Hello all,
I'm trying to install the intersect tool from the main Tool Shed,
https://toolshed.g2.bx.psu.edu/view/devteam/intersect
One of the dependencies fails to install, with the cryptic message
"Initializing repository installation failed [OK]":
https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7
Un-installing and reinstalling also fails.
$ hg log | head
changeset: 14342:db520d154716
branch: stable
tag: tip
user: Nate Coraor <nate(a)bx.psu.edu>
date: Thu Sep 04 10:00:23 2014 -0400
summary: Update tag latest_2014.08.11 for changeset e8453771b1db
This looks like the relevant chunk from the pasteur.log file:
143.xx.xx.120 - - [19/Mar/2015:12:21:46 +0100] "POST
/galaxy/admin_toolshed/deactivate_or_uninstall_repository?id=31fe793505d893ac
HTTP/1.1" 302 - "http://ppserver/galaxy/admin_
toolshed/deactivate_or_uninstall_repository?id=31fe793505d893ac"
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10.10; rv:36.0) Gecko/20100101
Firefox/36.0"
/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/ven
+++++++++++++++++++++++++++++++++++++++++++++++++
Usage of try_run is deprecated: please do not
use it anymore, and avoid configuration checks
involving running executable on the target machine.
+++++++++++++++++++++++++++++++++++++++++++++++++
Traceback (most recent call last):
File
"/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/bin/pip",
line 8, in <module>
File
"/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/__init__.py",
line 149, in main
File
"/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/basecommand.py",
line 181, in main
File
"/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/log.py",
line 48, in fatal
File
"/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/log.py",
line 75, in log
File
"/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/backwardcompat/__init__.py",
line 88, in fwrite
ValueError: I/O operation on closed file
143.xx.xx.120 - - [19/Mar/2015:12:21:47 +0100] "GET
/galaxy/admin_toolshed/browse_repositories?status=done&message=The+repository+named+%3Cb%3Epackage_bx_python_0_7%3C%2Fb%3E+has+been+uninstalled.++
HTTP/1.1" 200 -
"http://ppserver/galaxy/admin_toolshed/deactivate_or_uninstall_repository?id=31fe793505d893ac"
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10.10; rv:36.0) Gecko/20100101
Firefox/36.0"
DeprecationWarning)
v/build/numpy/numpy/distutils/command/config.py:40: DeprecationWarning:
C compiler: gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC
-fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2
-fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64
-mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC
compile options: '-Inumpy/core/src/private -Inumpy/core/src
-Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray
-Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include
-I/usr/include/python2.6 -c'
gcc: _configtest.c
gcc -pthread _configtest.o -o _configtest
failure.
removing: _configtest.c _configtest.o _configtest
building data_files sources
build_src: building npy-pkg config files
Downloading/unpacking bx-python==0.7.1 (from -r
/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/requirements.txt
(line 3))
Running setup.py egg_info for package bx-python
_configtest
Downloading
http://pypi.python.org/packages/source/d/distribute/distribute-0.6.10.tar.gz
Now working in
/mnt/galaxy/galaxy-dist/database/tmp/tmpes1qm8/distribute-0.6.10
Extracting in /mnt/galaxy/galaxy-dist/database/tmp/tmpes1qm8
Building a Distribute egg in
/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/build/bx-python
ute-0.6.10-py2.6.egg
Installed
/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/build/bx-python/nose-1.3.4-py2.6.egg
Installing collected packages: numpy, bx-python
Running setup.py install for numpy
Error unknown encoding: string-escape while executing command
/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/bin/python
-c "import
setuptools;__file__='/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/build/numpy/setup.py';exec(compile(open(__file__).read().replace('\r\n',
'\n'), __file__, 'exec'))" install --record
/mnt/galaxy/galaxy-dist/database/tmp/pip-wvcoo6-record/install-record.txt
--single-version-externally-managed --install-headers
/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/include/site/python2.6
Exception:
/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/build/bx-python/distrib
no previously-included directories found matching 'doc/.build'
Traceback (most recent call last):
/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/basecommand.py",
line 139, in main
28bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/commands/install.py",
line 271, in run
File
"/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/req.py",
line 1185, in install
File
"/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-
File
"/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/lib/python2.6/site-packages/pip-1.3.1-py2.6.egg/pip/util.py",
line 627, in call_subprocess
File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/subprocess.py", line 1230, in _execute_child
child_exception = pickle.loads(data)
File
"/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca
File
"/mnt/galaxy/galaxy-dist-shed-deps/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c087packages/pip-1.3.1-py2.6.egg/pip/req.py",
line 592, in install
File "/usr/lib64/python2.6/pickle.py", line 1374, in loads
return Unpickler(file).load()
File "/usr/lib64/python2.6/pickle.py", line 858, in load
File "/usr/lib64/python2.6/pickle.py", line 971, in load_string
dispatch[key](self)
LookupError: unknown encoding: string-escape
self.append(rep.decode("string-escape"))
Storing complete log in /mnt/galaxy/.pip/pip.log
143.xx.xx.120 - - [19/Mar/2015:12:20:13 +0100] "POST
/galaxy/admin_toolshed/manage_repositories HTTP/1.1" 302 -
"http://ppserver/galaxy/admin_toolshed/prepare_for_install"
"Mozilla/5.0 (Macintosh; Intel Mac OS X 10.10; rv:36.0) Gecko/20100101
Firefox/36.0"
Other than updating this Galaxy to the March 2015 release, is there
anything which looks suspicious on my side?
Peter