| Traceback (most recent call last): | |
| File "/usr/local/bin/bcbio_nextgen.py", line 216, in <module> | |
| main(**kwargs) | |
| File "/usr/local/bin/bcbio_nextgen.py", line 42, in main | |
| run_main(**kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 36, in run_main | |
| fc_dir, run_info_yaml) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 82, in _run_toplevel | |
| for xs in pipeline.run(config, config_file, parallel, dirs, pipeline_items): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 183, in run | |
| samples = run_parallel("postprocess_alignment", samples) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel | |
| return run_multicore(fn, items, config, parallel=parallel) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 84, in run_multicore | |
| for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 653, in __call__ | |
| self.dispatch(function, args, kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 400, in dispatch | |
| job = ImmediateApply(func, args, kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 138, in __init__ | |
| self.results = func(*args, **kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 63, in wrapper | |
| return apply(f, *args, **kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 31, in postprocess_alignment | |
| return sample.postprocess_alignment(*args) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 161, in postprocess_alignment | |
| data = _recal_no_markduplicates(data) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 167, in _recal_no_markduplicates | |
| data = recalibrate.prep_recal(data)[0][0] | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/variation/recalibrate.py", line 39, in prep_recal | |
| platform, dbsnp_file, intervals, data) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/variation/recalibrate.py", line 78, in _gatk_base_recalibrator | |
| if broad_runner.gatk_type() == "lite": | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/broad/__init__.py", line 311, in gatk_type | |
| if LooseVersion(self.gatk_major_version()) > LooseVersion("2.3"): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/broad/__init__.py", line 322, in gatk_major_version | |
| full_version = self.get_gatk_version() | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/broad/__init__.py", line 294, in get_gatk_version | |
| gatk_jar = self._get_jar("GenomeAnalysisTK", ["GenomeAnalysisTKLite"]) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/broad/__init__.py", line 373, in _get_jar | |
| raise ValueError("Could not find jar %s in %s:%s" % (command, self._picard_ref, self._gatk_dir)) | |
| ValueError: Could not find jar GenomeAnalysisTK in /usr/local/share/java/picard:/usr/local/share/java/gatk | |
| ERROR | |
| Allow BAM files as input to pipeline. ... [2014-10-03 01:42] Using input YAML configuration: /home/vagrant/bcbio-nextgen/tests/data/automated/run_info-bam.yaml | |
| [2014-10-03 01:42] Checking sample YAML configuration: /home/vagrant/bcbio-nextgen/tests/data/automated/run_info-bam.yaml | |
| [2014-10-03 01:42] Testing minimum versions of installed programs | |
| [2014-10-03 01:42] Resource requests: bwa, sambamba, samtools; memory: 2.0; cores: 16, 1, 16 | |
| [2014-10-03 01:42] Configuring 1 jobs to run, using 1 cores each with 2.2g of memory reserved for each job | |
| [2014-10-03 01:42] Timing: alignment preparation | |
| [2014-10-03 01:42] multiprocessing: prep_align_inputs | |
| [2014-10-03 01:42] BAM to bgzipped fastq | |
| [2014-10-03 01:42] top - 01:42:34 up 2:57, 1 user, load average: 0.73, 0.37, 0.18 | |
| [2014-10-03 01:42] Tasks: 83 total, 1 running, 82 sleeping, 0 stopped, 0 zombie | |
| [2014-10-03 01:42] %Cpu(s): 11.1 us, 3.9 sy, 15.8 ni, 65.9 id, 3.1 wa, 0.0 hi, 0.3 si, 0.0 st | |
| [2014-10-03 01:42] KiB Mem: 1017856 total, 789180 used, 228676 free, 11784 buffers | |
| [2014-10-03 01:42] KiB Swap: 0 total, 0 used, 0 free. 516136 cached Mem | |
| [2014-10-03 01:42] | |
| [2014-10-03 01:42] PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND | |
| [2014-10-03 01:42] 1 root 20 0 37080 5080 96 S 0.0 0.5 0:00.66 init | |
| [2014-10-03 01:42] 2 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kthreadd | |
| [2014-10-03 01:42] 3 root 20 0 0 0 0 S 0.0 0.0 0:00.88 ksoftirqd/0 | |
| [2014-10-03 01:42] 4 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0 | |
| [2014-10-03 01:42] 5 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0H | |
| [2014-10-03 01:42] 7 root 20 0 0 0 0 S 0.0 0.0 0:02.41 rcu_sched | |
| [2014-10-03 01:42] 8 root 20 0 0 0 0 S 0.0 0.0 0:05.11 rcuos/0 | |
| [2014-10-03 01:42] 9 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcu_bh | |
| [2014-10-03 01:42] 10 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcuob/0 | |
| [2014-10-03 01:42] 11 root rt 0 0 0 0 S 0.0 0.0 0:00.00 migration/0 | |
| [2014-10-03 01:42] 12 root rt 0 0 0 0 S 0.0 0.0 0:00.26 watchdog/0 | |
| [2014-10-03 01:42] 13 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 khelper | |
| [2014-10-03 01:42] 14 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kdevtmpfs | |
| [2014-10-03 01:42] 15 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 netns | |
