[Debian-med-packaging] Bug#1037700: ivar: ftbfs with GCC-13
Matthias Klose
doko at debian.org
Wed Jun 14 10:25:52 BST 2023
Package: src:ivar
Version: 1.3.1+dfsg-7
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/ivar_1.3.1+dfsg-7_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
[...]
primer_bed.cpp:283:115: error: ‘class primer’ has no member named ‘get_start’; did you mean ‘set_start’?
283 | auto minmax_start = std::minmax_element(primers.begin(), primers.end(), [] (primer lhs, primer rhs) {return lhs.get_start() < rhs.get_start();});
| ^~~~~~~~~
| set_start
primer_bed.cpp:283:133: error: ‘class primer’ has no member named ‘get_start’; did you mean ‘set_start’?
283 | auto minmax_start = std::minmax_element(primers.begin(), primers.end(), [] (primer lhs, primer rhs) {return lhs.get_start() < rhs.get_start();});
| ^~~~~~~~~
| set_start
primer_bed.cpp: In lambda function:
primer_bed.cpp:288:115: error: ‘class primer’ has no member named ‘get_end’; did you mean ‘set_end’?
288 | auto minmax_start = std::minmax_element(primers.begin(), primers.end(), [] (primer lhs, primer rhs) {return lhs.get_end() < rhs.get_end();});
| ^~~~~~~
| set_end
primer_bed.cpp:288:131: error: ‘class primer’ has no member named ‘get_end’; did you mean ‘set_end’?
288 | auto minmax_start = std::minmax_element(primers.begin(), primers.end(), [] (primer lhs, primer rhs) {return lhs.get_end() < rhs.get_end();});
| ^~~~~~~
| set_end
make[3]: *** [Makefile:398: remove_reads_from_amplicon.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: *** [Makefile:398: primer_bed.o] Error 1
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
as -v -I . -I .. --gdwarf-5 --64 -o alignment.o /tmp/ccIpCNHF.s
GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'alignment.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
as -v -I . -I .. --gdwarf-5 --64 -o ivar.o /tmp/ccAKmKbn.s
GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'ivar.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
as -v -I . -I .. --gdwarf-5 --64 -o suffix_tree.o /tmp/ccSaN496.s
GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
as -v -I . -I .. --gdwarf-5 --64 -o call_variants.o /tmp/ccnPgGJ4.s
GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_variants.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
as -v -I . -I .. --gdwarf-5 --64 -o trim_primer_quality.o /tmp/ccsysYgc.s
GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'suffix_tree.'
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'trim_primer_quality.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
as -v -I . -I .. --gdwarf-5 --64 -o call_consensus_pileup.o /tmp/ccLUcmne.s
GNU assembler version 2.40 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.40
MAKEFLAGS=w -j8
COMPILER_PATH=/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/13/:/usr/libexec/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/13/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/13/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_consensus_pileup.'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: *** [Makefile:371: all-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:312: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 returned exit code 2
make: *** [debian/rules:12: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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