[Debian-med-packaging] Bug#853687: trinityrnaseq: ftbfs with GCC-7

[Matthias Klose]

Package: src:trinityrnaseq
Version: 2.2.0+dfsg-2
Severity: normal
Tags: sid buster
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-7

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-7/g++-7, but succeeds to build with gcc-6/g++-6. The
severity of this report may be raised before the buster release.
There is no need to fix this issue in time for the stretch release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc7-20170126/trinityrnaseq_2.2.0+dfsg-2_unstable_gcc7.log
The last lines of the build log are at the end of this report.

To build with GCC 7, either set CC=gcc-7 CXX=g++-7 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-7/porting_to.html

[...]
make[4]: Leaving directory '/<<BUILDDIR>>/trinityrnaseq-2.2.0+dfsg/Inchworm'
make[3]: Leaving directory '/<<BUILDDIR>>/trinityrnaseq-2.2.0+dfsg/Inchworm'
make[2]: Leaving directory '/<<BUILDDIR>>/trinityrnaseq-2.2.0+dfsg/Inchworm'
	make -j64 install DESTDIR=/<<BUILDDIR>>/trinityrnaseq-2.2.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no
make[2]: Entering directory '/<<BUILDDIR>>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust'
X=`pwd`; \
for i in src; \
do echo '<<<' $i '>>>'; cd $X/$i; make install; done
<<< src >>>
make[3]: Entering directory '/<<BUILDDIR>>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust/src'
mv slclust ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust/src'
make[2]: Leaving directory '/<<BUILDDIR>>/trinityrnaseq-2.2.0+dfsg/trinity-plugins/slclust'
make[1]: Leaving directory '/<<BUILDDIR>>/trinityrnaseq-2.2.0+dfsg'
   debian/rules override_dh_install-arch
make[1]: Entering directory '/<<BUILDDIR>>/trinityrnaseq-2.2.0+dfsg'
dh_install -a
dh_install: Cannot find (any matches for) "Chrysalis/TranscriptomeFromVaryK" (tried in "." and "debian/tmp")
dh_install: trinityrnaseq missing files: Chrysalis/TranscriptomeFromVaryK
dh_install: Cannot find (any matches for) "Chrysalis/RunButterfly" (tried in "." and "debian/tmp")
dh_install: trinityrnaseq missing files: Chrysalis/RunButterfly
dh_install: Cannot find (any matches for) "Chrysalis/ReadsToTranscripts_MPI_chang" (tried in "." and "debian/tmp")
dh_install: trinityrnaseq missing files: Chrysalis/ReadsToTranscripts_MPI_chang
dh_install: Cannot find (any matches for) "Chrysalis/ReadsToTranscripts_MPI" (tried in "." and "debian/tmp")
dh_install: trinityrnaseq missing files: Chrysalis/ReadsToTranscripts_MPI
dh_install: Cannot find (any matches for) "Chrysalis/ReadsToTranscripts" (tried in "." and "debian/tmp")
dh_install: trinityrnaseq missing files: Chrysalis/ReadsToTranscripts
dh_install: Cannot find (any matches for) "Chrysalis/QuantifyGraph" (tried in "." and "debian/tmp")
dh_install: trinityrnaseq missing files: Chrysalis/QuantifyGraph
dh_install: Cannot find (any matches for) "Chrysalis/JoinTransByPairs" (tried in "." and "debian/tmp")
dh_install: trinityrnaseq missing files: Chrysalis/JoinTransByPairs
dh_install: Cannot find (any matches for) "Chrysalis/IsoformAugment" (tried in "." and "debian/tmp")
dh_install: trinityrnaseq missing files: Chrysalis/IsoformAugment
dh_install: Cannot find (any matches for) "Chrysalis/GraphFromFasta_MPI" (tried in "." and "debian/tmp")
dh_install: trinityrnaseq missing files: Chrysalis/GraphFromFasta_MPI
dh_install: Cannot find (any matches for) "Chrysalis/GraphFromFasta" (tried in "." and "debian/tmp")
dh_install: trinityrnaseq missing files: Chrysalis/GraphFromFasta
dh_install: Cannot find (any matches for) "Chrysalis/CreateIwormFastaBundle" (tried in "." and "debian/tmp")
dh_install: trinityrnaseq missing files: Chrysalis/CreateIwormFastaBundle
dh_install: Cannot find (any matches for) "Chrysalis/Chrysalis" (tried in "." and "debian/tmp")
dh_install: trinityrnaseq missing files: Chrysalis/Chrysalis
dh_install: Cannot find (any matches for) "Chrysalis/BreakTransByPairs" (tried in "." and "debian/tmp")
dh_install: trinityrnaseq missing files: Chrysalis/BreakTransByPairs
dh_install: missing files, aborting
debian/rules:47: recipe for target 'override_dh_install-arch' failed
make[1]: *** [override_dh_install-arch] Error 255
make[1]: Leaving directory '/<<BUILDDIR>>/trinityrnaseq-2.2.0+dfsg'
debian/rules:20: recipe for target 'binary' failed
make: *** [binary] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit status 2