Package: src:vienna-rna Version: 2.6.4+dfsg-1 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:vienna-rna, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_clean rm -f doc/RNAlib* rm -f doc/*.db rm -f interfaces/Perl/Makefile.perl.old rm -f interfaces/Python/install.record rm -rf doc/html rm -rf doc/latex rm -rf src/cthreadpool #find . \( -type f -a \( -name config.status -o -name config.sub -o -name config.guess \) \) -delete find src/ViennaRNA -name "*.hex" -delete [... snipped ...] checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking xargs -n works... yes checking dependency style of gcc... none checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu 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 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 how to run the C preprocessor... gcc -E checking whether g++ supports C++11 features by default... yes checking for strchr... yes checking for strdup... yes checking for strtol... yes checking for limits.h... yes checking for _Bool... yes checking for stdbool.h that conforms to C99 or later... yes checking for inline... inline checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for working strtod... yes checking for size_t... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for RNAlib2... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands configure: ====================================== ViennaRNA Package 2.6.4 ====================================== Successfully configured with the following options: Sub Packages ------------ * Kinfold : yes * RNAforester : no * Analyse{Dists,Seqs} : yes * RNAlocmin : yes * Kinwalker : no * RNAxplorer : no (missing fortran compiler) Extra Libraries --------------- * Support Vector Machine : no * GNU Scientific Library : yes * GNU MPFR : yes Features -------- * Use hash for NR Sampling : no * C11 features : yes * TTY colors : yes * Float Precision(PF} : no * Deprecation Warnings : no Optimizations ------------- * Auto Vectorization : yes * Explicit SIMD Extension : yes * Link Time Optimization : no * POSIX Threads : yes * OpenMP : yes Scripting Language Interfaces ----------------------------- * Perl 5 : yes * Python 3.x : yes * Python 2.x : no Documentation ------------- * Reference Manual (PDF) : no (no sphinx-build, LaTeX packages missing) * Reference Manual (HTML) : no (no sphinx-build) * Tutorial (PDF) : no * Tutorial (HTML) : no * CLA (PDF) : yes Unit Tests ---------- * Executable Programs : yes * C-Library : no * Perl 5 Interface : yes * Python 3.x Interface : yes * Python 2.x Interface : no MacOS X ------- * Universal Binary : no * Installer : no * SDK : no Install Directories ------------------- * Executables : /usr/bin * Libraries : /usr/lib/x86_64-linux-gnu * Header files : /usr/include * Extra Data : /usr/share * Man pages : /usr/share/man * Documentation : /usr/share/doc/ViennaRNA (HTML) : (PDF) : * Perl5 Interface : (binaries) : /usr/lib/x86_64-linux-gnu/perl/5.40.1 (scripts) : /usr/share/perl/5.40.1 * Python 3.x Interface : (binaries) : /usr/local/lib/python3.13/dist-packages (scripts) : /usr/local/lib/python3.13/dist-packages * Python 2.x Interface : Not to be installed (binaries) : (scripts) : You can run 'make', 'make check', and 'make install' now! if [ -r man/help2manWrapper.sh ] \ ; then chmod +x man/help2manWrapper.sh \ ; fi make[1]: Leaving directory '/<<PKGBUILDDIR>>' debian/rules override_dh_auto_build make[1]: Entering directory '/<<PKGBUILDDIR>>' if [ ! -d src/cthreadpool ]; then \ mkdir -p src/cthreadpool && \ cd src/cthreadpool && \ ln -s /usr/include/cthreadpool/thpool.h . && \ ln -s /usr/share/cthreadpool/thpool.c . ; \ fi # Using --no-parallel to avoid some problems with missing files during the build dh_auto_build --no-parallel make -j1 make[2]: Entering directory '/<<PKGBUILDDIR>>' make all-recursive make[3]: Entering directory '/<<PKGBUILDDIR>>' Making all in src make[4]: Entering directory '/<<PKGBUILDDIR>>/src' Making all in ViennaRNA make[5]: Entering directory '/<<PKGBUILDDIR>>/src/ViennaRNA' Making all in static make[6]: Entering directory '/<<PKGBUILDDIR>>/src/ViennaRNA/static' /usr/bin/xxd -i < postscript/structure_plot_macro_base.ps > postscript/structure_plot_macro_base.hex && echo ',0x00' >> postscript/structure_plot_macro_base.hex /usr/bin/xxd -i < postscript/structure_plot_macro_extras.ps > postscript/structure_plot_macro_extras.hex && echo ',0x00' >> postscript/structure_plot_macro_extras.hex /usr/bin/xxd -i < postscript/dot_plot_macro_base.ps > postscript/dot_plot_macro_base.hex && echo ',0x00' >> postscript/dot_plot_macro_base.hex /usr/bin/xxd -i < postscript/dot_plot_macro_turn.ps > postscript/dot_plot_macro_turn.hex && echo ',0x00' >> postscript/dot_plot_macro_turn.hex /usr/bin/xxd -i < postscript/dot_plot_macro_sd.ps > postscript/dot_plot_macro_sd.hex && echo ',0x00' >> postscript/dot_plot_macro_sd.hex /usr/bin/xxd -i < postscript/dot_plot_macro_ud.ps > postscript/dot_plot_macro_ud.hex && echo ',0x00' >> postscript/dot_plot_macro_ud.hex /usr/bin/xxd -i < postscript/dot_plot_macro_sc_motifs.ps > postscript/dot_plot_macro_sc_motifs.hex && echo ',0x00' >> postscript/dot_plot_macro_sc_motifs.hex /usr/bin/xxd -i < postscript/dot_plot_macro_linear_data.ps > postscript/dot_plot_macro_linear_data.hex && echo ',0x00' >> postscript/dot_plot_macro_linear_data.hex /usr/bin/xxd -i < postscript/aln_macro_base.ps > postscript/aln_macro_base.hex && echo ',0x00' >> postscript/aln_macro_base.hex /usr/bin/xxd -i < svg/structure_plot_header.svg > svg/structure_plot_header.hex && echo ',0x00' >> svg/structure_plot_header.hex /usr/bin/xxd -i < svg/structure_plot_footer.svg > svg/structure_plot_footer.hex && echo ',0x00' >> svg/structure_plot_footer.