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&gt; 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