Your message dated Wed, 07 Aug 2024 16:53:45 +0000
with message-id <e1sbjuz-00ckob...@fasolo.debian.org>
and subject line Bug#1075397: fixed in prime-phylo 1.0.11-12
has caused the Debian Bug report #1075397,
regarding prime-phylo: ftbfs with GCC-14
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 ow...@bugs.debian.org
immediately.)
--
1075397: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075397
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:prime-phylo
Version: 1.0.11-11
Severity: important
Tags: sid trixie
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-14
[This bug is targeted to the upcoming trixie release]
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-14/g++-14, but succeeds to build with gcc-13/g++-13. The
severity of this report will be raised before the trixie release.
The full build log can be found at:
http://qa-logs.debian.net/2024/07/01/prime-phylo_1.0.11-11_unstable_gccexp.log
The last lines of the build log are at the end of this report.
To build with GCC 14, either set CC=gcc-14 CXX=g++-14 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-14/porting_to.html
[...]
[ 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 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-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,::::::::::::::::::::
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 4%] Built target prime-phylo-sfile
make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make
src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
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-d -o /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c
NHXparse.y
NHXparse.y:108.1-7: warning: POSIX Yacc does not support %expect [-Wyacc]
108 | %expect 4
| ^~~~~~~
[ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4
cd /<<PKGBUILDDIR>>/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_
-o/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends
"Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/libraries/prime
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DependInfo.cmake
"--color="
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cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc
-DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK
-DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE
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-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime
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-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx
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/usr/lib/x86_64-linux-gnu/openmpi/include -isystem
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall
-fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phyl
o.dir/NHXnode.c.o -MF CMakeFiles/prime-phylo.dir/NHXnode.c.o.d -o
CMakeFiles/prime-phylo.dir/NHXnode.c.o -c
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXnode.c
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc
-DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK
-DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE
-Dprime_phylo_EXPORTS
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime
-I/<<PKGBUILDDIR>>/src/cxx/libraries/prime
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx
-I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx
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/usr/lib/x86_64-linux-gnu/openmpi/include -isystem
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall
-fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phyl
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-DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK
-DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE
-Dprime_phylo_EXPORTS
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime
-I/<<PKGBUILDDIR>>/src/cxx/libraries/prime
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx
-I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries
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/usr/lib/x86_64-linux-gnu/openmpi/include -isystem
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wall
-fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phyl
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-DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK
-DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE
-Dprime_phylo_EXPORTS
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime
-I/<<PKGBUILDDIR>>/src/cxx/libraries/prime
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx
-I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries
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cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime &&
/usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB
-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB
-DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime
-I/<<PKGBUILDDIR>>/src/cxx/libraries/prime
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-I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries
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/usr/lib/x86_64-linux-gnu/openmpi/include -isystem
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
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-fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.
o -MF CMakeFiles/prime-phylo.dir/Beep.cc.o.d -o
CMakeFiles/prime-phylo.dir/Beep.cc.o -c
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/Beep.cc
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-DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK
-DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE
-Dprime_phylo_EXPORTS
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime
-I/<<PKGBUILDDIR>>/src/cxx/libraries/prime
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx
-I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx
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-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
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-fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phyl
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CMakeFiles/prime-phylo.dir/NHXparse.c.o -c
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/NHXparse.c
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime &&
/usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB
-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB
-DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime
-I/<<PKGBUILDDIR>>/src/cxx/libraries/prime
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx
-I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx
-I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem
/usr/lib/x86_64-linux-gnu/openmpi/include -isystem
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g
-fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.
cc.o -MF CMakeFiles/prime-phylo.dir/AnError.cc.o.d -o
CMakeFiles/prime-phylo.dir/AnError.cc.o -c
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/AnError.cc
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime &&
/usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB
-DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB
-DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS
-I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime
-I/<<PKGBUILDDIR>>/src/cxx/libraries/prime
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx
-I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx
-I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem
/usr/lib/x86_64-linux-gnu/openmpi/include -isystem
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g
-fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOpti
on.cc.o -MF CMakeFiles/prime-phylo.dir/BeepOption.cc.o.d -o
CMakeFiles/prime-phylo.dir/BeepOption.cc.o -c
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepOption.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXnode.c: In function
‘NHX_debug_print’:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXnode.c:155:32: warning: format ‘%d’
expects argument of type ‘int’, but argument 3 has type ‘double’ [-Wformat=]
155 | fprintf(stderr, "BW:\t%d\n", l->arg.t);
| ~^ ~~~~~~~~
| | |
| int double
| %f
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1597:16:
warning: ‘input’ defined but not used [-Wunused-function]
1597 | static int input (void)
| ^~~~~
/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime/lexer.c:1554:17:
warning: ‘yyunput’ defined but not used [-Wunused-function]
1554 | static void yyunput (int c, char * yy_bp )
| ^~~~~~~
NHXparse.y: In function ‘read_tree’:
NHXparse.y:354:11: error: passing argument 1 of ‘close’ makes integer from
pointer without a cast [-Wint-conversion]
In file included from NHXparse.y:5:
/usr/include/unistd.h:358:23: note: expected ‘int’ but argument is of type
‘FILE *’
358 | extern int close (int __fd);
| ~~~~^~~~
NHXparse.y: In function ‘read_tree_string’:
NHXparse.y:402:20: warning: passing argument 1 of ‘read_from_string’ discards
‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
NHXparse.y:19:36: note: expected ‘char *’ but argument is of type ‘const char *’
make[3]: ***
[src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make:147:
src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o] Error 1
make[3]: *** Waiting for unfinished jobs....
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXannotation.c: In function
‘new_annotation’:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXannotation.c:80:3: warning:
‘__builtin_strncpy’ specified bound 5 equals destination size
[-Wstringop-truncation]
80 | strncpy(a->anno_type, tag, MAX_ANNOTATION_ID_LENGTH);
| ^
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:314:
src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[1]: *** [Makefile:159: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 "INSTALL=install
--strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:12: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: prime-phylo
Source-Version: 1.0.11-12
Done: Étienne Mollier <emoll...@debian.org>
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 1075...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 07 Aug 2024 16:56:11 +0200
Source: prime-phylo
Architecture: source
Version: 1.0.11-12
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1075397
Changes:
prime-phylo (1.0.11-12) unstable; urgency=medium
.
* gcc-14.patch: fix improper use of close(2) by using fclose(3).
(Closes: #1075397)
* typos.patch: new: fix multiple typos caught by lintian.
* d/control: declare compliance to standards version 4.7.0.
* d/lintian-overrides: new: flag false positive typos.
* d/control: add myself to uploaders.
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prime-phylo_1.0.11-12.debian.tar.xz
Checksums-Sha256:
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prime-phylo_1.0.11-12.debian.tar.xz
Files:
51b328f9fb4d4a53f8742d589d06a3b5 2366 science optional
prime-phylo_1.0.11-12.dsc
c7758ed00392a5375596398c1a0f6570 10472 science optional
prime-phylo_1.0.11-12.debian.tar.xz
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