gistcli - Paste

file1.txt

tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2015-06-17 15:09:12,936 Creating repository dependency objects...
tool_shed.util.shed_util_common DEBUG 2015-06-17 15:09:14,291 Updating an existing row for repository 'package_r_ggplot2_0_9_3' in the tool_shed_repository table, status set to 'New'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2015-06-17 15:09:14,328 Skipping installation of revision 5824d2b3bc8b of repository 'package_r_2_11_0' because it was installed with the (possibly updated) revision 5824d2b3bc8b and its current installation status is 'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager DEBUG 2015-06-17 15:09:14,328 Building repository dependency relationships...
warning: toolshed.g2.bx.psu.edu certificate with fingerprint bb:68:8f:9b:a4:ba:4e:6d:b6:59:7c:f2:43:19:c5:fc:95:a3:38:ea not verified (check hostfingerprints or web.cacerts config setting)
tool_shed.galaxy_install.install_manager ERROR 2015-06-17 15:09:17,554 No content returned from tool shed repository version request to https://toolshed.g2.bx.psu.edu/repository/get_tool_versions?name=package_r_ggplot2_0_9_3&owner=iuc&changeset_revision=87a27fc31fb5
tool_shed.util.tool_dependency_util DEBUG 2015-06-17 15:09:18,272 Updating an existing record for version 2.11.0 of tool dependency R for revision 87a27fc31fb5 of repository package_r_ggplot2_0_9_3 by updating the status from Uninstalled to Never installed.
tool_shed.util.tool_dependency_util DEBUG 2015-06-17 15:09:18,311 Updating an existing record for version 0.9.3 of tool dependency ggplot2 for revision 87a27fc31fb5 of repository package_r_ggplot2_0_9_3 by updating the status from Uninstalled to Never installed.
tool_shed.util.tool_dependency_util DEBUG 2015-06-17 15:09:18,487 Updating an existing record for version 0.9.3 of tool dependency ggplot2 for revision 87a27fc31fb5 of repository package_r_ggplot2_0_9_3 by updating the status from Never installed to Installing.
tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG 2015-06-17 15:09:18,538 Handling setup_r_environment for tool dependency ggplot2 with install_environment.env_shell_file_paths:
['/scicore/projects/galaxy/galaxy-dist/tools_dependencies/R/2.11.0/devteam/package_r_2_11_0/5824d2b3bc8b/env.sh']

ERROR: this R is version 2.11.0, package 'colorspace' requires R >=  2.13.0
Warning message:
In install.packages(c("colorspace_1.2-4.tar.gz"), lib = "/scicore/projects/galaxy/galaxy-dist/tools_dependencies/ggplot2/0.9.3/iuc/package_r_ggplot2_0_9_3/87a27fc31fb5",  :
  installation of package 'colorspace_1.2-4.tar.gz' had non-zero exit status
ERROR: this R is version 2.11.0, package 'stringr' requires R >= 2.14
Warning message:
In install.packages(c("stringr_0.6.2.tar.gz"), lib = "/scicore/projects/galaxy/galaxy-dist/tools_dependencies/ggplot2/0.9.3/iuc/package_r_ggplot2_0_9_3/87a27fc31fb5",  :
  installation of package 'stringr_0.6.2.tar.gz' had non-zero exit status
* 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’ ...
** 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 ‘munsell’ ...
** R
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths())) :
  there is no package called 'colorspace'
ERROR: lazy loading failed for package ‘munsell’
* removing ‘/scicore/projects/galaxy/galaxy-dist/tools_dependencies/ggplot2/0.9.3/iuc/package_r_ggplot2_0_9_3/87a27fc31fb5/munsell’
Warning message:
In install.packages(c("munsell_0.4.2.tar.gz"), lib = "/scicore/projects/galaxy/galaxy-dist/tools_dependencies/ggplot2/0.9.3/iuc/package_r_ggplot2_0_9_3/87a27fc31fb5",  :
  installation of package 'munsell_0.4.2.tar.gz' had non-zero exit status
* installing *source* package ‘labeling’ ...
** R
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (labeling)
* installing *source* package ‘plyr’ ...
