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 > _______________________________________________ > Debian-med-packaging mailing list > debian-med-packag...@alioth-lists.debian.net > https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging -- http://fam-tille.de
