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 <n...@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
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