[Debian-med-packaging] Bug#1020031: khmer: FTBFS: ld: cannot find build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o: No such file or directory

[Lucas Nussbaum]

Source: khmer
Version: 3.0.0~a3+dfsg-3
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20220917 ftbfs-bookworm

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.


Relevant part (hopefully):
> x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-310/khmer/_oxli/oxli_exception_convert.o build/temp.linux-x86_64-cpython-310/khmer/_oxli/readaligner.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o build/temp.linux-x86_64-3.10/src/oxli/hashtable.o build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o build/temp.linux-x86_64-3.10/src/oxli/labelhash.o build/temp.linux-x86_64-3.10/src/oxli/subset.o build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o build/temp.linux-x86_64-3.10/src/oxli/traversal.o build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o build/temp.linux-x86_64-3.10/src/oxli/assembler.o build/temp.linux-x86_64-3.10/src/oxli/alphabets.o build/temp.linux-x86_64-3.10/src/oxli/storage.o build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o third-party/cqf/gqf.o -L/usr/lib/x86_64-linux-gnu -lz -lbz2 -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_khmer/build/khmer/_oxli/readaligner.cpython-310-x86_64-linux-gnu.so -fopenmp
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/khmer/_cpy_khmer.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/khmer/_cpy_utils.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/khmer/_cpy_readparsers.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/oxli/read_parsers.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/oxli/kmer_hash.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/oxli/hashtable.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/oxli/hashgraph.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/oxli/labelhash.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/oxli/subset.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/oxli/read_aligner.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/oxli/hllcounter.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/oxli/traversal.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/oxli/kmer_filters.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/oxli/assembler.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/oxli/alphabets.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/src/oxli/storage.o: No such file or directory
> /usr/bin/ld: cannot find build/temp.linux-x86_64-3.10/third-party/smhasher/MurmurHash3.o: No such file or directory
> collect2: error: ld returned 1 exit status


The full build log is available from:
http://qa-logs.debian.net/2022/09/17/khmer_3.0.0~a3+dfsg-3_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20220917;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220917&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.