[Debian-med-packaging] Bug#957793: sigma-align: ftbfs with GCC-10

[Matthias Klose]

Package: src:sigma-align
Version: 1.1.3-6
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/sigma-align_1.1.3-6_unstable_gcc10.log
The last lines of the build log are at the end of this report.

To build with GCC 10, either set CC=gcc-10 CXX=g++-10 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-10/porting_to.html

[...]
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking glib.h usability... yes
checking glib.h presence... yes
checking for glib.h... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for gettimeofday... yes
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 config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
   dh_auto_build
	make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make  all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parseopts.o parseopts.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o readfasta.o readfasta.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getbgprobs.o getbgprobs.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o setbgprobs.o setbgprobs.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o initseqfrags.o initseqfrags.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o commonroutines.o commonroutines.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o setbgw.o setbgw.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o printhelp.o printhelp.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o blockseq.o blockseq.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble_frags_to_seqs.o assemble_frags_to_seqs.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o print_routines.o print_routines.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o getopt_long.o getopt_long.c
getopt_long.c: In function ‘getopt_internal’:
getopt_long.c:295:4: warning: implicit declaration of function ‘warnx’ [-Wimplicit-function-declaration]
  295 |    warnx(illoptchar, optchar);
      |    ^~~~~
gcc -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -DDEBUG -O2 -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -o sigma main.o parseopts.o readfasta.o getbgprobs.o setbgprobs.o initseqfrags.o commonroutines.o setbgw.o printhelp.o blockseq.o assemble_frags_to_seqs.o print_routines.o getopt_long.o -lglib-2.0 -lm 
/usr/bin/ld: parseopts.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here
/usr/bin/ld: getbgprobs.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here
/usr/bin/ld: setbgprobs.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here
/usr/bin/ld: initseqfrags.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here
/usr/bin/ld: commonroutines.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here
/usr/bin/ld: setbgw.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here
/usr/bin/ld: blockseq.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here
/usr/bin/ld: assemble_frags_to_seqs.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here
/usr/bin/ld: print_routines.o:./src/sigma.h:48: multiple definition of `swmat'; main.o:./src/sigma.h:48: first defined here
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:359: sigma] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: *** [Makefile:435: all-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:333: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 returned exit code 2
make: *** [debian/rules:4: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2