| [2014-10-03 01:42] 16 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 writeback | |
| [2014-10-03 01:42] 17 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kintegrityd | |
| [2014-10-03 01:42] 18 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 bioset | |
| [2014-10-03 01:42] 19 root 0 -20 0 0 0 S 0.0 0.0 0:00.15 kworker/u3:0 | |
| [2014-10-03 01:42] 20 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kblockd | |
| [2014-10-03 01:42] 21 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 ata_sff | |
| [2014-10-03 01:42] 22 root 20 0 0 0 0 S 0.0 0.0 0:00.00 khubd | |
| [2014-10-03 01:42] 23 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 md | |
| [2014-10-03 01:42] 24 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 devfreq_wq | |
| [2014-10-03 01:42] 25 root 20 0 0 0 0 S 0.0 0.0 0:03.02 kworker/0:1 | |
| [2014-10-03 01:42] 26 root 20 0 0 0 0 S 0.0 0.0 0:00.00 khungtaskd | |
| [2014-10-03 01:42] 27 root 20 0 0 0 0 S 0.0 0.0 0:06.86 kswapd0 | |
| [2014-10-03 01:42] 28 root 25 5 0 0 0 S 0.0 0.0 0:00.00 ksmd | |
| [2014-10-03 01:42] 29 root 39 19 0 0 0 S 0.0 0.0 0:00.39 khugepaged | |
| [2014-10-03 01:42] 30 root 20 0 0 0 0 S 0.0 0.0 0:00.00 fsnotify_ma+ | |
| [2014-10-03 01:42] 31 root 20 0 0 0 0 S 0.0 0.0 0:00.00 ecryptfs-kt+ | |
| [2014-10-03 01:42] 32 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 crypto | |
| [2014-10-03 01:42] 44 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kthrotld | |
| [2014-10-03 01:42] 64 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 deferwq | |
| [2014-10-03 01:42] 65 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 charger_man+ | |
| [2014-10-03 01:42] 106 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kpsmoused | |
| [2014-10-03 01:42] 107 root 20 0 0 0 0 S 0.0 0.0 0:00.00 scsi_eh_0 | |
| [2014-10-03 01:42] 154 root 20 0 0 0 0 S 0.0 0.0 0:00.80 jbd2/sda1-8 | |
| [2014-10-03 01:42] 155 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 ext4-rsv-co+ | |
| [2014-10-03 01:42] 351 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 iprt | |
| [2014-10-03 01:42] 471 root 20 0 10224 2288 0 S 0.0 0.2 0:00.00 dhclient | |
| [2014-10-03 01:42] 555 root 20 0 23420 324 36 S 0.0 0.0 0:00.02 rpcbind | |
| [2014-10-03 01:42] 597 statd 20 0 21544 456 0 S 0.0 0.0 0:00.00 rpc.statd | |
| [2014-10-03 01:42] 598 root 0 -20 0 0 0 S 0.0 0.0 0:00.17 kworker/u3:1 | |
| [2014-10-03 01:42] 796 message+ 20 0 39360 856 316 S 0.0 0.1 0:00.32 dbus-daemon | |
| [2014-10-03 01:42] 799 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 rpciod | |
| [2014-10-03 01:42] 814 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 nfsiod | |
| [2014-10-03 01:42] 862 root 20 0 25544 220 0 S 0.0 0.0 0:00.00 rpc.idmapd | |
| [2014-10-03 01:42] 896 syslog 20 0 257912 684 0 S 0.0 0.1 0:00.03 rsyslogd | |
| [2014-10-03 01:42] 1014 root 20 0 14540 168 4 S 0.0 0.0 0:00.00 getty | |
| [2014-10-03 01:42] 1017 root 20 0 14540 156 4 S 0.0 0.0 0:00.00 getty | |
| [2014-10-03 01:42] 1022 root 20 0 14540 152 4 S 0.0 0.0 0:00.00 getty | |
| [2014-10-03 01:42] 1023 root 20 0 14540 164 4 S 0.0 0.0 0:00.00 getty | |
| [2014-10-03 01:42] 1025 root 20 0 14540 164 4 S 0.0 0.0 0:00.00 getty | |
| [2014-10-03 01:42] 1060 root 20 0 4368 144 0 S 0.0 0.0 0:00.00 acpid | |
| [2014-10-03 01:42] 1061 root 20 0 23656 272 48 S 0.0 0.0 0:00.02 cron | |
| [2014-10-03 01:42] 1062 daemon 20 0 19140 184 12 S 0.0 0.0 0:00.00 atd | |
| [2014-10-03 01:42] 1095 root 20 0 216612 344 0 S 0.0 0.0 0:02.35 VBoxService | |
| [2014-10-03 01:42] 1181 root 20 0 61364 676 0 S 0.0 0.1 0:00.00 sshd | |
| [2014-10-03 01:42] 1201 root 20 0 182528 32860 1072 S 0.0 3.2 0:01.92 puppet | |
| [2014-10-03 01:42] 1229 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kauditd | |
| [2014-10-03 01:42] 1250 root 20 0 112692 33624 184 S 0.0 3.3 0:00.00 ruby | |
| [2014-10-03 01:42] 1281 root 20 0 14540 156 4 S 0.0 0.0 0:00.00 getty | |
| [2014-10-03 01:42] 4983 root 20 0 107696 992 0 S 0.0 0.1 0:00.00 sshd | |
| [2014-10-03 01:42] 5025 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/u2:1 | |
| [2014-10-03 01:42] 5036 vagrant 20 0 107696 1332 332 S 0.0 0.1 0:11.42 sshd | |
| [2014-10-03 01:42] 5037 vagrant 20 0 21592 2440 160 S 0.0 0.2 0:00.08 bash | |
| [2014-10-03 01:42] 8448 root 20 0 15276 208 0 S 0.0 0.0 0:00.02 upstart-fil+ | |
| [2014-10-03 01:42] 8451 root 20 0 15260 200 0 S 0.0 0.0 0:00.02 upstart-soc+ | |
| [2014-10-03 01:42] 8488 root 20 0 19476 196 0 S 0.0 0.0 0:00.00 upstart-ude+ | |
| [2014-10-03 01:42] 8491 root 20 0 49864 608 4 S 0.0 0.1 0:00.00 systemd-ude+ | |
| [2014-10-03 01:42] 8748 root 20 0 43452 340 0 S 0.0 0.0 0:00.00 systemd-log+ | |
| [2014-10-03 01:42] 9503 vagrant 20 0 11132 428 208 S 0.0 0.0 0:00.00 bash | |
| [2014-10-03 01:42] 9509 vagrant 20 0 110076 15916 1388 S 0.0 1.6 0:00.21 nosetests | |
| [2014-10-03 01:42] 9822 vagrant 20 0 547608 113044 15744 S 0.0 11.1 0:01.17 bcbio_nextg+ | |
| [2014-10-03 01:42] 9903 vagrant 20 0 11136 1396 1176 S 0.0 0.1 0:00.00 bash | |
| [2014-10-03 01:42] 9904 vagrant 20 0 11136 592 368 S 0.0 0.1 0:00.00 bash | |
| [2014-10-03 01:42] 9905 vagrant 20 0 11136 592 368 S 0.0 0.1 0:00.00 bash | |
