[Debian-med-packaging] Bug#984328: seer: ftbfs with GCC-11
Matthias Klose
doko at debian.org
Wed Mar 3 16:17:13 GMT 2021
Package: src:seer
Version: 1.1.4-4
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/seer_1.1.4-4_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.
[...]
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -b -rfakeroot
dpkg-buildpackage: info: source package seer
dpkg-buildpackage: info: source version 1.1.4-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Helmut Grohne <helmut at subdivi.de>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -f *.o ~* seer kmds map_back combineKmers filter_seer
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
cd test && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
rm -f *.o ~* tests_passed
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- LDFLAGS+=-L/usr/lib/x86_64-linux-gnu/hdf5/serial
make -j4 "INSTALL=install --strip-program=true" LDFLAGS\+=-L/usr/lib/x86_64-linux-gnu/hdf5/serial
make[2]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make all
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o sample.o sample.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o significant_kmer.o significant_kmer.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o kmer.o kmer.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o covar.o covar.cpp
significant_kmer.cpp: In function ‘std::istream& operator>>(std::istream&, Significant_kmer&)’:
significant_kmer.cpp:50:31: error: ‘numeric_limits’ is not a member of ‘std’
50 | line_stream.ignore(std::numeric_limits<std::streamsize>::max(), '\t');
| ^~~~~~~~~~~~~~
significant_kmer.cpp:50:61: error: expected primary-expression before ‘>’ token
50 | line_stream.ignore(std::numeric_limits<std::streamsize>::max(), '\t');
| ^
significant_kmer.cpp:50:64: error: ‘::max’ has not been declared; did you mean ‘std::max’?
50 | line_stream.ignore(std::numeric_limits<std::streamsize>::max(), '\t');
| ^~~
| std::max
In file included from /usr/include/c++/11/algorithm:62,
from significant_kmer.hpp:13,
from significant_kmer.cpp:9:
/usr/include/c++/11/bits/stl_algo.h:3467:5: note: ‘std::max’ declared here
3467 | max(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1 -DARMA_USE_HDF5=1 -c -o seerCommon.o seerCommon.cpp
make[3]: *** [<builtin>: significant_kmer.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: *** [Makefile:5: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" LDFLAGS\+=-L/usr/lib/x86_64-linux-gnu/hdf5/serial returned exit code 2
make[1]: *** [debian/rules:14: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:26: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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