[Debian-med-packaging] Bug#923382: libseqlib: FTBFS (dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file)
Santiago Vila
sanvila at debian.org
Wed Feb 27 09:21:25 GMT 2019
Package: src:libseqlib
Version: 1.1.2+dfsg-2
Severity: serious
Tags: ftbfs
Hello Andreas et al.
I tried to build this package in buster but it failed:
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[...]
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac,
libtoolize: and rerunning libtoolize and aclocal.
libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
libtoolize: 'AC_PROG_RANLIB' is rendered obsolete by 'LT_INIT'
configure.ac:17: installing './compile'
configure.ac:19: installing './config.guess'
configure.ac:19: installing './config.sub'
configure.ac:4: installing './missing'
src/Makefile.am: installing './depcomp'
dh_auto_configure -a
./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for ranlib... ranlib
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... (cached) ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for library containing gzopen... -lz
checking for library containing clock_gettime... none required
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/seqtools/Makefile
config.status: creating libseqlib.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
dh_auto_build -a
make -j1
make[1]: Entering directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg'
make all-recursive
make[2]: Entering directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg'
Making all in src
make[3]: Entering directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg/src'
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_la-FastqReader.lo `test -f 'FastqReader.cpp' || echo './'`FastqReader.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c FastqReader.cpp -fPIC -DPIC -o .libs/libseqlib_la-FastqReader.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c FastqReader.cpp -o libseqlib_la-FastqReader.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_la-BFC.lo `test -f 'BFC.cpp' || echo './'`BFC.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c BFC.cpp -fPIC -DPIC -o .libs/libseqlib_la-BFC.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c BFC.cpp -o libseqlib_la-BFC.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_la-ReadFilter.lo `test -f 'ReadFilter.cpp' || echo './'`ReadFilter.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c ReadFilter.cpp -fPIC -DPIC -o .libs/libseqlib_la-ReadFilter.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c ReadFilter.cpp -o libseqlib_la-ReadFilter.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_la-SeqPlot.lo `test -f 'SeqPlot.cpp' || echo './'`SeqPlot.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c SeqPlot.cpp -fPIC -DPIC -o .libs/libseqlib_la-SeqPlot.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c SeqPlot.cpp -o libseqlib_la-SeqPlot.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_la-GenomicRegion.lo `test -f 'GenomicRegion.cpp' || echo './'`GenomicRegion.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c GenomicRegion.cpp -fPIC -DPIC -o .libs/libseqlib_la-GenomicRegion.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c GenomicRegion.cpp -o libseqlib_la-GenomicRegion.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_la-RefGenome.lo `test -f 'RefGenome.cpp' || echo './'`RefGenome.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c RefGenome.cpp -fPIC -DPIC -o .libs/libseqlib_la-RefGenome.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c RefGenome.cpp -o libseqlib_la-RefGenome.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_la-BamWriter.lo `test -f 'BamWriter.cpp' || echo './'`BamWriter.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c BamWriter.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamWriter.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c BamWriter.cpp -o libseqlib_la-BamWriter.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_la-BamReader.lo `test -f 'BamReader.cpp' || echo './'`BamReader.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c BamReader.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamReader.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c BamReader.cpp -o libseqlib_la-BamReader.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_la-BWAWrapper.lo `test -f 'BWAWrapper.cpp' || echo './'`BWAWrapper.