Package: src:disulfinder Version: 1.2.11-12 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, your package failed to build. Below you will find how the build ends (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202509/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you could not reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:disulfinder, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean dh_auto_clean make -j2 distclean make[1]: Entering directory '/<<PKGBUILDDIR>>' if [ -e "disulfind/src/Makefile" ]; then make -C disulfind/src clean; fi make[2]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src' make -C NN clean make -C Common clean make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/NN' rm -f *~ *.o brnn-train brnn-test make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/Common' make -C eig clean make[4]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/Common/eig' rm *.o libeig.a *~ -f make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/NN' make -C SVM clean make[4]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/Common/eig' make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f rm *.o libCommon.a Eig Norm *~ -f make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/SVM' make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/Common' cd SVM && make clean make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/SVM' rm *~ *.o *.a *.exe SVMClassifier -f make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/SVM' cd Input && make clean make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/Input' rm *.o makeWindow makeSparseVector globalDescriptor createKernelDataset createBRNNDataset buildXfolds *~ -f make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/Input' cd Output && make clean make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/Output' rm *.o makeASCIIOutput makeHTMLOutput *~ -f make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/Output' cd FSA-Alignment && make clean make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/FSA-Alignment' rm *.o fold_automata viterbi_aligner timed_transitions *~ -f make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/FSA-Alignment' cd BRNN && make clean make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src/BRNN' rm -f *.o core rm -f ./RNNs/*.o ./RNNs/core disulfind-conn make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src/BRNN' rm disulfinder disultrainer *.o *~ -f make[2]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src' rm -f *.[12345678] *.[12345678].gz #if [ -d "disulfind" ]; then rm -rf disulfind; fi if [ -d "disulfinder-1.2.11" ]; then rm -rf "disulfinder-1.2.11"; fi rm -rf patch-stamp \ initial-clean-stamp \ "disulfinder-1.2.11.tar.gz" \ .pc make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/disulfinder.substvars debian/disulfinder-data.substvars debian/files rm -fr -- debian/disulfinder/ debian/tmp/ debian/disulfinder-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_build --no-parallel make -j1 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<<PKGBUILDDIR>>' make -C disulfind/src disulfinder make[3]: Entering directory '/<<PKGBUILDDIR>>/disulfind/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/GlobalDescriptor.cpp -o Input/GlobalDescriptor.o In file included from Input/utils.h:2, from Input/GlobalDescriptor.cpp:3: Input/Protein.h:19:20: warning: âaa_three_codesâ defined but not used [-Wunused-variable] 19 | static const char *aa_three_codes[23] = { | ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: âtdb_aa_codesâ defined but not used [-Wunused-variable] 17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files | ^~~~~~~~~~~~ Input/Protein.h:16:20: warning: âaa_codesâ defined but not used [-Wunused-variable] 16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createBRNNDataset.cpp -o Input/createBRNNDataset.o In file included from Input/utils.h:2, from Input/createBRNNDataset.h:1, from Input/createBRNNDataset.cpp:2: Input/Protein.h:19:20: warning: âaa_three_codesâ defined but not used [-Wunused-variable] 19 | static const char *aa_three_codes[23] = { | ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: âtdb_aa_codesâ defined but not used [-Wunused-variable] 17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files | ^~~~~~~~~~~~ Input/Protein.h:16:20: warning: âaa_codesâ defined but not used [-Wunused-variable] 16 | static const char *aa_codes = "VLIMFWYGAPSTCHRKQENDBZX"; // as ordered in profile files | ^~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/createKernelDataset.cpp -o Input/createKernelDataset.o In file included from Input/utils.h:2, from Input/createKernelDataset.h:1, from Input/createKernelDataset.cpp:2: Input/Protein.h:19:20: warning: âaa_three_codesâ defined but not used [-Wunused-variable] 19 | static const char *aa_three_codes[23] = { | ^~~~~~~~~~~~~~ Input/Protein.h:17:20: warning: âtdb_aa_codesâ defined but not used [-Wunused-variable] 17 | static const char *tdb_aa_codes = "ARNDCQEGHILKMFPSTWYVBZX"; // as ordered in tdb profile files | ^~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeWindow.cpp -o Input/makeWindow.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/makeSparseVector.cpp -o Input/makeSparseVector.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/Protein.cpp -o Input/Protein.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Input/buildXfolds.cpp -o Input/buildXfolds.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c SVM/SVMClassifier.cpp -o SVM/SVMClassifier.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/makeHTMLOutput.cpp -o Output/makeHTMLOutput.o Output/makeHTMLOutput.cpp: In function âvoid makeHTMLOutput(std::string, const char*, int, std::string, std::ostream&)â: Output/makeHTMLOutput.cpp:162:24: warning: ISO C++ forbids converting a string constant to âchar*â [-Wwrite-strings] 162 | char * altname[2] = {"Second","Third"}; | ^~~~~~~~ Output/makeHTMLOutput.cpp:162:33: warning: ISO C++ forbids converting a string constant to âchar*â [-Wwrite-strings] 162 | char * altname[2] = {"Second","Third"}; | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/utils.cpp -o Output/utils.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c Output/makeASCIIOutput.cpp -o Output/makeASCIIOutput.o Output/makeASCIIOutput.cpp: In function âvoid makeASCIIOutput(std::string, const char*, int, std::string, std::ostream&)â: Output/makeASCIIOutput.cpp:144:24: warning: ISO C++ forbids converting a string constant to âchar*â [-Wwrite-strings] 144 | char * altname[2] = {"SECOND","THIRD"}; | ^~~~~~~~ Output/makeASCIIOutput.cpp:144:33: warning: ISO C++ forbids converting a string constant to âchar*â [-Wwrite-strings] 144 | char * altname[2] = {"SECOND","THIRD"}; | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++14 -DDEFAULT_PKGDATADIR=\"/usr/share/disulfinder\" -O3 -Wall -Wno-deprecated -IBRNN/RNNs -c FSA-Alignment/fsa.cpp -o FSA-Alignment/fsa.o In file included from FSA-Alignment/../Common/Matrix.h:13, from FSA-Alignment/../Common/CommonMethods.h:15, from FSA-Alignment/fsa.cpp:2: /usr/include/f2c.h:135:9: error: reference to âcomplexâ is ambiguous 135 | complex c; | ^~~~~~~ In file included from /usr/include/c++/15/bits/stl_algobase.h:64, from /usr/include/c++/15/vector:64, from FSA-Alignment/fsa.h:3, from FSA-Alignment/fsa.cpp:1: /usr/include/c++/15/bits/stl_pair.h:105:11: note: candidates are: âtemplate<class _Tp> class std::complexâ 105 | class complex; | ^~~~~~~ /usr/include/f2c.h:17:31: note: âtypedef struct complex complexâ 17 | typedef struct { real r, i; } complex; | ^~~~~~~ make[3]: *** [Makefile:48: FSA-Alignment/fsa.o] Error 1 make[3]: Leaving directory '/<<PKGBUILDDIR>>/disulfind/src' make[2]: *** [Makefile:24: disulfinder] Error 2 make[2]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true" returned exit code 2 make[1]: *** [debian/rules:17: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:14: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 --------------------------------------------------------------------------------
