Your message dated Sat, 5 Aug 2017 18:50:49 +0300
with message-id <20170805155048.3kripm6r4fdx6ud2@localhost>
and subject line The version currently in unstable/testing builds with gcc 7
has caused the Debian Bug report #853482,
regarding libbpp-seq-omics: ftbfs with GCC-7
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
853482: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=853482
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:libbpp-seq-omics
Version: 2.2.0-1
Severity: normal
Tags: sid buster
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-7
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-7/g++-7, but succeeds to build with gcc-6/g++-6. The
severity of this report may be raised before the buster release.
There is no need to fix this issue in time for the stretch release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc7-20170126/libbpp-seq-omics_2.2.0-1_unstable_gcc7.log
The last lines of the build log are at the end of this report.
To build with GCC 7, either set CC=gcc-7 CXX=g++-7 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-7/porting_to.html
[...]
^~~~~
/<<PKGBUILDDIR>>/src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp:73:60: warning:
dynamic exception specifications are deprecated in C++11; use 'noexcept'
instead [-Wdeprecated]
const BasicSequenceFeature GtfFeatureReader::nextFeature() throw (Exception)
^~~~~
[ 93%] Linking CXX static library libbpp-seq-omics.a
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P
CMakeFiles/bppseqomics-static.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E
cmake_link_script CMakeFiles/bppseqomics-static.dir/link.txt --verbose=1
/usr/bin/ar qc libbpp-seq-omics.a
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Fastq.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/MafParser.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/MafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/SequenceFilterMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/ChromosomeMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/DuplicateFilterMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/ConcatenateMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/FullGapFilterMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/M
af/EntropyFilterMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/MaskFilterMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/QualityFilterMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/OutputMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/WindowSplitMafIterator.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/MafSequence.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Io/Maf/MafStatistics.cpp.o
CMakeFiles/bppseqomics-static
.dir/Bpp/Seq/Io/Maf/IterationListener.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Feature/SequenceFeature.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Feature/SequenceFeatureTools.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Feature/Gff/GffFeatureReader.cpp.o
CMakeFiles/bppseqomics-static.dir/Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp.o
/usr/bin/ranlib libbpp-seq-omics.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 93%] Built target bppseqomics-static
make -f test/CMakeFiles/test_fastq.dir/build.make
test/CMakeFiles/test_fastq.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends
"Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/test
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/test
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/test/CMakeFiles/test_fastq.dir/DependInfo.cmake
--color=
Scanning dependencies of target test_fastq
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f test/CMakeFiles/test_fastq.dir/build.make
test/CMakeFiles/test_fastq.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 95%] Building CXX object test/CMakeFiles/test_fastq.dir/test_fastq.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/test && /usr/bin/c++
-I/<<PKGBUILDDIR>>/test/../src -Wall -Weffc++ -Wshadow -Wconversion -o
CMakeFiles/test_fastq.dir/test_fastq.cpp.o -c
/<<PKGBUILDDIR>>/test/test_fastq.cpp
In file included from /<<PKGBUILDDIR>>/test/test_fastq.cpp:41:0:
/<<PKGBUILDDIR>>/test/../src/Bpp/Seq/Io/Fastq.h:121:67: warning: dynamic
exception specifications are deprecated in C++11; use 'noexcept' instead
[-Wdeprecated]
bool nextSequence(std::istream& input, Sequence& seq) const throw
(Exception);
^~~~~
/<<PKGBUILDDIR>>/test/../src/Bpp/Seq/Io/Fastq.h:133:75: warning: dynamic
exception specifications are deprecated in C++11; use 'noexcept' instead
[-Wdeprecated]
void writeSequence(std::ostream& output, const Sequence& seq) const
throw (Exception);
^~~~~
[ 96%] Linking CXX executable test_fastq
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E
cmake_link_script CMakeFiles/test_fastq.dir/link.txt --verbose=1
/usr/bin/c++ -Wall -Weffc++ -Wshadow -Wconversion -Wl,-z,relro
CMakeFiles/test_fastq.dir/test_fastq.cpp.o -o test_fastq -rdynamic -lbpp-core
-lbpp-seq -L../src -lbpp-seq-omics
CMakeFiles/test_fastq.dir/test_fastq.cpp.o:(.data.rel.ro._ZTVN3bpp19SequenceWithQualityE[_ZTVN3bpp19SequenceWithQualityE]+0x110):
undefined reference to `virtual thunk to
bpp::EdSymbolList::toString[abi:cxx11]() const'
CMakeFiles/test_fastq.dir/test_fastq.cpp.o:(.data.rel.ro._ZTVN3bpp19SequenceWithQualityE[_ZTVN3bpp19SequenceWithQualityE]+0x140):
undefined reference to `virtual thunk to
bpp::EdSymbolList::getChar[abi:cxx11](unsigned long) const'
CMakeFiles/test_fastq.dir/test_fastq.cpp.o:(.data.rel.ro._ZTCN3bpp19SequenceWithQualityE0_NS_22SequenceWithAnnotationE[_ZTVN3bpp19SequenceWithQualityE]+0x110):
undefined reference to `virtual thunk to
bpp::EdSymbolList::toString[abi:cxx11]() const'
CMakeFiles/test_fastq.dir/test_fastq.cpp.o:(.data.rel.ro._ZTCN3bpp19SequenceWithQualityE0_NS_22SequenceWithAnnotationE[_ZTVN3bpp19SequenceWithQualityE]+0x140):
undefined reference to `virtual thunk to
bpp::EdSymbolList::getChar[abi:cxx11](unsigned long) const'
CMakeFiles/test_fastq.dir/test_fastq.cpp.o:(.data.rel.ro._ZTCN3bpp19SequenceWithQualityE8_NS_12EdSymbolListE[_ZTVN3bpp19SequenceWithQualityE]+0x2f8):
undefined reference to `virtual thunk to
bpp::EdSymbolList::toString[abi:cxx11]() const'
CMakeFiles/test_fastq.dir/test_fastq.cpp.o:(.data.rel.ro._ZTCN3bpp19SequenceWithQualityE8_NS_12EdSymbolListE[_ZTVN3bpp19SequenceWithQualityE]+0x328):
undefined reference to `virtual thunk to
bpp::EdSymbolList::getChar[abi:cxx11](unsigned long) const'
collect2: error: ld returned 1 exit status
test/CMakeFiles/test_fastq.dir/build.make:99: recipe for target
'test/test_fastq' failed
make[3]: *** [test/test_fastq] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
CMakeFiles/Makefile2:1240: recipe for target
'test/CMakeFiles/test_fastq.dir/all' failed
make[2]: *** [test/CMakeFiles/test_fastq.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
Makefile:163: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: make -j1 returned exit code 2
debian/rules:6: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
--- End Message ---
--- Begin Message ---
The version currently in unstable/testing builds with gcc 7:
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/libbpp-seq-omics.html
Most likely the new upstream version fixed it.
cu
Adrian
--
"Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
"Only a promise," Lao Er said.
Pearl S. Buck - Dragon Seed
--- End Message ---
