[Debian-med-packaging] Bug#907358: ncbi-vdb: fix broken library on i386

[Steve Langasek]

On Tue, Aug 28, 2018 at 09:38:50PM +0200, Andreas Tille wrote:
> > Also, this broken library package would have been detectable at build time
> > if you were building with -Wl,-z,defs in LDFLAGS, as that would have
> > prevented ever generating a shared library with missing symbols.  That's a
> > good idea to do anyway, but in particular it would mean that if you didn't
> > want to support i386 anymore, you could just add this to build flags and not
> > have to worry about changing the architecture list explicitly.

> So I did but was running into new problems which are caused by the hand
> craftet build system (yes, I tried to convince upstream to use some of
> the usual candidates but failed :-((( ).  I was able to add some missing
> libs in pbuilder chroot but whatever trick I try[1] the build system
> always constructs a different command line than I tested inside the
> pbuilder chroot.

> Do you have any idea to stop this insane messing up with library options?

> [1] https://salsa.debian.org/med-team/ncbi-vdb/blob/master/debian/patches/fix_linking.patch

Failure I see in a local build is:

Try to add extra libs to LDFLAGS ... unfortunately this fails as well
CMD=gcc -shared -o /tmp/ncbi-vdb/debian/tmp/usr/ncbi-vdb/linux/gcc/x86_64/dbg/lib/libkdf5.so.2.9.2 -Wl,-soname,libkdf5.so.2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-z,defs -Wl,--as-needed -g    -g    hdf5dir.pic.o hdf5file.pic.o hdf5arrayfile.pic.o -L/tmp/ncbi-vdb/debian/tmp/usr/ncbi-vdb/linux/gcc/x86_64/dbg/lib -L/tmp/ncbi-vdb/debian/tmp/usr/ncbi-vdb/linux/gcc/x86_64/dbg/ilib -lhdf5_serial -lz -lmbedx509 -lmbedtls -lmbedcrypto -Wl,-Bstatic -Wl,-whole-archive -lklib -lkfs -Wl,-no-whole-archive -Wl,-Bdynamic -lbz2 -ldl -lpthread -lm -lkproc -lkfs -lkdb -lkns -lkfg
gcc -shared -o /tmp/ncbi-vdb/debian/tmp/usr/ncbi-vdb/linux/gcc/x86_64/dbg/lib/libkdf5.so.2.9.2 -Wl,-soname,libkdf5.so.2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-z,defs -Wl,--as-needed -g    -g    hdf5dir.pic.o hdf5file.pic.o hdf5arrayfile.pic.o -L/tmp/ncbi-vdb/debian/tmp/usr/ncbi-vdb/linux/gcc/x86_64/dbg/lib -L/tmp/ncbi-vdb/debian/tmp/usr/ncbi-vdb/linux/gcc/x86_64/dbg/ilib -lhdf5_serial -lz -lmbedx509 -lmbedtls -lmbedcrypto -Wl,-Bstatic -Wl,-whole-archive -lklib -lkfs -Wl,-no-whole-archive -Wl,-Bdynamic -lbz2 -ldl -lpthread -lm
/tmp/ncbi-vdb/debian/tmp/usr/ncbi-vdb/linux/gcc/x86_64/dbg/ilib/libklib.a(hashfile.pic.o): In function `map_calloc':
/tmp/ncbi-vdb/libs/klib/hashfile.c:288: undefined reference to `KLockAcquire'
/tmp/ncbi-vdb/libs/klib/hashfile.c:321: undefined reference to `KLockUnlock'
/tmp/ncbi-vdb/libs/klib/hashfile.c:328: undefined reference to `KLockUnlock'
[...]

When using -Wl,--as-needed, each object needs to be listed on the
commandline /after/ those objects that use it.

A correct commandline would be:

gcc -shared -o /tmp/ncbi-vdb/debian/tmp/usr/ncbi-vdb/linux/gcc/x86_64/dbg/lib/libkdf5.so.2.9.2 -Wl,-soname,libkdf5.so.2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -Wl,-z,defs -Wl,--as-needed -g    -g    hdf5dir.pic.o hdf5file.pic.o hdf5arrayfile.pic.o -L/tmp/ncbi-vdb/debian/tmp/usr/ncbi-vdb/linux/gcc/x86_64/dbg/lib -L/tmp/ncbi-vdb/debian/tmp/usr/ncbi-vdb/linux/gcc/x86_64/dbg/ilib -lhdf5_serial -lz -Wl,-Bstatic -Wl,-whole-archive -lklib -lkfs -Wl,-no-whole-archive -Wl,-Bdynamic -lbz2 -ldl -lpthread -lm -lkfs -lkq -lkproc -lkdb -lkns -lkfg -lksproc -lmbedx509 -lmbedtls -lmbedcrypto -lz

So this seems to be sufficient:

    CMD="$CMD -lkfs -lkq -lkproc -lkdb -lkns -lkfg -lksproc -lmbedx509 -lmbedtls -lmbedcrypto -lz"

Though there is another similar error when trying to link libdiagnose.so
later.

-- 
Steve Langasek                   Give me a lever long enough and a Free OS
Debian Developer                   to set it on, and I can move the world.
Ubuntu Developer                                   https://www.debian.org/
slangasek at ubuntu.com                                     vorlon at debian.org
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 833 bytes
Desc: not available
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20180828/989c75d1/attachment.sig>