Hi Greg,
Good progress - no sign of the unicode error :)
I now have the following three repositories shown under
"Latest revision: installation errors"
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
(Seems to list both a failed and a successful BLAST+ 2.2.29 install?)
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26
(No error?)
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_28
(No error?)
On the other hand,
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_27
(No test/install results?)
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_29
Looks good.
So it seems there is still something not quite right here…
We've eliminated the use of fabric for installing tool dependencies on the test tool shed, and with this change I've seen the test tool shed fail at the same point the past 3 runs. It fails attempting to compile boost where it times out ( we have abuildbot timeout set at 36000 seconds if nothing occurs). This error occurs about half way through Stage 1 of the test run, so about 1/2 of the tool dependency definition repositories are not tested and no tests are run for repositories with tools.
The following log shows the repeaated compilation error. We'll be investigating approaches for handling issues like this. Now that we've eliminated fabric we'll have many more options for handling installation issues like this. Of course, if it turns out that our new code that eliminated fabric caused this, we'll get a fix in.
fabric_util.STDOUT DEBUG 2014-02-23 20:20:14,740 -- NUMBER_OF_JOBS: 2 (maximal number of concurrent compile jobs)
fabric_util.STDOUT DEBUG 2014-02-23 20:20:14,741 -- Extracting BOOST ..
fabric_util.STDOUT DEBUG 2014-02-23 20:20:20,006 -- Extracting BOOST .. done
fabric_util.STDOUT DEBUG 2014-02-23 20:20:20,006 -- Bootstrapping Boost libraries (./bootstrap.sh --prefix=/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/tmp/tmpShf1jI/tmp-toolshed-mtdq8JEyP/OpenMS-1.11.1/contrib --with-libraries=date_time,iostreams,math,regex) ...
fabric_util.STDOUT DEBUG 2014-02-23 20:20:37,231 -- Bootstrapping Boost libraries (./bootstrap.sh --prefix=/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/tmp/tmpShf1jI/tmp-toolshed-mtdq8JEyP/OpenMS-1.11.1/contrib --with-libraries=iostreams,math,date_time,regex) ... done
fabric_util.STDOUT DEBUG 2014-02-23 20:20:37,232 -- Installing Boost libraries (./bjam -j 2 -sZLIB_SOURCE=/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/tmp/tmpShf1jI/tmp-toolshed-mtdq8JEyP/OpenMS-1.11.1/contrib/src/zlib-1.2.5 -sBZIP2_SOURCE=/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/tmp/tmpShf1jI/tmp-toolshed-mtdq8JEyP/OpenMS-1.11.1/contrib/src/bzip2-1.0.5 link=static cxxflags=-fPIC install --build-type=complete --layout=tagged --threading=single,multi) ...
fabric_util.STDOUT DEBUG 2014-02-23 20:36:11,619 -- Installing Boost libraries (./bjam -j 2 -sZLIB_SOURCE=/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/tmp/tmpShf1jI/tmp-toolshed-mtdq8JEyP/OpenMS-1.11.1/contrib/src/zlib-1.2.5 -sBZIP2_SOURCE=/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/tmp/tmpShf1jI/tmp-toolshed-mtdq8JEyP/OpenMS-1.11.1/contrib/src/bzip2-1.0.5 link=static cxxflags=-fPIC install --build-type=complete --layout=tagged --threading=single,multi) ... failed
Thanks,
Peter