[Debian-med-packaging] Bug#956136: nanopolish: FTBFS (undefined references)

[Bas Couwenberg]

Source: nanopolish
Version: 0.12.1-1
Severity: serious
Tags: ftbfs
Justification: makes the package in question unusable or mostly so
Control: block 954654 by -1

Dear Maintainer,

Your packages fails to build in unstable:

 /usr/bin/ld: /tmp/nanopolish.HEB8tw.ltrans12.ltrans.o: in function `populate_maps_from_fastq(OutputHandles&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::unordered_map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&, std::unordered_map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::vector<bam1_t*, std::allocator<bam1_t*> >, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::vector<bam1_t*, std::allocator<bam1_t*> > > > >&, sam_hdr_t*, mm_mapopt_t, mm_idx_t*) [clone ._omp_fn.0]':
 ./src/nanopolish_call_methylation.cpp:536: undefined reference to `mm_map'
 /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:551: undefined reference to `mm_write_sam'
 /usr/bin/ld: /tmp/nanopolish.HEB8tw.ltrans12.ltrans.o: in function `run_watch_mode(__faidx_t const*)':
 ./src/nanopolish_call_methylation.cpp:668: undefined reference to `mm_verbose'
 /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:669: undefined reference to `mm_set_opt'
 /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:674: undefined reference to `mm_idx_reader_open'
 /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:677: undefined reference to `mm_idx_reader_read'
 /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:678: undefined reference to `mm_mapopt_update'
 /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:681: undefined reference to `mm_idx_reader_read'
 /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:758: undefined reference to `mm_idx_destroy'
 /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:759: undefined reference to `mm_idx_reader_close'
 /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:520: undefined reference to `mm_tbuf_init'
 /usr/bin/ld: /tmp/nanopolish.HEB8tw.ltrans12.ltrans.o:./src/nanopolish_call_methylation.cpp:577: undefined reference to `mm_tbuf_destroy'
 collect2: error: ld returned 1 exit status
 make[1]: *** [Makefile:165: nanopolish] Error 1

https://buildd.debian.org/status/fetch.php?pkg=nanopolish&arch=amd64&ver=0.12.1-1&stamp=1586252670&raw=0

Kind Regards,

Bas