Error installing tool dependency X version Y: coercing to Unicode: need string or buffer, NoneType found

Question: Error installing tool dependency X version Y: coercing to Unicode: need string or buffer, NoneType found

3.1 years ago by

France

Hi there,

I noticed that I have the same error for several dependency. I expect a single problem leading to this behaviour.

Error installing tool dependency libpng version 1.6.7: coercing to Unicode: need string or buffer, NoneType found

Error installing tool dependency pixman version 0.32.4: coercing to Unicode: need string or buffer, NoneType found

Here is the complete log for libpng for example :

tool_shed.galaxy_install.install_manager ERROR 2015-10-26 13:27:38,068 Error installing tool dependency libpng version 1.6.7: coercing to Unicode: need string or buffer, NoneType found
Traceback (most recent call last):
  File "/home/galaxy/diag_19102015/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 217, in install_specified_tool_dependencies
    from_tool_migration_manager=from_tool_migration_manager )
  File "/home/galaxy/diag_19102015/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 317, in install_package
    tool_dependency_db_records=None )
  File "/home/galaxy/diag_19102015/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 96, in process_tag_set
    tool_dependency_db_records=tool_dependency_db_records )
  File "/home/galaxy/diag_19102015/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py", line 520, in process_tag_set
    from_tool_migration_manager=from_tool_migration_manager )
  File "/home/galaxy/diag_19102015/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py", line 472, in handle_complex_repository_dependency_for_package
    tool_dependencies_config = suc.get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
  File "/home/galaxy/diag_19102015/galaxy/lib/tool_shed/util/shed_util_common.py", line 210, in get_absolute_path_to_file_in_repository
    for root, dirs, files in os.walk( repo_files_dir ):
  File "/usr/lib/python2.7/os.py", line 276, in walk
    names = listdir(top)
TypeError: coercing to Unicode: need string or buffer, NoneType found

I am looking for your guidance to solve this problem.

Thank you

Christ

coercing to unicode dependency • 1.1k views

ADD COMMENT • link •

modified 2.7 years ago by Nicola Soranzo • 70 • written 3.1 years ago by christophe.habib • 340

I noticed as well that I have dissonant informations about the packages status. For example if I go on package_cairo I see that there are missing package.

http://img11.hostingpics.net/pics/236587packagecairo.png

But if I click on "package_freetype_2_5_2" I can see this :

http://www.hostingpics.net/viewer.php?id=800032packagelibpng.png

So I can see first than package libpng 1.6.7 has "installed" status, but then the very same package has "Uninstalled" status. How can this be possible? Did I misunderstood something here?

ADD REPLY • link modified 3.1 years ago • written 3.1 years ago by christophe.habib • 340

package_libpng_1_6_7 repository dependency is "Installed" in both the pictures you posted.

ADD REPLY • link written 2.7 years ago by Nicola Soranzo • 70

In the second picture libpng appear in the missing tool dependencies as well right after the installed status..

ADD REPLY • link written 2.7 years ago by christophe.habib • 340

2.7 years ago by

Nicola Soranzo • 70

Norwich, UK

Nicola Soranzo • 70 wrote:

I think this is caused by repo_files_dir being None or '' in method handle_complex_repository_dependency_for_package() from file lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py . In Galaxy releases 16.01 a check has been, which will raise an Exception with a message like "Unable to locate the repository directory for revision %s of installed repository %s owned by %s."

I'd suggest to upgrade to 16.01 if you have not already done so and then try to uninstall/reinstall the tool dependency and see if it works or what new errors you'll see in the server logs.

ADD COMMENT • link written 2.7 years ago by Nicola Soranzo • 70

I did the upgrade. I tried to uninstall libpng version 1.6.7, now I have this error :

Error installing tool dependency libpng version 1.6.7: Unable to locate the repository directory for revision 05df724aefbb of installed repository package_libpng_1_6_7 owned by iuc.

Same goes for ncurses 6.0 :

Error installing tool dependency ncurses version 6.0: Unable to locate the repository directory for revision c921f7ce9ca7 of installed repository package_ncurses_6_0 owned by iuc.

ADD REPLY • link written 2.6 years ago by christophe.habib • 340

3.0 years ago by

christophe.habib • 340

France

christophe.habib • 340 wrote:

Hi again,

I still have the very same error message for many packages/tools. Here is the list :

ncurses	6.0
matplotlib	1.2.1
numpy	1.7.1
readline	6.2
libpng	1.6.7
freetype	2.4.11
atlas	3.10.2
libxml2	2.9.1

Do you know where I should investigate to get a clue about these errors please?

Thank you!

ADD COMMENT • link written 3.0 years ago by christophe.habib • 340

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