[Debian-med-packaging] Bug#897877: trinityrnaseq: ftbfs with GCC-8

[Matthias Klose]

Package: src:trinityrnaseq
Version: 2.5.1+dfsg-2
Severity: normal
Tags: sid buster
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-8

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-8/g++-8, but succeeds to build with gcc-7/g++-7. The
severity of this report will be raised before the buster release.

The full build log can be found at:
http://aws-logs.debian.net/2018/05/01/gcc8/trinityrnaseq_2.5.1+dfsg-2_unstable_gcc8.log.gz
The last lines of the build log are at the end of this report.

To build with GCC 8, either set CC=gcc-8 CXX=g++-8 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-8/porting_to.html

[...]
mv slclust ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/trinityrnaseq-2.5.1+dfsg/trinity-plugins/slclust/src'
make[1]: Leaving directory '/<<BUILDDIR>>/trinityrnaseq-2.5.1+dfsg'
   debian/rules override_dh_install-arch
make[1]: Entering directory '/<<BUILDDIR>>/trinityrnaseq-2.5.1+dfsg'
dh_install -a
dh_install: Cannot find (any matches for) "Chrysalis/TranscriptomeFromVaryK" (tried in ., debian/tmp)

dh_install: trinityrnaseq missing files: Chrysalis/TranscriptomeFromVaryK
dh_install: Cannot find (any matches for) "Chrysalis/RunButterfly" (tried in ., debian/tmp)

dh_install: trinityrnaseq missing files: Chrysalis/RunButterfly
dh_install: Cannot find (any matches for) "Chrysalis/ReadsToTranscripts_MPI_chang" (tried in ., debian/tmp)

dh_install: trinityrnaseq missing files: Chrysalis/ReadsToTranscripts_MPI_chang
dh_install: Cannot find (any matches for) "Chrysalis/ReadsToTranscripts_MPI" (tried in ., debian/tmp)

dh_install: trinityrnaseq missing files: Chrysalis/ReadsToTranscripts_MPI
dh_install: Cannot find (any matches for) "Chrysalis/ReadsToTranscripts" (tried in ., debian/tmp)

dh_install: trinityrnaseq missing files: Chrysalis/ReadsToTranscripts
dh_install: Cannot find (any matches for) "Chrysalis/QuantifyGraph" (tried in ., debian/tmp)

dh_install: trinityrnaseq missing files: Chrysalis/QuantifyGraph
dh_install: Cannot find (any matches for) "Chrysalis/JoinTransByPairs" (tried in ., debian/tmp)

dh_install: trinityrnaseq missing files: Chrysalis/JoinTransByPairs
dh_install: Cannot find (any matches for) "Chrysalis/IsoformAugment" (tried in ., debian/tmp)

dh_install: trinityrnaseq missing files: Chrysalis/IsoformAugment
dh_install: Cannot find (any matches for) "Chrysalis/GraphFromFasta_MPI" (tried in ., debian/tmp)

dh_install: trinityrnaseq missing files: Chrysalis/GraphFromFasta_MPI
dh_install: Cannot find (any matches for) "Chrysalis/GraphFromFasta" (tried in ., debian/tmp)

dh_install: trinityrnaseq missing files: Chrysalis/GraphFromFasta
dh_install: Cannot find (any matches for) "Chrysalis/CreateIwormFastaBundle" (tried in ., debian/tmp)

dh_install: trinityrnaseq missing files: Chrysalis/CreateIwormFastaBundle
dh_install: Cannot find (any matches for) "Chrysalis/Chrysalis" (tried in ., debian/tmp)

dh_install: trinityrnaseq missing files: Chrysalis/Chrysalis
dh_install: Cannot find (any matches for) "Chrysalis/BreakTransByPairs" (tried in ., debian/tmp)

dh_install: trinityrnaseq missing files: Chrysalis/BreakTransByPairs
dh_install: missing files, aborting
make[1]: *** [debian/rules:46: override_dh_install-arch] Error 25
make[1]: Leaving directory '/<<BUILDDIR>>/trinityrnaseq-2.5.1+dfsg'
make: *** [debian/rules:19: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2