[Debian-med-packaging] Bug#1049535: igor: Fails to build binary packages again after successful build
Lucas Nussbaum
lucas at debian.org
Wed Aug 16 08:42:49 BST 2023
Source: igor
Version: 1.4.0+dfsg-4
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild
Hi,
This package fails to do build a binary-only build (not source) after a
successful build (dpkg-buildpackage ; dpkg-buildpackage -b).
This is probably a clear violation of Debian Policy section 4.9 (clean target),
but this is filed as severity:minor for now, because a discussion on
debian-devel showed that we might want to revisit the requirement of a working
'clean' target.
More information about this class of issues, included common problems and
solutions, is available at
https://wiki.debian.org/qa.debian.org/FTBFS/DoubleBuild
Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b
> --------------------------------------------------------------------------------------------------------------------
>
> dpkg-buildpackage: info: source package igor
> dpkg-buildpackage: info: source version 1.4.0+dfsg-4
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
> dpkg-source --before-build .
> dpkg-buildpackage: info: host architecture amd64
> debian/rules clean
> dh clean
> debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> make -j8 distclean
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> Making distclean in igor_src
> make[3]: Entering directory '/<<PKGBUILDDIR>>/igor_src'
> rm -rf .libs _libs
> rm -f *.o
> rm -f *.lo
> rm -f *.tab.c
> rm -f igor
> test -z "" || rm -f
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f ./.deps/igor-Aligner.Po
> rm -f ./.deps/igor-Bestscenarioscounter.Po
> rm -f ./.deps/igor-CDR3SeqData.Po
> rm -f ./.deps/igor-Counter.Po
> rm -f ./.deps/igor-Coverageerrcounter.Po
> rm -f ./.deps/igor-Deletion.Po
> rm -f ./.deps/igor-Dinuclmarkov.Po
> rm -f ./.deps/igor-Errorrate.Po
> rm -f ./.deps/igor-Errorscounter.Po
> rm -f ./.deps/igor-ExtractFeatures.Po
> rm -f ./.deps/igor-GenModel.Po
> rm -f ./.deps/igor-Genechoice.Po
> rm -f ./.deps/igor-HypermutationfullNmererrorrate.Po
> rm -f ./.deps/igor-Hypermutationglobalerrorrate.Po
> rm -f ./.deps/igor-Insertion.Po
> rm -f ./.deps/igor-IntStr.Po
> rm -f ./.deps/igor-Model_Parms.Po
> rm -f ./.deps/igor-Model_marginals.Po
> rm -f ./.deps/igor-Pgencounter.Po
> rm -f ./.deps/igor-Rec_Event.Po
> rm -f ./.deps/igor-Singleerrorrate.Po
> rm -f ./.deps/igor-Utils.Po
> rm -f ./.deps/igor-main.Po
> rm -f Makefile
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/igor_src'
> make[3]: Entering directory '/<<PKGBUILDDIR>>'
> rm -rf .libs _libs
> rm -f *.lo
> test -z "" || rm -f
> rm -f config.h stamp-h1
> rm -f libtool config.lt
> rm -f TAGS ID GTAGS GRTAGS GSYMS GPATH tags
> test . = "." || test -z "" || rm -f
> rm -f cscope.out cscope.in.out cscope.po.out cscope.files
> make[3]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -f config.status config.cache config.log configure.lineno config.status.lineno
> rm -f Makefile
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> rm -rf docs/latex
> rm -rf docs/html
> rm -rf config.guess config.sub
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_autoreconf_clean
> dh_clean
> debian/rules binary
> dh binary
> dh_update_autotools_config
> dh_autoreconf
> libtoolize: putting auxiliary files in '.'.
