[Debian-med-packaging] Bug#701348: rnahybrid: ftbfs with GCC-4.8

[Matthias Klose]

Package: src:rnahybrid
Version: 2.1.1-1
Severity: important
Tags: sid jessie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-4.8

The package fails to build in a test rebuild on at least amd64 with
gcc-4.8/g++-4.8, but succeeds to build with gcc-4.7/g++-4.7. The
severity of this report may be raised before the jessie release.

  XXX

The full build log can be found at:
http://people.debian.org/~doko/logs-20130217/gcc48/rnahybrid_2.1.1-1_unstable_gcc48.log
The last lines of the build log are at the end of this report.

To build with GCC 4.8, either set CC=gcc-4.8 CXX=g++-4.8 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t experimental install g++ g++-4.7 g++-4.8 libc6-dev

The test rebuild was done with eglibc-2.17 and GCC-4.8, so some issues
might be caused by the updated glibc.

[...]
rnaeffective.c:288:16: warning: incompatible implicit declaration of built-in function 'strlen' [enabled by default]
       seqlen = strlen(query_sq);
                ^
rnaeffective.c:299:20: warning: incompatible implicit declaration of built-in function 'strchr' [enabled by default]
  index_one = (int) strchr(alphabet,letter_one);
                    ^
rnaeffective.c:299:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  index_one = (int) strchr(alphabet,letter_one);
              ^
rnaeffective.c:300:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  index_two = (int) strchr(alphabet,letter_two);
              ^
rnaeffective.c:303:22: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
    freq_di[index_one-(int) alphabet][index_two-(int) alphabet]++;
                      ^
rnaeffective.c:303:48: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
    freq_di[index_one-(int) alphabet][index_two-(int) alphabet]++;
                                                ^
rnaeffective.c:346:15: warning: incompatible implicit declaration of built-in function 'strlen' [enabled by default]
   for (i=0; i<strlen(alphabet); i++) {
               ^
rnaeffective.c:436:6: warning: incompatible implicit declaration of built-in function 'strcpy' [enabled by default]
      strcpy(x, " ");                             
      ^
rnaeffective.c:437:6: warning: incompatible implicit declaration of built-in function 'strcat' [enabled by default]
      strcat(x, target_sq);
      ^
rnaeffective.c:565:6: warning: incompatible implicit declaration of built-in function 'strcpy' [enabled by default]
      strcpy(x, " ");                             
      ^
rnaeffective.c:566:6: warning: incompatible implicit declaration of built-in function 'strcat' [enabled by default]
      strcat(x, target_sq);
      ^
x86_64-linux-gnu-gcc  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security  -Wl,-z,defs -o RNAeffective  rnaeffective.o hybrid_core.o numerical.o energy.o input.o fasta.o random.o mt19937-1.o plot.o  -lg2 -lm 
make[3]: Leaving directory `/«PKGBUILDDIR»/src'
Making all in man
make[3]: Entering directory `/«PKGBUILDDIR»/man'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/«PKGBUILDDIR»/man'
make[3]: Entering directory `/«PKGBUILDDIR»'
make[3]: Leaving directory `/«PKGBUILDDIR»'
make[2]: Leaving directory `/«PKGBUILDDIR»'
make[1]: Leaving directory `/«PKGBUILDDIR»'
   debian/rules override_dh_auto_test
make[1]: Entering directory `/«PKGBUILDDIR»'
src/RNAhybrid -s 3utr_worm -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta
make[1]: *** [override_dh_auto_test] Segmentation fault
make[1]: Leaving directory `/«PKGBUILDDIR»'
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2