[Debian-med-packaging] Bug#1037672: genomicsdb: ftbfs with GCC-13
Matthias Klose
doko at debian.org
Wed Jun 14 10:24:56 BST 2023
Package: src:genomicsdb
Version: 1.4.4-3
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/genomicsdb_1.4.4-3_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
[...]
| (
/<<PKGBUILDDIR>>/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc:69:49: error: expected primary-expression before ‘>’ token
69 | return do_code(reinterpret_cast<uint64_t *>(tile), tile_size, this);
| ^
/<<PKGBUILDDIR>>/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc: In member function ‘virtual int CodecDeltaEncode::decode(unsigned char*, size_t)’:
/<<PKGBUILDDIR>>/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc:104:41: error: ‘uint32_t’ does not name a type
104 | return do_decode(reinterpret_cast<uint32_t *>(tile), tile_size, this);
| ^~~~~~~~
/<<PKGBUILDDIR>>/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc:104:41: note: ‘uint32_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
/<<PKGBUILDDIR>>/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc:104:50: error: expected ‘>’ before ‘*’ token
104 | return do_decode(reinterpret_cast<uint32_t *>(tile), tile_size, this);
| ^
/<<PKGBUILDDIR>>/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc:104:50: error: expected ‘(’ before ‘*’ token
104 | return do_decode(reinterpret_cast<uint32_t *>(tile), tile_size, this);
| ^
| (
/<<PKGBUILDDIR>>/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc:104:51: error: expected primary-expression before ‘>’ token
104 | return do_decode(reinterpret_cast<uint32_t *>(tile), tile_size, this);
| ^
/<<PKGBUILDDIR>>/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc:106:41: error: ‘uint64_t’ does not name a type
106 | return do_decode(reinterpret_cast<uint64_t *>(tile), tile_size, this);
| ^~~~~~~~
/<<PKGBUILDDIR>>/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc:106:41: note: ‘uint64_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’?
/<<PKGBUILDDIR>>/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc:106:50: error: expected ‘>’ before ‘*’ token
106 | return do_decode(reinterpret_cast<uint64_t *>(tile), tile_size, this);
| ^
/<<PKGBUILDDIR>>/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc:106:50: error: expected ‘(’ before ‘*’ token
106 | return do_decode(reinterpret_cast<uint64_t *>(tile), tile_size, this);
| ^
| (
/<<PKGBUILDDIR>>/genomicsdb-tiledb/core/src/codec/codec_filter_delta_encode.cc:106:51: error: expected primary-expression before ‘>’ token
106 | return do_decode(reinterpret_cast<uint64_t *>(tile), tile_size, this);
| ^
make[4]: *** [genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/build.make:247: genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/src/codec/codec_filter_delta_encode.cc.o] Error 1
make[4]: *** Waiting for unfinished jobs....