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/dna_mathews1999.par > misc/dna_mathews1999.hex && echo ',0x00' >> misc/dna_mathews1999.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/dna_mathews2004.par > misc/dna_mathews2004.hex && echo ',0x00' >> misc/dna_mathews2004.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_andronescu2007.par > misc/rna_andronescu2007.hex && echo ',0x00' >> misc/rna_andronescu2007.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_langdon2018.par > misc/rna_langdon2018.hex && echo ',0x00' >> misc/rna_langdon2018.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_misc_special_hairpins.par > misc/rna_misc_special_hairpins.hex && echo ',0x00' >> misc/rna_misc_special_hairpins.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_turner1999.par > misc/rna_turner1999.hex && echo ',0x00' >> misc/rna_turner1999.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_turner2004.par > misc/rna_turner2004.hex && echo ',0x00' >> misc/rna_turner2004.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_mod_7DA_parameters.json > misc/rna_mod_7DA_parameters.hex && echo ',0x00' >> misc/rna_mod_7DA_parameters.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_mod_inosine_parameters.json > misc/rna_mod_inosine_parameters.hex && echo ',0x00' >> misc/rna_mod_inosine_parameters.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_mod_m6A_parameters.json > misc/rna_mod_m6A_parameters.hex && echo ',0x00' >> misc/rna_mod_m6A_parameters.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_mod_pseudouridine_parameters.json > misc/rna_mod_pseudouridine_parameters.hex && echo ',0x00' >> misc/rna_mod_pseudouridine_parameters.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_mod_purine_parameters.json > misc/rna_mod_purine_parameters.hex && echo ',0x00' >> misc/rna_mod_purine_parameters.hex /usr/bin/mkdir -p misc && /usr/bin/xxd -i < ../../../misc/rna_mod_dihydrouridine_parameters.json > misc/rna_mod_dihydrouridine_parameters.hex && echo ',0x00' >> misc/rna_mod_dihydrouridine_parameters.hex make all-am make[7]: Entering directory '/<<PKGBUILDDIR>>/src/ViennaRNA/static' make[7]: Nothing to be done for 'all-am'. make[7]: Leaving directory '/<<PKGBUILDDIR>>/src/ViennaRNA/static' make[6]: Leaving directory '/<<PKGBUILDDIR>>/src/ViennaRNA/static' Making all in plotting/naview make[6]: Entering directory '/<<PKGBUILDDIR>>/src/ViennaRNA/plotting/naview' /bin/bash ../../../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../../../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o naview.lo naview.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c naview.c -fPIC -DPIC -o .libs/naview.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../../../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../../../src -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c naview.c -fPIC -DPIC -o naview.o >/dev/null 2>&1 /bin/bash ../../../../libtool --tag=CC --mode=link gcc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -fno-strict-aliasing -lpthread -Wl,-z,relro -o libRNA_naview.la naview.lo -lgsl -lgslcblas -lm libtool: link: ar cr .libs/libRNA_naview.a .libs/naview.o libtool: link: ranlib .libs/libRNA_naview.a libtool: link: ( cd ".libs" && rm -f "libRNA_naview.la" && ln -s "../libRNA_naview.la" "libRNA_naview.la" ) make[6]: Leaving directory '/<<PKGBUILDDIR>>/src/ViennaRNA/plotting/naview' make[6]: Entering directory '/<<PKGBUILDDIR>>/src/ViennaRNA' /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o fold_compound.lo fold_compound.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c fold_compound.c -fPIC -DPIC -o .libs/fold_compound.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c fold_compound.c -fPIC -DPIC -o fold_compound.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o dist_vars.lo dist_vars.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c dist_vars.c -fPIC -DPIC -o .libs/dist_vars.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c dist_vars.c -fPIC -DPIC -o dist_vars.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o part_func.lo part_func.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c part_func.c -fPIC -DPIC -o .libs/part_func.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c part_func.c -fPIC -DPIC -o part_func.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o part_func_wrappers.lo part_func_wrappers.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c part_func_wrappers.c -fPIC -DPIC -o .libs/part_func_wrappers.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c part_func_wrappers.c -fPIC -DPIC -o part_func_wrappers.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o pf_fold.lo pf_fold.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c pf_fold.c -fPIC -DPIC -o .libs/pf_fold.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c pf_fold.c -fPIC -DPIC -o pf_fold.