Your message dated Wed, 16 Sep 2020 01:05:17 +0530
with message-id
<CAJN192-0GhJh=tewfhez804-9vmd8jcsp9ckqgo5ozfo+zo...@mail.gmail.com>
and subject line Re: mrbayes: ftbfs with GCC-10
has caused the Debian Bug report #957564,
regarding mrbayes: ftbfs with GCC-10
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
957564: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957564
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:mrbayes
Version: 3.2.6+dfsg-2
Severity: normal
Tags: sid bullseye
User: [email protected]
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
--- End Message ---
--- Begin Message ---
Hi,
this has been fixed in the new upstream version, as can be seen in build
logs[1]
Hence closing this manually.
[1]: https://buildd.debian.org/status/package.php?p=mrbayes
Kind regards
Nilesh
--- End Message ---
