[Debichem-devel] Bug#1013017: psi4: ftbfs with GCC-12
Matthias Klose
doko at debian.org
Thu Jun 16 13:12:34 BST 2022
Package: src:psi4
Version: 1:1.3.2+dfsg-2.1
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-12
[This bug is targeted to the upcoming bookworm 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-12/g++-12, but succeeds to build with gcc-11/g++-11. The
severity of this report will be raised before the bookworm release.
The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/gcc12/psi4_1.3.2+dfsg-2.1_unstable_gcc12.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.
[...]
[ 99%] Building CXX object src/CMakeFiles/core.dir/export_misc.cc.o
[ 99%] Building CXX object src/CMakeFiles/core.dir/export_blas_lapack.cc.o
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/export_benchmarks.cc.o -MF CMakeFiles/core.dir/export_benchmarks.cc.o.d -o CMakeFiles/core.dir/export_benchmarks.cc.o -c /<<PKGBUILDDIR>>/psi4/src/export_benchmarks.cc
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/export_cubeprop.cc.o -MF CMakeFiles/core.dir/export_cubeprop.cc.o.d -o CMakeFiles/core.dir/export_cubeprop.cc.o -c /<<PKGBUILDDIR>>/psi4/src/export_cubeprop.cc
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/export_diis.cc.o -MF CMakeFiles/core.dir/export_diis.cc.o.d -o CMakeFiles/core.dir/export_diis.cc.o -c /<<PKGBUILDDIR>>/psi4/src/export_diis.cc
[ 99%] Building CXX object src/CMakeFiles/core.dir/export_functional.cc.o
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/export_mints.cc.o -MF CMakeFiles/core.dir/export_mints.cc.o.d -o CMakeFiles/core.dir/export_mints.cc.o -c /<<PKGBUILDDIR>>/psi4/src/export_mints.cc
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/export_misc.cc.o -MF CMakeFiles/core.dir/export_misc.cc.o.d -o CMakeFiles/core.dir/export_misc.cc.o -c /<<PKGBUILDDIR>>/psi4/src/export_misc.cc
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/export_blas_lapack.cc.o -MF CMakeFiles/core.dir/export_blas_lapack.cc.o.d -o CMakeFiles/core.dir/export_blas_lapack.cc.o -c /<<PKGBUILDDIR>>/psi4/src/export_blas_lapack.cc
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/export_functional.cc.o -MF CMakeFiles/core.dir/export_functional.cc.o.d -o CMakeFiles/core.dir/export_functional.cc.o -c /<<PKGBUILDDIR>>/psi4/src/export_functional.cc
[ 99%] Building CXX object src/CMakeFiles/core.dir/export_oeprop.cc.o
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/export_oeprop.cc.o -MF CMakeFiles/core.dir/export_oeprop.cc.o.d -o CMakeFiles/core.dir/export_oeprop.cc.o -c /<<PKGBUILDDIR>>/psi4/src/export_oeprop.cc
[ 99%] Building CXX object src/CMakeFiles/core.dir/export_pcm.cc.o
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/export_pcm.cc.o -MF CMakeFiles/core.dir/export_pcm.cc.o.d -o CMakeFiles/core.dir/export_pcm.cc.o -c /<<PKGBUILDDIR>>/psi4/src/export_pcm.cc
[ 99%] Building CXX object src/CMakeFiles/core.dir/export_plugins.cc.o
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/export_plugins.cc.o -MF CMakeFiles/core.dir/export_plugins.cc.o.d -o CMakeFiles/core.dir/export_plugins.cc.o -c /<<PKGBUILDDIR>>/psi4/src/export_plugins.cc
[ 99%] Building CXX object src/CMakeFiles/core.dir/export_psio.cc.o
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/export_psio.cc.o -MF CMakeFiles/core.dir/export_psio.cc.o.d -o CMakeFiles/core.dir/export_psio.cc.o -c /<<PKGBUILDDIR>>/psi4/src/export_psio.cc
[ 99%] Building CXX object src/CMakeFiles/core.dir/export_trans.cc.o
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/export_trans.cc.o -MF CMakeFiles/core.dir/export_trans.cc.o.d -o CMakeFiles/core.dir/export_trans.cc.o -c /<<PKGBUILDDIR>>/psi4/src/export_trans.cc
[ 99%] Building CXX object src/CMakeFiles/core.dir/export_wavefunction.cc.o
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/export_wavefunction.cc.o -MF CMakeFiles/core.dir/export_wavefunction.cc.o.d -o CMakeFiles/core.dir/export_wavefunction.cc.o -c /<<PKGBUILDDIR>>/psi4/src/export_wavefunction.cc
/<<PKGBUILDDIR>>/psi4/src/export_wavefunction.cc: In function ‘void export_wavefunction(pybind11::module&)’:
/<<PKGBUILDDIR>>/psi4/src/export_wavefunction.cc:142:51: warning: ‘psi::SharedVector psi::Wavefunction::frequencies() const’ is deprecated: Using `Wavefunction.frequencies` c-side instead of `Wavefunction.frequencies` py-side is deprecated, and in 1.4 it will stop working [-Wdeprecated-declarations]
142 | .def("legacy_frequencies", &Wavefunction::frequencies, "Returns the frequencies of the Hessian.")