| [2014-10-03 01:42] 9906 vagrant 20 0 91152 2932 2040 S 0.0 0.3 0:00.00 bamtofastq | |
| [2014-10-03 01:42] 9907 vagrant 20 0 9084 420 320 S 0.0 0.0 0:00.00 bgzip | |
| [2014-10-03 01:42] 9908 vagrant 20 0 9084 420 320 S 0.0 0.0 0:00.00 bgzip | |
| [2014-10-03 01:42] 9909 vagrant 20 0 4444 656 556 S 0.0 0.1 0:00.00 sh | |
| [2014-10-03 01:42] 9910 vagrant 20 0 23536 1392 1052 R 0.0 0.1 0:00.00 top | |
| [2014-10-03 01:42] 32158 root 20 0 0 0 0 S 0.0 0.0 0:04.95 kworker/u2:0 | |
| [2014-10-03 01:42] AutoArray<unsigned long,alloc_type_cxx> failed to allocate 134217728 elements (1073741824 bytes) | |
| [2014-10-03 01:42] Uncaught exception occurred | |
| Traceback (most recent call last): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/alignprep.py", line 308, in _bgzip_from_bam | |
| log_error=False) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| CalledProcessError: Command 'set -o pipefail; /usr/local/bin/bamtofastq filename=/home/vagrant/bcbio-nextgen/tests/data/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam T=/home/vagrant/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/8bde12dc-4a9e-11e4-ba80-080027201064/tmplLZDgQ/7_100326_FC6107FAAXX-1.fq-sort F=>(/usr/local/bin/bgzip -c /dev/stdin > /home/vagrant/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/8bde12dc-4a9e-11e4-ba80-080027201064/tmplLZDgQ/7_100326_FC6107FAAXX-1.fq.gz) F2=>(/usr/local/bin/bgzip -c /dev/stdin > /home/vagrant/bcbio-nextgen/tests/test_automated_output/align_prep/7_100326_FC6107FAAXX-2.fq.gz) S=/dev/null O=/dev/null O2=/dev/null collate=1 colsbs=1073741824 | |
| KiB Swap: 0 total, 0 used, 0 free. 516136 cached Mem | |
| PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND | |
| 1 root 20 0 37080 5080 96 S 0.0 0.5 0:00.66 init | |
| 2 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kthreadd | |
| 3 root 20 0 0 0 0 S 0.0 0.0 0:00.88 ksoftirqd/0 | |
| 4 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0 | |
| 5 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0H | |
| 7 root 20 0 0 0 0 S 0.0 0.0 0:02.41 rcu_sched | |
| 8 root 20 0 0 0 0 S 0.0 0.0 0:05.11 rcuos/0 | |
| 9 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcu_bh | |
| 10 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcuob/0 | |
| 11 root rt 0 0 0 0 S 0.0 0.0 0:00.00 migration/0 | |
| 12 root rt 0 0 0 0 S 0.0 0.0 0:00.26 watchdog/0 | |
| 13 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 khelper | |
| 14 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kdevtmpfs | |
| 15 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 netns | |
| 16 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 writeback | |
| 17 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kintegrityd | |
| 18 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 bioset | |
| 19 root 0 -20 0 0 0 S 0.0 0.0 0:00.15 kworker/u3:0 | |
| 20 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kblockd | |
| 21 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 ata_sff | |
| 22 root 20 0 0 0 0 S 0.0 0.0 0:00.00 khubd | |
| 23 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 md | |
| 24 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 devfreq_wq | |
| 25 root 20 0 0 0 0 S 0.0 0.0 0:03.02 kworker/0:1 | |
| 26 root 20 0 0 0 0 S 0.0 0.0 0:00.00 khungtaskd | |
| 27 root 20 0 0 0 0 S 0.0 0.0 0:06.86 kswapd0 | |
| 28 root 25 5 0 0 0 S 0.0 0.0 0:00.00 ksmd | |
| 29 root 39 19 0 0 0 S 0.0 0.0 0:00.39 khugepaged | |
| 30 root 20 0 0 0 0 S 0.0 0.0 0:00.00 fsnotify_ma+ | |
| 31 root 20 0 0 0 0 S 0.0 0.0 0:00.00 ecryptfs-kt+ | |
| 32 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 crypto | |
| 44 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kthrotld | |
| 64 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 deferwq | |
| 65 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 charger_man+ | |
| 106 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kpsmoused | |
| 107 root 20 0 0 0 0 S 0.0 0.0 0:00.00 scsi_eh_0 | |
| 154 root 20 0 0 0 0 S 0.0 0.0 0:00.80 jbd2/sda1-8 | |
| 155 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 ext4-rsv-co+ | |
| 351 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 iprt | |
| 471 root 20 0 10224 2288 0 S 0.0 0.2 0:00.00 dhclient | |
| 555 root 20 0 23420 324 36 S 0.0 0.0 0:00.02 rpcbind | |
| 597 statd 20 0 21544 456 0 S 0.0 0.0 0:00.00 rpc.statd | |
| 598 root 0 -20 0 0 0 S 0.0 0.0 0:00.17 kworker/u3:1 | |
| 796 message+ 20 0 39360 856 316 S 0.0 0.1 0:00.32 dbus-daemon | |
| 799 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 rpciod | |
| 814 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 nfsiod | |
| 862 root 20 0 25544 220 0 S 0.0 0.0 0:00.00 rpc.idmapd | |
| 896 syslog 20 0 257912 684 0 S 0.0 0.1 0:00.03 rsyslogd | |
| 1014 root 20 0 14540 168 4 S 0.0 0.0 0:00.00 getty | |
| 1017 root 20 0 14540 156 4 S 0.0 0.0 0:00.00 getty | |
| 1022 root 20 0 14540 152 4 S 0.0 0.0 0:00.00 getty | |
| 1023 root 20 0 14540 164 4 S 0.0 0.0 0:00.00 getty | |
| 1025 root 20 0 14540 164 4 S 0.0 0.0 0:00.00 getty | |
| 1060 root 20 0 4368 144 0 S 0.0 0.0 0:00.00 acpid | |
| 1061 root 20 0 23656 272 48 S 0.0 0.0 0:00.02 cron | |
