[Debian-med-packaging] Bug#957564: mrbayes: ftbfs with GCC-10

[Matthias Klose]

Package: src:mrbayes
Version: 3.2.6+dfsg-2
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/mrbayes_3.2.6+dfsg-2_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

[...]
      |                             ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
                 from bayes.h:10,
                 from sumpt.c:37:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 15 and 144 bytes into a destination of size 120
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sumpt.c:7161:32: warning: ‘.tree’ directive writing 5 bytes into a region of size between 1 and 120 [-Wformat-overflow=]
 7161 |         sprintf (tFilename, "%s.tree%d.trprobs", sumtParams.sumtOutfile, treeNo+1);
      |                                ^~~~~
sumpt.c:7161:29: note: directive argument in the range [-2147483647, 2147483647]
 7161 |         sprintf (tFilename, "%s.tree%d.trprobs", sumtParams.sumtOutfile, treeNo+1);
      |                             ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
                 from bayes.h:10,
                 from sumpt.c:37:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 15 and 144 bytes into a destination of size 120
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sumpt.c: In function ‘PrintBrlensToFile’:
sumpt.c:7257:29: warning: ‘%s’ directive writing up to 119 bytes into a region of size 100 [-Wformat-overflow=]
 7257 |         sprintf (filename, "%s.brlens", sumtParams.sumtOutfile);
      |                             ^~          ~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
                 from bayes.h:10,
                 from sumpt.c:37:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 8 and 127 bytes into a destination of size 100
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sumpt.c:7255:29: warning: ‘%s’ directive writing up to 119 bytes into a region of size 100 [-Wformat-overflow=]
 7255 |         sprintf (filename, "%s.tree%d.brlens", sumtParams.sumtOutfile, treeNo+1);
      |                             ^~                 ~~~~~~~~~~~~~~~~~~~~~~
sumpt.c:7255:28: note: directive argument in the range [-2147483647, 2147483647]
 7255 |         sprintf (filename, "%s.tree%d.brlens", sumtParams.sumtOutfile, treeNo+1);
      |                            ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
                 from bayes.h:10,
                 from sumpt.c:37:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 14 and 143 bytes into a destination of size 100
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mpicc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2  -c -o utils.o utils.c
mpicc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2  -c -o mbbeagle.o mbbeagle.c
mpicc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2  -c -o best.o best.c
mpicc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle -DUSECONFIG_H -o mb bayes.o command.o model.o mcmc.o likelihood.o proposal.o sumpt.o utils.o mbbeagle.o best.o -Wl,-z,relro -L/usr/lib -lhmsbeagle -lreadline -lm
/usr/bin/ld: model.o:./src/model.c:150: multiple definition of `toJ'; command.o:./src/command.c:365: first defined here
/usr/bin/ld: model.o:./src/model.c:150: multiple definition of `fromI'; command.o:./src/command.c:365: first defined here
/usr/bin/ld: model.o:./src/model.c:150: multiple definition of `foundDash'; command.o:./src/command.c:365: first defined here
/usr/bin/ld: model.o:./src/model.c:150: multiple definition of `foundEqual'; command.o:./src/command.c:367: first defined here
/usr/bin/ld: model.o:./src/model.c:151: multiple definition of `foundExp'; command.o:./src/command.c:366: first defined here
/usr/bin/ld: model.o:./src/model.c:152: multiple definition of `isNegative'; command.o:./src/command.c:366: first defined here
/usr/bin/ld: likelihood.o:./src/likelihood.h:43: multiple definition of `preLikeR'; mcmc.o:./src/likelihood.h:43: first defined here
/usr/bin/ld: likelihood.o:./src/likelihood.h:42: multiple definition of `preLikeL'; mcmc.o:./src/likelihood.h:42: first defined here
/usr/bin/ld: likelihood.o:./src/likelihood.h:44: multiple definition of `preLikeA'; mcmc.o:./src/likelihood.h:44: first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:18: mb] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
dh_auto_build: error: cd src && make -j1 returned exit code 2
make[1]: *** [debian/rules:24: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:10: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2