[Debian-med-packaging] Bug#831110: trinityrnaseq: FTBFS with GCC 6: ./aligns/KmerAlignCore.cc:6:34: fatal error: aligns/KmerAlignCore.h: No such file or directory

[Lucas Nussbaum]

Source: trinityrnaseq
Version: 2.2.0+dfsg-1
Severity: serious
Tags: stretch sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20160713 qa-ftbfs
Justification: FTBFS with GCC 6 on amd64

Hi,

During a rebuild of all packages in sid using the gcc-defaults package
available in experimental to make GCC default to version 6, your package failed
to build on amd64. For more information about GCC 6 and Stretch, see:
- https://wiki.debian.org/GCC6
- https://lists.debian.org/debian-devel-announce/2016/06/msg00007.html

Relevant part (hopefully):
> g++  -W -Wall -Wno-unused -Wno-deprecated -ansi -pedantic -Wno-long-long -fno-nonansi-builtins -Wctor-dtor-privacy -Wsign-promo -Woverloaded-virtual -Wendif-labels  -O3  -ggdb3 -DMAKE_DATE='"Mon May 23 18:46:45 UTC 2016"' -DMAKE_OS_RELEASE='"3.16.0-4-amd64"' -DMAKE_RELEASE='"3.0"' -DNEW_MAKEFILE -imacros system/BigFileDefines.h -pthread  -ftemplate-depth-30 -fno-strict-aliasing -mieee-fp   -fopenmp      -Wdate-time -D_FORTIFY_SOURCE=2  -c ./aligns/KmerAlignCore.cc -o obj/aligns/KmerAlignCore.o
> ./aligns/KmerAlignCore.cc:6:34: fatal error: aligns/KmerAlignCore.h: No such file or directory
>  #include "aligns/KmerAlignCore.h"
>                                   ^
> compilation terminated.
> make[2]: *** [aligns/KmerAlignCore.o] Error 1

The full build log is available from:
   http://people.debian.org/~lucas/logs/2016/07/13/trinityrnaseq_2.2.0+dfsg-1_unstable_gcc6.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.