[Debian-med-packaging] Help in gcc-5 migration needed (Was: Bug#778161: velvet: ftbfs with GCC-5)

[Andreas Tille]

Hi,

any idea how to deal with this kind of errors?  I noticed that this
problem also occures when velvet is built with clang but have no idea
how to fix it.

> Package: src:velvet
> Version: 1.2.10+dfsg1-1
> ...
> 
> gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/autoOpen.c -o obj/autoOpen.o 
> gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -Wl,-z,relro -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm
> obj/run.o: In function `main':
> /??BUILDDIR??/velvet-1.2.10+dfsg1/src/run.c:245: undefined reference to `isCreateBinary'
> /??BUILDDIR??/velvet-1.2.10+dfsg1/src/run.c:291: undefined reference to `isCreateBinary'
> obj/splayTable.o: In function `inputSequenceArrayIntoSplayTableAndArchive':
> /??BUILDDIR??/velvet-1.2.10+dfsg1/src/splayTable.c:982: undefined reference to `isCreateBinary'
> collect2: error: ld returned 1 exit status
> make[2]: *** [velveth] Error 1

Any help would be welcome

    Andreas.

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