Source: igor Version: 1.4.0+dfsg-4 Severity: minor Tags: trixie sid ftbfs User: [email protected] Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build User: [email protected] 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 <[email protected]> > 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 âvirtual 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&)â: > 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: âoperator+(const char*, long > int)â (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: âstd::string operator+(const > std::string&, Gene_class)â > 68 | std::string operator+(const std::string& , Gene_class ); > | ^~~~~~~~ > Deletion.cpp: In member function âvirtual 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&)â: > 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: âoperator+(const char*, long > int)â (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: âstd::string operator+(const > std::string&, Seq_side)â > 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 âvirtual 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&) constâ: > 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: âoperator+(const char*, long > int)â (built-in) > Utils.h:68:13: note: candidate 2: âstd::string operator+(const > std::string&, Gene_class)â > 68 | std::string operator+(const std::string& , Gene_class ); > | ^~~~~~~~ > Deletion.cpp:1173:88: note: candidate 1: âoperator+(const char*, long > int)â (built-in) > Utils.h:68:13: note: candidate 2: âstd::string operator+(const > std::string&, Gene_class)â > 68 | std::string operator+(const std::string& , Gene_class ); > | ^~~~~~~~ > Dinuclmarkov.cpp: In member function âvirtual 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&) constâ: > 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: âoperator+(const char*, long > int)â (built-in) > Utils.h:68:13: note: candidate 2: âstd::string operator+(const > std::string&, Gene_class)â > 68 | std::string operator+(const std::string& , Gene_class ); > | ^~~~~~~~ > Utils.h: In member function âMatrix<T>& Matrix<T>::operator=(const > Matrix<T>&) [with T = double]â: > Utils.h:142:9: warning: control reaches end of non-void function > [-Wreturn-type] > 142 | } > | ^ > Deletion.cpp: In member function âvirtual bool > Deletion::has_effect_on(Seq_type) constâ: > 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 âvirtual 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&)â: > 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: âoperator+(const char*, long > int)â (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: âstd::string operator+(const > std::string&, Gene_class)â > 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 âMatrix<T>& Matrix<T>::operator=(const > Matrix<T>&) [with T = double]â: > 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 âvirtual 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&)â: > 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: âoperator+(const char*, long > int)â (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: âstd::string operator+(const > std::string&, Gene_class)â > 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 âMatrix<T>& Matrix<T>::operator=(const > Matrix<T>&) [with T = double]â: > 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 âMatrix<T>& Matrix<T>::operator=(const > Matrix<T>&) [with T = double]â: > 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 âint main(int, char**)â: > main.cpp:257:31: warning: ignoring return value of âint system(const > char*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 257 | system(&("man igor")[0]); > | ~~~~~~^~~~~~~~~~~~~~~~~~ > main.cpp:289:32: warning: ignoring return value of âFILE* freopen(const > char*, const char*, FILE*)â declared with attribute > âwarn_unused_resultâ [-Wunused-result] > 289 | freopen(argv[++carg_i],"a+",stdout); > | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ > main.cpp:1565:23: warning: ignoring return value of âint system(const > char*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1565 | system(&("mkdir " + cl_path )[0]); > | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ > main.cpp:1716:23: warning: ignoring return value of âint system(const > char*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1716 | system(&("mkdir " + cl_path + "run_demo")[0]); > | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > main.cpp:1750:31: warning: ignoring return value of âint system(const > char*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 1750 | system(&("mkdir " + cl_path + "aligns")[0]); > | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > main.cpp:2058:31: warning: ignoring return value of âint system(const > char*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 2058 | system(&("mkdir " + cl_path + batchname + > "output")[0]); > | > ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > main.cpp:2062:39: warning: ignoring return value of âint system(const > char*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 2062 | system(&("mkdir " + cl_path + > batchname + "inference")[0]); > | > ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > main.cpp:2068:39: warning: ignoring return value of âint system(const > char*)â declared with attribute âwarn_unused_resultâ [-Wunused-result] > 2068 | system(&("mkdir " + cl_path + > batchname + "evaluate")[0]); > | > ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > main.cpp:2078:31: warning: ignoring return value of âint system(const > char*)â declared with attribute âwarn_unused_resultâ [-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 âMatrix<T>& Matrix<T>::operator=(const > Matrix<T>&) [with T = double]â: > 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.
