[Debian-med-packaging] Bug#892223: fixed in seqan2 2.4.0+dfsg-9

Michael Crusoe michael.crusoe at gmail.com
Wed Dec 26 10:01:23 GMT 2018


FYI, in building +dfsg-9 we are seeing new bus errors on armhf (which
previously passed the tests)
https://buildd.debian.org/status/logs.php?arch=armhf&pkg=seqan2

https://buildd.debian.org/status/fetch.php?pkg=seqan2&arch=armhf&ver=2.4.0%2Bdfsg-9&stamp=1544194851&raw=0

And on mips there is a new test failure (tests previously passed here):

https://buildd.debian.org/status/fetch.php?pkg=seqan2&arch=mips&ver=2.4.0%2Bdfsg-9&stamp=1544151238&raw=0

Given that these architectures (and sparc64) previously built fine for
Debian, I suggest we revert this patch for now.

===
armel bus errors:
===

 39/400 Test  #46: test_test_index_crosscompare_dna
..................................................Bus error***Exception:
 0.01 sec
TEST SUITE test_index
SEQAN_ENABLE_DEBUG == 1
SEQAN_ENABLE_TESTING == 1
SEQAN_CXX_FLAGS == "SEQAN_CXX_FLAGS_NOT_SET"
SEQAN_ASYNC_IO == 1
testIndexCrossCompareDna OK

 46/400 Test  #52: test_test_index_fm_rank_dictionary
................................................Bus error***Exception:
0.01 sec
TEST SUITE tests
SEQAN_ENABLE_DEBUG == 1
SEQAN_ENABLE_TESTING == 1
SEQAN_CXX_FLAGS == "SEQAN_CXX_FLAGS_NOT_SET"
SEQAN_ASYNC_IO == 1
RankDictionaryTest_Constructor type parameter seqan::RankDictionary<bool,
seqan::Naive<void, seqan::RDConfig<unsigned int, seqan::Alloc<void>, 1u,
1u> > > OK
RankDictionaryTest_Constructor type parameter seqan::RankDictionary<bool,
seqan::Levels<void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>,
1u, 1u> > > OK
RankDictionaryTest_Constructor type parameter
seqan::RankDictionary<seqan::SimpleType<unsigned char, seqan::Dna_>,
seqan::Levels<void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>,
1u, 1u> > > OK
RankDictionaryTest_Constructor type parameter
seqan::RankDictionary<seqan::SimpleType<unsigned char, seqan::Dna5_>,
seqan::Levels<void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>,
1u, 1u> > > OK
RankDictionaryTest_Constructor type parameter
seqan::RankDictionary<seqan::SimpleType<unsigned char, seqan::Dna5Q_>,
seqan::Levels<void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>,
1u, 1u> > > OK
RankDictionaryTest_Constructor type parameter
seqan::RankDictionary<seqan::SimpleType<unsigned char,
seqan::ReducedAminoAcid_<seqan::Tag<seqan::Murphy10_> > >,
seqan::Levels<void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>,
1u, 1u> > > OK
RankDictionaryTest_Constructor type parameter
seqan::RankDictionary<seqan::SimpleType<unsigned char, seqan::AminoAcid_>,
seqan::Levels<void, seqan::LevelsRDConfig<unsigned int, seqan::Alloc<void>,
1u, 1u> > > OK

===
mips test failure
===

  5/397 Test   #7: test_align_parallel_data_structures
...............................................Child aborted***Exception:
 0.10 sec
TEST SUITE test_align_parallel_data_structures
SEQAN_ENABLE_DEBUG == 1
SEQAN_ENABLE_TESTING == 1
SEQAN_CXX_FLAGS == "SEQAN_CXX_FLAGS_NOT_SET"
SEQAN_ASYNC_IO == 1
test_align_parallel_wavefront_task_scheduler_construct OK
test_align_parallel_wavefront_task_scheduler_async OK
test_align_parallel_wavefront_alignment_scheduler_construct OK
test_align_parallel_wavefront_alignment_scheduler_async OK
double free or corruption (out)
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