[Debian-med-packaging] Bug#1037886: vsearch: ftbfs with GCC-13

[Matthias Klose]

Package: src:vsearch
Version: 2.22.1-1
Severity: normal
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-13

[This bug is targeted to the upcoming trixie release]

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-13/g++-13, but succeeds to build with gcc-12/g++-12. The
severity of this report will be raised before the trixie release.

The full build log can be found at:
http://qa-logs.debian.net/2023/05/22/logs/vsearch_2.22.1-1_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 13, either set CC=gcc-13 CXX=g++-13 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-13/porting_to.html

[...]
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -march=x86-64 -mtune=generic -std=c++11 -msse2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -std=c++11 -c -o libcpu_sse2_a-cpu.o `test -f 'cpu.cc' || echo './'`cpu.cc
rm -f libcityhash.a
ar cru libcityhash.a libcityhash_a-city.o 
ar: `u' modifier ignored since `D' is the default (see `U')
ar: libcityhash_a-city.o: plugin needed to handle lto object
ranlib libcityhash.a
ranlib: libcityhash.a(libcityhash_a-city.o): plugin needed to handle lto object
rm -f libcpu_ssse3.a
ar cru libcpu_ssse3.a libcpu_ssse3_a-cpu.o  
ar: `u' modifier ignored since `D' is the default (see `U')
ar: libcpu_ssse3_a-cpu.o: plugin needed to handle lto object
ranlib libcpu_ssse3.a
ranlib: libcpu_ssse3.a(libcpu_ssse3_a-cpu.o): plugin needed to handle lto object
rm -f libcpu_sse2.a
ar cru libcpu_sse2.a libcpu_sse2_a-cpu.o  
ar: `u' modifier ignored since `D' is the default (see `U')
ar: libcpu_sse2_a-cpu.o: plugin needed to handle lto object
ranlib libcpu_sse2.a
ranlib: libcpu_sse2.a(libcpu_sse2_a-cpu.o): plugin needed to handle lto object
g++ -Wall -Wsign-compare -march=x86-64 -mtune=generic -std=c++11 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -flto -std=c++11  -Wl,-z,relro -Wl,-z,now -flto -o ../bin/vsearch  align.o align_simd.o allpairs.o arch.o attributes.o bitmap.o chimera.o cluster.o cut.o db.o dbhash.o dbindex.o derep.o derepsmallmem.o dynlibs.o eestats.o fa2fq.o fasta.o fastq.o fastqjoin.o fastqops.o fastx.o filter.o getseq.o kmerhash.o linmemalign.o maps.o mask.o md5.o mergepairs.o minheap.o msa.o orient.o otutable.o rerep.o results.o search.o searchcore.o searchexact.o sffconvert.o sha1.o showalign.o shuffle.o sintax.o sortbylength.o sortbysize.o subsample.o tax.o udb.o unique.o userfields.o util.o vsearch.o libcityhash.a libcpu_ssse3.a libcpu_sse2.a -ldl -lpthread 
derep.cc:65:8: warning: type ‘struct bucket’ violates the C++ One Definition Rule [-Wodr]
   65 | struct bucket
      |        ^
derepsmallmem.cc:65:8: note: a different type is defined in another translation unit
   65 | struct bucket
      |        ^
derep.cc:67:12: note: the first difference of corresponding definitions is field ‘hash’
   67 |   uint64_t hash;
      |            ^
derepsmallmem.cc:67:11: note: a field of same name but different type is defined in another translation unit
   67 |   uint128 hash;
      |           ^
derep.cc:65:8: note: type ‘uint64_t’ should match type ‘struct uint128’
   65 | struct bucket
      |        ^
lto-wrapper: warning: using serial compilation of 5 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
/usr/bin/ld: /tmp/ccjFEVxz.ltrans0.ltrans.o: in function `dbhash_search_first(char*, unsigned long, dbhash_search_info_s*)':
./src/./src/util.cc:194: undefined reference to `CityHash64(char const*, unsigned long)'
/usr/bin/ld: /tmp/ccjFEVxz.ltrans0.ltrans.o: in function `derep(char*, bool)':
./src/./src/util.cc:194: undefined reference to `CityHash64(char const*, unsigned long)'
/usr/bin/ld: ./src/./src/util.cc:194: undefined reference to `CityHash64(char const*, unsigned long)'
/usr/bin/ld: ./src/./src/util.cc:194: undefined reference to `CityHash64(char const*, unsigned long)'
/usr/bin/ld: /tmp/ccjFEVxz.ltrans0.ltrans.o: in function `derep_smallmem(char*)':
./src/./src/util.cc:199: undefined reference to `CityHash128(char const*, unsigned long)'
/usr/bin/ld: ./src/./src/util.cc:199: undefined reference to `CityHash128(char const*, unsigned long)'
/usr/bin/ld: ./src/./src/util.cc:199: undefined reference to `CityHash128(char const*, unsigned long)'
/usr/bin/ld: ./src/./src/util.cc:199: undefined reference to `CityHash128(char const*, unsigned long)'
/usr/bin/ld: /tmp/ccjFEVxz.ltrans0.ltrans.o: in function `cluster_core_parallel()':
./src/./src/unique.cc:365: undefined reference to `CityHash64(char const*, unsigned long)'
/usr/bin/ld: /tmp/ccjFEVxz.ltrans2.ltrans.o: in function `search_topscores(searchinfo_s*)':
./src/./src/searchcore.cc:239: undefined reference to `increment_counters_from_bitmap_ssse3(unsigned short*, unsigned char*, unsigned int)'
/usr/bin/ld: ./src/./src/searchcore.cc:244: undefined reference to `increment_counters_from_bitmap_sse2(unsigned short*, unsigned char*, unsigned int)'
/usr/bin/ld: /tmp/ccjFEVxz.ltrans1.ltrans.o: in function `process(merge_data_s*, kh_handle_s*)':
./src/./src/kmerhash.cc:110: undefined reference to `CityHash64(char const*, unsigned long)'
/usr/bin/ld: ./src/./src/kmerhash.cc:283: undefined reference to `CityHash64(char const*, unsigned long)'
/usr/bin/ld: /tmp/ccjFEVxz.ltrans3.ltrans.o: in function `unique_count_hash(uhandle_s*, int, int, char*, unsigned int*, unsigned int**, int)':
./src/./src/unique.cc:300: undefined reference to `CityHash64(char const*, unsigned long)'
collect2: error: ld returned 1 exit status
make[4]: *** [Makefile:650: ../bin/vsearch] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: *** [Makefile:376: all-recursive] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: *** [Makefile:317: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 returned exit code 2
make[1]: *** [debian/rules:34: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:31: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2