| 1062 daemon 20 0 19140 184 12 S 0.0 0.0 0:00.00 atd | |
| 1095 root 20 0 216612 344 0 S 0.0 0.0 0:02.35 VBoxService | |
| 1181 root 20 0 61364 676 0 S 0.0 0.1 0:00.00 sshd | |
| 1201 root 20 0 182528 32860 1072 S 0.0 3.2 0:01.92 puppet | |
| 1229 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kauditd | |
| 1250 root 20 0 112692 33624 184 S 0.0 3.3 0:00.00 ruby | |
| 1281 root 20 0 14540 156 4 S 0.0 0.0 0:00.00 getty | |
| 4983 root 20 0 107696 992 0 S 0.0 0.1 0:00.00 sshd | |
| 5025 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/u2:1 | |
| 5036 vagrant 20 0 107696 1332 332 S 0.0 0.1 0:11.42 sshd | |
| 5037 vagrant 20 0 21592 2440 160 S 0.0 0.2 0:00.08 bash | |
| 8448 root 20 0 15276 208 0 S 0.0 0.0 0:00.02 upstart-fil+ | |
| 8451 root 20 0 15260 200 0 S 0.0 0.0 0:00.02 upstart-soc+ | |
| 8488 root 20 0 19476 196 0 S 0.0 0.0 0:00.00 upstart-ude+ | |
| 8491 root 20 0 49864 608 4 S 0.0 0.1 0:00.00 systemd-ude+ | |
| 8748 root 20 0 43452 340 0 S 0.0 0.0 0:00.00 systemd-log+ | |
| 9503 vagrant 20 0 11132 428 208 S 0.0 0.0 0:00.00 bash | |
| 9509 vagrant 20 0 110076 15916 1388 S 0.0 1.6 0:00.21 nosetests | |
| 9822 vagrant 20 0 547608 113044 15744 S 0.0 11.1 0:01.17 bcbio_nextg+ | |
| 9903 vagrant 20 0 11136 1396 1176 S 0.0 0.1 0:00.00 bash | |
| 9904 vagrant 20 0 11136 592 368 S 0.0 0.1 0:00.00 bash | |
| 9905 vagrant 20 0 11136 592 368 S 0.0 0.1 0:00.00 bash | |
| 9906 vagrant 20 0 91152 2932 2040 S 0.0 0.3 0:00.00 bamtofastq | |
| 9907 vagrant 20 0 9084 420 320 S 0.0 0.0 0:00.00 bgzip | |
| 9908 vagrant 20 0 9084 420 320 S 0.0 0.0 0:00.00 bgzip | |
| 9909 vagrant 20 0 4444 656 556 S 0.0 0.1 0:00.00 sh | |
| 9910 vagrant 20 0 23536 1392 1052 R 0.0 0.1 0:00.00 top | |
| 32158 root 20 0 0 0 0 S 0.0 0.0 0:04.95 kworker/u2:0 | |
| AutoArray<unsigned long,alloc_type_cxx> failed to allocate 134217728 elements (1073741824 bytes) | |
| current total allocation 1074215981 | |
| /usr/local/lib/libmaus.so.0(_ZN7libmaus4util10StackTraceC1Ev+0x4c) [0x7f22312be866:??:0] | |
| /usr/local/bin/bamtofastq(_ZN7libmaus9exception16LibMausExceptionC2Ev+0x1d) [0x412873:??:?] | |
| /usr/local/bin/bamtofastq(_ZN7libmaus9autoarray9AutoArrayImLNS0_10alloc_typeE0EE13allocateArrayEm+0x79) [0x41cc45:??:?] | |
| /usr/local/bin/bamtofastq(_ZN7libmaus9autoarray9AutoArrayImLNS0_10alloc_typeE0EEC2Emb+0x27) [0x41cd95:??:?] | |
| /usr/local/bin/bamtofastq() [0x443274:??:?] | |
| /usr/local/bin/bamtofastq() [0x40ef57:??:?] | |
| /usr/local/bin/bamtofastq() [0x40feea:??:?] | |
| /usr/local/bin/bamtofastq() [0x40bde8:??:?] | |
| /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f2230179ec5:??:0] | |
| /usr/local/bin/bamtofastq() [0x40d978:??:?] | |
| ' returned non-zero exit status 1 | |
| Traceback (most recent call last): | |
| File "/usr/local/bin/bcbio_nextgen.py", line 216, in <module> | |
| main(**kwargs) | |
| File "/usr/local/bin/bcbio_nextgen.py", line 42, in main | |
| run_main(**kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 36, in run_main | |
| fc_dir, run_info_yaml) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 82, in _run_toplevel | |
| for xs in pipeline.run(config, config_file, parallel, dirs, pipeline_items): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 175, in run | |
| samples = run_parallel("prep_align_inputs", samples) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel | |
| return run_multicore(fn, items, config, parallel=parallel) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 84, in run_multicore | |
| for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items): | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 653, in __call__ | |
| self.dispatch(function, args, kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 400, in dispatch | |
| job = ImmediateApply(func, args, kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 138, in __init__ | |
| self.results = func(*args, **kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 63, in wrapper | |
| return apply(f, *args, **kwargs) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 39, in prep_align_inputs | |
| return alignprep.create_inputs(*args) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/alignprep.py", line 37, in create_inputs | |
| ready_files = _prep_grabix_indexes(data["files"], data["dirs"], data) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/alignprep.py", line 153, in _prep_grabix_indexes | |
| out = _bgzip_from_bam(in_files[0], dirs, data["config"]) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/alignprep.py", line 308, in _bgzip_from_bam | |
| log_error=False) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run | |
| _do_run(cmd, checks, log_stdout) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run | |
| raise subprocess.CalledProcessError(exitcode, error_msg) | |
