[Debian-med-packaging] Bug#1078882: sra-sdk: FTBFS against HDF5 1.14

[Gilles Filippini]

Source: sra-sdk
Version: 3.0.3+dfsg-8
Severity: important

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Hi,

The sra-sdk package fails to build from source in a test rebuild against
hdf5 1.14 currently in experimental:

cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tools/loaders/pacbio-load && /usr/bin/cc -DLINUX -DNDEBUG -DUNIX -D_ARCH_BITS=64 -D_GNU_SOURCE -D__mod__=\"tools/pacbio-load\" -Dx86_64 -I/usr/include/ncbi-vdb -I/usr/inc
lude/ncbi-vdb/cc/gcc -I/usr/include/ncbi-vdb/cc/gcc/x86_64 -I/usr/include/ncbi-vdb/os/linux -I/usr/include/ncbi-vdb/os/unix -I/<<PKGBUILDDIR>>/ngs/ngs-sdk -I/<<PKGBUILDDIR>>/libs/inc -I/<<PKGBUILDDIR>>/tools/loa
ders/pacbio-load -I/usr/include/hdf5/serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -f
cf-protection -fsigned-char -Wdate-time -D_FORTIFY_SOURCE=2 -std=c11   -rdynamic -Wall -MD -MT tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o -MF CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.
o.d -o CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o -c /<<PKGBUILDDIR>>/tools/loaders/pacbio-load/hdf5/hdf5dir.c
In file included from /usr/include/hdf5/serial/H5public.h:31,
                 from /usr/include/hdf5/serial/hdf5.h:21,
                 from /<<PKGBUILDDIR>>/tools/loaders/pacbio-load/hdf5/hdf5dir.c:35:
/<<PKGBUILDDIR>>/tools/loaders/pacbio-load/hdf5/hdf5dir.c: In function ‘HDF5DirPathTypeOnBuffer’:
/usr/include/hdf5/serial/H5version.h:947:31: error: too few arguments to function ‘H5Oget_info_by_name3’
  947 |   #define H5Oget_info_by_name H5Oget_info_by_name3
      |                               ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/tools/loaders/pacbio-load/hdf5/hdf5dir.c:295:18: note: in expansion of macro ‘H5Oget_info_by_name’
  295 |     herr_t h5e = H5Oget_info_by_name( self->hdf5_handle, buffer, &obj_info, H5P_DEFAULT );
      |                  ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/hdf5/serial/H5Apublic.h:21,
                 from /usr/include/hdf5/serial/hdf5.h:22:
/usr/include/hdf5/serial/H5Opublic.h:541:15: note: declared here
  541 | H5_DLL herr_t H5Oget_info_by_name3(hid_t loc_id, const char *name, H5O_info2_t *oinfo, unsigned fields,
      |               ^~~~~~~~~~~~~~~~~~~~
make[3]: *** [tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/build.make:93: tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/hdf5/hdf5dir.c.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:5938: tools/loaders/pacbio-load/CMakeFiles/pacbio-load.dir/all] Error 2


Full build log attached.

Please note that adding -DH5_USE_110_API to CFLAGS and CXXFLAGS solves the issue.

Best,
_g.


- -- System Information:
Debian Release: 12.0
Architecture: amd64 (x86_64)

Kernel: Linux 6.1.0-21-amd64 (SMP w/12 CPU threads; PREEMPT)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

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