Source: sra-sdk Version: 3.0.3+dfsg-8 Severity: important -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512
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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sra-sdk_3.0.3+dfsg-8_amd64.build.gz
Description: application/gzip
