I found this: https://gitlab.com/gromacs/gromacs/-/commit/64740ad3ac2748d6b93f398fef5c5ddcec62bcf2 It should be a similar issue, but I couldn't find the pending affected files to fix it, and that patch is not enough :/ AILED: src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o /usr/lib/ccache/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7_float/src -I/var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/external/thread_mpi/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/external -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/external/tng_io/include -isystem /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7_float/tng/include -isystem /usr/include/include -O2 -pipe -march=native -fno-stack-protector -std=c++17 -fPIC -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -fopenmp -MD -MT src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -MF src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o.d -o src/gromacs/CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/analysisdata/dataframe.cpp In file included from /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/analysisdata/dataframe.h:49, from /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/analysisdata/dataframe.cpp:44: /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h:126:5: error: ‘uint64_t’ does not name a type 126 | uint64_t flags_; | ^~~~~~~~ /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h:1:1: note: ‘uint64_t’ is defined in header ‘<cstdint>’; did you forget to ‘#include <cstdint>’? +++ |+#include <cstdint> 1 | /* /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h: In constructor ‘gmx::FlagsTemplate<FlagType>::FlagsTemplate()’: /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h:73:23: error: class ‘gmx::FlagsTemplate<FlagType>’ does not have any field named ‘flags_’ 73 | FlagsTemplate() : flags_(0) {} | ^~~~~~ /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h: In constructor ‘gmx::FlagsTemplate<FlagType>::FlagsTemplate(FlagType)’: /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h:75:36: error: class ‘gmx::FlagsTemplate<FlagType>’ does not have any field named ‘flags_’ 75 | FlagsTemplate(FlagType flag) : flags_(flag) {} | ^~~~~~ /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h: In member function ‘bool gmx::FlagsTemplate<FlagType>::test(FlagType) const’: /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h:83:46: error: ‘flags_’ was not declared in this scope; did you mean ‘flag’? 83 | bool test(FlagType flag) const { return (flags_ & flag) != 0; } | ^~~~~~ | flag /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h: In member function ‘void gmx::FlagsTemplate<FlagType>::clearAll()’: /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h:85:23: error: ‘flags_’ was not declared in this scope 85 | void clearAll() { flags_ = 0; } | ^~~~~~ /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h: In member function ‘void gmx::FlagsTemplate<FlagType>::set(FlagType)’: /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h:87:31: error: ‘flags_’ was not declared in this scope; did you mean ‘flag’? 87 | void set(FlagType flag) { flags_ |= flag; } | ^~~~~~ | flag /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h: In member function ‘void gmx::FlagsTemplate<FlagType>::clear(FlagType)’: /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h:89:33: error: ‘flags_’ was not declared in this scope; did you mean ‘flag’? 89 | void clear(FlagType flag) { flags_ &= ~flag; } | ^~~~~~ | flag /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h: In member function ‘gmx::FlagsTemplate<FlagType> gmx::FlagsTemplate<FlagType>::operator|(const gmx::FlagsTemplate<FlagType>&) const’: /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h:106:40: error: ‘flags_’ was not declared in this scope 106 | return FlagsTemplate<FlagType>(flags_ | other.flags_); | ^~~~~~ /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h: In member function ‘gmx::FlagsTemplate<FlagType>& gmx::FlagsTemplate<FlagType>::operator|=(const gmx::FlagsTemplate<FlagType>&)’: /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h:111:9: error: ‘flags_’ was not declared in this scope 111 | flags_ |= other.flags_; | ^~~~~~ /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h: In member function ‘gmx::FlagsTemplate<FlagType> gmx::FlagsTemplate<FlagType>::operator&(const gmx::FlagsTemplate<FlagType>&) const’: /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h:117:40: error: ‘flags_’ was not declared in this scope 117 | return FlagsTemplate<FlagType>(flags_ & other.flags_); | ^~~~~~ /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h: In member function ‘gmx::FlagsTemplate<FlagType> gmx::FlagsTemplate<FlagType>::operator~() const’: /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h:120:81: error: ‘flags_’ was not declared in this scope 120 | FlagsTemplate<FlagType> operator~() const { return FlagsTemplate<FlagType>(~flags_); } | ^~~~~~ /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h: In constructor ‘gmx::FlagsTemplate<FlagType>::FlagsTemplate(long unsigned int)’: /var/tmp/portage/sci-chemistry/gromacs-2021.7-r1/work/gromacs-2021.7/src/gromacs/utility/flags.h:124:51: error: class ‘gmx::FlagsTemplate<FlagType>’ does not have any field named ‘flags_’ 124 | explicit FlagsTemplate(unsigned long flags) : flags_(flags) {} | ^~~~~~
Just add the includes the errors say to? What do you get then?
Created attachment 872953 [details, diff] 1.patch Sorry, I needed to leave and I couldn't test Indeed, the attached patch works fine!
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=05f1ec32b757a08781ce81f883ec0873b7ee6d99 commit 05f1ec32b757a08781ce81f883ec0873b7ee6d99 Author: Pacho Ramos <pacho@gentoo.org> AuthorDate: 2023-10-20 12:11:55 +0000 Commit: Pacho Ramos <pacho@gentoo.org> CommitDate: 2023-10-20 13:14:37 +0000 sci-chemistry/gromacs: Fix compilation with gcc-13 Closes: https://bugs.gentoo.org/915694 Signed-off-by: Pacho Ramos <pacho@gentoo.org> .../gromacs/files/gromacs-2021-cstdint-include.patch | 12 ++++++++++++ sci-chemistry/gromacs/gromacs-2021.7-r1.ebuild | 1 + 2 files changed, 13 insertions(+)
