Greg,

I still get the same traceback. The issue is with installing a repository from testtoolshed, which is running code on the default branch, to a galaxy instance running on the stable branch. My understanding was that the default branch is supposed to be backward- compatible to the stable branch. Please let me know if this is not the case (which would mean that this is not a bug).


The atlas and lapack errors are begin caused by http:// testtoolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7. I'm cc'ing galaxy-iuc so they can look into it further.

Thanks for the report on phast. I'll probably need to use the architecture-dependent compilation stuff you're working on to fix this.

-rico

On Sep 20, 2013, at 11:21 AM, Greg Von Kuster wrote:

Hi Rico,

The test tool shed is now running my latest commit - 10629:ab20415126a7. I was successful with installing the genome diversity repository and all of it's dependencies using that changeset in my local Galaxy environment (although 3 tool dependencies encountered the following errors while attempting to compile).

Can you try again and let me know if you encounter additonal problems?

atlas 3.10.1 package Error cat: ..//CONFIG/src/Makefile: No such file or directory cp: ..//CONFIG/src/atlcomp.txt: No such file or directory make: *** No rule to make target `xconfig'. Stop. /bin/ sh: line 1: ./xconfig: No such file or directory

lapack 3.4.2 package Error CMake Error: your Fortran compiler: "CMAKE_Fortran_COMPILER-NOTFOUND" was not found. Please set CMAKE_Fortran_COMPILER to a valid compiler path or name. CMake Error at /opt/local/share/cmake-2.8/Modules/ CMakeFortranInformation.cmake:27 (get_filename_component): get_filename_component called with incorrect number of arguments Call Stack (most recent call first): CMakeLists.txt:2 (project) CMake Error: CMAKE_Fortran_COMPILER not set, after EnableLanguage CMake Error: Internal CMake error, TryCompile configure of cmake failed CMake Error at /opt/local/share/cmake-2.8/Modules/ CMakeFortranInformation.cmake:27 (get_filename_component): get_filename_component called with incorrect number of arguments Call Stack (most recent call first): CMakeLists.txt:2 (project) CMake Error: CMAKE_Fortran_COMPILER not set, after EnableLanguage CMake Error: Internal CMake error, TryCompile configure of cmake failed CMake Error at /opt/local/share/cmake-2.8/Modules/ CMakeFortranInformation.cmake:27 (get_filename_component): get_filename_component called with incorrect number of arguments Call Stack (most recent call first): CMakeLists.txt:2 (project) CMake Error: CMAKE_Fortran_COMPILER not set, after EnableLanguage CMake Error: Internal CMake error, TryCompile configure of cmake failed CMake Error at /opt/local/share/cmake-2.8/Modules/ CMakeFortranInformation.cmake:27 (get_filename_component): get_filename_component called with incorrect number of arguments Call Stack (most recent call first): CMakeLists.txt:2 (project) CMake Error: CMAKE_Fortran_COMPILER not set, after EnableLanguage CMake Error: Internal CMake error, TryCompile configure of cmake failed CMake Error at /opt/local/share/cmake-2.8/Modules/ CMakeFortranInformation.cmake:27 (get_filename_component): get_filename_component called with incorrect number of arguments Call Stack (most recent call first): CMakeLists.txt:2 (project) CMake Error: CMAKE_Fortran_COMPILER not set, after EnableLanguage CMake Error: Internal CMake error, TryCompile configure of cmake failed


