Hello Peter,

On Feb 24, 2014, at 3:32 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> 
> 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.

Thanks,

Greg Von Kuster

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

command timed out: 36000 seconds without output, attempting to kill
process killed by signal 9



> 
> Thanks,
> 
> Peter

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