[Debian-med-packaging] Bug#948926: Help for linking library needed (Was: Bug#948926: blasr ftbfs with libpbbam1.0.6)

[Andrey Rahmatullin]

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 at 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,$ORIGIN/' -Wl,-rpath-link,/build/blasr-5.3.3+dfsg/build/
> FAILED: toAfg
> c++  -o toAfg 'toAfg at exe/utils_ToAfg.cpp.o' -I/usr/include/pbseq -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 - g -O2 -fdebug-prefix-map=/build/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -std=c++14 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a -pthread -lblasr / usr/lib/x86_64-linux-gnu/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/build/blasr-5.3.3+dfsg/build/
> /usr/bin/ld: toAfg at 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 at sputnik:/build/blasr-5.3.3+dfsg/build# c++  -o toAfg 'toAfg at 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 at 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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