[Debian-med-packaging] Bug#962550: libgclib breaks gffread autopkgtest: Segmentation fault

Paul Gevers elbrus at debian.org
Tue Jun 9 20:25:27 BST 2020 

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: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
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: -----------------------]

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