| subprocess.CalledProcessError: Command 'set -o pipefail; /usr/local/bin/bamtofastq filename=/home/vagrant/bcbio-nextgen/tests/data/100326_FC6107FAAXX/7_100326_FC6107FAAXX.bam T=/home/vagrant/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/8bde12dc-4a9e-11e4-ba80-080027201064/tmplLZDgQ/7_100326_FC6107FAAXX-1.fq-sort F=>(/usr/local/bin/bgzip -c /dev/stdin > /home/vagrant/bcbio-nextgen/tests/test_automated_output/tmptest/bcbiotx/8bde12dc-4a9e-11e4-ba80-080027201064/tmplLZDgQ/7_100326_FC6107FAAXX-1.fq.gz) F2=>(/usr/local/bin/bgzip -c /dev/stdin > /home/vagrant/bcbio-nextgen/tests/test_automated_output/align_prep/7_100326_FC6107FAAXX-2.fq.gz) S=/dev/null O=/dev/null O2=/dev/null collate=1 colsbs=1073741824 | |
| KiB Swap: 0 total, 0 used, 0 free. 516136 cached Mem | |
| PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND | |
| 1 root 20 0 37080 5080 96 S 0.0 0.5 0:00.66 init | |
| 2 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kthreadd | |
| 3 root 20 0 0 0 0 S 0.0 0.0 0:00.88 ksoftirqd/0 | |
| 4 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0 | |
| 5 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kworker/0:0H | |
| 7 root 20 0 0 0 0 S 0.0 0.0 0:02.41 rcu_sched | |
| 8 root 20 0 0 0 0 S 0.0 0.0 0:05.11 rcuos/0 | |
| 9 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcu_bh | |
| 10 root 20 0 0 0 0 S 0.0 0.0 0:00.00 rcuob/0 | |
| 11 root rt 0 0 0 0 S 0.0 0.0 0:00.00 migration/0 | |
| 12 root rt 0 0 0 0 S 0.0 0.0 0:00.26 watchdog/0 | |
| 13 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 khelper | |
| 14 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kdevtmpfs | |
| 15 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 netns | |
| 16 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 writeback | |
| 17 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kintegrityd | |
| 18 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 bioset | |
| 19 root 0 -20 0 0 0 S 0.0 0.0 0:00.15 kworker/u3:0 | |
| 20 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kblockd | |
| 21 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 ata_sff | |
| 22 root 20 0 0 0 0 S 0.0 0.0 0:00.00 khubd | |
| 23 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 md | |
| 24 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 devfreq_wq | |
| 25 root 20 0 0 0 0 S 0.0 0.0 0:03.02 kworker/0:1 | |
| 26 root 20 0 0 0 0 S 0.0 0.0 0:00.00 khungtaskd | |
| 27 root 20 0 0 0 0 S 0.0 0.0 0:06.86 kswapd0 | |
| 28 root 25 5 0 0 0 S 0.0 0.0 0:00.00 ksmd | |
| 29 root 39 19 0 0 0 S 0.0 0.0 0:00.39 khugepaged | |
| 30 root 20 0 0 0 0 S 0.0 0.0 0:00.00 fsnotify_ma+ | |
| 31 root 20 0 0 0 0 S 0.0 0.0 0:00.00 ecryptfs-kt+ | |
| 32 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 crypto | |
| 44 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kthrotld | |
| 64 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 deferwq | |
| 65 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 charger_man+ | |
| 106 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 kpsmoused | |
| 107 root 20 0 0 0 0 S 0.0 0.0 0:00.00 scsi_eh_0 | |
| 154 root 20 0 0 0 0 S 0.0 0.0 0:00.80 jbd2/sda1-8 | |
| 155 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 ext4-rsv-co+ | |
| 351 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 iprt | |
| 471 root 20 0 10224 2288 0 S 0.0 0.2 0:00.00 dhclient | |
| 555 root 20 0 23420 324 36 S 0.0 0.0 0:00.02 rpcbind | |
| 597 statd 20 0 21544 456 0 S 0.0 0.0 0:00.00 rpc.statd | |
| 598 root 0 -20 0 0 0 S 0.0 0.0 0:00.17 kworker/u3:1 | |
| 796 message+ 20 0 39360 856 316 S 0.0 0.1 0:00.32 dbus-daemon | |
| 799 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 rpciod | |
| 814 root 0 -20 0 0 0 S 0.0 0.0 0:00.00 nfsiod | |
| 862 root 20 0 25544 220 0 S 0.0 0.0 0:00.00 rpc.idmapd | |
| 896 syslog 20 0 257912 684 0 S 0.0 0.1 0:00.03 rsyslogd | |
| 1014 root 20 0 14540 168 4 S 0.0 0.0 0:00.00 getty | |
| 1017 root 20 0 14540 156 4 S 0.0 0.0 0:00.00 getty | |
| 1022 root 20 0 14540 152 4 S 0.0 0.0 0:00.00 getty | |
| 1023 root 20 0 14540 164 4 S 0.0 0.0 0:00.00 getty | |
| 1025 root 20 0 14540 164 4 S 0.0 0.0 0:00.00 getty | |
| 1060 root 20 0 4368 144 0 S 0.0 0.0 0:00.00 acpid | |
| 1061 root 20 0 23656 272 48 S 0.0 0.0 0:00.02 cron | |
| 1062 daemon 20 0 19140 184 12 S 0.0 0.0 0:00.00 atd | |
| 1095 root 20 0 216612 344 0 S 0.0 0.0 0:02.35 VBoxService | |
| 1181 root 20 0 61364 676 0 S 0.0 0.1 0:00.00 sshd | |
| 1201 root 20 0 182528 32860 1072 S 0.0 3.2 0:01.92 puppet | |
| 1229 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kauditd | |
| 1250 root 20 0 112692 33624 184 S 0.0 3.3 0:00.00 ruby | |
| 1281 root 20 0 14540 156 4 S 0.0 0.0 0:00.00 getty | |
| 4983 root 20 0 107696 992 0 S 0.0 0.1 0:00.00 sshd | |
| 5025 root 20 0 0 0 0 S 0.0 0.0 0:00.00 kworker/u2:1 | |
| 5036 vagrant 20 0 107696 1332 332 S 0.0 0.1 0:11.42 sshd | |
| 5037 vagrant 20 0 21592 2440 160 S 0.0 0.2 0:00.08 bash | |
| 8448 root 20 0 15276 208 0 S 0.0 0.0 0:00.02 upstart-fil+ | |
| 8451 root 20 0 15260 200 0 S 0.0 0.0 0:00.02 upstart-soc+ | |
| 8488 root 20 0 19476 196 0 S 0.0 0.0 0:00.00 upstart-ude+ | |
| 8491 root 20 0 49864 608 4 S 0.0 0.1 0:00.00 systemd-ude+ | |
| 8748 root 20 0 43452 340 0 S 0.0 0.0 0:00.00 systemd-log+ | |
| 9503 vagrant 20 0 11132 428 208 S 0.0 0.0 0:00.00 bash | |
| 9509 vagrant 20 0 110076 15916 1388 S 0.0 1.6 0:00.21 nosetests | |
| 9822 vagrant 20 0 547608 113044 15744 S 0.0 11.1 0:01.17 bcbio_nextg+ | |
| 9903 vagrant 20 0 11136 1396 1176 S 0.0 0.1 0:00.00 bash | |
