[Debian-med-packaging] Bug#984067: ivar: ftbfs with GCC-11

[Matthias Klose]

Package: src:ivar
Version: 1.3+dfsg-1
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-11

[This bug is not targeted to the upcoming bullseye 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-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.

The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/ivar_1.3+dfsg-1_unstable_gcc11.log
The last lines of the build log are at the end of this report.

To build with GCC 11, either set CC=gcc-11 CXX=g++-11 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-11/porting_to.html

GCC 11 defaults to the GNU++17 standard.  If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.

[...]
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-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.'
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -v -g -std=c++11 -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp
Using built-in specs.
COLLECT_GCC=g++
OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 11-20210227-1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/packages/gcc/11/gcc-11-11-20210227/debian/tmp-nvptx/usr,amdgcn-amdhsa=/packages/gcc/11/gcc-11-11-20210227/debian/tmp-gcn/usr --without-cuda-driver --enable-checking=yes,extra,rtl --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=32
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 11.0.1 20210227 (experimental) [master revision ded7355b3d9:aa8bb3da10e:06a9f20f97e788bdff139dcf62d055955debcc8d] (Debian 11-20210227-1) 
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
 /usr/lib/gcc/x86_64-linux-gnu/11/cc1plus -quiet -v -I . -I .. -imultiarch x86_64-linux-gnu -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -dumpbase-ext .cpp -mtune=generic -march=x86-64 -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -fasynchronous-unwind-tables -o /tmp/ccHC7IGP.s
GNU C++11 (Debian 11-20210227-1) version 11.0.1 20210227 (experimental) [master revision ded7355b3d9:aa8bb3da10e:06a9f20f97e788bdff139dcf62d055955debcc8d] (x86_64-linux-gnu)
	compiled by GNU C version 11.0.1 20210227 (experimental) [master revision ded7355b3d9:aa8bb3da10e:06a9f20f97e788bdff139dcf62d055955debcc8d], GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP

GGC heuristics: --param ggc-min-expand=30 --param ggc-min-heapsize=4096
ignoring duplicate directory "/usr/include/x86_64-linux-gnu/c++/11"
ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/11/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/11/../../../../x86_64-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
 .
 ..
 /usr/include/c++/11
 /usr/include/x86_64-linux-gnu/c++/11
 /usr/include/c++/11/backward
 /usr/lib/gcc/x86_64-linux-gnu/11/include
 /usr/local/include
 /usr/include/x86_64-linux-gnu
 /usr/include
End of search list.
GNU C++11 (Debian 11-20210227-1) version 11.0.1 20210227 (experimental) [master revision ded7355b3d9:aa8bb3da10e:06a9f20f97e788bdff139dcf62d055955debcc8d] (x86_64-linux-gnu)
	compiled by GNU C version 11.0.1 20210227 (experimental) [master revision ded7355b3d9:aa8bb3da10e:06a9f20f97e788bdff139dcf62d055955debcc8d], GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP

GGC heuristics: --param ggc-min-expand=30 --param ggc-min-heapsize=4096
Compiler executable checksum: 2900c290e29b54415706f52c8eebe364
cc1plus: all warnings being treated as errors
make[3]: *** [Makefile:389: ivar.o] Error 1
make[3]: *** Waiting for unfinished jobs....
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-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/ccjBTk0p.s
GNU assembler version 2.35.2 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2
MAKEFLAGS=w -j4 
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-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' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
 as -v -I . -I .. --gdwarf-5 --64 -o remove_reads_from_amplicon.o /tmp/cc1GXrdE.s
GNU assembler version 2.35.2 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2
MAKEFLAGS=w -j4 
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'remove_reads_from_amplicon.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-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/ccHC7IGP.s
GNU assembler version 2.35.2 (x86_64-linux-gnu) using BFD version (GNU Binutils for Debian) 2.35.2
MAKEFLAGS=w -j4 
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/11/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/11/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mtune=generic' '-march=x86-64' '-dumpdir' 'call_variants.'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: *** [Makefile:362: all-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:303: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 returned exit code 2
make: *** [debian/rules:9: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2