Created attachment 210595 [details] svn diff for biology/infernal to 1.1.3 Update biology/infernal to 1.1.3 *'make test' now requires python3 *Makefile sync'ed with biology/hmmer (bug #243244) please note that the MAINTAINER mail address is modified. The port passed poudriere testport in my environment (11.3 amd64/i386).
Build info is available at https://gitlab.com/swills/freebsd-ports/pipelines/108425851
Hi Motomichi, Thanks for the patch. I noticed that 3 tests fail. Is this a known issue? ... ... exercise 297 [ hmmpgmd_ga] ... FAILED [command failed] exercise 298 [ rewind] ... ok. exercise 299 [ hmmpgmd_shard_ga] ... FAILED [command failed] exercise 300 [ bad-fasta] ... ok. exercise 301 [ brute-itest] ... ok. exercise 302 [ hmmpress-itest] ... ok. exercise 303 [ h39] ... ok. exercise 304 [ h45] ... ok. exercise 305 [ h50] ... ok. exercise 306 [ h82] ... ok. exercise 307 [ iss159] ... FAILED [command failed]
(In reply to Fernando Apesteguía from comment #2) I have never seen these fails in my environment. The tests can be performed separately after build as follows: % cd ${WRKSRC}/hmmer/testsuite % ./i19-hmmpgmd-ga.pl .. .. tmppfx % ./i22-hmmpgmd-shard-ga.pl .. .. tmpprx % ./iss159-nhmmer-overlap.py .. .. tmppfx These would emit (a little) detailed error messages upon fails.
(In reply to Motomichi Matsuzaki from comment #3) $ cd work/infernal-1.1.3/hmmer/testsuite/ $ ./i19-hmmpgmd-ga.pl $ FAIL: didn't find hmmpgmd executable in /src Any special setup needed?
Sorry, my bad. Here are the test executions: $ ./i19-hmmpgmd-ga.pl .. .. tmppfx FAIL: hmmc2 returned non-zero exit code of 256 at ./i19-hmmpgmd-ga.pl line 107. $ ./iss159-nhmmer-overlap.py .. .. tmppfx FAIL: hmmbuild failed ./i22-hmmpgmd-shard-ga.pl .. .. tmppfx FAIL: hmmc2 returned non-zero exit code of 256 at ./i22-hmmpgmd-shard-ga.pl line 89.
Created attachment 210784 [details] diff for testing i19 & i22 could be network-related problems. as for iss159, I have no idea. Could you please apply the patch to obtain directly the error messages? % make clean; make % cd ${WRKSRC}/hmmer/testsuite % patch <patch.diff % ./i19-hmmpgmd-ga.pl .. .. tmppfx % ./i22-hmmpgmd-shard-ga.pl .. .. tmppfx % ./iss159-nhmmer-overlap.py .. .. tmppfx
FWIW, I tried on a different computer and the same tests fail. Also, 1.1.2 seems to work: ./i19-hmmpgmd-ga.pl .. .. tmppfx ok It seems a regression in the new version.
Created attachment 211100 [details] svn diff for biology/infernal to 1.1.3 (revised) a revised patch to pass "make test" in 13-CURRENT
(In reply to Fernando Apesteguía from comment #7) Now I have reproduced the problem. The fail in iss159 is dependent on previous fails (hmmpgmd_ga & hmmpgmd_shard_ga), and there is no problems in iss159 itself. The fails in hmmpgmd_ga & hmmpgmd_shard_ga are caused by the binary hmm2c, which has hardcoded errno in its shutdown process. The revised patch is tested on 13-CURRENT & 11.3R (both amd64), and "make test" successed cleanly.
A commit references this bug: Author: fernape Date: Mon Jan 27 17:57:15 UTC 2020 New revision: 524268 URL: https://svnweb.freebsd.org/changeset/ports/524268 Log: biology/infernal: update to 1.1.3 PR: 243247 Submitted by: mzaki@e-mail.ne.jp (maintainer) Changes: head/biology/infernal/Makefile head/biology/infernal/distinfo head/biology/infernal/files/patch-configure head/biology/infernal/files/patch-hmmer_src_hmmc2.c head/biology/infernal/files/patch-src_Makefile.in
Committed, Thanks!
(In reply to Fernando Apesteguía from comment #11) Thanks so much. Could you handle Bug #243244 too? It comes from the same author, and has quite similar structure. (In fact, Infernal 1.1.3 contains a whole package of Hmmer 3.3)
(In reply to Motomichi Matsuzaki from comment #12) Sure!