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 <[email protected]> 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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