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

[Adrian Bunk]

Control: tags -1 ftbfs fixed-upstream

On Fri, May 04, 2018 at 12:23:56PM +0000, Matthias Klose wrote:
>...
> 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

Upstream fix:
https://github.com/trinityrnaseq/trinityrnaseq/commit/a3d279c17f868fd51d56f8e1a6f9a3c223480fbf

There is now a second FTBFS afterwards:
   dh_installdocs
dh_installdocs: Cannot find (any matches for) "hpc_conf" (tried in .)

This second FTBFS is unrelated, it is due to the #902355 fix.

cu
Adrian

-- 

       "Is there not promise of rain?" Ling Tan asked suddenly out
        of the darkness. There had been need of rain for many days.
       "Only a promise," Lao Er said.
                                       Pearl S. Buck - Dragon Seed