Your message dated Fri, 17 Jul 2020 10:00:14 +0000
with message-id <[email protected]>
and subject line Bug#962550: fixed in libgclib 0.11.9-2
has caused the Debian Bug report #962550,
regarding libgclib1: ABI break without soname change
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
962550: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=962550
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: libgclib, gffread
Control: found -1 libgclib/0.11.9-1
Control: found -1 gffread/0.11.8-1
Severity: serious
Tags: sid bullseye
X-Debbugs-CC: [email protected]
User: [email protected]
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of libgclib the autopkgtest of gffread fails in
testing when that autopkgtest is run with the binary packages of
libgclib from unstable. It passes when run with only packages from
testing. In tabular form:
pass fail
libgclib from testing 0.11.9-1
gffread from testing 0.11.8-1
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of libgclib to
testing [1]. Due to the nature of this issue, I filed this bug report
against both packages. Can you please investigate the situation and
reassign the bug to the right package?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=libgclib
https://ci.debian.net/data/autopkgtest/testing/amd64/g/gffread/5834728/log.gz
/usr/share/doc/augustus/tutorial/data/hints.rnaseq.intron.gff:
/usr/share/doc/augustus/tutorial/results/abinitio-browser.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8435 Segmentation fault gffread ${gff} > /dev/null
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8436 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/augustus/tutorial/results/augustus-ppx.gff:
GHash.hh(244): ASSERT(hash[i].hash<0) failed.
/usr/share/doc/augustus/tutorial/results/hints.est.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8438 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/augustus/tutorial/results/hints.gff:
/usr/share/doc/augustus/tutorial/results/hints.rnaseq.ep.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8439 Segmentation fault gffread ${gff} > /dev/null
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8440 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/augustus/tutorial/results/output-abinitio.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8441 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/augustus/tutorial/results/output-browser.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8442 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/augustus/tutorial/results/output.gff: GHash.hh(244):
ASSERT(hash[i].hash<0) failed.
/usr/share/doc/augustus/tutorial/results/scipio.gff: GHash.hh(244):
ASSERT(hash[i].hash<0) failed.
/usr/share/bedtools/test/fisher/tumor.gff: GHash.hh(244):
ASSERT(hash[i].hash<0) failed.
/usr/share/bedtools/test/intersect/b.issue311.gff:
/usr/share/bedtools/test/intersect/gdc.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8450 Segmentation fault gffread ${gff} > /dev/null
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8451 Segmentation fault gffread ${gff} > /dev/null
/usr/share/bedtools/test/map/test.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8452 Segmentation fault gffread ${gff} > /dev/null
/usr/share/bedtools/test/merge/a.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8453 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/cnvkit/examples/test/formats/example.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8458 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/data/Efeatures.gff2:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8463 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/data/Efeatures.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8464 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/data/Etags.gff2:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8465 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/data/Etags.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8466 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/test/data/bioperl.gff3: GHash.hh(244):
ASSERT(hash[i].hash<0) failed.
/usr/share/EMBOSS/test/data/eden1.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8472 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/test/data/featexample1.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8473 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/test/data/gmod-align.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8474 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/test/data/gmod-discontinuous.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8475 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/test/data/gmod-eden1.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8476 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/test/data/gmod-sonic1.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8477 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/test/data/gmod-sonic2.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8478 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/test/data/gmod-sonic3.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8479 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/test/data/hba.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8480 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/test/data/noid.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8481 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/test/data/paamir.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8482 Segmentation fault gffread ${gff} > /dev/null
/usr/share/EMBOSS/test/data/paamir.gff3: GHash.hh(244):
ASSERT(hash[i].hash<0) failed.
/usr/share/EMBOSS/test/data/seqexample.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8484 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/elegans_acceptor.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8489 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/elegans_core.gff3:
GHash.hh(244): ASSERT(hash[i].hash<0) failed.
