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biology/bcftools: update to 1.9
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Authored by fernape on Aug 1 2018, 4:29 PM.

Details

Summary

Reported in PR 230169

While here:

  • Update LICENSE handling
  • Move all commands to bin/
Test Plan
  • portlint -AC OK (see note below)
  • poudriere builds for {10.4,11.1}{amd64,i386},11.2 amd64, 12i386 OK
  • run test in 10.4 amd64 OK

During make, this error shows up:

find: /usr/home/fernape/FreeBSD-repos/ports/head/biology/bcftools/work/stage/usr/local/lib/perl5/site_perl: No such file or directory

This is present before the update.

Also, I added USE_LDCONFIG, but portlint complains with:

You have defined USE_LDCONFIG, but this port does not install any shared objects

Diff Detail

Repository
rP FreeBSD ports repository
Lint
Automatic diff as part of commit; lint not applicable.
Unit
Automatic diff as part of commit; unit tests not applicable.

Event Timeline

fernape created this revision.Aug 1 2018, 4:29 PM
tcberner accepted this revision.Aug 1 2018, 5:47 PM
tcberner added a subscriber: wen.

Looks good to me -- note that @wen is assigned the PR though.

This revision is now accepted and ready to land.Aug 1 2018, 5:47 PM

Looks good to me -- note that @wen is assigned the PR though.

Yes, I noticed that (also, we need to wait for maintainer timeout, due on August 12th).

About the other two things: USE_LDCONFIG warning seems a false positive. What about the perl thing? I can not trace the origin of the problem.

Looks good to me -- note that @wen is assigned the PR though.

Yes, I noticed that (also, we need to wait for maintainer timeout, due on August 12th).

About the other two things: USE_LDCONFIG warning seems a false positive. What about the perl thing? I can not trace the origin of the problem.

I think the maintainer set a "+" flag, so I assume it's fine ^^

As for the perl messages, checkout Mk/Uses/perl5.mk's fix-perl-things target:

[...]
/usr/bin/find /wrkdirs/poudriere/ports/reviews/biology/bcftools/work/stage -name '*.bs' -size 0 -delete || :
/bin/rm -f /wrkdirs/poudriere/ports/reviews/biology/bcftools/work/stage/usr/local/lib/perl5/5.26/mach/perllocal.pod* || :
/bin/rmdir -p /wrkdirs/poudriere/ports/reviews/biology/bcftools/work/stage/usr/local/lib/perl5/5.26/mach 2>/dev/null || :
[ -d "/wrkdirs/poudriere/ports/reviews/biology/bcftools/work/stage/usr/local/lib/perl5/site_perl/man/man3" ] &&  /usr/bin/find /wrkdirs/poudriere/ports/reviews/biology/bcftools/work/stage/usr/local/lib/perl5/site_perl/man/man3 -name '*::README.3' -delete || :
/usr/bin/find /wrkdirs/poudriere/ports/reviews/biology/bcftools/work/stage/usr/local/lib/perl5/site_perl -name README.pod -delete || :
find: /wrkdirs/poudriere/ports/reviews/biology/bcftools/work/stage/usr/local/lib/perl5/site_perl: No such file or directory
[...]

Maintainer here. I approve updating this port as long as htslib, samtools, and bcftools are updated together.

mat added a comment.Aug 2 2018, 9:14 AM

The Perl related error was fixed in rP476224.

biology/bcftools/Makefile
12 ↗(On Diff #46134)

LICENSE_FILE. The _<lic> only work when you have more than one license.

43–44 ↗(On Diff #46134)

I think this should be LICENSE+=, and adding LICENSE_COMB.
Also, as it is the same file, only using LICENSE_FILE works.

In D16543#351577, @mat wrote:

The Perl related error was fixed in rP476224.

Terrific, thanks!

fernape added inline comments.Aug 2 2018, 10:51 AM
biology/bcftools/Makefile
43–44 ↗(On Diff #46134)

That was my first attempt, but when reading INSTALL file, I had some doubts. It says that if we use gsl the resultant software MUST be GPL compatible, but it also says that the default building is dual MIT-GPL and that we can choose which one to use. I'm no expert in licenses but sounds a bit confusing to me.

fernape updated this revision to Diff 46187.Aug 2 2018, 3:26 PM

Update LICENSE handling.

The INSTALL file states that by default the software is dual licensed (MIT and
GPL) and we can choose (so we choose MIT by default). If using gsl, we can no
longer choose and we need to ship the resultant software with terms compatible
with GPL, so add GPLv3 to LICENSE and set LICENSE_COMB to multi.

This revision now requires review to proceed.Aug 2 2018, 3:26 PM
fernape marked 3 inline comments as done.Aug 2 2018, 3:26 PM
tcberner added inline comments.Aug 2 2018, 6:07 PM
biology/bcftools/Makefile
39 ↗(On Diff #46187)

^ you could use USES=localbase

fernape updated this revision to Diff 46206.Aug 2 2018, 6:27 PM

Add localbase to USES

fernape marked an inline comment as done.Aug 2 2018, 6:28 PM
tcberner accepted this revision.Aug 2 2018, 6:34 PM

still looks fine to me

This revision is now accepted and ready to land.Aug 2 2018, 6:34 PM
This revision was automatically updated to reflect the committed changes.