Biosamtools with libxml2 dep

[hajgato]

PR #1062 and #992 merged... If I did everything right ;)

[hpcugentbot]

Automatic reply from Jenkins: Can I test this?

[boegel]

Jenkins: ok to test

[boegel]

@hajgato: there's a patch for BioPerl available at https://github.com/hpcugent/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/p/Perl/BioPerl-1.6.923_remove-broken-tests.patch that disables the broken tests for BioPerl v1.6.923 that I ran into in #992

Can you get that included here as well? (copy it to the BioPerl dir, include it in the easyconfig(s))

[hajgato]

@boegel: I do not understand this. I do not see any broken tests for me after adding XML-LibXML. And I am installing BioPerl-1.6.924

[hajgato]

This seems to be dead. Anybody wiling to test this?

[verdurin]

I'll take a look at this, given it's been requested by our users this week...

[boegel]

@verdurin: you should try and take @hajgato's branch, and update it with develop to start... let me know if you need help with this

[hpcugentbot]

Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/4353/console for more details).

This pull request is now ready for review/testing.

Please try and find someone who can tackle this; contact @boegel if you're not sure what to do.

[pescobar]

Test report by @pescobar
FAILED
Build succeeded for 5 out of 71 (15 easyconfigs in this PR)
Linux centos 6.5, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/1c9e087f1027800045d6 for a full test report.

[boegel]

Jenkins: test this please

[boegel]

Test report by @boegel
FAILED
Build succeeded for 48 out of 54 (15 easyconfigs in this PR)
Linux SL 6.6, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.6.6
See https://gist.github.com/2fdb480387032bb22c3c for a full test report.

[hpcugentbot]

Easyconfigs unit test suite PASSed (see https://jenkins1.ugent.be/job/easybuild-easyconfigs-pr-builder/4476/console for more details).

This pull request is now ready for review/testing.

Please try and find someone who can tackle this; contact @boegel if you're not sure what to do.

[boegel]

@hajgato: can you look into a test report for this?

[hajgato]

@boegel: defaults changed since I have did this: it checks for bin, but it does not have.

[hajgato]

@boegel maybe in the past the builddependency was present in the test phase, and not anymore?

[boegel]

@hajgato: ah, sorry, didn't actually check whether the dep was already there or not, sorry >_<

build dependencies get loaded at the start of the build sequence, and stay there (I think) for the entire process

I'll check on that, and see if I can figure out something on my end.

Meanwhile, can you check whether you have XML::LibXML in your system?

I'm getting this:

$ perldoc -lm XML::LibXML 
No module found for "XML::LibXML".

[hajgato]

@boegel Its on it.

# perldoc -lm XML::LibXML 
/usr/lib64/perl5/XML/LibXML.pm

[boegel]

@hajgato: may be related to #643; it's probably not a bad idea to try and figure out why the tests are broken (I see you've disabled them too here)

[boegel]

Maybe it has something to do with -T? http://perldoc.perl.org/perlsec.html#Taint-mode-and-%40INC

[migueldiascosta]

@hajgato, this PR is being closed for the following reason(s): no activity for > 6 months.
Please don't hesitate to reopen this PR or add a comment if you feel this contribution is still relevant.
For more information on our policy w.r.t. closing PRs, see https://easybuild.readthedocs.io/en/latest/Contributing.html#why-a-pull-request-may-be-closed-by-a-maintainer