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c BWAWrapper.cpp -fPIC -DPIC -o .libs/libseqlib_la-BWAWrapper.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c BWAWrapper.cpp -o libseqlib_la-BWAWrapper.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_la-BamRecord.lo `test -f 'BamRecord.cpp' || echo './'`BamRecord.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c BamRecord.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamRecord.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c BamRecord.cpp -o libseqlib_la-BamRecord.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_la-FermiAssembler.lo `test -f 'FermiAssembler.cpp' || echo './'`FermiAssembler.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c FermiAssembler.cpp -fPIC -DPIC -o .libs/libseqlib_la-FermiAssembler.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c FermiAssembler.cpp -o libseqlib_la-FermiAssembler.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libseqlib_la-BamHeader.lo `test -f 'BamHeader.cpp' || echo './'`BamHeader.cpp
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c BamHeader.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamHeader.o
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c BamHeader.cpp -o libseqlib_la-BamHeader.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=link g++ -g -Wno-unknown-pragmas -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libseqlib-1.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0 -Wl,-z,relro -Wl,-z,now -o libseqlib.la -rpath /usr/lib/x86_64-linux-gnu libseqlib_la-FastqReader.lo libseqlib_la-BFC.lo libseqlib_la-ReadFilter.lo libseqlib_la-SeqPlot.lo libseqlib_la-GenomicRegion.lo libseqlib_la-RefGenome.lo libseqlib_la-BamWriter.lo libseqlib_la-BamReader.lo libseqlib_la-BWAWrapper.lo libseqlib_la-BamRecord.lo libseqlib_la-FermiAssembler.lo libseqlib_la-BamHeader.lo -lz -pthread
libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/8/crtbeginS.o .libs/libseqlib_la-FastqReader.o .libs/libseqlib_la-BFC.o .libs/libseqlib_la-ReadFilter.o .libs/libseqlib_la-SeqPlot.o .libs/libseqlib_la-GenomicRegion.o .libs/libseqlib_la-RefGenome.o .libs/libseqlib_la-BamWriter.o .libs/libseqlib_la-BamReader.o .libs/libseqlib_la-BWAWrapper.o .libs/libseqlib_la-BamRecord.o .libs/libseqlib_la-FermiAssembler.o .libs/libseqlib_la-BamHeader.o -lz -L/usr/lib/gcc/x86_64-linux-gnu/8 -L/usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/8/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/8/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/crtn.o -g -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -pthread -Wl,-soname -Wl,libseqlib.so.1 -o .libs/libseqlib.so.1.0.0
libtool: link: (cd ".libs" && rm -f "libseqlib.so.1" && ln -s "libseqlib.so.1.0.0" "libseqlib.so.1")
libtool: link: (cd ".libs" && rm -f "libseqlib.so" && ln -s "libseqlib.so.1.0.0" "libseqlib.so")
libtool: link: ar cru .libs/libseqlib.a libseqlib_la-FastqReader.o libseqlib_la-BFC.o libseqlib_la-ReadFilter.o libseqlib_la-SeqPlot.o libseqlib_la-GenomicRegion.o libseqlib_la-RefGenome.o libseqlib_la-BamWriter.o libseqlib_la-BamReader.o libseqlib_la-BWAWrapper.o libseqlib_la-BamRecord.o libseqlib_la-FermiAssembler.o libseqlib_la-BamHeader.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libseqlib.a
libtool: link: ( cd ".libs" && rm -f "libseqlib.la" && ln -s "../libseqlib.la" "libseqlib.la" )
make[3]: Leaving directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg'
dh_auto_test -a
make -j1 check VERBOSE=1
make[1]: Entering directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg'
Making check in src
make[2]: Entering directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg/src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j1 install DESTDIR=/<<BUILDDIR>>/libseqlib-1.1.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg'
echo "mkdir -p bin && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a htslib/libhts.a bin"
mkdir -p bin && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a htslib/libhts.a bin
make[1]: Leaving directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg'
dh_install
# Trick to get also headers moved by d-shlibmove
cp -a SeqLib debian # note: also GenomicRegionCollection.cpp is really needed by freebayes
d-shlibmove --commit \
--multiarch \
--devunversioned \
--exclude-la \
--movedev debian/SeqLib usr/include \
src/.libs/libseqlib.so
Library package automatic movement utility
--> zlib1g-dev package exists.
