[Debian-med-packaging] Bug#892222: seqan2: FTBFS on hppa: app_test_seqan_tcoffee fails on 2trx.mlcs.fasta

[Andreas Tille]

Hi Aaron,

I had a quick look at this bug and realises that currently the source
code does not even build any more[1] thus not even reaching the test you
spotted as failing:

...
[  3%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o
cd /<<PKGBUILDDIR>>/obj-hppa-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2  -W -Wall -pedantic -fopenmp    -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -MF CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o.d -o CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -c /<<PKGBUILDDIR>>/apps/pair_align/lib/pair_align_global.cpp
malloc(): unaligned tcache chunk detected
malloc(): unaligned tcache chunk detected
c++: internal compiler error: Aborted signal terminated program cc1plus
Please submit a full bug report,
with preprocessed source if appropriate.


Kind regards

     Andreas.


[1] https://buildd.debian.org/status/fetch.php?pkg=seqan2&arch=hppa&ver=2.4.0%2Bdfsg-14&stamp=1638150140&raw=0

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