Hi Greg! I don't know if it's the same problem, but I've not been able to see test results for this repository for a while: http://toolshed.g2.bx.psu.edu/view/crs4/blat Best, Nicola Il giorno mar, 10/12/2013 alle 09.46 -0500, Greg Von Kuster ha scritto:

There are several "flags" for each repository revision that determine if and how the revision is tested. If tested, flags also detemine which category the latest revision falls into when clicking on the links in the Tool Shed's menu. One of these flags is "tools_functionally_correct", which was incorrectly set on http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/ee10017fcd8... due to a bug introduced during the reengineering of the Topll Shed's install and test framework that I recently did. This bug was corrected in the following change set.

https://bitbucket.org/galaxy/galaxy-central/commits/ca25579a90e97157e32b527e...

I've corrected the setting for the tools_functionally_correct flag for your repository so it should no longer be displayed in the "Latest revision: failing tool tests" category.

Thanks for letting us know about this, and please let us know if you discover other reposiory revisions that require the same correction.

Greg Von Kuster

On Dec 9, 2013, at 5:06 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

...

Hi Dave & Greg,

Could you double check how the "Skip automated testing of tools in this revision" setting is being used on the Test Tool Shed?

e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/ee10017fcd8...

Test runs Automated test environment Not tested Licensing issues restrict automated tool dependency installation. 2013-11-29 17:19:34 Automated test environment Not tested Licensing issues restrict automated tool dependency installation.

(Ticked) Skip automated testing of tools in this revision

That all looks fine, and it is listed under "Latest revision: skip tool tests".

However, this tool is also listed under "Latest revision: failing tool tests".

Regards,

Peter ___________________________________________________________ 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: http://lists.bx.psu.edu/

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Hi Greg, thanks for looking at this! Unfortunately still no test results displayed for http://toolshed.g2.bx.psu.edu/view/crs4/blat Best, Nicola Il giorno mar, 10/12/2013 alle 10.43 -0500, Greg Von Kuster ha scritto:

Hello Nicola,

The main tool shed is running a bit behind the test tool shed since it is on the stable branch. I've commited a fix for the main tool shed in 11664:3bf805dfa14e that should correct the problem resulting in no test results being displayed. Results should begin being displayed with the test run tomorrow morning. I'll make sure to inspect the test runs for the main tool shed more closely from here on (I've been focusing more on the test tool shed) to make sure the different issues that arise on the stable branch are handled more quickly.

Thanks for letting me know about this.

Greg Von Kuster

On Dec 10, 2013, at 10:09 AM, Nicola Soranzo <soranzo@crs4.it> wrote:

...

Hi Greg! I don't know if it's the same problem, but I've not been able to see test results for this repository for a while:

http://toolshed.g2.bx.psu.edu/view/crs4/blat

Best, Nicola

Il giorno mar, 10/12/2013 alle 09.46 -0500, Greg Von Kuster ha scritto:

...

There are several "flags" for each repository revision that determine if and how the revision is tested. If tested, flags also detemine which category the latest revision falls into when clicking on the links in the Tool Shed's menu. One of these flags is "tools_functionally_correct", which was incorrectly set on http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/ee10017fcd8... due to a bug introduced during the reengineering of the Topll Shed's install and test framework that I recently did. This bug was corrected in the following change set.

https://bitbucket.org/galaxy/galaxy-central/commits/ca25579a90e97157e32b527e...

I've corrected the setting for the tools_functionally_correct flag for your repository so it should no longer be displayed in the "Latest revision: failing tool tests" category.

Thanks for letting us know about this, and please let us know if you discover other reposiory revisions that require the same correction.

Greg Von Kuster

On Dec 9, 2013, at 5:06 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

...

Hi Dave & Greg,

Could you double check how the "Skip automated testing of tools in this revision" setting is being used on the Test Tool Shed?

e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/ee10017fcd8...

Test runs Automated test environment Not tested Licensing issues restrict automated tool dependency installation. 2013-11-29 17:19:34 Automated test environment Not tested Licensing issues restrict automated tool dependency installation.

(Ticked) Skip automated testing of tools in this revision

That all looks fine, and it is listed under "Latest revision: skip tool tests".

However, this tool is also listed under "Latest revision: failing tool tests".

Regards,

Peter ___________________________________________________________ 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: http://lists.bx.psu.edu/

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: http://lists.bx.psu.edu/

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: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Thanks Greg for the heads-up! These are great news, I can surely wait until mid-January (the wait will be mostly vacation time :). Just let us know when we can start checking again the test results on the main Tool Shed. Nicola Il 2013-12-17 21:15 Greg Von Kuster ha scritto:

Hi Nicola,

There's some bad news and good new regarding this issue.