set -e
install -d -m 755 debian/libseqlib-dev/usr/lib/x86_64-linux-gnu
install -d -m 755 debian/libseqlib1/usr/lib/x86_64-linux-gnu
mv src/.libs/libseqlib.a debian/libseqlib-dev/usr/lib/x86_64-linux-gnu
mv src/.libs/libseqlib.so debian/libseqlib-dev/usr/lib/x86_64-linux-gnu
mv /<<BUILDDIR>>/libseqlib-1.1.2+dfsg/src/.libs/libseqlib.so.1 debian/libseqlib1/usr/lib/x86_64-linux-gnu
mv /<<BUILDDIR>>/libseqlib-1.1.2+dfsg/src/.libs/libseqlib.so.1.0.0 debian/libseqlib1/usr/lib/x86_64-linux-gnu
PKGDEV=libseqlib-dev
PKGSHL=libseqlib1
install -d -m 755 debian/libseqlib-dev/usr/include
mv debian/SeqLib debian/libseqlib-dev/usr/include
mkdir -p /<<BUILDDIR>>/libseqlib-1.1.2+dfsg/debian/libseqlib-dev/usr/lib/x86_64-linux-gnu/pkgconfig
mv libseqlib.pc /<<BUILDDIR>>/libseqlib-1.1.2+dfsg/debian/libseqlib-dev/usr/lib/x86_64-linux-gnu/pkgconfig
make[1]: Leaving directory '/<<BUILDDIR>>/libseqlib-1.1.2+dfsg'
dh_installdocs -a
dh_installchangelogs -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see diff output below
dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below
dpkg-gensymbols: warning: debian/libseqlib1/DEBIAN/symbols doesn't match completely debian/libseqlib1.symbols
--- debian/libseqlib1.symbols (libseqlib1_1.1.2+dfsg-2_amd64)
+++ dpkg-gensymbols768fxC 2019-02-26 19:47:16.636319594 +0000
@@ -108,8 +108,8 @@
_ZN6SeqLib6Filter10ReadFilterD1Ev at Base 1.1.1+dfsg
_ZN6SeqLib6Filter10ReadFilterD2Ev at Base 1.1.1+dfsg
_ZN6SeqLib6Filter11AhoCorasick12TrieFromFileERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 1.1.1+dfsg
- _ZN6SeqLib6Filter11AhoCorasickD1Ev at Base 1.1.1+dfsg
- _ZN6SeqLib6Filter11AhoCorasickD2Ev at Base 1.1.1+dfsg
+#MISSING: 1.1.2+dfsg-2# _ZN6SeqLib6Filter11AhoCorasickD1Ev at Base 1.1.1+dfsg
+#MISSING: 1.1.2+dfsg-2# _ZN6SeqLib6Filter11AhoCorasickD2Ev at Base 1.1.1+dfsg
_ZN6SeqLib6Filter12AbstractRule12addMotifRuleERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb at Base 1.1.1+dfsg
_ZN6SeqLib6Filter12AbstractRule12parseSeqLineERKN4Json5ValueE at Base 1.1.1+dfsg
_ZN6SeqLib6Filter12AbstractRule12parseSubLineERKN4Json5ValueE at Base 1.1.1+dfsg
@@ -235,9 +235,9 @@
_ZNK6SeqLib9BamRecord11CountNBasesEv at Base 1.1.1+dfsg
_ZNK6SeqLib9BamRecord11PositionEndEv at Base 1.1.2+dfsg
_ZNK6SeqLib9BamRecord14GetSmartIntTagERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 1.1.1+dfsg
-#MISSING: 1.1.2+dfsg-1# _ZNK6SeqLib9BamRecord14ParseReadGroupB5cxx11Ev at Base 1.1.1+dfsg
+ _ZNK6SeqLib9BamRecord14ParseReadGroupB5cxx11Ev at Base 1.1.2+dfsg-2
_ZNK6SeqLib9BamRecord15AsGenomicRegionEv at Base 1.1.1+dfsg
-#MISSING: 1.1.2+dfsg-1# _ZNK6SeqLib9BamRecord15PairOrientationEv at Base 1.1.1+dfsg
+ _ZNK6SeqLib9BamRecord15PairOrientationEv at Base 1.1.2+dfsg-2
_ZNK6SeqLib9BamRecord15PositionEndMateEv at Base 1.1.2+dfsg
_ZNK6SeqLib9BamRecord15QualitySequenceB5cxx11Ev at Base 1.1.1+dfsg
_ZNK6SeqLib9BamRecord17GetSmartDoubleTagERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 1.1.1+dfsg
