perl version 5.18.1 repository error

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perl version 5.18.1 repository error

Rathert, Philipp, Dr.
perl version 5.18.1 repository error

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:


package_perl_xml_parser_expat_2_41
 
1ce3818a8eb9
 
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_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 



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Re: perl version 5.18.1 repository error

Nicola Soranzo-2
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:
perl version 5.18.1 repository error

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:


package_perl_xml_parser_expat_2_41
 
1ce3818a8eb9
 
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_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 




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Re: perl version 5.18.1 repository error

Rathert, Philipp, Dr.
perl version 5.18.1 repository error

Hi Nicola,

 

Now I get this:

perl

5.18.1

package

Error

  File "lib/tool_shed/galaxy_install/install_manager.py", line 123, in install_and_build_package_via_fabric
    tool_dependency = self.install_and_build_package( install_environment, tool_dependency, actions_dict )
  File "lib/tool_shed/galaxy_install/install_manager.py", line 108, in install_and_build_package
    initial_download=False )
  File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step
    initial_download=initial_download )
  File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 1881, in execute_step
    job_name=package_name )
  File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 118, in handle_command
    self.log_results( cmd, output, os.path.join( self.install_dir, basic_util.INSTALLATION_LOG ) )
  File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py", line 250, in log_results
    logfile = open( file_path, 'wb' )

[Errno 2] No such file or directory: u'/galaxy-central/tool_deps/perl/5.18.1/iuc/package_perl_5_18/d905bb415eca/INSTALLATION.log'

 

 

 

From: Nicola Soranzo [mailto:[hidden email]] On Behalf Of Nicola Soranzo
Sent: Mittwoch, 23. März 2016 12:49
To: Rathert, Philipp, Dr. <[hidden email]>; [hidden email]
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 






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Re: perl version 5.18.1 repository error

Rathert, Philipp, Dr.
In reply to this post by Rathert, Philipp, Dr.
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_coreutils8.22packageErrorShutting 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 <[hidden email]>
Sent: Wednesday 23rd March 2016 12:49
To: Rathert, Philipp, Dr. <[hidden email]>; [hidden email]
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:


package_perl_xml_parser_expat_2_41
1ce3818a8eb9
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_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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Re: perl version 5.18.1 repository error

Marius van den Beek
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. <[hidden email]> wrote:

Dear Nicola,


now it looks like package_gnu_coreutils_8_22

is generating an error



gnu_coreutils8.22packageErrorShutting 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 <[hidden email]>
Sent: Wednesday 23rd March 2016 12:49
To: Rathert, Philipp, Dr. <[hidden email]>; [hidden email]
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:


package_perl_xml_parser_expat_2_41
1ce3818a8eb9
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_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:
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To search Galaxy mailing lists use the unified search at:
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Re: perl version 5.18.1 repository error

Rathert, Philipp, Dr.

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:[hidden email]]
Sent: Donnerstag, 24. März 2016 11:49
To: Rathert, Philipp, Dr. <[hidden email]>
Cc: Nicola Soranzo <[hidden email]>; [hidden email]
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. <[hidden email]> wrote:

Dear Nicola,

 

now it looks like package_gnu_coreutils_8_22

is generating an error

 

 

gnu_coreutils

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 <[hidden email]>
Sent: Wednesday 23rd March 2016 12:49
To: Rathert, Philipp, Dr. <[hidden email]>; [hidden email]
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:
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To search Galaxy mailing lists use the unified search at:
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