phast 1.3 package Error make[1]: *** No rule to make target `/Users/ gvk/workspace/tool_dependencies/clapack/3.2.1/rico/ package_clapack_3_2_1/56a949e5f998/lapack.a', needed by `/Users/gvk/ workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/ phast-1.3/src/lib/../../lib/liblapack.a'. Stop. make[1]: *** No rule to make target `/Users/gvk/workspace/galaxy-central/database/ tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/dless/../../lib/ libphast.a', needed by `/Users/gvk/workspace/galaxy-central/ database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/dless/../../bin/ dless'. Stop. make[1]: *** No rule to make target `/Users/gvk/ workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/ phast-1.3/src/exoniphy/../../lib/libphast.a', needed by `/Users/ gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/ phast-1.3/src/exoniphy/../../bin/exoniphy'. Stop. make[1]: *** No rule to make target `/Users/gvk/workspace/galaxy-central/database/ tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phastCons/../../lib/ libphast.a', needed by `/Users/gvk/workspace/galaxy-central/ database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phastCons/../../ bin/phastCons'. Stop. make[1]: *** No rule to make target `/Users/ gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/ phast-1.3/src/phastOdds/../../lib/libphast.a', needed by `/Users/ gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/ phast-1.3/src/phastOdds/../../bin/phastOdds'. Stop. make[1]: *** No rule to make target `/Users/gvk/workspace/galaxy-central/database/ tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phastMotif/../../lib/ libphast.a', needed by `/Users/gvk/workspace/galaxy-central/ database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phastMotif/../../ bin/phastMotif'. Stop. make[1]: *** No rule to make target `/Users/ gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/ phast-1.3/src/phyloFit/../../lib/libphast.a', needed by `/Users/gvk/ workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/ phast-1.3/src/phyloFit/../../bin/phyloFit'. Stop. make[1]: *** No rule to make target `/Users/gvk/workspace/galaxy-central/database/ tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phyloBoot/../../lib/ libphast.a', needed by `/Users/gvk/workspace/galaxy-central/ database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/phyloBoot/../../ bin/phyloBoot'. Stop. make[1]: *** No rule to make target `/Users/ gvk/workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/ phast-1.3/src/phyloP/../../lib/libphast.a', needed by `/Users/gvk/ workspace/galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/ phast-1.3/src/phyloP/../../bin/phyloP'. Stop. make[1]: *** No rule to make target `/Users/gvk/workspace/galaxy-central/database/tmp/ tmp-toolshed-mtdM9orSY/phast-1.3/src/prequel/../../lib/libphast.a', needed by `/Users/gvk/workspace/galaxy-central/database/tmp/tmp- toolshed-mtdM9orSY/phast-1.3/src/prequel/../../bin/pbsDecode'. Stop. make[1]: *** No rule to make target `/Users/gvk/workspace/ galaxy-central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/ util/../../lib/libphast.a', needed by `/Users/gvk/workspace/galaxy- central/database/tmp/tmp-toolshed-mtdM9orSY/phast-1.3/src/ util/../../bin/all_dists'. Stop. make: *** [all] Error 2



On Sep 19, 2013, at 6:28 PM, Richard Burhans <r...@bx.psu.edu> wrote:

my galaxy instance:
        parent: 10587:1f34ec186fcf
         Pack script.
        branch: stable
        commit: 3 modified, 91 unknown
        update: (current)

testtoolshed.g2.bx.psu.edu:
        parent: 10592:ea0c57f1cdf0 tip
         Fix for unicode values in rst_to_html.
        branch: default
        commit: 34 unknown (clean)
        update: (current)

Try to install this repository:
        http://testtoolshed.g2.bx.psu.edu/view/rico/genome_diversity

URL: https://oocyte.bx.psu.edu/admin_toolshed/prepare_for_install? tool_shed_url=http://testtoolshed.g2.bx.psu.edu/ &repository_ids=d43c67507430e220&changeset_revisions=b63d27fdf040 File '/scratch/galaxy/home/oocyte/galaxy_oocyte/eggs/WebError-0.8a- py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond
 app_iter = self.application(environ, detect_start_response)
File '/scratch/galaxy/home/oocyte/galaxy_oocyte/eggs/Paste-1.7.5.1- py2.7.egg/paste/recursive.py', line 84 in __call__
 return self.application(environ, start_response)
File '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/galaxy/web/ framework/middleware/remoteuser.py', line 91 in __call__
 return self.app( environ, start_response )
File '/scratch/galaxy/home/oocyte/galaxy_oocyte/eggs/Paste-1.7.5.1- py2.7.egg/paste/httpexceptions.py', line 633 in __call__
 return self.application(environ, start_response)
File '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/galaxy/web/ framework/base.py', line 132 in __call__
 return self.handle_request( environ, start_response )
File '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/galaxy/web/ framework/base.py', line 190 in handle_request
 body = method( trans, **kwargs )
File '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/galaxy/web/ framework/__init__.py', line 221 in decorator
 return func( self, trans, *args, **kwargs )
File '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/galaxy/webapps/ galaxy/controllers/admin_toolshed.py', line 911 in prepare_for_install
 includes_tool_dependencies )
File '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/tool_shed/util/ common_install_util.py', line 85 in get_dependencies_for_repository installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install ( trans, repo_info_tuple ) File '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/tool_shed/util/ common_install_util.py', line 214 in get_installed_and_missing_repository_dependencies_for_new_install tool_shed, name, owner, changeset_revision, prior_installation_required = suc.parse_repository_dependency_tuple ( rd_tup ) File '/scratch/galaxy/home/oocyte/galaxy_oocyte/lib/tool_shed/util/ shed_util_common.py', line 1197 in parse_repository_dependency_tuple
 prior_installation_required = str( prior_installation_required )
UnboundLocalError: local variable 'prior_installation_required' referenced before assignment

contains_error = False
repository_dependency_tuple = ['http:// testtoolshed.g2.bx.psu.edu/', 'package_clapack_3_2_1', 'rico', '56a949e5f998', 'True', 'False']

-rico

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