Your message dated Wed, 17 Jul 2024 19:51:44 +0000
with message-id <[email protected]>
and subject line Bug#1075186: fixed in libmems 1.6.0+4725-11
has caused the Debian Bug report #1075186,
regarding libmems: 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.
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--
1075186: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075186
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:libmems
Version: 1.6.0+4725-10
Severity: important
Tags: sid trixie
User: [email protected]
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/libmems_1.6.0+4725-10_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
[...]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
-I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
Aligner.cpp -o Aligner.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I..
-Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer
-ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE -g
-O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o
homologymain.lo `test -f 'HomologyHMM/homologymain.cc' || echo
'./'`HomologyHMM/homologymain.cc
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
-I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
HomologyHMM/homologymain.cc -fPIC -DPIC -o .libs/homologymain.o
In file included from /usr/include/c++/14/ext/hash_map:60,
from HomologyHMM/dptables.h:43,
from HomologyHMM/homology.h:27,
from HomologyHMM/homologymain.cc:21:
/usr/include/c++/14/backward/backward_warning.h:32:2: warning: #warning This
file includes at least one deprecated or antiquated header which may be removed
without further notice at a future date. Please use a non-deprecated interface
with equivalent functionality instead. For a listing of replacement headers and
interfaces, consult the file backward_warning.h. To disable this warning use
-Wno-deprecated. [-Wcpp]
32 | #warning \
| ^~~~~~~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
-I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
HomologyHMM/homology.cc -o homology.o >/dev/null 2>&1
In file included from HomologyHMM/homology.h:28:
HomologyHMM/algebras.h: In function ‘BFloat double2bfloat(double)’:
HomologyHMM/algebras.h:190:21: warning: ISO C++17 does not allow ‘register’
storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
HomologyHMM/algebras.h: In function ‘BFloat bfloat_pr_product(const BFloat&,
const BFloat&)’:
HomologyHMM/algebras.h:209:19: warning: ISO C++17 does not allow ‘register’
storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.e+b.e);
| ^~
HomologyHMM/algebras.h: In function ‘BFloat bfloat_pr_double_product(const
BFloat&, double)’:
HomologyHMM/algebras.h:216:19: warning: ISO C++17 does not allow ‘register’
storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
HomologyHMM/algebras.h: In function ‘void
bfloat_pr_double_product_accum(BFloat&, double)’:
HomologyHMM/algebras.h:229:19: warning: ISO C++17 does not allow ‘register’
storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
HomologyHMM/algebras.h: In function ‘BFloat bfloat_pr_quotient(const BFloat&,
const BFloat&)’:
HomologyHMM/algebras.h:236:19: warning: ISO C++17 does not allow ‘register’
storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
-I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
HomologyHMM/homologymain.cc -o homologymain.o >/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer
-ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE
-DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o
asyncio.lo `test -f 'dmSML/asyncio.c' || echo './'`dmSML/asyncio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
-I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -c dmSML/asyncio.c -fPIC -DPIC -o
.libs/asyncio.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
-I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -c dmSML/asyncio.c -o asyncio.o
>/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer
-ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE
-DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o
alinuxaio.lo `test -f 'dmSML/alinuxaio.c' || echo './'`dmSML/alinuxaio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
-I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -c dmSML/alinuxaio.c -fPIC -DPIC -o
.libs/alinuxaio.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
-I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -c dmSML/alinuxaio.c -o alinuxaio.o
>/dev/null 2>&1
/bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-Wdate-time -D_FORTIFY_SOURCE=2 -O2 -funroll-loops -fomit-frame-pointer
-ftree-vectorize -I/usr/include/libGenome -I/usr/include/libMUSCLE
-DUSE_POSIX_AIO -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o
aPOSIXaio.lo `test -f 'dmSML/aPOSIXaio.c' || echo './'`dmSML/aPOSIXaio.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
-I/usr/include/libGenome -I/usr/include/libMUSCLE -DUSE_POSIX_AIO -g -O2
-Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -c dmSML/aPOSIXaio.c -fPIC -DPIC -o
.libs/aPOSIXaio.o
dmSML/aPOSIXaio.c: In function ‘QueryLastCompletePAIO’:
dmSML/aPOSIXaio.c:115:28: error: passing argument 1 of ‘aio_suspend’ from
incompatible pointer type [-Wincompatible-pointer-types]
115 | rval = aio_suspend(request_array, 1, &zero_wait);
| ^~~~~~~~~~~~~
| |
| struct aiocb **
In file included from /usr/include/features.h:502,
from /usr/include/x86_64-linux-gnu/sys/types.h:25,
from ../libMems/dmSML/asyncio.h:24,
from ../libMems/dmSML/aPOSIXaio.h:8,
from dmSML/aPOSIXaio.c:5:
/usr/include/aio.h:202:12: note: expected ‘const struct aiocb * const*’ but
argument is of type ‘struct aiocb **’
202 | extern int __REDIRECT_NTH (aio_suspend,
| ^~~~~~~~~~~~~~
make[3]: *** [Makefile:675: aPOSIXaio.lo] Error 1
make[3]: *** Waiting for unfinished jobs....
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
-I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
GreedyBreakpointElimination.cpp -o GreedyBreakpointElimination.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
-I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
Backbone.cpp -o Backbone.o >/dev/null 2>&1
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2
-O2 -funroll-loops -fomit-frame-pointer -ftree-vectorize
-I/usr/include/libGenome -I/usr/include/libMUSCLE -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c
ProgressiveAligner.cpp -o ProgressiveAligner.o >/dev/null 2>&1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/libMems'
make[2]: *** [Makefile:549: all-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:457: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j8 returned exit code 2
make: *** [debian/rules:6: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: libmems
Source-Version: 1.6.0+4725-11
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
libmems, 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.
Étienne Mollier <[email protected]> (supplier of updated libmems 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: Wed, 17 Jul 2024 20:45:19 +0200
Source: libmems
Architecture: source
Version: 1.6.0+4725-11
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1075186
Changes:
libmems (1.6.0+4725-11) unstable; urgency=medium
.
* gcc-14.patch: new: hint a constant type to fix a build failure.
(Closes: #1075186)
* d/control: declare compliance to standards version 4.7.0.
* d/control: migrate from pkg-config to pkgconf.
* d/libmems1t64.lintian-overrides: fix a mismatch.
* d/rules: convert leftover header file with national encoding to utf8.
* d/s/lintian-overrides: new: flag error caused by t64 transission.
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libmems_1.6.0+4725-11.debian.tar.xz
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Files:
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