[Debian-med-packaging] Bug#778161: velvet: ftbfs with GCC-5

[Matthias Klose]

Package: src:velvet
Version: 1.2.10+dfsg1-1
Severity: normal
Tags: sid stretch
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-5

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-5/g++-5, but succeeds to build with gcc-4.9/g++-4.9. The
severity of this report may be raised before the stretch release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc5-20150205/velvet_1.2.10+dfsg1-1_unstable_gcc5.log
The last lines of the build log are at the end of this report.

To build with GCC 5, either set CC=gcc-5 CXX=g++-5 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t experimental install g++ 

Common build failures are C11 as the default C mode, 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-5/porting_to.html

[...]
In file included from src/scaffold.c:32:0:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
                    ^
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
 extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
                           ^
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
 extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
                    ^
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
 extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
                          ^
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o 
In file included from src/kmerOccurenceTable.c:29:0:
src/readSet.h:64:16: warning: inline function 'isCreateBinary' declared but never defined
 inline boolean isCreateBinary();
                ^
In file included from src/kmerOccurenceTable.c:27:0:
src/graph.h:178:20: warning: inline function 'setShortReadMarkerOffset' declared but never defined
 extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
                    ^
src/graph.h:177:27: warning: inline function 'getShortReadMarkerOffset' declared but never defined
 extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker * marker);
                           ^
src/graph.h:174:20: warning: inline function 'setShortReadMarkerPosition' declared but never defined
 extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
                    ^
src/graph.h:173:26: warning: inline function 'getShortReadMarkerPosition' declared but never defined
 extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker * marker);
                          ^
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/allocArray.c -o obj/allocArray.o 
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
Makefile:70: recipe for target 'velveth' failed
make[2]: Leaving directory '/«BUILDDIR»/velvet-1.2.10+dfsg1'
dh_auto_build: make -j1 LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 CPPFLAGS=-D_FORTIFY_SOURCE=2 CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security LDFLAGS=-Wl,-z,relro returned exit code 2
make[1]: *** [build_long_versions] Error 2
debian/rules:23: recipe for target 'build_long_versions' failed
make[1]: Leaving directory '/«BUILDDIR»/velvet-1.2.10+dfsg1'
make: *** [build-arch] Error 2
debian/rules:7: recipe for target 'build-arch' failed
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2