| 9904 vagrant 20 0 11136 592 368 S 0.0 0.1 0:00.00 bash | |
| 9905 vagrant 20 0 11136 592 368 S 0.0 0.1 0:00.00 bash | |
| 9906 vagrant 20 0 91152 2932 2040 S 0.0 0.3 0:00.00 bamtofastq | |
| 9907 vagrant 20 0 9084 420 320 S 0.0 0.0 0:00.00 bgzip | |
| 9908 vagrant 20 0 9084 420 320 S 0.0 0.0 0:00.00 bgzip | |
| 9909 vagrant 20 0 4444 656 556 S 0.0 0.1 0:00.00 sh | |
| 9910 vagrant 20 0 23536 1392 1052 R 0.0 0.1 0:00.00 top | |
| 32158 root 20 0 0 0 0 S 0.0 0.0 0:04.95 kworker/u2:0 | |
| AutoArray<unsigned long,alloc_type_cxx> failed to allocate 134217728 elements (1073741824 bytes) | |
| current total allocation 1074215981 | |
| /usr/local/lib/libmaus.so.0(_ZN7libmaus4util10StackTraceC1Ev+0x4c) [0x7f22312be866:??:0] | |
| /usr/local/bin/bamtofastq(_ZN7libmaus9exception16LibMausExceptionC2Ev+0x1d) [0x412873:??:?] | |
| /usr/local/bin/bamtofastq(_ZN7libmaus9autoarray9AutoArrayImLNS0_10alloc_typeE0EE13allocateArrayEm+0x79) [0x41cc45:??:?] | |
| /usr/local/bin/bamtofastq(_ZN7libmaus9autoarray9AutoArrayImLNS0_10alloc_typeE0EEC2Emb+0x27) [0x41cd95:??:?] | |
| /usr/local/bin/bamtofastq() [0x443274:??:?] | |
| /usr/local/bin/bamtofastq() [0x40ef57:??:?] | |
| /usr/local/bin/bamtofastq() [0x40feea:??:?] | |
| /usr/local/bin/bamtofastq() [0x40bde8:??:?] | |
| /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x7f2230179ec5:??:0] | |
| /usr/local/bin/bamtofastq() [0x40d978:??:?] | |
| ' returned non-zero exit status 1 | |
| ERROR | |
| Create a project template from input files and metadata configuration. ... variant_regions ../data/100326_FC6107FAAXX/test.bed | |
| sex female | |
| description 7_1 | |
| batch 1a | |
| variant_regions ../data/100326_FC6107FAAXX/test.bed | |
| sex | |
| description 8_1 | |
| batch 1a | |
| Configuration file created at: /home/vagrant/bcbio-nextgen/tests/test_automated_output/100326/config/100326.yaml | |
| Edit to finalize and run with: | |
| cd /home/vagrant/bcbio-nextgen/tests/test_automated_output/100326/work | |
| bcbio_nextgen.py ../config/100326.yaml | |
| ok | |
| Identify programs and versions used in analysis. ... [{'program': 'bcbio-nextgen', 'version': '0.8.3a-9f027b9'}, {'program': 'alientrimmer', 'version': '0.3.2'}, {'program': 'bamtools', 'version': '2.3.0'}, {'program': 'bcbio_variation', 'version': '0.1.7'}, {'program': 'bcftools', 'version': '1.1'}, {'program': 'bedtools', 'version': '2.21.0'}, {'program': 'biobambam', 'version': '0.0.154'}, {'program': 'bowtie2', 'version': '2.2.3'}, {'program': 'bwa', 'version': '0.7.10'}, {'program': 'chanjo', 'version': '2.1.2'}, {'program': 'cn.mops', 'version': '1.10.1'}, {'program': 'cufflinks', 'version': '2.1.1'}, {'program': 'cutadapt', 'version': '1.4.2'}, {'program': 'fastqc', 'version': '0.11.2'}, {'program': 'featurecounts', 'version': '1.4.4'}, {'program': 'freebayes', 'version': '0.9.14-15'}, {'program': 'gatk-framework', 'version': '3.2-4'}, {'program': 'gemini', 'version': '0.7.0'}, {'program': 'htseq', 'version': '0.6.1p1'}, {'program': 'mutect', 'version': '1.1.5'}, {'program': 'novoalign', 'version': '3.02.02'}, {'program': 'novosort', 'version': 'V3.00.02'}, {'program': 'oncofuse', 'version': '1.0.7'}, {'program': 'picard', 'version': '1.96'}, {'program': 'platypus-variant', 'version': '0.7.9.2'}, {'program': 'qualimap', 'version': '0.7.1'}, {'program': 'rnaseqc', 'version': '1.1.7'}, {'program': 'sambamba', 'version': '0.4.7'}, {'program': 'samtools', 'version': '1.1'}, {'program': 'snpeff', 'version': '3.6c'}, {'program': 'tophat', 'version': '2.0.9'}, {'program': 'varscan', 'version': '2.3.7'}, {'program': 'vcflib', 'version': '2014-08-13'}, {'program': 'vt', 'version': '2014-08-16'}, {'program': 'gatk', 'version': ''}] | |
| ok | |
| Parallel combination of VCF files, split by chromosome. ... [2014-10-03 01:42] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: bgzip S1-variants.vcf | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bgzip -c /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants.vcf > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmph3pj0F/S1-variants.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: tabix index S1-variants.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpIwuhxw/S1-variants.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: bgzip S2-variants.vcf | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bgzip -c /home/vagrant/bcbio-nextgen/tests/data/variants/S2-variants.vcf > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpmrXBs8/S2-variants.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: tabix index S2-variants.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpQuaySZ/S2-variants.vcf.gz | |