** libs
g++ -I/scicore/projects/galaxy/galaxy-dist/tools_dependencies/R/2.11.0/devteam/package_r_2_11_0/5824d2b3bc8b/lib/R/include  -I/galaxy/builds/Linux-x86_64/install_dir/include    -fpic  -I/galaxy/builds/Linux-x86_64/install_dir/include -c RcppExports.cpp -o RcppExports.o
RcppExports.cpp:4:18: error: Rcpp.h: No such file or directory
RcppExports.cpp:6: error: ‘Rcpp’ is not a namespace-name
RcppExports.cpp:6: error: expected namespace-name before ‘;’ token
RcppExports.cpp:9: error: ‘List’ does not name a type
RcppExports.cpp:10: error: ‘RcppExport’ does not name a type
RcppExports.cpp:25: error: expected constructor, destructor, or type conversion before ‘<’ token
RcppExports.cpp:26: error: ‘RcppExport’ does not name a type
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘plyr’
* removing ‘/scicore/projects/galaxy/galaxy-dist/tools_dependencies/ggplot2/0.9.3/iuc/package_r_ggplot2_0_9_3/87a27fc31fb5/plyr’
Warning message:
In install.packages(c("plyr_1.8.1.tar.gz"), lib = "/scicore/projects/galaxy/galaxy-dist/tools_dependencies/ggplot2/0.9.3/iuc/package_r_ggplot2_0_9_3/87a27fc31fb5",  :
  installation of package 'plyr_1.8.1.tar.gz' had non-zero exit status
* installing *source* package ‘digest’ ...
** libs
install_environment.STDOUT DEBUG 2015-06-17 15:09:53,973 -I/galaxy/builds/Linux-x86_64/install_dir/include -c aes.c -o aes.o
-I/galaxy/builds/Linux-x86_64/install_dir/include -c aes.c -o aes.o
install_environment.STDOUT DEBUG 2015-06-17 15:09:54,364 e    -fpic  -I/galaxy/builds/Linux-x86_64/install_dir/include -c crc32.c -o crc32.o
e    -fpic  -I/galaxy/builds/Linux-x86_64/install_dir/include -c crc32.c -o crc32.o
gcc -std=gnu99 -I/scicore/projects/galaxy/galaxy-dist/tools_dependencies/R/2.11.0/devteam/package_r_2_11_0/5824d2b3bc8b/lib/R/include  -I/galaxy/builds/Linux-x86_64/install_dir/include    -fpic  gcc -std=gnu99 -I/scicore/projects/galaxy/galaxy-dist/tools_dependencies/R/2.11.0/devteam/package_r_2_11_0/5824d2b3bc8b/lib/R/include  -I/galaxy/builds/Linux-x86_64/install_dir/includgcc -std=gnu99 -I/scicore/projects/galaxy/galaxy-dist/tools_dependencies/R/2.11.0/devteam/pack -I/galaxy/builds/Linux-x86_64/install_dir/include -c digest.c -o digest.o
install_environment.STDOUT DEBUG 2015-06-17 15:09:55,037 age_r_2_11_0/5824d2b3bc8b/lib/R/include  -I/galaxy/builds/Linux-x86_64/install_dir/include    -fpic /include  -I/galaxy/buildude    -fpic  -I/galaxy/builds/Linux-x86_64/install_dir/include -c md5.c -o md5.o
age_r_2_11_0/5824d2b3bc8b/lib/R/include  -I/galaxy/builds/Linux-x86_64/install_dir/include    -fpic /include  -I/galaxy/buildude    -fpic  -I/galaxy/builds/Linux-x86_64/install_dir/include -c md5.c -o md5.o
install_environment.STDOUT DEBUG 2015-06-17 15:09:55,206 ilds/Linux-x86_64/install_dir/include    -fpic  -I/galaxy/builds/Linux-x86_64/install_dir/include -c raes.c -o raes.o
ilds/Linux-x86_64/install_dir/include    -fpic  -I/galaxy/builds/Linux-x86_64/install_dir/include -c raes.c -o raes.o
gcc -std=gnu99 -I/scicore/projects/galaxy/galaxy-dist/tools_dependencies/R/2.11.0/devteam/package_r_2_11_0/5824d2b3bc8b/lib/Rs/Linux-x86_64/install_dir/inclgcc -std=gnu99 -I/scicore/projects/galaxy/galaxy-dist/tools_dependencies/R/2.11.0/devteam/package_r_2_11_0/5824d2b3bc8b/lib/R/include  -I/galaxy/bugcc -std=gnu99 -I/scicore/projects/galaxy/galaxy-dist/tools_dependencies/R/2.11.0/devteam/package_r_2_11_0/5824d2b3bc8b/lib/R/include  -I/galaxy/builds/Linux-x86_64/install_dir/include    -fpic  -I/galaxy/builds/Linux-x86_64/install_dir/include -c sha1.c -o sha1.o
x-x86_64/install_dir/include    -fpic  -I/galaxy/builds/Linux-x86_64/install_dir/include -c sha2.c -o sha2.o
am/package_r_2_11_0/5824d2b3bc8b/lib/R/include  -I/galaxy/builds/Linux-x86_64/install_dir/include    sha256.c -o sha256.o
gcc -std=gnu99 -shared -Wl,-rpath,$ORIGIN/../lib -L/galaxy/builds/Linux-x86_64/install_dir/lib -o digest.so aes.o crc32.o dig-dist/tools_dependencies/R/2.11.0/devteam/package_r_2_11_0/5824d2b3bc8b/lib/R/lib -lR
