Add perl-bio-searchio-hmmer

[0xaf1f]

Bio::SearchIO::hmmer was formerly part of the core bioperl distribution until version 1.7.3 when it and a bunch of other components were split out into separate development repositories (thanks @rpetit3 for digging this up), so later bioperl packages here caused problems for the prokka package (#33356), which uses this component.

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[0xaf1f]

@bioconda/core, when a PR touches multiple packages, why doesn't the package builder use the newly built ones when building the remaining packages? It's not reasonable to have to wait for each change to hit the archive before submitting the next one.

There's an issue with a missing dependency in perl-bioperl-core. That package gets built first, then thrown away. Then, when perl-bio-searchio-hmmer is being built, the broken package from the archive is being pulled in and the package build has no chance. It should use the perl-bioperl-core that was just built...

[BiocondaBot]

Reposting for @0xaf1f to enable pings (courtesy of the BiocondaBot):

@bioconda/core, when a PR touches multiple packages, why doesn't the package builder use the newly built ones when building the remaining packages? It's not reasonable to have to wait for each change to hit the archive before submitting the next one.

There's an issue with a missing dependency in perl-bioperl-core. That package gets built first, then thrown away. Then, when perl-bio-searchio-hmmer is being built, the broken package from the archive is being pulled in and the package build has no chance. It should use the perl-bioperl-core that was just built...

[0xaf1f]

Due to inadequacies of the builder here, I'm forced to make this 3 4 PRs instead of 1.

[0xaf1f]

@dpryan79 I added the missing dependency on perl-test-most for perl-bio-searchio-hmmer to get rid of a bunch of the noise in the log (speaking of noise, the container doesn't seem to like C.UTF-8) and hopefully what I was saying before on gitter is more clear. I get what you said about the package build order being problematic, but this is an issue too:

When perl-bio-searchio-hmmer is being built (on its retry after perl-bioperl-core is successfully built), it's getting

01:10:42 BIOCONDA INFO (OUT)     perl-bioperl-core:           1.7.8-pl5321h9ee0642_0  bioconda

instead of the freshly built from just a few minutes prior

01:04:09 BIOCONDA INFO (ERR) [Mar 21 01:04:09] SOUT perl-bioperl-core  conda-bld/noarch::perl-bioperl-core-1.7.8-pl5321hdfd78af_1

which results in this subtle test failure:

01:11:45 BIOCONDA INFO (OUT) Test Summary Report
01:11:45 BIOCONDA INFO (OUT) -------------------
01:11:45 BIOCONDA INFO (OUT) t/LocalDB-Index.t      (Wstat: 256 Tests: 4 Failed: 1)
01:11:45 BIOCONDA INFO (OUT)   Failed test:  3
01:11:45 BIOCONDA INFO (OUT)   Non-zero exit status: 1
01:11:45 BIOCONDA INFO (OUT) Files=7, Tests=1166,  4 wallclock secs ( 0.10 usr  0.00 sys +  2.98 cusr  0.33 csys =  3.41 CPU)
01:11:45 BIOCONDA INFO (OUT) Result: FAIL
01:11:45 BIOCONDA INFO (OUT) Failed 1/7 test programs. 1/1166 subtests failed.

[dpryan79]

@BiocondaBot please update

[0xaf1f]

so it's a general conda solver problem to not pull in the latest build of a package? Or is it channel priority not preferring local over bioconda/conda-forge?

[0xaf1f]

It looks like the mulled-build correctly picks up the new local packages, but the original build doesn't. Do you know why the two procedures behave differently?

[0xaf1f]

@BiocondaBot please add label.

I'm still curious about why the regular build and mulled build don't resolve dependencies the same way.

[dpryan79]

@0xaf1f The classic conda solver doesn't prioritize the most recent build, or even the most recent version. This has caused a LOT of headaches. Starting in conda 4.12 there's the option to use the mamba solver instead, which will try to use the highest build number and version, which should generally do more what people expect.

[dpryan79]

@BiocondaBot please merge

[BiocondaBot]

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.

[0xaf1f]

The classic conda solver doesn't prioritize the most recent build, or even the most recent version. This has caused a LOT of headaches. Starting in conda 4.12 there's the option to use the mamba solver instead, which will try to use the highest build number and version, which should generally do more what people expect.

Ah, got it. Many thanks for getting this working!