@@ -259,6 +259,7 @@
_ZNKSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_N6SeqLib4_BamEESaISA_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSC_18_Mod_range_hashingENSC_20_Default_ranged_hashENSC_20_Prime_rehash_policyENSC_17_Hashtable_traitsILb1ELb0ELb1EEEE5countERS7_ at Base 1.1.1+dfsg
_ZNKSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESaIS8_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb1ELb0ELb1EEEE19_M_find_before_nodeEmRS7_m at Base 1.1.1+dfsg
_ZNKSt5ctypeIcE8do_widenEc at Base 1.1.1+dfsg
+ _ZNKSt6vectorIN6SeqLib13GenomicRegionESaIS1_EE12_M_check_lenEmPKc at Base 1.1.2+dfsg-2
_ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_N6SeqLib4_BamEESaISA_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSC_18_Mod_range_hashingENSC_20_Default_ranged_hashENSC_20_Prime_rehash_policyENSC_17_Hashtable_traitsILb1ELb0ELb1EEEE10_M_emplaceIJS6_IS5_S9_EEEES6_INSC_14_Node_iteratorISA_Lb0ELb1EEEbESt17integral_constantIbLb1EEDpOT_ at Base 1.1.1+dfsg
#MISSING: 1.1.2+dfsg-1# _ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_N6SeqLib4_BamEESaISA_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSC_18_Mod_range_hashingENSC_20_Default_ranged_hashENSC_20_Prime_rehash_policyENSC_17_Hashtable_traitsILb1ELb0ELb1EEEE21_M_insert_unique_nodeEmmPNSC_10_Hash_nodeISA_Lb1EEE at Base 1.1.1+dfsg
_ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_N6SeqLib4_BamEESaISA_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSC_18_Mod_range_hashingENSC_20_Default_ranged_hashENSC_20_Prime_rehash_policyENSC_17_Hashtable_traitsILb1ELb0ELb1EEEE21_M_insert_unique_nodeEmmPNSC_10_Hash_nodeISA_Lb1EEEm at Base 1.1.2+dfsg
@@ -270,11 +271,13 @@
_ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESaIS8_ENSt8__detail10_Select1stESt8equal_toIS5_ESt4hashIS5_ENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb1ELb0ELb1EEEED2Ev at Base 1.1.1+dfsg
_ZNSt10_HashtableIiSt4pairIKiN6SeqLib13TIntervalTreeIimEEESaIS5_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb0ELb0ELb1EEEE10_M_emplaceIJS0_IiS4_EEEES0_INS7_14_Node_iteratorIS5_Lb0ELb0EEEbESt17integral_constantIbLb1EEDpOT_ at Base 1.1.2+dfsg
#MISSING: 1.1.2+dfsg-1# _ZNSt10_HashtableIiSt4pairIKiN6SeqLib13TIntervalTreeIimEEESaIS5_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb0ELb0ELb1EEEE21_M_insert_unique_nodeEmmPNS7_10_Hash_nodeIS5_Lb0EEE at Base 1.1.1+dfsg
+ _ZNSt10_HashtableIiSt4pairIKiN6SeqLib13TIntervalTreeIimEEESaIS5_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb0ELb0ELb1EEEE21_M_insert_unique_nodeEmmPNS7_10_Hash_nodeIS5_Lb0EEEm at Base 1.1.2+dfsg-2
_ZNSt10_HashtableIiSt4pairIKiN6SeqLib13TIntervalTreeIimEEESaIS5_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb0ELb0ELb1EEEE5clearEv at Base 1.1.1+dfsg
_ZNSt10_HashtableIiSt4pairIKiN6SeqLib13TIntervalTreeIimEEESaIS5_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb0ELb0ELb1EEEE9_M_rehashEmRKm at Base 1.1.1+dfsg
