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lzamparo/conda info

Created December 18, 2015 00:48
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conda install scikit-bio fail
Raw
conda info
mski1743:Submission zamparol$ conda info
Current conda install:
platform : osx-64
conda version : 3.19.0
conda-build version : 1.11.0
python version : 2.7.11.final.0
requests version : 2.9.0
root environment : /Users/zamparol/anaconda (writable)
default environment : /Users/zamparol/anaconda
envs directories : /Users/zamparol/anaconda/envs
package cache : /Users/zamparol/anaconda/pkgs
channel URLs : https://repo.continuum.io/pkgs/free/osx-64/
https://repo.continuum.io/pkgs/free/noarch/
https://repo.continuum.io/pkgs/pro/osx-64/
https://repo.continuum.io/pkgs/pro/noarch/
config file : None
is foreign system : False
Raw
conda install scikit-bio
mski1743:Submission zamparol$ conda install scikit-bio
Fetching package metadata: ....
Solving package specifications: ...............................
Package plan for installation in environment /Users/zamparol/anaconda:
The following packages will be downloaded:
package | build
---------------------------|-----------------
appnope-0.1.0 | py27_0 4 KB
bz2file-0.98 | py27_0 10 KB
contextlib2-0.4.0 | py27_0 6 KB
decorator-4.0.4 | py27_0 11 KB
future-0.15.2 | py27_0 616 KB
ipython_genutils-0.1.0 | py27_0 32 KB
lockfile-0.10.2 | py27_0 14 KB
natsort-4.0.3 | py27_0 39 KB
path.py-8.1.2 | py27_1 45 KB
pexpect-3.3 | py27_0 60 KB
python.app-1.2 | py27_4 7 KB
simplegeneric-0.8.1 | py27_0 6 KB
cachecontrol-0.11.5 | py27_0 19 KB
pickleshare-0.5 | py27_0 8 KB
scipy-0.16.1 | np110py27_p0 11.8 MB
traitlets-4.0.0 | py27_0 88 KB
ipython-4.0.1 | py27_0 917 KB
pandas-0.17.1 | np110py27_0 6.3 MB
scikit-bio-0.4.0 | np110py27_0 744 KB
------------------------------------------------------------
Total: 20.7 MB
The following NEW packages will be INSTALLED:
appnope: 0.1.0-py27_0
bz2file: 0.98-py27_0
cachecontrol: 0.11.5-py27_0
contextlib2: 0.4.0-py27_0
future: 0.15.2-py27_0
ipython_genutils: 0.1.0-py27_0
lockfile: 0.10.2-py27_0
natsort: 4.0.3-py27_0
path.py: 8.1.2-py27_1
pexpect: 3.3-py27_0
pickleshare: 0.5-py27_0
scikit-bio: 0.4.0-np110py27_0
simplegeneric: 0.8.1-py27_0
traitlets: 4.0.0-py27_0
The following packages will be UPDATED:
decorator: 3.4.0-py27_0 --> 4.0.4-py27_0
ipython: 3.0.0-py27_0 --> 4.0.1-py27_0
pandas: 0.17.0-np110py27_0 --> 0.17.1-np110py27_0
python.app: 1.2-py27_3 --> 1.2-py27_4
scipy: 0.16.0-np19py27_p1 [mkl] --> 0.16.1-np110py27_p0 [mkl]
Proceed ([y]/n)? y
Fetching packages ...
appnope-0.1.0- 100% |#######################################################################################################| Time: 0:00:00 1.91 MB/s
bz2file-0.98-p 100% |#######################################################################################################| Time: 0:00:00 1.26 MB/s
contextlib2-0. 100% |#######################################################################################################| Time: 0:00:00 2.69 MB/s
decorator-4.0. 100% |#######################################################################################################| Time: 0:00:00 9.97 MB/s
future-0.15.2- 100% |#######################################################################################################| Time: 0:00:00 7.35 MB/s
ipython_genuti 100% |#######################################################################################################| Time: 0:00:00 2.40 MB/s
lockfile-0.10. 100% |#######################################################################################################| Time: 0:00:00 1.35 MB/s
natsort-4.0.3- 100% |#######################################################################################################| Time: 0:00:00 2.17 MB/s
path.py-8.1.2- 100% |#######################################################################################################| Time: 0:00:00 3.70 MB/s
pexpect-3.3-py 100% |#######################################################################################################| Time: 0:00:00 3.01 MB/s
python.app-1.2 100% |#######################################################################################################| Time: 0:00:00 2.21 MB/s
simplegeneric- 100% |#######################################################################################################| Time: 0:00:00 2.68 MB/s
cachecontrol-0 100% |#######################################################################################################| Time: 0:00:00 2.55 MB/s
pickleshare-0. 100% |#######################################################################################################| Time: 0:00:00 3.08 MB/s
scipy-0.16.1-n 100% |#######################################################################################################| Time: 0:00:01 8.87 MB/s
traitlets-4.0. 100% |#######################################################################################################| Time: 0:00:00 4.77 MB/s
ipython-4.0.1- 100% |#######################################################################################################| Time: 0:00:00 7.96 MB/s
pandas-0.17.1- 100% |#######################################################################################################| Time: 0:00:00 8.85 MB/s
scikit-bio-0.4 100% |#######################################################################################################| Time: 0:00:00 5.66 MB/s
Extracting packages ...
[ COMPLETE ]|##########################################################################################################################| 100%
Unlinking packages ...
[ COMPLETE ]|##########################################################################################################################| 100%
Linking packages ...