| ^~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/psi4/src/psi4/cc/ccwave.h:34,
from /<<PKGBUILDDIR>>/psi4/src/export_wavefunction.cc:46:
/<<PKGBUILDDIR>>/psi4/src/psi4/libmints/wavefunction.h:642:18: note: declared here
642 | SharedVector frequencies() const;
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/psi4/src/export_wavefunction.cc:143:55: warning: ‘void psi::Wavefunction::set_frequencies(std::shared_ptr<psi::Vector>)’ is deprecated: Using `Wavefunction.set_frequencies` is deprecated, and in 1.4 it will stop working [-Wdeprecated-declarations]
143 | .def("set_legacy_frequencies", &Wavefunction::set_frequencies, "Sets the frequencies of the Hessian.")
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/psi4/src/psi4/libmints/wavefunction.h:646:10: note: declared here
646 | void set_frequencies(std::shared_ptr<Vector> freqs);
| ^~~~~~~~~~~~~~~
[ 99%] Building CXX object src/CMakeFiles/core.dir/export_options.cc.o
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/export_options.cc.o -MF CMakeFiles/core.dir/export_options.cc.o.d -o CMakeFiles/core.dir/export_options.cc.o -c /<<PKGBUILDDIR>>/psi4/src/export_options.cc
[ 99%] Building CXX object src/CMakeFiles/core.dir/create_new_plugin.cc.o
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/create_new_plugin.cc.o -MF CMakeFiles/core.dir/create_new_plugin.cc.o.d -o CMakeFiles/core.dir/create_new_plugin.cc.o -c /<<PKGBUILDDIR>>/psi4/src/create_new_plugin.cc
/<<PKGBUILDDIR>>/psi4/src/create_new_plugin.cc: In member function ‘void psi::PluginFileManager::process()’:
/<<PKGBUILDDIR>>/psi4/src/create_new_plugin.cc:114:68: error: ‘ostream_iterator’ is not a member of ‘std’
114 | std::copy(source_files_.begin(), source_files_.end(), std::ostream_iterator<std::string>(imploded, " "));
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/psi4/src/create_new_plugin.cc:41:1: note: ‘std::ostream_iterator’ is defined in header ‘<iterator>’; did you forget to ‘#include <iterator>’?
40 | #include "psi4/libpsi4util/process.h"
+++ |+#include <iterator>
41 |
/<<PKGBUILDDIR>>/psi4/src/create_new_plugin.cc:114:96: error: expected primary-expression before ‘>’ token
114 | std::copy(source_files_.begin(), source_files_.end(), std::ostream_iterator<std::string>(imploded, " "));
| ^
[100%] Building CXX object src/CMakeFiles/core.dir/read_options.cc.o
cd /<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build/src && /usr/bin/c++ -DUSING_CheMPS2 -Dcore_EXPORTS -I/<<PKGBUILDDIR>>/psi4/include -I/<<PKGBUILDDIR>>/psi4/src -isystem /usr/include/hdf5/serial -isystem /usr/include/python3.10 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -g -DNDEBUG -fPIC -fvisibility=hidden -fvisibility-inlines-hidden -fopenmp -std=c++14 -MD -MT src/CMakeFiles/core.dir/read_options.cc.o -MF CMakeFiles/core.dir/read_options.cc.o.d -o CMakeFiles/core.dir/read_options.cc.o -c /<<PKGBUILDDIR>>/psi4/src/read_options.cc
make[6]: *** [src/CMakeFiles/core.dir/build.make:289: src/CMakeFiles/core.dir/create_new_plugin.cc.o] Error 1
make[6]: *** Waiting for unfinished jobs....
make[6]: Leaving directory '/<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build'
make[5]: *** [CMakeFiles/Makefile2:1044: src/CMakeFiles/core.dir/all] Error 2
make[5]: Leaving directory '/<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build'
make[4]: *** [Makefile:139: all] Error 2
make[4]: Leaving directory '/<<PKGBUILDDIR>>/builddir/psi4-core-prefix/src/psi4-core-build'
make[3]: *** [CMakeFiles/psi4-core.dir/build.make:89: psi4-core-prefix/src/psi4-core-stamp/psi4-core-build] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make[2]: *** [CMakeFiles/Makefile2:8310: CMakeFiles/psi4-core.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
make[1]: *** [Makefile:149: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/builddir'
dh_auto_build: error: cd builddir && make -j8 VERBOSE=1 returned exit code 2
make: *** [debian/rules:11: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
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