Question: python_mysqldb and R depenedencies missing after installation
0
gravatar for Mic
3.3 years ago by
Mic70
Australia
Mic70 wrote:

I installed ceas (Owner:pjbriggs, Revision:f411ce97a351), but I have got problems with the following "Installed, missing tool dependencies":

R 3.1.2

configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: you cannot build PDF versions of vignettes and help pages
configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: error: --with-readline=yes (default) and headers/libs are not available

python_mysqldb 1.2.5

File "/galaxy-central/lib/tool_shed/galaxy_install/install_manager.py", line 142, in install_and_build_package_via_fabric
    tool_dependency = self.install_and_build_package( tool_shed_repository, tool_dependency, actions_dict )
  File "/galaxy-central/lib/tool_shed/galaxy_install/install_manager.py", line 100, in install_and_build_package
    initial_download=True )
  File "/galaxy-central/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step
    initial_download=initial_download )
  File "/galaxy-central/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 685, in execute_step
    dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums )
  File "/galaxy-central/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 223, in url_download
    extraction_path = archive.extract( install_dir )
  File "/galaxy-central/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in extract
    os.chmod( absolute_filepath, unix_permissions )

[Errno 2] No such file or directory: '/export/galaxy-central/database/files/tmp-toolshed-mtdk8TtAR/MySQL-python-1.2.5/MySQL-python-1.2.5/GPL-2.0'

How is it possible to fix it?

Thank you in advance.

Mic

ceas galaxy docker • 783 views
ADD COMMENTlink written 3.3 years ago by Mic70

Which OS are you on? Is this OS-X?

ADD REPLYlink written 3.3 years ago by Bjoern Gruening5.1k

I was creating a docker image based on bgruening/galaxy-stable:dev. Docker 1.7.1 is running on CentOS 6.6.

ADD REPLYlink written 3.3 years ago by Mic70
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