[Debian-med-packaging] Bug#897867: spades: ftbfs with GCC-8
Matthias Klose
doko at debian.org
Fri May 4 13:23:45 BST 2018
Package: src:spades
Version: 3.11.1+dfsg-1
Severity: normal
Tags: sid buster
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-8
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-8/g++-8, but succeeds to build with gcc-7/g++-7. The
severity of this report will be raised before the buster release.
The full build log can be found at:
http://aws-logs.debian.net/2018/05/01/gcc8/spades_3.11.1+dfsg-1_unstable_gcc8.log.gz
The last lines of the build log are at the end of this report.
To build with GCC 8, either set CC=gcc-8 CXX=g++-8 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are 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-8/porting_to.html
[...]
cd /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/io && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/io -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/io -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src/include -I/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/include -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src/common -isystem /<<BUILDDIR>>/spades-3.11.1+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/spades-3.11.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++11 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/input.dir/sam/sam_reader.cpp.o -c /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/io/sam/sam_reader.cpp
[ 52%] Linking CXX static library libinput.a
cd /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/io && /usr/bin/cmake -P CMakeFiles/input.dir/cmake_clean_target.cmake
cd /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/io && /usr/bin/cmake -E cmake_link_script CMakeFiles/input.dir/link.txt --verbose=1
/usr/bin/ar qc libinput.a CMakeFiles/input.dir/reads/parser.cpp.o CMakeFiles/input.dir/sam/read.cpp.o CMakeFiles/input.dir/sam/sam_reader.cpp.o
/usr/bin/ranlib libinput.a
make[4]: Leaving directory '/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades'
[ 52%] Built target input
make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades'
cd /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/spades-3.11.1+dfsg/src /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake --color=
Dependee "/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline/CMakeFiles/pipeline.dir/DependInfo.cmake" is newer than depender "/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline/CMakeFiles/pipeline.dir/depend.internal".
Dependee "/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline/CMakeFiles/pipeline.dir/depend.internal".
Scanning dependencies of target pipeline
make[4]: Leaving directory '/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades'
make -f common/pipeline/CMakeFiles/pipeline.dir/build.make common/pipeline/CMakeFiles/pipeline.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades'
[ 52%] Building CXX object common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o
cd /<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline && /usr/bin/c++ -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/common/pipeline -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src/include -I/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades/include -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src -I/<<BUILDDIR>>/spades-3.11.1+dfsg/src/common -isystem /<<BUILDDIR>>/spades-3.11.1+dfsg/src/../ext/include -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/spades-3.11.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++11 -O2 -g -DNDEBUG -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/pipeline.dir/stage.cpp.o -c /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline/stage.cpp
In file included from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/sequence/seq.hpp:38,
from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/sequence/sequence.hpp:16,
from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/io/reads/single_read.hpp:12,
from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/assembly_graph/index/edge_position_index.hpp:11,
from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline/graph_pack.hpp:10,
from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline/stage.hpp:11,
from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline/stage.cpp:8:
/<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/sequence/nucl.hpp: In member function 'bool nucl_complement_functor::operator()(char) const':
/<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/sequence/nucl.hpp:84:19: warning: ?: using integer constants in boolean context [-Wint-in-bool-context]
return cc ? cc : 'N';
~~~^~~~~~~~~~
In file included from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/assembly_graph/handlers/edges_position_handler.hpp:20,
from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/visualization/graph_labeler.hpp:12,
from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/assembly_graph/handlers/id_track_handler.hpp:12,
from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline/graph_pack.hpp:13,
from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline/stage.hpp:11,
from /<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/pipeline/stage.cpp:8:
/<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/assembly_graph/paths/mapping_path.hpp: In member function 'bool omnigraph::GapDescription<Graph>::has_filling() const':
/<<BUILDDIR>>/spades-3.11.1+dfsg/src/common/assembly_graph/paths/mapping_path.hpp:390:16: error: cannot convert 'const boost::optional<Sequence>' to 'bool' in return
return filling_seq_;
^~~~~~~~~~~~
make[4]: *** [common/pipeline/CMakeFiles/pipeline.dir/build.make:63: common/pipeline/CMakeFiles/pipeline.dir/stage.cpp.o] Error 1
make[4]: Leaving directory '/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades'
make[3]: *** [CMakeFiles/Makefile2:815: common/pipeline/CMakeFiles/pipeline.dir/all] Error 2
make[3]: Leaving directory '/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades'
make[2]: *** [Makefile:152: all] Error 2
make[2]: Leaving directory '/<<BUILDDIR>>/spades-3.11.1+dfsg/build_spades'
make[1]: *** [debian/rules:41: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/spades-3.11.1+dfsg'
make: *** [debian/rules:23: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
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