> libtoolize: copying file './ltmain.sh'
> libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
> libtoolize: copying file 'm4/libtool.m4'
> libtoolize: copying file 'm4/ltoptions.m4'
> libtoolize: copying file 'm4/ltsugar.m4'
> libtoolize: copying file 'm4/ltversion.m4'
> libtoolize: copying file 'm4/lt~obsolete.m4'
> configure.ac:14: installing './compile'
> configure.ac:14: installing './config.guess'
> configure.ac:14: installing './config.sub'
> configure.ac:7: installing './install-sh'
> configure.ac:7: installing './missing'
> igor_src/Makefile.am: installing './depcomp'
> dh_auto_configure
> ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${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 race-free 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 build system type... x86_64-pc-linux-gnu
> checking host system type... x86_64-pc-linux-gnu
> checking how to print strings... printf
> checking whether make supports the include directive... yes (GNU style)
> checking for gcc... gcc
> 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 the compiler supports GNU C... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to enable C11 features... none needed
> checking whether gcc understands -c and -o together... yes
> checking dependency style of gcc... none
> 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 file... file
> 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... 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 for stdio.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for strings.h... yes
> checking for sys/stat.h... yes
> checking for sys/types.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 for g++... g++
> checking whether the compiler supports GNU C++... yes
> checking whether g++ accepts -g... yes
> checking for g++ option to enable C++11 features... none needed
> checking dependency style of g++... none
> 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 for gcc... (cached) gcc
> checking whether the compiler supports GNU C... (cached) yes
> checking whether gcc accepts -g... (cached) yes
> checking for gcc option to enable C11 features... (cached) none needed
> checking whether gcc understands -c and -o together... (cached) yes
> checking dependency style of gcc... (cached) none
> checking whether g++ supports C++11 features by default... yes
> checking for g++ option to support OpenMP... -fopenmp
> checking for _Bool... no
> checking for stdbool.h that conforms to C99... yes
> checking for inline... inline
> checking for size_t... yes
> checking for pow... yes
> checking for sqrt... yes
> checking that generated files are newer than configure... done
> configure: creating ./config.status
> config.status: creating Makefile
> config.status: creating igor_src/Makefile
> config.status: creating config.h
> config.status: executing depfiles commands
> config.status: executing libtool commands
> === configuring in igor_src (/<<PKGBUILDDIR>>/igor_src)
> configure: WARNING: no configuration information is in igor_src
> dh_auto_build
> make -j8
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> make all-recursive
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> Making all in igor_src
> make[3]: Entering directory '/<<PKGBUILDDIR>>/igor_src'
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Bestscenarioscounter.o `test -f 'Bestscenarioscounter.cpp' || echo './'`Bestscenarioscounter.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-CDR3SeqData.o `test -f 'CDR3SeqData.cpp' || echo './'`CDR3SeqData.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Counter.o `test -f 'Counter.cpp' || echo './'`Counter.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Coverageerrcounter.o `test -f 'Coverageerrcounter.cpp' || echo './'`Coverageerrcounter.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Deletion.o `test -f 'Deletion.cpp' || echo './'`Deletion.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Dinuclmarkov.o `test -f 'Dinuclmarkov.cpp' || echo './'`Dinuclmarkov.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Errorscounter.o `test -f 'Errorscounter.cpp' || echo './'`Errorscounter.cpp
> Deletion.cpp:1590:44: warning: multi-character character constant [-Wmultichar]
> 1590 | else if ((*iter)=='14'){
> | ^~~~
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Errorrate.o `test -f 'Errorrate.cpp' || echo './'`Errorrate.cpp