| [2014-10-03 01:42] INFO: bcbio-nextgen: multiprocessing: merge_variant_files | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Merge variants | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools merge -O z -r chrM `cat /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/S1_S2-combined-chrM-files.txt` > /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmpoNQJLy/S1_S2-combined-chrM.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: tabix index S1_S2-combined-chrM.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmp5ZWzL1/S1_S2-combined-chrM.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Merge variants | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools merge -O z -r chr22 `cat /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/S1_S2-combined-chr22-files.txt` > /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmpErtpA7/S1_S2-combined-chr22.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: tabix index S1_S2-combined-chr22.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-regions/tx/tmp7j4JNd/S1_S2-combined-chr22.vcf.gz | |
| [2014-10-03 01:42] INFO: bcbio-nextgen: multiprocessing: concat_variant_files | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Concat variant files | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/gatk-framework org.broadinstitute.gatk.tools.CatVariants -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-files.list -out /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpPKLNAO/S1_S2-combined.vcf.gz -assumeSorted -Xms500m -Xmx3500m -XX:+UseSerialGC | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:45,840 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:45,844 HelpFormatter - Program Name: org.broadinstitute.gatk.tools.CatVariants | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:45,847 HelpFormatter - Program Args: -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa -V /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined-files.list -out /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpPKLNAO/S1_S2-combined.vcf.gz -assumeSorted | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:45,872 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_65-b32. | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:45,873 HelpFormatter - Date/Time: 2014/10/03 01:42:45 | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:45,873 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:45,873 HelpFormatter - ------------------------------------------------------- | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: .. | |
| ok | |
| Exclude samples from VCF files. ... [2014-10-03 01:42] DEBUG: bcbio-nextgen: Exclude samples: ['S1'] | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools view -O z -s S2 /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined.vcf.gz > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpIVS2MF/S1_S2-combined-exclude.vcf.gz | |
| ok | |
| Split a VCF file into SNPs and indels, then combine back together. ... [2014-10-03 01:42] DEBUG: bcbio-nextgen: Subset to SNPs and indels | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools view -O v /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants.vcf --types snps > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpeeO6MI/S1-variants-snp.vcf | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Subset to SNPs and indels | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools view -O v /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants.vcf --exclude-types snps > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmp1Jn0i6/S1-variants-indel.vcf | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Resource requests: ; memory: 1.0; cores: 1 | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Configuring 1 jobs to run, using 1 cores each with 1.2g of memory reserved for each job | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: bgzip S1-variants-snp.vcf | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bgzip -c /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-snp.vcf > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpn5tLKi/S1-variants-snp.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: tabix index S1-variants-snp.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpXvxMKj/S1-variants-snp.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: bgzip S1-variants-indel.vcf | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bgzip -c /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-indel.vcf > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpJ2nKJF/S1-variants-indel.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: tabix index S1-variants-indel.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpuwgsra/S1-variants-indel.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: Combine variant files | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/gatk-framework -Xms500m -Xmx3500m -XX:+UseSerialGC -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --out /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpznICnq/S1-variants-merge.vcf.gz --variant:v0 /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-snp.vcf.gz --variant:v1 /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:47,834 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:47,836 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-18-g478145d, Compiled 2014/09/19 01:24:53 | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:47,837 HelpFormatter - Copyright (c) 2010 The Broad Institute | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:47,837 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:47,840 