installing to /scicore/projects/galaxy/galaxy-dist/tools_dependencies/ggplot2/0.9.3/iuc/package_r_ggplot2_0_9_3/87a27fc31fb5/digest/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
install_environment.STDOUT DEBUG 2015-06-17 15:09:57,281 gcc -std=gnu99 -I/scicore/projects/galaxy/galaxy-dist/tools_dependencies/R/2.11.0/devteam/package_r_2_11_0/5824d2b3bc8b/lib/R/include  -I/galaxy/builds/Linugcc -std=gnu99 -I/scicore/projects/galaxy/galaxy-dist/tools_dependencies/R/2.11.0/devte -fpic  -I/galaxy/builds/Linux-x86_64/install_dir/include -cest.o md5.o raes.o sha1.o sha2.o sha256.o -L/scicore/projects/galaxy/galaxy
gcc -std=gnu99 -I/scicore/projects/galaxy/galaxy-dist/tools_dependencies/R/2.11.0/devteam/package_r_2_11_0/5824d2b3bc8b/lib/R/include  -I/galaxy/builds/Linugcc -std=gnu99 -I/scicore/projects/galaxy/galaxy-dist/tools_dependencies/R/2.11.0/devte -fpic  -I/galaxy/builds/Linux-x86_64/install_dir/include -cest.o md5.o raes.o sha1.o sha2.o sha256.o -L/scicore/projects/galaxy/galaxy
* DONE (digest)
ERROR: this R is version 2.11.0, package 'gtable' requires R >= 2.14
Warning message:
In install.packages(c("gtable_0.1.2.tar.gz"), lib = "/scicore/projects/galaxy/galaxy-dist/tools_dependencies/ggplot2/0.9.3/iuc/package_r_ggplot2_0_9_3/87a27fc31fb5",  :
  installation of package 'gtable_0.1.2.tar.gz' had non-zero exit status
* installing *source* package ‘reshape2’ ...
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths())) :
  there is no package called 'plyr'
ERROR: lazy loading failed for package ‘reshape2’
* removing ‘/scicore/projects/galaxy/galaxy-dist/tools_dependencies/ggplot2/0.9.3/iuc/package_r_ggplot2_0_9_3/87a27fc31fb5/reshape2’
Warning message:
In install.packages(c("reshape2_1.2.2.tar.gz"), lib = "/scicore/projects/galaxy/galaxy-dist/tools_dependencies/ggplot2/0.9.3/iuc/package_r_ggplot2_0_9_3/87a27fc31fb5",  :
  installation of package 'reshape2_1.2.2.tar.gz' had non-zero exit status
ERROR: this R is version 2.11.0, package 'scales' requires R >= 2.12
Warning message:
In install.packages(c("scales_0.2.3.tar.gz"), lib = "/scicore/projects/galaxy/galaxy-dist/tools_dependencies/ggplot2/0.9.3/iuc/package_r_ggplot2_0_9_3/87a27fc31fb5",  :
  installation of package 'scales_0.2.3.tar.gz' had non-zero exit status
* installing *source* package ‘proto’ ...
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (proto)
Debug at: https://galaxy.scicore.unibas.ch/_debug/view/1433419623
ERROR: this R is version 2.11.0, package 'ggplot2' requires R >= 2.14
Warning message:
In install.packages(c("ggplot2_0.9.3.1.tar.gz"), lib = "/scicore/projects/galaxy/galaxy-dist/tools_dependencies/ggplot2/0.9.3/iuc/package_r_ggplot2_0_9_3/87a27fc31fb5",  :
  installation of package 'ggplot2_0.9.3.1.tar.gz' had non-zero exit status
tool_shed.galaxy_install.install_manager DEBUG 2015-06-17 15:10:16,229 Changing status for tool dependency ggplot2 from Installing to Installed.
tool_shed.galaxy_install.install_manager DEBUG 2015-06-17 15:10:16,277 Tool dependency ggplot2 version 0.9.3 has been installed in /scicore/projects/galaxy/galaxy-dist/tools_dependencies/ggplot2/0.9.3/iuc/package_r_ggplot2_0_9_3/87a27fc31fb5.
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 38165)
Traceback (most recent call last):
  File "/scicore/projects/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/usr/lib64/python2.7/SocketServer.py", line 334, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib64/python2.7/SocketServer.py", line 657, in __init__
    self.finish()
  File "/usr/lib64/python2.7/SocketServer.py", line 716, in finish
    self.wfile.close()
  File "/usr/lib64/python2.7/socket.py", line 279, in close
    self.flush()
  File "/usr/lib64/python2.7/socket.py", line 303, in flush
    self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
----------------------------------------