[Debian-med-packaging] Bug#667201: hhsuite: ftbfs with GCC-4.7

[Matthias Klose]

Package: hhsuite
Version: 2.0.13-1
Severity: important
Tags: sid wheezy
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-4.7

The package fails to build in a test rebuild on at least amd64 with
gcc-4.7/g++-4.7, but succeeds to build with gcc-4.6/g++-4.6. The
severity of this report may be raised before the wheezy release.

hhsearch.C:1374:65: error: 'R_OK' was not declared in this scope

The full build log can be found at:
http://people.debian.org/~lucas/logs/2012/03/29-clang-gcc47/unstable-gcc47/hhsuite_2.0.13-1_unstable-gcc47.log
The last lines of the build log are at the end of this report.

Some hints on fixing these issues can be found at
http://gcc.gnu.org/gcc-4.7/porting_to.html

To build with GCC 4.7, either set CC=gcc-4.7 CXX=g++-4.7 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

[...]
make[2]: Entering directory `/«PKGBUILDDIR»/data'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/«PKGBUILDDIR»/data'
make -C src all
make[2]: Entering directory `/«PKGBUILDDIR»/src'
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics  -DHH_SSE3 -msse3 -fopenmp -c cs/aa.cc -o cs/aa.o
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics  -DHH_SSE3 -msse3 -fopenmp -c cs/application.cc -o cs/application.o
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics  -DHH_SSE3 -msse3 -fopenmp -c cs/as.cc -o cs/as.o
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics  -DHH_SSE3 -msse3 -fopenmp -c cs/assert_helpers.cc -o cs/assert_helpers.o
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics  -DHH_SSE3 -msse3 -fopenmp -c cs/blosum_matrix.cc -o cs/blosum_matrix.o
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics  -DHH_SSE3 -msse3 -fopenmp -c cs/getopt_pp.cc -o cs/getopt_pp.o
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics  -DHH_SSE3 -msse3 -fopenmp -c cs/log.cc -o cs/log.o
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics  -DHH_SSE3 -msse3 hhblits.C -o hhblits  cs/aa.o  cs/application.o  cs/as.o  cs/assert_helpers.o  cs/blosum_matrix.o  cs/getopt_pp.o  cs/log.o -lpthread -fopenmp -lrt -lffindex
In file included from hhblits.C:263:0:
hhprefilter.C: In function 'void prefilter_db()':
hhprefilter.C:1048:38: warning: capture of variable 'cpu' with non-automatic storage duration [enabled by default]
hhblits.C:173:5: note: 'int cpu' declared here
g++ -O3 -Wall -Wno-deprecated -Wno-char-subscripts -fno-strict-aliasing -Ics  -DHH_SSE3 -msse3 hhsearch.C -o hhsearch  cs/aa.o  cs/application.o  cs/as.o  cs/assert_helpers.o  cs/blosum_matrix.o  cs/getopt_pp.o  cs/log.o -lpthread -lrt
hhsearch.C: In function 'int main(int, char**)':
hhsearch.C:1374:65: error: 'R_OK' was not declared in this scope
hhsearch.C:1374:69: error: 'access' was not declared in this scope
hhsearch.C:1387:57: error: 'R_OK' was not declared in this scope
hhsearch.C:1387:61: error: 'access' was not declared in this scope
make[2]: *** [hhsearch] Error 1
make[2]: Leaving directory `/«PKGBUILDDIR»/src'
make[1]: *** [all] Error 2
dh_auto_build: make -j1 returned exit code 2
make[1]: Leaving directory `/«PKGBUILDDIR»'
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2