Re: [galaxy-dev] perl version 5.18.1 repository error
Dear Nicola, now it looks like package_gnu_coreutils_8_22 is generating an error gnu_coreutils <http://129.69.102.42/admin_toolshed/manage_repository_tool_dependencies?repository_id=e4c0e60daf76dabb&operation=browse&tool_dependency_ids=e96c6ce43a3d239a> 8.22 package Error Shutting down process id 23231 because it generated no output for the defined timeout period of 3600.0 seconds. I didn't find anything an this error on the web and I am not sure how I can fix this... cheers, philipp -----Original message----- From: Nicola Soranzo <nsoranzo@tiscali.it> Sent: Wednesday 23rd March 2016 12:49 To: Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de>; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] perl version 5.18.1 repository error Hi Philipp, can you try to reinstall the tool dependency? Go to the Admin interface, "Manage installed tools", click on the "package_perl_xml_parser_expat_2_41", then from the "Repository Actions" menu select "Manage tool dependencies", select the dependency in error and "Uninstall", then select it again and "Install" it. Cheers, Nicola On 23/03/16 08:06, Rathert, Philipp, Dr. wrote: Dear all, i am trying to install tool (meme-fimo) which needs package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency. however, although the tool installs just fine it shows that package_perl_xml_parser_expat_2_41 has missing dependencies: Tool shed repository:package_perl_xml_parser_expat_2_41 Tool shed repository changeset revision:1ce3818a8eb9 Tool dependency status:Error Tool dependency installation error:Error installing tool dependency perl version 5.18.1: Unable to locate the repository directory for revision d905bb415eca of installed repository package_perl_5_18 owned by iuc. Tool dependency installation directory:././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9 Is this an error of my local instance or is the revision missing on the toolshed? Thank you very much for your help. Cheers, philipp ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Philipp, I believe you have run into a rather complicated problem with perl's dependencies. We (the IUC) have changed from coreutils-8.22 to coreutils-8.25 for exactly the reason you are reporting (`...generated no output for the defined timeout period of 3600.0 seconds`). So you should update your installation of package_perl_5_18_1. Unfortunately, no stable release of galaxy up till now can handle this change of dependencies cleanly. (16.04 will be the first release that should have no problem with this). When you are doing an update of package_perl_5_18_1, you should have gnu-coreutils-8.25 listed as one of perl's dependencies, as well as gnu-coreutils-8.22. For the moment the best thing you can do is to ignore the status of gnu-coreutils-8.22. Once you upgrade galaxy to release_16.04 or newer, repairing package_perl_5_18_1 will remove gnu-coreutils-8.22 from the list of dependencies of perl. This should not affect the functionality of perl or meme. Let us know how it goes Marius On 24 March 2016 at 09:23, Rathert, Philipp, Dr. < philipp.rathert@ibc.uni-stuttgart.de> wrote:
Dear Nicola,
now it looks like package_gnu_coreutils_8_22
is generating an error
gnu_coreutils <http://129.69.102.42/admin_toolshed/manage_repository_tool_dependencies?repository_id=e4c0e60daf76dabb&operation=browse&tool_dependency_ids=e96c6ce43a3d239a> 8.22 package Error Shutting down process id 23231 because it generated no output for the defined timeout period of 3600.0 seconds.
I didn't find anything an this error on the web and I am not sure how I can fix this...
cheers,
philipp
-----Original message----- *From:* Nicola Soranzo <nsoranzo@tiscali.it> *Sent:* Wednesday 23rd March 2016 12:49 *To:* Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de>; galaxy-dev@lists.galaxyproject.org *Subject:* Re: [galaxy-dev] perl version 5.18.1 repository error
Hi Philipp, can you try to reinstall the tool dependency? Go to the Admin interface, "Manage installed tools", click on the "package_perl_xml_parser_expat_2_41", then from the "Repository Actions" menu select "Manage tool dependencies", select the dependency in error and "Uninstall", then select it again and "Install" it.
Cheers, Nicola
On 23/03/16 08:06, Rathert, Philipp, Dr. wrote:
Dear all,
i am trying to install tool (meme-fimo) which needs package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency.
however, although the tool installs just fine it shows that package_perl_xml_parser_expat_2_41 has missing dependencies:
Tool shed repository:package_perl_xml_parser_expat_2_41 Tool shed repository changeset revision:1ce3818a8eb9 Tool dependency status:Error Tool dependency installation error:Error installing tool dependency perl version 5.18.1: Unable to locate the repository directory for revision d905bb415eca of installed repository package_perl_5_18 owned by iuc. Tool dependency installation directory: ././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9
Is this an error of my local instance or is the revision missing on the toolshed?