/usr/share/gbrowse/htdocs/tutorial/data_files/elegans_deletion.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8491 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/elegans_expression.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8492 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/elegans_extra.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8493 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/elegans_repeats.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8494 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/elegans_sts.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8495 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_array.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8496 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_domains.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8497 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_est.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8498 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_est_targets.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8499 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_geneproducts.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8500 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_genes.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8501 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_genes_simple.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8502 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_matches.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8503 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_microarray.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8504 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_phyloalign.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8505 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_phyloalign_wigentries.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8506 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_remarks.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8507 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_trace.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8508 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/elegans_acceptor.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8509 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/elegans_core.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8510 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/elegans_deletion.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8511 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/elegans_expression.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8512 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/elegans_extra.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8513 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/elegans_repeats.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8514 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/elegans_sts.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8515 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox1.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8516 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox2.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8517 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox3.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8518 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox4.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8519 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox4a.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8520 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox4b.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8521 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox5.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8522 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox6.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8523 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox7.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8524 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox8.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8525 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox9.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8526 Segmentation fault gffread ${gff} > /dev/null
/usr/share/gbrowse/htdocs/tutorial/dbgff/data_files/volvox_all.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8527 Segmentation fault gffread ${gff} > /dev/null
/usr/share/genometools/gtdata/doc/csa_example_consensus_spliced_alignments.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8532 Segmentation fault gffread ${gff} > /dev/null
/usr/share/genometools/gtdata/doc/csa_example_spliced_alignments.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8533 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sgp1.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8538 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/mhcregion/hs.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8539 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/mhcregion/mm.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8540 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/splice_sites/KCRB.AG.hs.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8541 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/splice_sites/KCRB.AG.mm.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8542 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/splice_sites/KCRB.GT.hs.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8543 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/splice_sites/KCRB.GT.mm.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8544 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/splice_sites/KCRB.hs.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8545 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/splice_sites/KCRB.hs_utr.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8546 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/splice_sites/KCRB.mm.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8547 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/splice_sites/KCRB.mm_utr.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8548 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/wublast/taf6.hs.gene.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8549 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/wublast/taf6.mm.gene.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8550 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/wublast/taf6.mmhs.genomic.blastn.aplot.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8551 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2aplot/examples/wublast/taf6.mmhs.genomic.blastn.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8552 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2ps/test-data/Hsap_BTK_annotation.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8557 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2ps/test-data/Hsap_BTK_geneid.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8558 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2ps/test-data/Hsap_BTK_genscan.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8559 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2ps/test-data/Hsap_BTK_sgp3X.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8560 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/gff2ps/test-data/Hsap_BTK_sgpFO.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8561 Segmentation fault gffread ${gff} > /dev/null
/usr/share/htslib-test/test/tabix/gff_file.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8566 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/libbio-graphics-perl/examples/feature_data.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8571 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/python3/dist-packages/optimir/resources/coordinates/hsa_miRBase_v21.gff3:
GHash.hh(244): ASSERT(hash[i].hash<0) failed.
/usr/lib/python3/dist-packages/optimir/resources/coordinates/hsa_miRBase_v22.gff3:
GHash.hh(244): ASSERT(hash[i].hash<0) failed.
/usr/lib/python3/dist-packages/optimir/resources/coordinates/hsa_miRgeneDB_v2.gff3:
GHash.hh(244): ASSERT(hash[i].hash<0) failed.
/usr/share/doc/proteinortho/examples/C.gff: GHash.hh(244):
ASSERT(hash[i].hash<0) failed.
/usr/share/doc/proteinortho/examples/C2.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8584 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/proteinortho/examples/E.gff: GHash.hh(244):
ASSERT(hash[i].hash<0) failed.
/usr/share/doc/proteinortho/examples/L.gff: GHash.hh(244):
ASSERT(hash[i].hash<0) failed.
/usr/share/doc/proteinortho/examples/M.gff: GHash.hh(244):
ASSERT(hash[i].hash<0) failed.
/usr/lib/python3/dist-packages/gffutils/test/data/FBgn0031208.gff:
GHash.hh(244): ASSERT(hash[i].hash<0) failed.
