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
> 
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
> 
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to