Thank you very much for your help.
Cheers,
philipp
___________________________________________________________ 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: https://lists.galaxyproject.org/
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___________________________________________________________ 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: https://lists.galaxyproject.org/
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HHi Marius, Many thanks for this detailed information. I reinstalled the pearl package and it has now the 8.25 version as an additional dependency. The tool seems to work as well. Thanks again, I will ignore the 8.22 version. Cheers, Philipp From: Marius van den Beek [mailto:m.vandenbeek@gmail.com] Sent: Donnerstag, 24. März 2016 11:49 To: Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de> Cc: Nicola Soranzo <nsoranzo@tiscali.it>; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] perl version 5.18.1 repository error Hi Philipp, I believe you have run into a rather complicated problem with perl's dependencies. We (the IUC) have changed from coreutils-8.22 to coreutils-8.25 for exactly the reason you are reporting (`...generated no output for the defined timeout period of 3600.0 seconds`). So you should update your installation of package_perl_5_18_1. Unfortunately, no stable release of galaxy up till now can handle this change of dependencies cleanly. (16.04 will be the first release that should have no problem with this). When you are doing an update of package_perl_5_18_1, you should have gnu-coreutils-8.25 listed as one of perl's dependencies, as well as gnu-coreutils-8.22. For the moment the best thing you can do is to ignore the status of gnu-coreutils-8.22. Once you upgrade galaxy to release_16.04 or newer, repairing package_perl_5_18_1 will remove gnu-coreutils-8.22 from the list of dependencies of perl. This should not affect the functionality of perl or meme. Let us know how it goes Marius On 24 March 2016 at 09:23, Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de <mailto:philipp.rathert@ibc.uni-stuttgart.de> > wrote: Dear Nicola, now it looks like package_gnu_coreutils_8_22 is generating an error gnu_coreutils <http://129.69.102.42/admin_toolshed/manage_repository_tool_dependencies?repository_id=e4c0e60daf76dabb&operation=browse&tool_dependency_ids=e96c6ce43a3d239a> 8.22 package Error Shutting down process id 23231 because it generated no output for the defined timeout period of 3600.0 seconds. I didn't find anything an this error on the web and I am not sure how I can fix this... cheers, philipp -----Original message----- From: Nicola Soranzo <nsoranzo@tiscali.it <mailto:nsoranzo@tiscali.it> > Sent: Wednesday 23rd March 2016 12:49 To: Rathert, Philipp, Dr. <philipp.rathert@ibc.uni-stuttgart.de <mailto:philipp.rathert@ibc.uni-stuttgart.de> >; galaxy-dev@lists.galaxyproject.org <mailto:galaxy-dev@lists.galaxyproject.org> Subject: Re: [galaxy-dev] perl version 5.18.1 repository error Hi Philipp, can you try to reinstall the tool dependency? Go to the Admin interface, "Manage installed tools", click on the "package_perl_xml_parser_expat_2_41", then from the "Repository Actions" menu select "Manage tool dependencies", select the dependency in error and "Uninstall", then select it again and "Install" it. Cheers, Nicola On 23/03/16 08:06, Rathert, Philipp, Dr. wrote: Dear all, i am trying to install tool (meme-fimo) which needs package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency. however, although the tool installs just fine it shows that package_perl_xml_parser_expat_2_41 has missing dependencies: Tool shed repository:package_perl_xml_parser_expat_2_41 Tool shed repository changeset revision:1ce3818a8eb9 Tool dependency status:Error Tool dependency installation error:Error installing tool dependency perl version 5.18.1: Unable to locate the repository directory for revision d905bb415eca of installed repository package_perl_5_18 owned by iuc. Tool dependency installation directory:././tool_deps/perl/5.18.1/iuc/package_perl_xml_parser_expat_2_41/1ce3818a8eb9 Is this an error of my local instance or is the revision missing on the toolshed? Thank you very much for your help. Cheers, philipp ___________________________________________________________ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
-
Marius van den Beek -
Philipp Rathert -
Rathert, Philipp, Dr.