_ZNSt10_HashtableIiSt4pairIKiN6SeqLib13TIntervalTreeIimEEESaIS5_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb0ELb0ELb1EEEED1Ev at Base 1.1.1+dfsg
_ZNSt10_HashtableIiSt4pairIKiN6SeqLib13TIntervalTreeIimEEESaIS5_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb0ELb0ELb1EEEED2Ev at Base 1.1.1+dfsg
#MISSING: 1.1.2+dfsg-1# _ZNSt10_HashtableIiSt4pairIKiSt6vectorIN6SeqLib9TIntervalIimEESaIS5_EEESaIS8_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb0ELb0ELb1EEEE21_M_insert_unique_nodeEmmPNSA_10_Hash_nodeIS8_Lb0EEE at Base 1.1.1+dfsg
+ _ZNSt10_HashtableIiSt4pairIKiSt6vectorIN6SeqLib9TIntervalIimEESaIS5_EEESaIS8_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb0ELb0ELb1EEEE21_M_insert_unique_nodeEmmPNSA_10_Hash_nodeIS8_Lb0EEEm at Base 1.1.2+dfsg-2
_ZNSt10_HashtableIiSt4pairIKiSt6vectorIN6SeqLib9TIntervalIimEESaIS5_EEESaIS8_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb0ELb0ELb1EEEE9_M_rehashEmRKm at Base 1.1.1+dfsg
_ZNSt10_HashtableIiSt4pairIKiSt6vectorIN6SeqLib9TIntervalIimEESaIS5_EEESaIS8_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb0ELb0ELb1EEEED1Ev at Base 1.1.1+dfsg
_ZNSt10_HashtableIiSt4pairIKiSt6vectorIN6SeqLib9TIntervalIimEESaIS5_EEESaIS8_ENSt8__detail10_Select1stESt8equal_toIiESt4hashIiENSA_18_Mod_range_hashingENSA_20_Default_ranged_hashENSA_20_Prime_rehash_policyENSA_17_Hashtable_traitsILb0ELb0ELb1EEEED2Ev at Base 1.1.1+dfsg
@@ -343,7 +346,7 @@
_ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEN6SeqLib4_BamEED2Ev at Base 1.1.1+dfsg
_ZNSt5dequeIPN12aho_corasick5stateIcEESaIS3_EE16_M_push_back_auxIJRKS3_EEEvDpOT_ at Base 1.1.1+dfsg
_ZNSt6vectorIN12aho_corasick7ahoemitIcEESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.1.1+dfsg
- _ZNSt6vectorIN12aho_corasick7ahoemitIcEESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.1.2+dfsg
+#MISSING: 1.1.2+dfsg-2# _ZNSt6vectorIN12aho_corasick7ahoemitIcEESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.1.2+dfsg
_ZNSt6vectorIN12aho_corasick7ahoemitIcEESaIS2_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS2_S4_EE at Base 1.1.1+dfsg
_ZNSt6vectorIN12aho_corasick7ahoemitIcEESaIS2_EE9push_backERKS2_ at Base 1.1.1+dfsg
_ZNSt6vectorIN12aho_corasick7ahoemitIcEESaIS2_EEC1ERKS4_ at Base 1.1.1+dfsg
@@ -364,7 +367,7 @@
_ZNSt6vectorIN6SeqLib6Filter12AbstractRuleESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.1.1+dfsg
_ZNSt6vectorIN6SeqLib9BamRecordESaIS1_EE17_M_realloc_insertIJRKS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 1.1.1+dfsg
_ZNSt6vectorIN6SeqLib9TIntervalIimEESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.1.1+dfsg
- _ZNSt6vectorIN6SeqLib9TIntervalIimEESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.1.2+dfsg
+#MISSING: 1.1.2+dfsg-2# _ZNSt6vectorIN6SeqLib9TIntervalIimEESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.1.2+dfsg
_ZNSt6vectorIN6SeqLib9TIntervalIimEESaIS2_EEaSERKS4_ at Base 1.1.1+dfsg
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 1.1.1+dfsg
