Package: src:netcdf-parallel
Version: 1:4.9.0-4
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary --buildsystem=cmake
dh_update_autotools_config -O--buildsystem=cmake
cp -an --reflink=auto config.guess
debian/.debhelper/bucket/files/af8a1922c9b3c240bf2119d4ec0965a0b5ec36b1016017ba66db44b3b53e9cea.tmp
mv
debian/.debhelper/bucket/files/af8a1922c9b3c240bf2119d4ec0965a0b5ec36b1016017ba66db44b3b53e9cea.tmp
debian/.debhelper/bucket/files/af8a1922c9b3c240bf2119d4ec0965a0b5ec36b1016017ba66db44b3b53e9cea
cp -f /usr/share/misc/config.guess ./config.guess
cp -an --reflink=auto config.sub
debian/.debhelper/bucket/files/d611751fba98e807c9684d253bb02aa73d6825fe0e0b9ae3cbf258a59171c9b0.tmp
mv
debian/.debhelper/bucket/files/d611751fba98e807c9684d253bb02aa73d6825fe0e0b9ae3cbf258a59171c9b0.tmp
debian/.debhelper/bucket/files/d611751fba98e807c9684d253bb02aa73d6825fe0e0b9ae3cbf258a59171c9b0
cp -f /usr/share/misc/config.sub ./config.sub
dh_autoreconf -O--buildsystem=cmake
find ! -ipath "./debian/*" -a ! \( -path '*/.git/*' -o -path '*/.hg/*' -o
-path '*/.bzr/*' -o -path '*/.svn/*' -o -path '*/CVS/*' \) -a -type f -exec md5sum {} + -o
-type l -printf "symlink %p
" > debian/autoreconf.before
grep -q ^XDT_ configure.ac
autoreconf -f -i
[... snipped ...]
[ 29%] Building C object ncgen/CMakeFiles/ncgen.dir/main.c.o
cd /<<PKGBUILDDIR>>/build-pnetcdf/ncgen && /usr/bin/mpicc -DCURL_STATICLIB=1 -DENABLE_SET_LOG_LEVEL -DH5_BUILT_AS_DYNAMIC_LIB -DHAVE_CONFIG_H -DRELAX_COORD_BOUND
-I/<<PKGBUILDDIR>>/build-pnetcdf/include -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/oc2 -I/<<PKGBUILDDIR>>/libsrc -I/usr/include/hdf5/openmpi
-I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/build-pnetcdf -I/<<PKGBUILDDIR>>/ncdump -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIE -MD -MT ncgen/CMakeFiles/ncgen.dir/main.c.o -MF CMakeFiles/ncgen.dir/main.c.o.d -o
CMakeFiles/ncgen.dir/main.c.o -c /<<PKGBUILDDIR>>/ncgen/main.c
/<<PKGBUILDDIR>>/ncgen/main.c: In function ‘main’:
/<<PKGBUILDDIR>>/ncgen/main.c:454:23: warning: ignoring return value of ‘fread’
declared with attribute ‘warn_unused_result’ [-Wunused-result]
454 | (void)fread(bom,1,1,fp);
| ^~~~~~~~~~~~~~~~~
[ 29%] Building C object ncgen/CMakeFiles/ncgen.dir/ncgeny.c.o
cd /<<PKGBUILDDIR>>/build-pnetcdf/ncgen && /usr/bin/mpicc -DCURL_STATICLIB=1 -DENABLE_SET_LOG_LEVEL -DH5_BUILT_AS_DYNAMIC_LIB -DHAVE_CONFIG_H -DRELAX_COORD_BOUND
-I/<<PKGBUILDDIR>>/build-pnetcdf/include -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/oc2 -I/<<PKGBUILDDIR>>/libsrc -I/usr/include/hdf5/openmpi
-I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/build-pnetcdf -I/<<PKGBUILDDIR>>/ncdump -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIE -MD -MT ncgen/CMakeFiles/ncgen.dir/ncgeny.c.o -MF CMakeFiles/ncgen.dir/ncgeny.c.o.d -o
CMakeFiles/ncgen.dir/ncgeny.c.o -c /<<PKGBUILDDIR>>/ncgen/ncgeny.c
[ 29%] Building C object ncgen/CMakeFiles/ncgen.dir/semantics.c.o
cd /<<PKGBUILDDIR>>/build-pnetcdf/ncgen && /usr/bin/mpicc -DCURL_STATICLIB=1 -DENABLE_SET_LOG_LEVEL -DH5_BUILT_AS_DYNAMIC_LIB -DHAVE_CONFIG_H -DRELAX_COORD_BOUND
-I/<<PKGBUILDDIR>>/build-pnetcdf/include -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/oc2 -I/<<PKGBUILDDIR>>/libsrc -I/usr/include/hdf5/openmpi
-I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/build-pnetcdf -I/<<PKGBUILDDIR>>/ncdump -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIE -MD -MT ncgen/CMakeFiles/ncgen.dir/semantics.c.o -MF CMakeFiles/ncgen.dir/semantics.c.o.d -o
CMakeFiles/ncgen.dir/semantics.c.o -c /<<PKGBUILDDIR>>/ncgen/semantics.c
[ 29%] Building C object ncgen/CMakeFiles/ncgen.dir/util.c.o
cd /<<PKGBUILDDIR>>/build-pnetcdf/ncgen && /usr/bin/mpicc -DCURL_STATICLIB=1 -DENABLE_SET_LOG_LEVEL -DH5_BUILT_AS_DYNAMIC_LIB -DHAVE_CONFIG_H -DRELAX_COORD_BOUND
-I/<<PKGBUILDDIR>>/build-pnetcdf/include -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/oc2 -I/<<PKGBUILDDIR>>/libsrc -I/usr/include/hdf5/openmpi
-I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/build-pnetcdf -I/<<PKGBUILDDIR>>/ncdump -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG -fPIE -MD -MT ncgen/CMakeFiles/ncgen.dir/util.c.o -MF CMakeFiles/ncgen.dir/util.c.o.d -o
CMakeFiles/ncgen.dir/util.c.o -c /<<PKGBUILDDIR>>/ncgen/util.c
[ 29%] Linking C executable ncgen
cd /<<PKGBUILDDIR>>/build-pnetcdf/ncgen && /usr/bin/cmake -E cmake_link_script
CMakeFiles/ncgen.dir/link.txt --verbose=1
/usr/bin/mpicc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=.
-specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -O3 -DNDEBUG
-specs=/usr/share/dpkg/no-pie-link.specs -Wl,-z,relro -Wl,-z,now
CMakeFiles/ncgen.dir/bindata.c.o CMakeFiles/ncgen.dir/bytebuffer.c.o
CMakeFiles/ncgen.dir/cdata.c.o CMakeFiles/ncgen.dir/cvt.c.o CMakeFiles/ncgen.dir/data.c.o
CMakeFiles/ncgen.dir/debug.c.o CMakeFiles/ncgen.dir/dump.c.o
CMakeFiles/ncgen.dir/escapes.c.o CMakeFiles/ncgen.dir/f77data.c.o
CMakeFiles/ncgen.dir/genbin.c.o CMakeFiles/ncgen.dir/genc.c.o
CMakeFiles/ncgen.dir/genchar.c.o CMakeFiles/ncgen.dir/generate.c.o
CMakeFiles/ncgen.dir/generr.c.o CMakeFiles/ncgen.dir/genf77.c.o
CMakeFiles/ncgen.dir/genj.c.o CMakeFiles/ncgen.dir/genlib.c.o
CMakeFiles/ncgen.dir/getfill.c.o CMakeFiles/ncgen.dir/jdata.c.o
CMakeFiles/ncgen.dir/list.c.o CMakeFiles/ncgen.dir/main.c.o CMakeFiles/ncgen.dir/ncgeny.c.o
CMakeFiles/ncgen.dir/semantics.c.o CMakeFiles/ncgen.dir/util.c.o -o ncgen
../liblib/libnetcdf_pnetcdf.so.19 /usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5_hl.so
/usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so /usr/lib/x86_64-linux-gnu/libcrypto.so
/usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libsz.so
/usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libdl.a -lm
/usr/lib/x86_64-linux-gnu/libblosc.so /usr/lib/x86_64-linux-gnu/libzstd.so
/usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libpnetcdf.so
/usr/lib/x86_64-linux-gnu/libxml2.so -ldl
/usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5_hl.so
/usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so /usr/lib/x86_64-linux-gnu/libcrypto.so
/usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libsz.so
/usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libdl.a -lm
/usr/lib/x86_64-linux-gnu/libblosc.so /usr/lib/x86_64-linux-gnu/libzstd.so
/usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libpnetcdf.so
/usr/lib/x86_64-linux-gnu/libxml2.so
/usr/bin/ld: warning: libmpi_cxx.so.40, needed by
/usr/lib/x86_64-linux-gnu/libpnetcdf.so, not found (try using -rpath or
-rpath-link)
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libpnetcdf.so: undefined reference to
`ompi_mpi_cxx_op_intercept'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libpnetcdf.so: undefined reference to
`MPI::Win::Free()'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libpnetcdf.so: undefined reference to
`MPI::Datatype::Free()'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libpnetcdf.so: undefined reference to
`ompi_op_set_cxx_callback'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libpnetcdf.so: undefined reference to
`MPI::Comm::Comm()'
collect2: error: ld returned 1 exit status
make[4]: *** [ncgen/CMakeFiles/ncgen.dir/build.make:495: ncgen/ncgen] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build-pnetcdf'
make[3]: *** [CMakeFiles/Makefile2:2939: ncgen/CMakeFiles/ncgen.dir/all] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build-pnetcdf'
make[2]: *** [Makefile:169: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build-pnetcdf'
make[1]: *** [debian/rules:66: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:29: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202410/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks.
