[Debian-med-packaging] Bug#957708: prime-phylo: ftbfs with GCC-10
Matthias Klose
doko at debian.org
Fri Apr 17 12:09:10 BST 2020
Package: src:prime-phylo
Version: 1.0.11-8
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/prime-phylo_1.0.11-8_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
[...]
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 1%] [BISON][MyParser2] Building parser with bison 3.5.1
[ 1%] [FLEX][MyScanner2] Building scanner with flex 2.6.4
cd /<<PKGBUILDDIR>>/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c gb.y
cd /<<PKGBUILDDIR>>/src/cxx/libraries/sfile && /usr/bin/flex -o/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l
gb.y: warning: 1 nonterminal useless in grammar [-Wother]
gb.y: warning: 1 rule useless in grammar [-Wother]
gb.y:258.1-12: warning: nonterminal useless in grammar: darwin_entry [-Wother]
258 | darwin_entry : TEXT {$$ = NULL; /* Not implemented yet */}
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/libraries/sfile /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/DependInfo.cmake --color=
Scanning dependencies of target prime-phylo-sfile
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o
[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o
[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o
[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/gbread.c
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -c /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/gbread.c: In function ‘main’:
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/gbread.c:17:10: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration]
17 | if (!strcmp(argv[opt], "-d")) {
| ^~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c: In function ‘seq_print’:
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:265:14: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=]
265 | printf("%9d", char_counter + 1);
| ^~~~~ ~~~~~~~~~~~~~~~~
| |
| long int
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:212:15: warning: variable ‘date’ set but not used [-Wunused-but-set-variable]
212 | char *top, *date;
| ^~~~
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c: In function ‘yyparse’:
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c:1335:16: warning: implicit declaration of function ‘yylex’ [-Wimplicit-function-declaration]
1335 | yychar = yylex ();
| ^~~~~
gb.y: In function ‘yyerror’:
gb.y:291:70: warning: implicit declaration of function ‘linenumber’ [-Wimplicit-function-declaration]
gb.y: In function ‘add_to_seq’:
gb.y:402:9: warning: unused variable ‘new_buf’ [-Wunused-variable]
seqreader.l: In function ‘seq_read’:
seqreader.l:270:9: warning: unused variable ‘code’ [-Wunused-variable]
At top level:
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1864:16: warning: ‘input’ defined but not used [-Wunused-function]
1864 | static int input (void)
| ^~~~~
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile/lexer.c:1821:17: warning: ‘yyunput’ defined but not used [-Wunused-function]
1821 | static void yyunput (int c, char * yy_bp )
| ^~~~~~~
[ 4%] Linking C shared library libprime-phylo-sfile.so
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo-sfile.dir/link.txt --verbose=1
/usr/bin/cc -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libprime-phylo-sfile.so -o libprime-phylo-sfile.so CMakeFiles/prime-phylo-sfile.dir/gbread.c.o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -Wl,-rpath,::::::::::::::::::::
/usr/bin/ld: CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o:(.bss+0x14): multiple definition of `yydebug'; CMakeFiles/prime-phylo-sfile.dir/gbread.c.o:./obj-x86_64-linux-gnu/src/cxx/libraries/sfile/./src/cxx/libraries/sfile/gbread.c:4: first defined here
collect2: error: ld returned 1 exit status
make[3]: *** [src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make:144: src/cxx/libraries/sfile/libprime-phylo-sfile.so] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:373: src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:155: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j4 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:12: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
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