[Debian-med-packaging] Bug#925678: ffindex: ftbfs with GCC-9

[Matthias Klose]

Package: src:ffindex
Version: 0.9.9.9-2
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-9

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-9/g++-9, but succeeds to build with gcc-8/g++-8. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc9-20190321/ffindex_0.9.9.9-2_unstable_gcc9.log
The last lines of the build log are at the end of this report.

To build with GCC 9, either set CC=gcc-9 CXX=g++-9 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-9/porting_to.html

GCC 9 also passes the linker option --as-needed by default; typical
build issues are passing libraries before object files to the linker,
or underlinking of convenience libraries built from the same source.

[...]
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
debian/rules:39: target 'ffindex_apply_mpi.1' given more than once in the same rule
rm -f ffindex_apply.1 ffindex_build.1 ffindex_from_fasta.1 ffindex_get.1 ffindex_modify.1 ffindex_unpack.1 ffindex_apply_mpi.1 ffindex_from_tsv.1 ffindex_apply_mpi.1
dh_clean
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
 debian/rules build-arch
debian/rules:39: target 'ffindex_apply_mpi.1' given more than once in the same rule
dh build-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
   dh_auto_build -a
	make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make -C src all
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o ffindex.o ffindex.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o ffindex_posix_search.o ffindex_posix_search.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o ffutil.o ffutil.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o ffindex_from_fasta.o ffindex_from_fasta.c
ffindex.c: In function 'ffindex_write':
ffindex.c:577:3: warning: ignoring return value of 'ftruncate', declared with attribute warn_unused_result [-Wunused-result]
  577 |   ftruncate(fileno(index_file), ftell(index_file));
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o ffindex_get.o ffindex_get.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o ffindex_build.o ffindex_build.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o ffindex_modify.o ffindex_modify.c
In file included from /usr/include/string.h:494,
                 from ffindex.c:26:
In function 'strncpy',
    inlined from 'ffindex_insert_dir' at ffindex.c:234:5:
/usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 255 bytes from a string of length 255 [-Wstringop-truncation]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o ffindex_unpack.o ffindex_unpack.c
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2  -c -o ffindex_from_tsv.o ffindex_from_tsv.c
cc -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_MPI -c ffindex_apply_mpi.c -o ffindex_apply_mpi.o 
cc -Wl,-z,relro -Wl,-z,now -Wl,-z,defs -Wl,-soname,libffindex.so.2.0.2 -shared -o libffindex.so.2.0.2 ffindex.o ffindex_posix_search.o ffutil.o
ar rcs libffindex.a ffindex.o ffindex_posix_search.o ffutil.o
ln -sf libffindex.so.2.0.2 libffindex.so
cc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c ffindex_apply_mpi.c -o ffindex_apply.o 
cc -o ffindex_from_fasta ffindex_from_fasta.o -Wl,-z,relro -Wl,-z,now -L. -lffindex
cc -o ffindex_get ffindex_get.o -Wl,-z,relro -Wl,-z,now -L. -lffindex
cc -o ffindex_build ffindex_build.o -Wl,-z,relro -Wl,-z,now -L. -lffindex
cc -o ffindex_modify ffindex_modify.o -Wl,-z,relro -Wl,-z,now -L. -lffindex
cc -o ffindex_unpack ffindex_unpack.o -Wl,-z,relro -Wl,-z,now -L. -lffindex
cc -o ffindex_from_tsv ffindex_from_tsv.o -Wl,-z,relro -Wl,-z,now -L. -lffindex
cc -pthread -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -std=c99 -O2 -g -fPIC -Wall -pedantic -D_GNU_SOURCE=1 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_MPI -o ffindex_apply_mpi  ffindex_apply_mpi.o -Wl,-z,relro -Wl,-z,now -L. -lffindex
/usr/bin/ld: ffindex_apply_mpi.o: in function `main':
./src/ffindex_apply_mpi.c:171: undefined reference to `MPI_Init'
/usr/bin/ld: ./src/ffindex_apply_mpi.c:361: undefined reference to `MPI_Finalize'
/usr/bin/ld: ./src/ffindex_apply_mpi.c:172: undefined reference to `ompi_mpi_comm_world'
/usr/bin/ld: ./src/ffindex_apply_mpi.c:172: undefined reference to `MPI_Comm_rank'
/usr/bin/ld: ./src/ffindex_apply_mpi.c:173: undefined reference to `ompi_mpi_comm_world'
/usr/bin/ld: ./src/ffindex_apply_mpi.c:173: undefined reference to `MPI_Comm_size'
/usr/bin/ld: ./src/ffindex_apply_mpi.c:320: undefined reference to `ompi_mpi_comm_world'
/usr/bin/ld: ./src/ffindex_apply_mpi.c:320: undefined reference to `MPI_Barrier'
/usr/bin/ld: ./src/ffindex_apply_mpi.c:349: undefined reference to `MPI_Finalize'
/usr/bin/ld: ./src/ffindex_apply_mpi.c:269: undefined reference to `MPI_Finalize'
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:67: ffindex_apply_mpi] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: *** [Makefile:2: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: make -j4 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:18: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2