An unexpected error has occurred, please consider sending the############################################################################# | 94%
following traceback to the conda GitHub issue tracker at:
https://github.com/conda/conda/issues
Include the output of the command 'conda info' in your report.
Traceback (most recent call last):
File "/Users/zamparol/anaconda/bin/conda", line 5, in <module>
sys.exit(main())
File "/Users/zamparol/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 195, in main
args_func(args, p)
File "/Users/zamparol/anaconda/lib/python2.7/site-packages/conda/cli/main.py", line 202, in args_func
args.func(args, p)
File "/Users/zamparol/anaconda/lib/python2.7/site-packages/conda/cli/main_install.py", line 45, in execute
install.install(args, parser, 'install')
File "/Users/zamparol/anaconda/lib/python2.7/site-packages/conda/cli/install.py", line 423, in install
plan.execute_actions(actions, index, verbose=not args.quiet)
File "/Users/zamparol/anaconda/lib/python2.7/site-packages/conda/plan.py", line 537, in execute_actions
inst.execute_instructions(plan, index, verbose)
File "/Users/zamparol/anaconda/lib/python2.7/site-packages/conda/instructions.py", line 148, in execute_instructions
cmd(state, arg)
File "/Users/zamparol/anaconda/lib/python2.7/site-packages/conda/instructions.py", line 91, in LINK_CMD
link(state['prefix'], arg, index=state['index'])
File "/Users/zamparol/anaconda/lib/python2.7/site-packages/conda/instructions.py", line 87, in link
install.link(pkgs_dir, prefix, dist, lt, index=index)
File "/Users/zamparol/anaconda/lib/python2.7/site-packages/conda/install.py", line 616, in link
os.makedirs(dst_dir)
File "/Users/zamparol/anaconda/lib/python2.7/os.py", line 157, in makedirs
mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/Users/zamparol/anaconda/lib/python2.7/site-packages/skbio/draw'
Raw
sudo pip install pyensembl
mski1743:Submission zamparol$ sudo pip install pyensembl
The directory '/Users/zamparol/Library/Caches/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/Users/zamparol/Library/Caches/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Collecting pyensembl
Requirement already satisfied (use --upgrade to upgrade): memoized-property>=1.0.2 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from pyensembl)
Requirement already satisfied (use --upgrade to upgrade): pandas>=0.15 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from pyensembl)
Requirement already satisfied (use --upgrade to upgrade): typechecks>=0.0.2 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from pyensembl)
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.7 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from pyensembl)
Collecting scikit-bio>=0.4.0 (from pyensembl)
Downloading scikit-bio-0.4.1.tar.gz (8.1MB)
100% |████████████████████████████████| 8.1MB 41kB/s
Requirement already satisfied (use --upgrade to upgrade): datacache>=0.4.16 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from pyensembl)
Collecting gtfparse>=0.0.3 (from pyensembl)
Requirement already satisfied (use --upgrade to upgrade): six>=1.9.0 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from pyensembl)
Requirement already satisfied (use --upgrade to upgrade): python-dateutil in /Users/zamparol/anaconda/lib/python2.7/site-packages (from pandas>=0.15->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): pytz>=2011k in /Users/zamparol/anaconda/lib/python2.7/site-packages (from pandas>=0.15->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): bz2file>=0.98 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): lockfile>=0.10.2 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): CacheControl>=0.11.5 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): contextlib2>=0.4.0 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): decorator>=3.4.2 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): future>=0.14.3 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): IPython>=3.2.0 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): matplotlib>=1.4.3 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): natsort>=4.0.3 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): scipy>=0.15.1 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): nose>=1.3.7 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): requests>=2.5.1 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from datacache>=0.4.16->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): appdirs>=1.4.0 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from datacache>=0.4.16->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): progressbar33>=2.4 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from datacache>=0.4.16->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): biopython>=1.65 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from datacache>=0.4.16->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): traitlets in /Users/zamparol/anaconda/lib/python2.7/site-packages (from IPython>=3.2.0->scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): pickleshare in /Users/zamparol/anaconda/lib/python2.7/site-packages (from IPython>=3.2.0->scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): simplegeneric>0.8 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from IPython>=3.2.0->scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): gnureadline in /Users/zamparol/anaconda/lib/python2.7/site-packages (from IPython>=3.2.0->scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): appnope in /Users/zamparol/anaconda/lib/python2.7/site-packages (from IPython>=3.2.0->scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): pexpect in /Users/zamparol/anaconda/lib/python2.7/site-packages (from IPython>=3.2.0->scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): cycler in /Users/zamparol/anaconda/lib/python2.7/site-packages (from matplotlib>=1.4.3->scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): pyparsing!=2.0.4,>=1.5.6 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from matplotlib>=1.4.3->scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): ipython-genutils in /Users/zamparol/anaconda/lib/python2.7/site-packages (from traitlets->IPython>=3.2.0->scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): path.py in /Users/zamparol/anaconda/lib/python2.7/site-packages (from pickleshare->IPython>=3.2.0->scikit-bio>=0.4.0->pyensembl)
Requirement already satisfied (use --upgrade to upgrade): ptyprocess>=0.5 in /Users/zamparol/anaconda/lib/python2.7/site-packages (from pexpect->IPython>=3.2.0->scikit-bio>=0.4.0->pyensembl)
Installing collected packages: scikit-bio, gtfparse, pyensembl
Running setup.py install for scikit-bio
Successfully installed gtfparse-0.0.5 pyensembl-0.8.4 scikit-bio-0.4.1
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