/usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: ../../test/.libs/libh5test.a(h5test.o): undefined reference to symbol 'ompi_mpi_comm_world' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpi.so.40: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make[2]: *** [Makefile:899: testhdf5] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-libs/hdf5-1.12.2-r6/work/hdf5-1.12.2/c++/test' make[1]: *** [Makefile:880: all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-libs/hdf5-1.12.2-r6/work/hdf5-1.12.2/c++' make: *** [Makefile:727: all-recursive] Error 1 * ERROR: sci-libs/hdf5-1.12.2-r6::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-libs/hdf5-1.12.2-r6::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/hdf5-1.12.2-r6::gentoo'`. * The complete build log is located at '/var/tmp/portage/sci-libs/hdf5-1.12.2-r6/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/hdf5-1.12.2-r6/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/hdf5-1.12.2-r6/work/hdf5-1.12.2' * S: '/var/tmp/portage/sci-libs/hdf5-1.12.2-r6/work/hdf5-1.12.2' Reproducible: Always Steps to Reproduce: 1.emerge --oneshot hdf5 2. 3.
Created attachment 860192 [details] emerge --info > /tmp/emerge--info.txt
Thank you for the report. We need to have all information at hand before ticket assignment. This includes * the complete build.log as attachment as described on https://wiki.gentoo.org/wiki/Attach_the_logs_to_the_bug_ticket Please reopen this ticket (Status:UNCONFIRMED) afterwards.
Created attachment 860212 [details] hdf5 build.log * The complete build log is located at '/var/tmp/portage/sci-libs/hdf5-1.12.2-r6/temp/build.log'.
Created attachment 860213 [details] environment * The ebuild environment file is located at '/var/tmp/portage/sci-libs/hdf5-1.12.2-r6/temp/environment'.
libtool: link: x86_64-pc-linux-gnu-g++ -Wall -Wcast-qual -Wconversion -Wctor-dtor-privacy -Weffc++ -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wnon-virtual-dtor -Wold-style-cast -Woverloaded-virtual -Wreorder -Wshadow -Wsign-promo -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wstrict-overflow=5 -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -Wno-deprecated-copy -fstdarg-opt -fdiagnostics-urls=never -fno-diagnostics-color -Wcast-align -Wmissing-declarations -Wpacked -Wredundant-decls -Wswitch -Wunused-but-set-variable -Wunused-function -Wunused-variable -Wunused-parameter -Wshadow -O3 -march=skylake -mabm -mrtm -O2 -pipe -Wl,-O1 -o .libs/testhdf5 testhdf5.o dsets.o tattr.o tarray.o tcompound.o tdspl.o tfile.o tfilter.o th5s.o tlinks.o tobject.o trefer.o ttypes.o tvlstr.o titerate.o h5cpputil.o -Wl,--as-needed ../../test/.libs/libh5test.a ../../c++/src/.libs/libhdf5_cpp.so /var/tmp/portage/sci-libs/hdf5-1.12.2-r6/work/hdf5-1.12.2/src/.libs/libhdf5.so ../../src/.libs/libhdf5.so -lpthread -lsz -lz -ldl -lm /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: ../../test/.libs/libh5test.a(h5test.o): undefined reference to symbol 'ompi_mpi_comm_world' /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libmpi.so.40: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make[2]: *** [Makefile:899: testhdf5] Error 1 Does -r4 build ok?
No but at that time I just masked it in hope that it will be solved in next version. Unfortunately it was not the case. My package.mask: cat package.mask =sci-libs/hdf5-1.12.2-r5:0 =sci-libs/hdf5-1.12.2-r4:0
Now I see, https://bugs.gentoo.org/show_bug.cgi?id=863089 Sorry, I did not find it earlier. So I add =sci-libs/hdf5-1.12.2-r6:0 to package.mask
(In reply to Petr Vokac from comment #7) > Now I see, https://bugs.gentoo.org/show_bug.cgi?id=863089 > Sorry, I did not find it earlier. > So I add =sci-libs/hdf5-1.12.2-r6:0 to package.mask Thanks for spotting that. *** This bug has been marked as a duplicate of bug 863089 ***
