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Perl: move to threaded libraries, dependencies 2 #735

Merged
merged 1 commit into from
Feb 3, 2016
Merged

Perl: move to threaded libraries, dependencies 2 #735

merged 1 commit into from
Feb 3, 2016

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chapmanb
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@chapmanb chapmanb commented Feb 3, 2016

Second and final rounds of perl dependencies moving to perl-threaded.
Final step in transition is a upcoming PR with high level packages
using Perl.

Second and final rounds of perl dependencies moving to perl-threaded.
Final step in transition is a upcoming PR with high level packages
using Perl.
chapmanb added a commit that referenced this pull request Feb 3, 2016
Perl: move to threaded libraries, dependencies 2
@chapmanb chapmanb merged commit bb4f3dd into bioconda:master Feb 3, 2016
@chapmanb chapmanb deleted the perl-to-threaded-deps-2 branch February 3, 2016 10:23
@acaprez
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acaprez commented Feb 4, 2016

Just wondering why the gcc requirement was dropped from perl-math-cdf? It builds a shared lib as part of the install. I thought best practice now was to explicitly require the conda gcc/libgcc as a build/run requirement for anything that needs it. Also, if perl-threaded is going to be the default now, it should likely be rebuilt using conda gcc for the reason here: #695.

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chapmanb commented Feb 4, 2016

Adam;
Sorry about that, I had missed #695, which explains exactly why gcc was getting dropped from the recipes since perl-threaded is not build that way. I guess the best path forward is to re-build perl-threaded and then re-add gcc to places that need it. All of the shared libraries now have been switched over so I can work on that or merge a patch, whatever works best for you. Thanks again for being on top of this.

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acaprez commented Feb 4, 2016

Hi Brad,
No problem. I actually didn't realize that perl-threaded == Perl itself with threading until now (don't do much with Perl really). Otherwise I could've done the same with it at the time. If you've got some time to work on re-adding gcc, that'd be great. I'm tied up with other things until the end of the week unfortunately.

So the reason for the separately named package is that the default channel perl was built without threads, and the install library path is different (x86_64-linux vs x86_64-linux-thread-multi)? Just wondering about rebuilding our perl with threading as an option.

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chapmanb commented Feb 4, 2016

Adam;
Thanks again for this. I pushed a new perl-threaded with gcc and will work on a final PR that rebuilds all the dependencies with gcc as well.

You're right on about perl versus perl-threaded. It doesn't change much beyond adding in threading capability, but does require that all library dependencies get rebuilt against the threaded version.

Thanks again for the help catching the gcc problems right away.

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2 participants