The bad news is that the old version of the tool shed's install and test framework required complete reengineering, and this resulted in it not being functional in the main tool shed's environment which runs the Galaxy stable branch. I've tried several approaches to committing and grafting changes to the stable branch in an attempt to piece together a functional environment for the main tool shed until the next Galaxy release, but the reengineering effort was so extensive that it made this extremely difficult.

So the main tool shed cannot be tested until the next-stable branch is created in preparation for the next Galaxy release. The next-stable branch is currently scheduled for mid January, 2014, with the Galaxy release currently scheduled for the first week of February, 2014.

The good news is that the reengineerig effort has resulted in a much more stable and functional install and test framework that will provide many more benefits than its previous incarnation. I am now working on enhancing the framework to include installing and testing repositories of type tool_dependency_definition. This enhancement will be included in the next-stable branch when it is created in mid-January.

Sorry for the inconvenience this may cause, but after mid-January things should be in good shape on the main tool shed.

Greg Von Kuster

On Dec 12, 2013, at 5:00 PM, Nicola Soranzo <soranzo@crs4.it> wrote:

...

Hi Greg, thanks for looking at this! Unfortunately still no test results displayed for http://toolshed.g2.bx.psu.edu/view/crs4/blat

Best, Nicola

Il giorno mar, 10/12/2013 alle 10.43 -0500, Greg Von Kuster ha scritto:

...

Hello Nicola,

The main tool shed is running a bit behind the test tool shed since it is on the stable branch. I've commited a fix for the main tool shed in 11664:3bf805dfa14e that should correct the problem resulting in no test results being displayed. Results should begin being displayed with the test run tomorrow morning. I'll make sure to inspect the test runs for the main tool shed more closely from here on (I've been focusing more on the test tool shed) to make sure the different issues that arise on the stable branch are handled more quickly.

Thanks for letting me know about this.

Greg Von Kuster

On Dec 10, 2013, at 10:09 AM, Nicola Soranzo <soranzo@crs4.it> wrote:

...

Hi Greg! I don't know if it's the same problem, but I've not been able to see test results for this repository for a while:

http://toolshed.g2.bx.psu.edu/view/crs4/blat

Best, Nicola

Il giorno mar, 10/12/2013 alle 09.46 -0500, Greg Von Kuster ha scritto:

...

There are several "flags" for each repository revision that determine if and how the revision is tested. If tested, flags also detemine which category the latest revision falls into when clicking on the links in the Tool Shed's menu. One of these flags is "tools_functionally_correct", which was incorrectly set on http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/ee10017fcd8... due to a bug introduced during the reengineering of the Topll Shed's install and test framework that I recently did. This bug was corrected in the following change set.

https://bitbucket.org/galaxy/galaxy-central/commits/ca25579a90e97157e32b527e...

I've corrected the setting for the tools_functionally_correct flag for your repository so it should no longer be displayed in the "Latest revision: failing tool tests" category.

Thanks for letting us know about this, and please let us know if you discover other reposiory revisions that require the same correction.

Greg Von Kuster

On Dec 9, 2013, at 5:06 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

...

Hi Dave & Greg,

Could you double check how the "Skip automated testing of tools in this revision" setting is being used on the Test Tool Shed?

e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/ee10017fcd8...

Test runs Automated test environment Not tested Licensing issues restrict automated tool dependency installation. 2013-11-29 17:19:34 Automated test environment Not tested Licensing issues restrict automated tool dependency installation.

(Ticked) Skip automated testing of tools in this revision

That all looks fine, and it is listed under "Latest revision: skip tool tests".

However, this tool is also listed under "Latest revision: failing tool tests".

Regards,

Peter ___________________________________________________________ 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: http://lists.bx.psu.edu/

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: http://lists.bx.psu.edu/

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: http://lists.bx.psu.edu/

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: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Hello Peter, I've corrected this one as well - no tool test results should now be displayed for the venn_list repository. Regarding roy, the test run that displayed that result was Nov 30, which is quite a while back and may have been due to an issue that has since been corrected. I believe ryp is now installing correctly for repositories requiring it, but I'll keep an eye on things to confirm. I'm also still working on the following Trello card which will help determine things like this, although it isnow in between other priorities. I'm hoping to have this card completed before the Christmas break. https://trello.com/c/HVGrShnC/60-tool-shed-should-test-installation-of-packa... Greg Von Kuster On Dec 10, 2013, at 10:59 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

Thanks Greg,

I'm seeing this tool listed under "Latest revision: failing tool tests", while it has been marked to skipped (missing R dependency, which I ought to be able to handle now with Bjoern's work):

http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list

Interestingly the error suggests rpy is missing on the Test Tool Shed, which if true ought to break a lot of the core tools as well...

ImportError: No module named rpy

Regards,

Peter ___________________________________________________________ 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: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/