[Debichem-devel] Bug#1114110: freesasa: FTBFS: cif.cc:294:51: error: 'const __gnu_cxx::__alloc_traits<std::allocator<gemmi::Model>, gemmi::Model>::value_type' {aka 'const struct gemmi::Model'} has no member named 'name'
Santiago Vila
sanvila at debian.org
Fri Sep 5 19:17:10 BST 2025
Package: src:freesasa
Version: 2.1.2-4
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:freesasa, so that this is still
visible in the BTS web page for this package.
Thanks.
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[...]
debian/rules clean
dh clean
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
configure.ac:42: warning: The macro 'AC_PROG_CC_C99' is obsolete.
configure.ac:42: You should run autoupdate.
./lib/autoconf/c.m4:1662: AC_PROG_CC_C99 is expanded from...
configure.ac:42: the top level
configure.ac:123: warning: AC_PROG_LEX without either yywrap or noyywrap is obsolete
./lib/autoconf/programs.m4:743: _AC_PROG_LEX is expanded from...
./lib/autoconf/programs.m4:736: AC_PROG_LEX is expanded from...
configure.ac:123: the top level
configure.ac:16: installing './compile'
configure.ac:46: installing './config.guess'
configure.ac:46: installing './config.sub'
configure.ac:6: installing './install-sh'
configure.ac:6: installing './missing'
src/Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
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 sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/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 xargs -n works... yes
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 whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
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 for ranlib... ranlib
checking for sqrt in -lm... yes
checking for dlsym in -ldl... yes
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 size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for inttypes.h... (cached) yes
checking for libintl.h... yes
checking for malloc.h... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for dlfcn.h... yes
checking for inline... inline
checking for size_t... (cached) yes
checking for C/C++ restrict keyword... __restrict__
checking for int16_t... yes
checking for int32_t... yes
checking for int8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for uint8_t... yes
checking for inline... (cached) inline
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for GNU libc compatible malloc... yes
checking for GNU libc compatible realloc... yes
checking for memset... yes
checking for mkdir... yes
checking for sqrt... yes
checking for strchr... yes
checking for strdup... yes
checking for strerror... yes
checking for strncasecmp... yes
checking for getopt_long... yes
checking for getline... yes
checking whether g++ supports C++14 features with -std=gnu++14... yes
checking for pthread_create in -lpthread... yes
checking for pthread.h... yes
checking for xmllint... no
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for libxml-2.0... yes
checking for json_object_get in -ljson-c... yes
checking for json-c/json_object.h... yes
checking for jsonlint... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating doc/Makefile
config.status: creating doc/Doxyfile
config.status: creating doc/man/freesasa.1
config.status: creating tests/Makefile
config.status: creating share/Makefile
config.status: creating tests/test-cli
config.status: creating config.h
config.status: executing depfiles commands
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- freesasa_LDADD='libfreesasa.a ${libdir}/libgemmi_cpp.a -lz -ljson-c -lxml2'
make -j2 "freesasa_LDADD=libfreesasa.a \${libdir}/libgemmi_cpp.a -lz -ljson-c -lxml2"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[3]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[4]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o main.o main.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o cif.o cif.cc
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -c -o classifier.o classifier.c
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -c -o classifier_protor.o classifier_protor.c
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -c -o classifier_oons.o classifier_oons.c
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -c -o classifier_naccess.o classifier_naccess.c
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -c -o coord.o coord.c
cif.cc: In function ‘std::vector<freesasa_structure*> freesasa_cif_structure_array(FILE*, int*, const freesasa_classifier*, int)’:
cif.cc:294:51: error: ‘const __gnu_cxx::__alloc_traits<std::allocator<gemmi::Model>, gemmi::Model>::value_type’ {aka ‘const struct gemmi::Model’} has no member named ‘name’
294 | __func__, models[i].name.c_str());
| ^~~~
cif.cc:300:85: error: ‘const __gnu_cxx::__alloc_traits<std::allocator<gemmi::Model>, gemmi::Model>::value_type’ {aka ‘const struct gemmi::Model’} has no member named ‘name’
300 | freesasa_structure *structure = structure_from_chain(doc, models[i].name, chain_name, classifier, options);
| ^~~~
cif.cc:321:53: error: ‘const __gnu_cxx::__alloc_traits<std::allocator<gemmi::Model>, gemmi::Model>::value_type’ {aka ‘const struct gemmi::Model’} has no member named ‘name’
321 | structure_from_model(doc, models[i].name, classifier, options));
| ^~~~
cif.cc: In function ‘int reset_freesasa_tables(gemmi::cif::Block&)’:
cif.cc:715:23: error: ‘struct gemmi::cif::Table’ has no member named ‘convert_pair_to_loop’
715 | table.convert_pair_to_loop();
| ^~~~~~~~~~~~~~~~~~~~
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -c -o pdb.o pdb.c
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -c -o log.o log.c
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -c -o sasa_lr.o sasa_lr.c
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -c -o sasa_sr.o sasa_sr.c
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -c -o structure.o structure.c
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -c -o node.o node.c
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -c -o freesasa.o freesasa.c
gcc -DHAVE_CONFIG_H -I. -I.. -I../third-party/gemmi/include/ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/libxml2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fPIC -c -o nb.o nb.c
make[4]: *** [Makefile:582: cif.o] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: *** [Makefile:397: all-recursive] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: *** [Makefile:336: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j2 "freesasa_LDADD=libfreesasa.a \${libdir}/libgemmi_cpp.a -lz -ljson-c -lxml2" returned exit code 2
make[1]: *** [debian/rules:11: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:7: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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