On Wed, Jan 15, 2020 at 05:50:03PM +0100, Andreas Tille wrote: > Control: tags -1 help > > On Tue, Jan 14, 2020 at 09:48:10PM +0100, Paul Gevers wrote: > > Did not find CMake 'cmake' > > Found CMake: NO > > Run-time dependency pbbam found: NO > > > > meson.build:54:0: ERROR: Could not generate cargs for pbbam: > > Package pbcopper was not found in the pkg-config search path. > > Perhaps you should add the directory containing `pbcopper.pc' > > to the PKG_CONFIG_PATH environment variable > > Package 'pbcopper', required by 'pbbam', not found > > I've fixed this specific issue (and others) in Git[1] but I'm running > into trouble I have no idea to fix. > > > ... > [22/25] c++ -o toAfg 'toAfg@exe/utils_ToAfg.cpp.o' -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wdate-time - D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl. a -pthread -lblasr /usr/lib/x86_64-linux-gnu/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/build/blasr-5.3.3+dfsg/build/ > FAILED: toAfg > c++ -o toAfg 'toAfg@exe/utils_ToAfg.cpp.o' -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 - g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a -pthread -lblasr / usr/lib/x86_64-linux-gnu/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/build/blasr-5.3.3+dfsg/build/ > /usr/bin/ld: toAfg@exe/utils_ToAfg.cpp.o: undefined reference to symbol '_ZN6PacBio3BAM9BamRecordD1Ev' > /usr/bin/ld: /usr/lib/x86_64-linux-gnu//libpbbam.so.0.23.0: error adding symbols: DSO missing from command line > collect2: error: ld returned 1 exit status It tells you to add libpbbam to the link command. > In the pbuilder chroot I tried to simplify the linker call and > reduced it to > > root@sputnik:/build/blasr-5.3.3+dfsg/build# c++ -o toAfg 'toAfg@exe/utils_ToAfg.cpp.o' -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -DHAVE_HDF5_1_10_1 -std=c++14 -lhdf5_cpp -lhdf5 ./libblasr_impl.a -pthread -lz -lpbdata -lpbihdf -lpbihdf -lblasr > /usr/bin/ld: toAfg@exe/utils_ToAfg.cpp.o: undefined reference to symbol '_ZN6PacBio3BAM9BamRecordD1Ev' > /usr/bin/ld: /usr/lib/x86_64-linux-gnu/libpbbam.so.0.23.0: error adding symbols: DSO missing from command line > collect2: error: ld returned 1 exit status Indeed libpbbam is still missing here. > I've checked that the symbol which is not found exists in the linked > libraries: It's not linked. Also, using grep for this is very wrong, you need to use nm -D and check it's defined there (it is though). -- WBR, wRAR
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