> Dinuclmarkov.cpp: In member function ‘virtual void Dinucl_markov::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::shared_ptr<Rec_Event*>&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map<Gene_class, std::vector<Alignment_data> >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr<Error_rate>&, std::map<long unsigned int, std::shared_ptr<Counter> >&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)’:
> Dinuclmarkov.cpp:147:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
> 147 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class);
> | ^~~~~~~~~~~
> Dinuclmarkov.cpp:147:95: note: candidate 1: ‘operator+(const char*, long int)’ (built-in)
> In file included from Errorrate.h:29,
> from Rec_Event.h:38,
> from Dinuclmarkov.h:32,
> from Dinuclmarkov.cpp:26:
> Utils.h:68:13: note: candidate 2: ‘std::string operator+(const std::string&, Gene_class)’
> 68 | std::string operator+(const std::string& , Gene_class );
> | ^~~~~~~~
> Deletion.cpp: In member function ‘virtual void Deletion::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::shared_ptr<Rec_Event*>&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map<Gene_class, std::vector<Alignment_data> >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr<Error_rate>&, std::map<long unsigned int, std::shared_ptr<Counter> >&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)’:
> Deletion.cpp:909:98: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
> 909 | throw invalid_argument("Unknown side for D deletion: " + (*this).event_side); //TODO explicitly throw the side used
> | ^~~~~~~~~~
> Deletion.cpp:909:98: note: candidate 1: ‘operator+(const char*, long int)’ (built-in)
> In file included from Errorrate.h:29,
> from Rec_Event.h:38,
> from Deletion.h:29,
> from Deletion.cpp:26:
> Utils.h:69:13: note: candidate 2: ‘std::string operator+(const std::string&, Seq_side)’
> 69 | std::string operator+(const std::string& , Seq_side );
> | ^~~~~~~~
> Deletion.cpp:1173:88: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
> 1173 | throw invalid_argument("Unknown gene for deletions : " + this->event_class);
> | ^~~~~~~~~~~
> Dinuclmarkov.cpp: In member function ‘virtual std::queue<int> Dinucl_markov::draw_random_realization(const Marginal_array_p&, std::unordered_map<std::__cxx11::basic_string<char>, int>&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::unordered_map<Seq_type, std::__cxx11::basic_string<char> >&, std::mt19937_64&) const’:
> Dinuclmarkov.cpp:211:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
> 211 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class);
> | ^~~~~~~~~~~
> Dinuclmarkov.cpp:211:95: note: candidate 1: ‘operator+(const char*, long int)’ (built-in)
> Utils.h:68:13: note: candidate 2: ‘std::string operator+(const std::string&, Gene_class)’
> 68 | std::string operator+(const std::string& , Gene_class );
> | ^~~~~~~~
> Deletion.cpp:1173:88: note: candidate 1: ‘operator+(const char*, long int)’ (built-in)
> Utils.h:68:13: note: candidate 2: ‘std::string operator+(const std::string&, Gene_class)’
> 68 | std::string operator+(const std::string& , Gene_class );
> | ^~~~~~~~
> Dinuclmarkov.cpp: In member function ‘virtual void Dinucl_markov::iterate_initialize_Len_proba(Seq_type, std::map<int, double>&, std::queue<std::shared_ptr<Rec_Event> >&, double&, const Marginal_array_p&, Index_map&, Seq_type_str_p_map&, int&) const’:
> Dinuclmarkov.cpp:565:95: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
> 565 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class);
> | ^~~~~~~~~~~
> Dinuclmarkov.cpp:565:95: note: candidate 1: ‘operator+(const char*, long int)’ (built-in)
> Utils.h:68:13: note: candidate 2: ‘std::string operator+(const std::string&, Gene_class)’
> 68 | std::string operator+(const std::string& , Gene_class );
> | ^~~~~~~~
> Utils.h: In member function ‘Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]’:
> Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type]
> 142 | }
> | ^
> Deletion.cpp: In member function ‘virtual bool Deletion::has_effect_on(Seq_type) const’:
> Deletion.cpp:1705:2: warning: control reaches end of non-void function [-Wreturn-type]
> 1705 | }
> | ^
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-ExtractFeatures.o `test -f 'ExtractFeatures.cpp' || echo './'`ExtractFeatures.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Genechoice.o `test -f 'Genechoice.cpp' || echo './'`Genechoice.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-GenModel.o `test -f 'GenModel.cpp' || echo './'`GenModel.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-HypermutationfullNmererrorrate.o `test -f 'HypermutationfullNmererrorrate.cpp' || echo './'`HypermutationfullNmererrorrate.cpp
