[Debian-med-packaging] Bug#1028713: Comment

[Andreas Tille]

Hi Dominik,

thanks for your attempt to track this down.  I'm wondering what might
happen if I refresh the pufferfish code in debian/external which I tried
in my last commit.  Unfortunately this failed as well:

   https://salsa.debian.org/med-team/salmon/-/jobs/3876351

Kind regards
   Andreas.

Am Sun, Jan 29, 2023 at 09:05:51PM +0100 schrieb Dominik Stadler:
> A stacktrace from the segmentation fault looks like follows.
> 
> It triggers consistently for me with the following steps in a source-tree
> 
> fakeroot debian/rules binary
> cd sample_data/
> /tmp/salmon-1.9.0+ds1/obj-x86_64-linux-gnu/src/salmon index -t
> transcripts.fasta -i sample_salmon_quasi_index
> 
> 
> #0  0x00007ffff7495993 in __GI__IO_fwrite (buf=0x7fffffffc978, size=1,
> count=82,
> fp=0x7ffff6060400) at ./libio/iofwrite.c:37
> #1  0x000055555560f55d in spdlog::details::file_helper::write
> (this=0x7ffff607f980,
> msg=...) at ./include/spdlog/details/../sinks/../details/file_helper.h:90
> #2  0x00005555556299dd in
> spdlog::sinks::simple_file_sink<spdlog::details::null_mutex>::_sink_it
> (msg=...,
> this=0x7ffff607f970) at ./include/spdlog/details/../sinks/file_sinks.h:45
> #3  spdlog::sinks::base_sink<spdlog::details::null_mutex>::log
> (this=0x7ffff607f970,
> msg=...) at ./include/spdlog/sinks/base_sink.h:37
> #4  0x0000555555618aa3 in spdlog::logger::_sink_it
> (this=0x7ffff6025810, msg=...)
> at /usr/include/c++/12/bits/shared_ptr_base.h:1665
> #5  0x0000555555a8ae19 in spdlog::logger::log<double> (fmt=0x555555cd7f0b
> "mphf size = {} MB", lvl=spdlog::level::info, this=0x7ffff6025810) at
> ./external/pufferfish/include/spdlog/details/logger_impl.h:74
> #6  spdlog::logger::info<double> (arg1=<optimized out>, fmt=0x555555cd7f0b
> "mphf size = {} MB", this=0x7ffff6025810) at
> ./external/pufferfish/include/spdlog/details/logger_impl.h:145
> #7  pufferfishIndex (indexOpts=...) at
> ./external/pufferfish/src/PufferfishIndexer.cpp:660
> #8  0x00005555556636ae in SalmonIndex::buildPuffIndex_ (idxOpt=...,
> indexDir=...,
> this=0x7ffff603e280) at ./include/SalmonIndex.hpp:111
> #9  SalmonIndex::build (idxOpt=..., indexDir=..., this=0x7ffff603e280) at
> ./include/SalmonIndex.hpp:76
> #10 salmonIndex (argc=<optimized out>, argv=<optimized out>) at
> ./src/BuildSalmonIndex.cpp:247
> #11 0x00005555555fe510 in std::function<int (int, char const**,
> std::unique_ptr<SalmonIndex, std::default_delete<SalmonIndex>
> >&)>::operator()(int, char const**, std::unique_ptr<SalmonIndex,
> std::default_delete<S
> almonIndex> >&) const (__args#2=std::unique_ptr<SalmonIndex> = {...},
> __args#1=<optimized out>, __args#0=<optimized out>, this=0x7ffff604e1a8) at
> /usr/include/c++/12/bits/std_function.h:591
> #12 main (argc=<optimized out>, argv=0x7fffffffe028) at ./src/Salmon.cpp:267

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