[Debian-med-packaging] Bug#778021: ncbi-blast+: ftbfs with GCC-5

Matthias Klose doko at debian.org
Thu Feb 12 10:34:46 UTC 2015

Package: src:ncbi-blast+
Version: 2.2.29-3
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:
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

Applying patch no_multiarch_rpath
patching file c++/src/build-system/configure
Hunk #1 succeeded at 6209 (offset 286 lines).
patching file c++/src/build-system/configure.ac
Hunk #1 succeeded at 1737 (offset 117 lines).

Applying patch use_pie_for_apps
patching file c++/src/build-system/Makefile.app.in

Applying patch skip_services_unit_test
patching file c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app

Applying patch fix_configure
patching file c++/configure.orig

Applying patch include_typeinfo
patching file c++/include/corelib/ncbistl.hpp

Now at patch include_typeinfo
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/ncbi-blast+-vl5_sw/ncbi-blast+-2.2.29'
cd c++  &&  LD_LIBRARY_PATH=/build/ncbi-blast+-vl5_sw/ncbi-blast+-2.2.29/c++/BUILD/lib${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH} \
    CONFIG_SHELL=/bin/bash ./configure --with-dll --with-mt --without-autodep --without-makefile-auto-update --with-flat-makefile --without-caution --without-dbapi --without-lzo --with-runpath=/usr/lib/ncbi-blast+ --with-build-root=BUILD --without-debug
configure: loading site script /build/ncbi-blast+-vl5_sw/ncbi-blast+-2.2.29/c++/src/build-system/config.site

configure: creating cache config.cache
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
adjusted C   compiler: /usr/bin/gcc 
adjusted C++ compiler: /usr/bin/g++ 
configure: error: Do not know how to build MT-safe with compiler /usr/bin/g++  5.0.0
make[1]: *** [override_dh_auto_configure] Error 1
debian/rules:40: recipe for target 'override_dh_auto_configure' failed
make[1]: Leaving directory '/build/ncbi-blast+-vl5_sw/ncbi-blast+-2.2.29'
make: *** [build-arch] Error 2
debian/rules:96: recipe for target 'build-arch' failed
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2

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