> Genechoice.cpp: In member function ‘virtual void Gene_choice::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::shared_ptr<Rec_Event*>&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map<Gene_class, std::vector<Alignment_data> >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr<Error_rate>&, std::map<long unsigned int, std::shared_ptr<Counter> >&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)’:
> Genechoice.cpp:908:94: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
> 908 | throw invalid_argument("Unknown gene_class for GeneChoice: " + this->event_class);
> | ^~~~~~~~~~~
> Genechoice.cpp:908:94: note: candidate 1: ‘operator+(const char*, long int)’ (built-in)
> In file included from Errorrate.h:29,
> from Rec_Event.h:38,
> from Genechoice.h:29,
> from Genechoice.cpp:26:
> Utils.h:68:13: note: candidate 2: ‘std::string operator+(const std::string&, Gene_class)’
> 68 | std::string operator+(const std::string& , Gene_class );
> | ^~~~~~~~
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Hypermutationglobalerrorrate.o `test -f 'Hypermutationglobalerrorrate.cpp' || echo './'`Hypermutationglobalerrorrate.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Insertion.o `test -f 'Insertion.cpp' || echo './'`Insertion.cpp
> In file included from Errorrate.h:29,
> from HypermutationfullNmererrorrate.h:30,
> from HypermutationfullNmererrorrate.cpp:27:
> Utils.h: In member function ‘Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]’:
> Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type]
> 142 | }
> | ^
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-IntStr.o `test -f 'IntStr.cpp' || echo './'`IntStr.cpp
> Insertion.cpp: In member function ‘virtual void Insertion::iterate(double&, Downstream_scenario_proba_bound_map&, const std::string&, const Int_Str&, Index_map&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::shared_ptr<Rec_Event*>&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map<Gene_class, std::vector<Alignment_data> >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr<Error_rate>&, std::map<long unsigned int, std::shared_ptr<Counter> >&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)’:
> Insertion.cpp:244:93: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
> 244 | throw invalid_argument("Unknown gene_class for Insertion: " + this->event_class);
> | ^~~~~~~~~~~
> Insertion.cpp:244:93: note: candidate 1: ‘operator+(const char*, long int)’ (built-in)
> In file included from Errorrate.h:29,
> from Rec_Event.h:38,
> from Insertion.h:30,
> from Insertion.cpp:27:
> Utils.h:68:13: note: candidate 2: ‘std::string operator+(const std::string&, Gene_class)’
> 68 | std::string operator+(const std::string& , Gene_class );
> | ^~~~~~~~
> In file included from Errorrate.h:29,
> from Hypermutationglobalerrorrate.h:30,
> from Hypermutationglobalerrorrate.cpp:27:
> Utils.h: In member function ‘Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]’:
> Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type]
> 142 | }
> | ^
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Model_marginals.o `test -f 'Model_marginals.cpp' || echo './'`Model_marginals.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Model_Parms.o `test -f 'Model_Parms.cpp' || echo './'`Model_Parms.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Pgencounter.o `test -f 'Pgencounter.cpp' || echo './'`Pgencounter.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Rec_Event.o `test -f 'Rec_Event.cpp' || echo './'`Rec_Event.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Singleerrorrate.o `test -f 'Singleerrorrate.cpp' || echo './'`Singleerrorrate.cpp
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Utils.o `test -f 'Utils.cpp' || echo './'`Utils.cpp
> In file included from Errorrate.h:29,
> from Singleerrorrate.h:30,
> from Singleerrorrate.cpp:27:
> Utils.h: In member function ‘Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]’:
> Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type]
> 142 | }
> | ^
> g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-main.o `test -f 'main.cpp' || echo './'`main.cpp
> main.cpp: In function ‘int main(int, char**)’:
> main.cpp:257:31: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 257 | system(&("man igor")[0]);
> | ~~~~~~^~~~~~~~~~~~~~~~~~
> main.cpp:289:32: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 289 | freopen(argv[++carg_i],"a+",stdout);
> | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
> main.cpp:1565:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 1565 | system(&("mkdir " + cl_path )[0]);
> | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
> main.cpp:1716:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 1716 | system(&("mkdir " + cl_path + "run_demo")[0]);
> | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> main.cpp:1750:31: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 1750 | system(&("mkdir " + cl_path + "aligns")[0]);
> | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> main.cpp:2058:31: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 2058 | system(&("mkdir " + cl_path + batchname + "output")[0]);
> | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> main.cpp:2062:39: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 2062 | system(&("mkdir " + cl_path + batchname + "inference")[0]);
> | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> main.cpp:2068:39: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 2068 | system(&("mkdir " + cl_path + batchname + "evaluate")[0]);
> | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> main.cpp:2078:31: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
> 2078 | system(&("mkdir " + cl_path + batchname + "generated")[0]);
> | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> In file included from Errorrate.h:29,
> from Rec_Event.h:38,
> from Deletion.h:29,
> from main.cpp:28:
> Utils.h: In member function ‘Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]’:
> Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type]
> 142 | }
> | ^
> /bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl
> libtool: link: g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl -fopenmp
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/igor_src'
> make[3]: Entering directory '/<<PKGBUILDDIR>>'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_auto_test
> make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> Making check in igor_src
> make[2]: Entering directory '/<<PKGBUILDDIR>>/igor_src'
> make[2]: Nothing to be done for 'check'.
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/igor_src'
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> create-stamp debian/debhelper-build-stamp
> dh_prep
> dh_installdirs
> dh_auto_install --destdir=debian/igor/
> make -j1 install DESTDIR=/<<BUILDDIR>>/igor-1.4.0\+dfsg/debian/igor AM_UPDATE_INFO_DIR=no
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> Making install in igor_src
> make[2]: Entering directory '/<<PKGBUILDDIR>>/igor_src'
> make[3]: Entering directory '/<<PKGBUILDDIR>>/igor_src'
> /bin/mkdir -p '/<<PKGBUILDDIR>>/debian/igor/usr/bin'
> /bin/bash ../libtool --mode=install /usr/bin/install -c igor '/<<PKGBUILDDIR>>/debian/igor/usr/bin'
> libtool: install: /usr/bin/install -c igor /<<PKGBUILDDIR>>/debian/igor/usr/bin/igor
> make[3]: Nothing to be done for 'install-data-am'.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/igor_src'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/igor_src'
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> make[3]: Entering directory '/<<PKGBUILDDIR>>'
> /bin/mkdir -p '/<<PKGBUILDDIR>>/debian/igor/usr/bin'
> /usr/bin/install -c scripts/igor-compute_pgen '/<<PKGBUILDDIR>>/debian/igor/usr/bin'
> mkdir -p /<<PKGBUILDDIR>>/debian/igor/usr/share/igor/models
> cp -r models/* /<<PKGBUILDDIR>>/debian/igor/usr/share/igor/models
> /bin/mkdir -p '/<<PKGBUILDDIR>>/debian/igor/usr/share/igor/demo'
> /usr/bin/install -c -m 644 demo/genomicVs_with_primers.fasta demo/genomicDs.fasta demo/genomicJs_all_curated.fasta demo/murugan_naive1_noncoding_demo_seqs.txt '/<<PKGBUILDDIR>>/debian/igor/usr/share/igor/demo'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_installdocs
> dh_installchangelogs
> dh_installexamples
> debian/rules override_dh_installman
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> mv debian/igor1 debian/igor.1
> mv: cannot stat 'debian/igor1': No such file or directory
> make[1]: *** [debian/rules:35: override_dh_installman] Error 1
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> make: *** [debian/rules:18: binary] Error 2
> dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
>
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -b' failed to run.
The full build log is available from:
http://qa-logs.debian.net/2023/08/16/igor_1.4.0+dfsg-4_unstable.log
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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