Your message dated Sun, 17 Nov 2024 06:04:36 +0000
with message-id <[email protected]>
and subject line Bug#1086305: fixed in netcdf-parallel 1:4.9.0-5
has caused the Debian Bug report #1086305,
regarding netcdf-parallel: FTBFS: undefined reference to
`ompi_mpi_cxx_op_intercept'
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1086305: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1086305
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Source: netcdf-parallel
Source-Version: 1:4.9.0-5
Done: Alastair McKinstry <[email protected]>
We believe that the bug you reported is fixed in the latest version of
netcdf-parallel, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Alastair McKinstry <[email protected]> (supplier of updated netcdf-parallel
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sun, 17 Nov 2024 05:28:43 +0000
Source: netcdf-parallel
Architecture: source
Version: 1:4.9.0-5
Distribution: unstable
Urgency: medium
Maintainer: Alastair McKinstry <[email protected]>
Changed-By: Alastair McKinstry <[email protected]>
Closes: 1086305
Changes:
netcdf-parallel (1:4.9.0-5) unstable; urgency=medium
.
* Build against openmpi >= 5.0.5-6. Closes: #1086305
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