biology/bcftools: update to 1.9

[fernape]

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

[tcberner]

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

[fernape]

In D16543#351284, @tcberner wrote:

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.

[tcberner]

In D16543#351292, @fernape wrote:

In D16543#351284, @tcberner wrote:

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
[...]

[cartwright_asu.edu]

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

[mat]

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.

[fernape]

In D16543#351577, @mat wrote:

The Perl related error was fixed in rP476224.

Terrific, thanks!

[fernape]

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]

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.

[tcberner]

biology/bcftools/Makefile

39 ↗

(On Diff #46187)

^ you could use USES=localbase

[fernape]

Add localbase to USES

[tcberner]

still looks fine to me