HelpFormatter - Program Args: -U LENIENT_VCF_PROCESSING --read_filter BadCigar --read_filter NotPrimaryAlignment -T CombineVariants -R /home/vagrant/bcbio-nextgen/tests/data/genomes/hg19/seq/hg19.fa --out /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpznICnq/S1-variants-merge.vcf.gz --variant:v0 /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-snp.vcf.gz --variant:v1 /home/vagrant/bcbio-nextgen/tests/data/variants/S1-variants-indel.vcf.gz --rod_priority_list v0,v1 --suppressCommandLineHeader --setKey null | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:47,850 HelpFormatter - Executing as vagrant@vagrant-ubuntu-trusty-64 on Linux 3.13.0-35-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_65-b32. | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:47,851 HelpFormatter - Date/Time: 2014/10/03 01:42:47 | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:47,851 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:47,852 HelpFormatter - --------------------------------------------------------------------------------- | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:47,945 GenomeAnalysisEngine - Strictness is SILENT | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:47,989 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: WARN 01:42:48,028 IndexDictionaryUtils - Track v0 doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: WARN 01:42:48,034 IndexDictionaryUtils - Track v1 doesn't have a sequence dictionary built in, skipping dictionary validation | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:48,145 GenomeAnalysisEngine - Preparing for traversal | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:48,146 GenomeAnalysisEngine - Done preparing for traversal | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:48,147 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:48,148 ProgressMeter - | processed | time | per 1M | | total | remaining | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:48,149 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:48,287 ProgressMeter - done 12.0 0.0 s 3.2 h 45.7% 0.0 s 0.0 s | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: INFO 01:42:48,288 ProgressMeter - Total runtime 0.14 secs, 0.00 min, 0.00 hours | |
| ok | |
| Select a sample from a VCF file. ... [2014-10-03 01:42] DEBUG: bcbio-nextgen: Select sample: S2 | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/bcftools view -O z /home/vagrant/bcbio-nextgen/tests/data/variants/S1_S2-combined.vcf.gz -s S2 > /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmp5hXUwl/S1_S2-combined-sampleselect.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen: tabix index S1_S2-combined-sampleselect.vcf.gz | |
| [2014-10-03 01:42] DEBUG: bcbio-nextgen-commands: /usr/local/bin/tabix -f -p vcf /home/vagrant/bcbio-nextgen/tests/data/variants/tx/tmpHIauLo/S1_S2-combined-sampleselect.vcf.gz | |
| ok | |
| Ensure we can correctly find paired fastq files. ... ok | |
| ====================================================================== | |
| ERROR: Test variant calling with GATK pipeline. | |
| ---------------------------------------------------------------------- | |
| Traceback (most recent call last): | |
| File "/home/vagrant/bcbio-nextgen/tests/test_automated_analysis.py", line 249, in test_1_variantcall | |
| subprocess.check_call(cl) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/subprocess.py", line 540, in check_call | |
| raise CalledProcessError(retcode, cmd) | |
| CalledProcessError: Command '['bcbio_nextgen.py', '/home/vagrant/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/home/vagrant/bcbio-nextgen/tests/data/automated/../100326_FC6107FAAXX', '/home/vagrant/bcbio-nextgen/tests/data/automated/run_info-variantcall.yaml']' returned non-zero exit status 1 | |
| ====================================================================== | |
| ERROR: Allow BAM files as input to pipeline. | |
| ---------------------------------------------------------------------- | |
| Traceback (most recent call last): | |
| File "/home/vagrant/bcbio-nextgen/tests/test_automated_analysis.py", line 261, in test_5_bam | |
| subprocess.check_call(cl) | |
| File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/subprocess.py", line 540, in check_call | |
| raise CalledProcessError(retcode, cmd) | |
| CalledProcessError: Command '['bcbio_nextgen.py', '/home/vagrant/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/home/vagrant/bcbio-nextgen/tests/data/automated/run_info-bam.yaml']' returned non-zero exit status 1 | |
| ---------------------------------------------------------------------- | |
| Ran 11 tests in 149.015s | |
| FAILED (errors=2) | |
| vagrant@vagrant-ubuntu-trusty-64:~/bcbio-nextgen/tests$ |
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Hi @pfaucon,
Thanks for the note and sorry for the trouble. Unfortunately we can't ship GATK due to licensing issues so you have to install that yourself. We have some instructions here:
http://bcbio-nextgen.readthedocs.org/en/latest/contents/installation.html#gatk-and-mutect
If you follow those instructions and install GATK, does it fix the issue?