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o pf_multifold.lo pf_multifold.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c pf_multifold.c -fPIC -DPIC -o .libs/pf_multifold.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c pf_multifold.c -fPIC -DPIC -o pf_multifold.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o treedist.lo treedist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c treedist.c -fPIC -DPIC -o .libs/treedist.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c treedist.c -fPIC -DPIC -o treedist.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o inverse.lo inverse.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c inverse.c -fPIC -DPIC -o .libs/inverse.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c inverse.c -fPIC -DPIC -o inverse.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o ProfileDist.lo ProfileDist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ProfileDist.c -fPIC -DPIC -o .libs/ProfileDist.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c ProfileDist.c -fPIC -DPIC -o ProfileDist.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o RNAstruct.lo RNAstruct.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c RNAstruct.c -fPIC -DPIC -o .libs/RNAstruct.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c RNAstruct.c -fPIC -DPIC -o RNAstruct.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o mfe.lo mfe.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe.c -fPIC -DPIC -o .libs/mfe.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe.c -fPIC -DPIC -o mfe.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o mfe_window.lo mfe_window.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe_window.c -fPIC -DPIC -o .libs/mfe_window.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe_window.c -fPIC -DPIC -o mfe_window.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o mfe_wrappers.lo mfe_wrappers.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe_wrappers.c -fPIC -DPIC -o .libs/mfe_wrappers.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe_wrappers.c -fPIC -DPIC -o mfe_wrappers.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o mfe_window_wrappers.lo mfe_window_wrappers.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe_window_wrappers.c -fPIC -DPIC -o .libs/mfe_window_wrappers.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c mfe_window_wrappers.c -fPIC -DPIC -o mfe_window_wrappers.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o fold.lo fold.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c fold.c -fPIC -DPIC -o .libs/fold.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c fold.c -fPIC -DPIC -o fold.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o stringdist.lo stringdist.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c stringdist.c -fPIC -DPIC -o .libs/stringdist.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c stringdist.c -fPIC -DPIC -o stringdist.o >/dev/null 2>&1 /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c -o subopt.lo subopt.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -I../../src -I../../src/json -Wdate-time -D_FORTIFY_SOURCE=2 -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -I/usr/include/json-c/ -I/usr/include/libsvm/ -c subopt.c -fPIC -DPIC -o .libs/subopt.o subopt.c: In function 'vrna_subopt_cb': subopt.c:618:28: error: passing argument 2 of 'lst_kill' from incompatible pointer type [-Wincompatible-pointer-types] 618 | lst_kill(env->Stack, free_state_node); | ^~~~~~~~~~~~~~~ | | | void (*)(STATE *) In file included from subopt.c:34: ../../src/ViennaRNA/datastructures/lists.h:58:33: note: expected 'void (*)(void)' but argument is of type 'void (*)(STATE *)' 58 | void lst_kill (LIST * l, void (*freeNode) ()); | ~~~~~~~^~~~~~~~~~~~ subopt.c:330:1: note: 'free_state_node' declared here 330 | free_state_node(STATE *node); | ^~~~~~~~~~~~~~~ subopt.c: In function 'free_state_node': subopt.c:795:31: error: passing argument 2 of 'lst_kill' from incompatible pointer type [-Wincompatible-pointer-types] 795 | lst_kill(node->Intervals, lst_freenode); | ^~~~~~~~~~~~ | | | void (*)(void *) ../../src/ViennaRNA/datastructures/lists.h:58:33: note: expected 'void (*)(void)' but argument is of type 'void (*)(void *)' 58 | void lst_kill (LIST * l, void (*freeNode) ()); | ~~~~~~~^~~~~~~~~~~~ ../../src/ViennaRNA/datastructures/lists.h:56:6: note: 'lst_freenode' declared here 56 | void lst_freenode (/*@only@*/ void *node); | ^~~~~~~~~~~~ make[6]: *** [Makefile:1784: subopt.lo] Error 1 make[6]: Leaving directory '/<<PKGBUILDDIR>>/src/ViennaRNA' make[5]: *** [Makefile:2140: all-recursive] Error 1 make[5]: Leaving directory '/<<PKGBUILDDIR>>/src/ViennaRNA' make[4]: *** [Makefile:571: all-recursive] Error 1 make[4]: Leaving directory '/<<PKGBUILDDIR>>/src' make[3]: *** [Makefile:751: all-recursive] Error 1 make[3]: Leaving directory '/<<PKGBUILDDIR>>' make[2]: *** [Makefile:632: all] Error 2 make[2]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_build: error: make -j1 returned exit code 2 make[1]: *** [debian/rules:25: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:5: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 --------------------------------------------------------------------------------