_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 1.1.1+dfsg
@@ -387,7 +390,7 @@
_ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 1.1.1+dfsg
_ZNSt7__cxx114listIN6SeqLib13GenomicRegionESaIS2_EE4sortEv at Base 1.1.1+dfsg
_ZNSt7__cxx114listIN6SeqLib13GenomicRegionESaIS2_EE5mergeEOS4_ at Base 1.1.1+dfsg
- _ZNSt8_Rb_treeIN12aho_corasick7ahoemitIcEES2_St9_IdentityIS2_ESt4lessIS2_ESaIS2_EE16_M_insert_uniqueIRKS2_EESt4pairISt17_Rb_tree_iteratorIS2_EbEOT_ at Base 1.1.2+dfsg
+#MISSING: 1.1.2+dfsg-2# _ZNSt8_Rb_treeIN12aho_corasick7ahoemitIcEES2_St9_IdentityIS2_ESt4lessIS2_ESaIS2_EE16_M_insert_uniqueIRKS2_EESt4pairISt17_Rb_tree_iteratorIS2_EbEOT_ at Base 1.1.2+dfsg
_ZNSt8_Rb_treeIN12aho_corasick7ahoemitIcEES2_St9_IdentityIS2_ESt4lessIS2_ESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 1.1.1+dfsg
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St9_IdentityIS5_ESt4lessIS5_ESaIS5_EE16_M_insert_uniqueIRKS5_EESt4pairISt17_Rb_tree_iteratorIS5_EbEOT_ at Base 1.1.1+dfsg
_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St9_IdentityIS5_ESt4lessIS5_ESaIS5_EE7_M_copyINSB_11_Alloc_nodeEEEPSt13_Rb_tree_nodeIS5_EPKSF_PSt18_Rb_tree_node_baseRT_ at Base 1.1.1+dfsg
@@ -406,7 +409,7 @@
_ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPN6SeqLib11PlottedReadESt6vectorIS3_SaIS3_EEEElS3_NS0_5__ops15_Iter_less_iterEEvT_T0_SC_T1_T2_ at Base 1.1.1+dfsg
_ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPN6SeqLib13GenomicRegionESt6vectorIS3_SaIS3_EEEElS3_NS0_5__ops15_Iter_less_iterEEvT_T0_SC_T1_T2_ at Base 1.1.1+dfsg
_ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPN6SeqLib9TIntervalIimEESt6vectorIS4_SaIS4_EEEElS4_NS0_5__ops15_Iter_comp_iterINS2_19IntervalStartSorterIimEEEEEvT_T0_SG_T1_T2_ at Base 1.1.1+dfsg
- _ZSt13__heap_selectIN9__gnu_cxx17__normal_iteratorIPN6SeqLib13GenomicRegionESt6vectorIS3_SaIS3_EEEENS0_5__ops15_Iter_less_iterEEvT_SB_SB_T0_ at Base 1.1.2+dfsg
+#MISSING: 1.1.2+dfsg-2# _ZSt13__heap_selectIN9__gnu_cxx17__normal_iteratorIPN6SeqLib13GenomicRegionESt6vectorIS3_SaIS3_EEEENS0_5__ops15_Iter_less_iterEEvT_SB_SB_T0_ at Base 1.1.2+dfsg
_ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E0_EEEvT_SK_T0_ at Base 1.1.1+dfsg
_ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E_EEEvT_SK_T0_ at Base 1.1.1+dfsg
_ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPN6SeqLib11PlottedReadESt6vectorIS3_SaIS3_EEEENS0_5__ops15_Iter_less_iterEEvT_SB_T0_ at Base 1.1.1+dfsg
dh_makeshlibs: failing due to earlier errors
make: *** [debian/rules:10: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
The build was made in my autobuilder with "dpkg-buildpackage -B"
and it also fails here:
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/libseqlib.html
If this is really a bug in one of the build-depends, please use reassign and affects,
so that this is still visible in the BTS web page for this package.
Thanks.
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