[ 15%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/<<PKGBUILDDIR>>/genomicsdb-htslib -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o -c /<<PKGBUILDDIR>>/genomicsdb-htslib/cram/cram_external.c
[ 15%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/<<PKGBUILDDIR>>/genomicsdb-htslib -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o -c /<<PKGBUILDDIR>>/genomicsdb-htslib/cram/cram_index.c
[ 15%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/<<PKGBUILDDIR>>/genomicsdb-htslib -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o -c /<<PKGBUILDDIR>>/genomicsdb-htslib/cram/cram_io.c
[ 16%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/<<PKGBUILDDIR>>/genomicsdb-htslib -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o -c /<<PKGBUILDDIR>>/genomicsdb-htslib/cram/cram_samtools.c
[ 16%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/<<PKGBUILDDIR>>/genomicsdb-htslib -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o -c /<<PKGBUILDDIR>>/genomicsdb-htslib/cram/cram_stats.c
[ 16%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/<<PKGBUILDDIR>>/genomicsdb-htslib -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o -c /<<PKGBUILDDIR>>/genomicsdb-htslib/cram/mFILE.c
[ 17%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/<<PKGBUILDDIR>>/genomicsdb-htslib -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o -c /<<PKGBUILDDIR>>/genomicsdb-htslib/cram/open_trace_file.c
[ 17%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/<<PKGBUILDDIR>>/genomicsdb-htslib -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o -c /<<PKGBUILDDIR>>/genomicsdb-htslib/cram/pooled_alloc.c
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:609: genomicsdb-tiledb/core/CMakeFiles/TILEDB_CORE_OBJECTS.dir/all] Error 2
[ 17%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/<<PKGBUILDDIR>>/genomicsdb-htslib -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o -c /<<PKGBUILDDIR>>/genomicsdb-htslib/cram/rANS_static.c
[ 17%] Building C object genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cc -DVCF_ALLOW_INT64=1 -Dgenomicsdb_hts_EXPORTS -I/<<PKGBUILDDIR>>/genomicsdb-htslib -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT genomicsdb-htslib/CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o -MF CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o.d -o CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o -c /<<PKGBUILDDIR>>/genomicsdb-htslib/cram/string_alloc.c
[ 18%] Linking C shared library libgenomicsdb-hts.so
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/genomicsdb-htslib && /usr/bin/cmake -E cmake_link_script CMakeFiles/genomicsdb-hts.dir/link.txt --verbose=1
/usr/bin/cc -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgenomicsdb-hts.so -o libgenomicsdb-hts.so "CMakeFiles/genomicsdb-hts.dir/kfunc.c.o" "CMakeFiles/genomicsdb-hts.dir/knetfile.c.o" "CMakeFiles/genomicsdb-hts.dir/kstring.c.o" "CMakeFiles/genomicsdb-hts.dir/bcf_sr_sort.c.o" "CMakeFiles/genomicsdb-hts.dir/bgzf.c.o" "CMakeFiles/genomicsdb-hts.dir/errmod.c.o" "CMakeFiles/genomicsdb-hts.dir/faidx.c.o" "CMakeFiles/genomicsdb-hts.dir/header.c.o" "CMakeFiles/genomicsdb-hts.dir/hfile.c.o" "CMakeFiles/genomicsdb-hts.dir/hfile_libcurl.c.o" "CMakeFiles/genomicsdb-hts.dir/hfile_net.c.o" "CMakeFiles/genomicsdb-hts.dir/hts.c.o" "CMakeFiles/genomicsdb-hts.dir/hts_os.c.o" "CMakeFiles/genomicsdb-hts.dir/md5.c.o" "CMakeFiles/genomicsdb-hts.dir/multipart.c.o" "CMakeFiles/genomicsdb-hts.dir/probaln.c.o" "CMakeFiles/genomicsdb-hts.dir/realn.c.o" "CMakeFiles/genomicsdb-hts.dir/regidx.c.o" "CMakeFiles/genomicsdb-hts.dir/region.c.o" "CMakeFiles/genomicsdb-hts.dir/sam.c.o" "CMakeFiles/genomicsdb-hts.dir/synced_bcf_reader.c.o" "CMakeFiles/genomicsdb-hts.dir/vcf_sweep.c.o" "CMakeFiles/genomicsdb-hts.dir/tbx.c.o" "CMakeFiles/genomicsdb-hts.dir/textutils.c.o" "CMakeFiles/genomicsdb-hts.dir/thread_pool.c.o" "CMakeFiles/genomicsdb-hts.dir/vcf.c.o" "CMakeFiles/genomicsdb-hts.dir/vcfutils.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_codecs.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_decode.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_encode.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_external.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_index.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_io.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_samtools.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/cram_stats.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/mFILE.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/open_trace_file.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/pooled_alloc.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/rANS_static.c.o" "CMakeFiles/genomicsdb-hts.dir/cram/string_alloc.c.o" /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/liblzma.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 18%] Built target genomicsdb-hts
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:149: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:55: override_dh_auto_build-arch] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:17: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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