/usr/lib/python3/dist-packages/gffutils/test/data/gff_example1.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8593 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/python3/dist-packages/gffutils/test/data/hybrid1.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8594 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/python3/dist-packages/gffutils/test/data/intro_docs_example.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8595 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/python3/dist-packages/gffutils/test/data/keyval_sep_in_attrs.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8596 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/python3/dist-packages/gffutils/test/data/random-chr.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8597 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/python3/dist-packages/gffutils/test/data/synthetic.gff3:
GHash.hh(244): ASSERT(hash[i].hash<0) failed.
/usr/lib/python3/dist-packages/pybedtools/test/data/d.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8603 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/python3/dist-packages/pybedtools/test/data/exons.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8604 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/python3/dist-packages/pybedtools/test/data/gdc.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8605 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/python3/dist-packages/pybedtools/test/data/hg19.gff:
GHash.hh(244): ASSERT(hash[i].hash<0) failed.
/usr/lib/R/site-library/GenomicFeatures/extdata/GFF3_files/NC_011025.gff:
GHash.hh(244): ASSERT(hash[i].hash<0) failed.
/usr/lib/R/site-library/GenomicFeatures/extdata/GFF3_files/TheCanonicalGene_v1.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8612 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/R/site-library/GenomicFeatures/extdata/GFF3_files/a.gff3:
GHash.hh(244): ASSERT(hash[i].hash<0) failed.
/usr/lib/R/site-library/GenomicFeatures/extdata/GFF3_files/dmel-1000-r5.11.filtered.gff:
GHash.hh(244): ASSERT(hash[i].hash<0) failed.
/usr/lib/R/site-library/Gviz/extdata/test.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8619 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/R/site-library/Gviz/extdata/test.gff1:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8620 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/R/site-library/Gviz/extdata/test.gff3:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8621 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/R/site-library/Rhtslib/testdata/tabix/gff_file.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8626 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/R/site-library/rtracklayer/tests/gtf.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8631 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/R/site-library/rtracklayer/tests/v1.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8632 Segmentation fault gffread ${gff} > /dev/null
/usr/lib/R/site-library/rtracklayer/tests/v3.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8633 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/seqan-apps/gustaf/example/stellar.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8638 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/seqan-apps/insegt/example/annotations.gff: GHash.hh(244):
ASSERT(hash[i].hash<0) failed.
/usr/share/doc/seqan-apps/insegt/example/readOutput.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8640 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/seqan-apps/insegt/example/tupleOutput.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8641 Segmentation fault gffread ${gff} > /dev/null
/usr/share/doc/seqan-apps/snp_store/example/exampleReads.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8642 Segmentation fault gffread ${gff} > /dev/null
/usr/share/trinityrnaseq/sample_data/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/isoform_pair.fasta.gmap.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8647 Segmentation fault gffread ${gff} > /dev/null
/usr/share/spades/test_dataset/genes_1K.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8652 Segmentation fault gffread ${gff} > /dev/null
/usr/share/spades/test_dataset/operons_1K.gff:
/tmp/autopkgtest-lxc.3lbnjzpz/downtmp/build.25M/src/debian/tests/run-tests:
line 109: 8653 Segmentation fault gffread ${gff} > /dev/null
autopkgtest [02:14:04]: test run-tests: -----------------------]
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: libgclib
Source-Version: 0.11.9-2
Done: [email protected] (Michael R. Crusoe)
We believe that the bug you reported is fixed in the latest version of
libgclib, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael R. Crusoe <[email protected]> (supplier of updated libgclib package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 14 Jul 2020 20:42:23 +0200
Source: libgclib
Binary: libgclib-dev libgclib2 libgclib2-dbgsym
Architecture: source amd64
Version: 0.11.9-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Description:
libgclib-dev - header files for Genome Code Lib (GCLib)
libgclib2 - C++ library to handle biological short sequence data
Closes: 962550
Changes:
libgclib (0.11.9-2) unstable; urgency=medium
.
* Bump soname. Closes: #962550
* debhelper-compat 13 (routine-update)
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