Your message dated Mon, 27 Jul 2020 10:34:49 +0000
with message-id <[email protected]>
and subject line Bug#957708: fixed in prime-phylo 1.0.11-9
has caused the Debian Bug report #957708,
regarding prime-phylo: 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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
957708: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957708
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:prime-phylo
Version: 1.0.11-8
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/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
--- End Message ---
--- Begin Message ---
Source: prime-phylo
Source-Version: 1.0.11-9
Done: Nilesh Patra <[email protected]>
We believe that the bug you reported is fixed in the latest version of
prime-phylo, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Nilesh Patra <[email protected]> (supplier of updated prime-phylo package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 26 Jul 2020 20:01:51 +0530
Source: prime-phylo
Architecture: source
Version: 1.0.11-9
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Nilesh Patra <[email protected]>
Closes: 957708
Changes:
prime-phylo (1.0.11-9) unstable; urgency=medium
.
* Team Upload.
* Fix gcc-10 FTBFS (Closes: #957708)
* compat version: 13
* Add "Rules-Requires-Root:no"
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--- End Message ---
