Package: src:libstatgen
Version: 1.0.14-1
Severity: serious
Tags: ftbfs
Dear maintainer:
I tried to build this package in sid but it failed:
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[...]
debian/rules build-indep
dh build-indep
dh_update_autotools_config -i
dh_autoreconf -i
dh_auto_configure -i
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
make -j1 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>/samtools'
ln -s ../samtools/bgzf.h ../include/bgzf.h
ln -s ../samtools/knetfile.h ../include/knetfile.h
ln -s ../samtools/khash.h ../include/khash.h
[... snipped ...]
ln -s ../general/SmithWaterman.h ../include/SmithWaterman.h
ln -s ../general/Sort.h ../include/Sort.h
ln -s ../general/STLUtilities.h ../include/STLUtilities.h
ln -s ../general/StatGenStatus.h ../include/StatGenStatus.h
ln -s ../general/StringAlias.h ../include/StringAlias.h
ln -s ../general/StringArray.h ../include/StringArray.h
ln -s ../general/StringBasics.h ../include/StringBasics.h
ln -s ../general/StringHash.h ../include/StringHash.h
ln -s ../general/StringMap.h ../include/StringMap.h
ln -s ../general/Tabix.h ../include/Tabix.h
ln -s ../general/UncompressedFileType.h ../include/UncompressedFileType.h
ln -s ../general/Constant.h ../include/Constant.h
ln -s ../general/CSG_MD5.h ../include/CSG_MD5.h
ln -s ../general/Generic.h ../include/Generic.h
ln -s ../general/GenomeSequenceHelpers.h ../include/GenomeSequenceHelpers.h
ln -s ../general/GreedyTupleAligner.h ../include/GreedyTupleAligner.h
ln -s ../general/InplaceMerge.h ../include/InplaceMerge.h
ln -s ../general/LongHash.h ../include/LongHash.h
ln -s ../general/LongInt.h ../include/LongInt.h
ln -s ../general/MathConstant.h ../include/MathConstant.h
ln -s ../general/PackedVector.h ../include/PackedVector.h
ln -s ../general/PedigreeAlleles.h ../include/PedigreeAlleles.h
ln -s ../general/Performance.h ../include/Performance.h
ln -s ../general/ReusableVector.h ../include/ReusableVector.h
ln -s ../general/SimpleStats.h ../include/SimpleStats.h
ln -s ../general/TrimSequence.h ../include/TrimSequence.h
ln -s ../general/UnitTest.h ../include/UnitTest.h
g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation
-Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__
-D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseAsciiMap.o -c
BaseAsciiMap.cpp -DVERSION="\"1.0.0\""
g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation
-Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__
-D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseQualityHelper.o -c
BaseQualityHelper.cpp -DVERSION="\"1.0.0\""
g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation
-Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__
-D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseUtilities.o -c
BaseUtilities.cpp -DVERSION="\"1.0.0\""
g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation
-Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__
-D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BasicHash.o -c
BasicHash.cpp -DVERSION="\"1.0.0\""
g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation
-Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__
-D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BgzfFileType.o -c
BgzfFileType.cpp -DVERSION="\"1.0.0\""
g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation
-Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__
-D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BgzfFileTypeRecovery.o -c
BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\""
g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation
-Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__
-D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CharBuffer.o -c
CharBuffer.cpp -DVERSION="\"1.0.0\""
g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation
-Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__
-D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Chromosome.o -c
Chromosome.cpp -DVERSION="\"1.0.0\""
Chromosome.cpp: In constructor 'Chromosome::Chromosome(const string&, unsigned
int, bool)':
Chromosome.cpp:42:15: error: '*<unknown>.Chromosome::gs' is used uninitialized
in this function [-Werror=uninitialized]
if (this->gs) delete gs;
~~~~~~^~
cc1plus: all warnings being treated as errors
make[3]: *** [../Makefiles/Makefile.common:81: obj/Chromosome.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/general'
make[2]: *** [Makefiles/Makefile.base:15: general] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: make -j1 "INSTALL=install --strip-program=true" returned exit
code 2
make[1]: *** [debian/rules:14: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:11: build-indep] Error 2
dpkg-buildpackage: error: debian/rules build-indep subprocess returned exit
status 2
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The build was made with "dpkg-buildpackage -A" in my autobuilder,
but it also fails here in every architecture:
https://buildd.debian.org/status/package.php?p=libstatgen
Thanks.
