Your message dated Thu, 15 Aug 2024 11:09:38 +0000
with message-id <e1seymm-000hij...@fasolo.debian.org>
and subject line Bug#1075638: fixed in wise 2.4.1-25
has caused the Debian Bug report #1075638,
regarding wise: 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.)
--
1075638: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075638
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:wise
Version: 2.4.1-24
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/wise_2.4.1-24_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
[...]
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~
|
|
|
Wise2_HSPDatabaseSegment *
cc -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 -c -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread
-I../base/ proteinindexcons.c
hsplookupthreaded.dy: In function
‘Wise2_one_off_ordered_HSPscan_scan_query_direct’:
hsplookupthreaded.dy:263:18: warning: format ‘%d’ expects argument of type
‘int’, but argument 3 has type ‘long int’ [-Wformat=]
263 | fprintf(stderr,"retrieved array with %d elements\n",current_oph);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~
| |
| long int
cc -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 -c -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread
-I../base/ dnaindexcons.c
cc -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 -c -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread
-I../base/ staticseq.c
ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o
shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o
hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o
hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar: creating libdyna_glib.a
if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/dynlibsrc'
(cd external ; make CC="cc" CFLAGS="-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 -c
`pkg-config --cflags glib-2.0`" all )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/external'
(cd mott; make CC="cc" CFLAGS="-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 -c -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread
" all)
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/external/mott'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make
rule.
cc -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 -c -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread
-Wdate-time -D_FORTIFY_SOURCE=2 -c -o mott_api.o mott_api.c
cc -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 -c -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread
-Wdate-time -D_FORTIFY_SOURCE=2 -c -o gaplib.o gaplib.c
cc -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 -c -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread
-I../../dynlibsrc -I../../base wise2_mott_bridge.c
ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar: creating libmott.a
if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/external/mott'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/external'
(cd socket ; make CC="cc" CFLAGS="-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 -c `pkg-config --cflags glib-2.0`"
libwisesocket.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/socket'
cc -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 -c -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread
-I../base/ functionserver.c
cc -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 -c -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread
-I../base/ functionclient.c
cc -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 -c -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread
-I../base/ anonobj.c
cc -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 -c -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread
-I../base/ transferinterface.c
cc -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 -c -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread
-I../base/ directsocketwrite.c
functionclient.dy: In function ‘Wise2_new_FunctionProxyCoordinator’:
functionclient.dy:193:24: error: passing argument 2 of ‘connect’ from
incompatible pointer type [-Wincompatible-pointer-types]
193 | connect(out->socket, &server, sizeof(server));
| ^~~~~~~
| |
| struct sockaddr_in *
In file included from functionclient.c:7:
/usr/include/x86_64-linux-gnu/sys/socket.h:126:52: note: expected ‘const struct
sockaddr *’ but argument is of type ‘struct sockaddr_in *’
126 | extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t
__len);
| ^
make[3]: *** [makefile:41: functionclient.o] Error 1
make[3]: *** Waiting for unfinished jobs....
functionserver.dy: In function ‘Wise2_main_loop_forking_FunctionServer’:
functionserver.dy:129:11: warning: ignoring return value of ‘write’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
129 | write(new_socket,buf,9);
| ^~~~~~~~~~~~~~~~~~~~~~~
functionserver.dy:141:9: warning: ignoring return value of ‘write’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
141 | write(new_socket,buf,6);
| ^~~~~~~~~~~~~~~~~~~~~~~
functionserver.dy:183:9: warning: ignoring return value of ‘write’ declared
with attribute ‘warn_unused_result’ [-Wunused-result]
183 | write(new_socket,buf,5);
| ^~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/socket'
make[2]: *** [makefile:93: realall] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
dh_auto_build: error: cd src && make -j8 "INSTALL=install --strip-program=true"
all returned exit code 2
make[1]: *** [debian/rules:21: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:18: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: wise
Source-Version: 2.4.1-25
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
wise, 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 wise 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: Thu, 15 Aug 2024 12:15:41 +0200
Source: wise
Architecture: source
Version: 2.4.1-25
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1075638
Changes:
wise (2.4.1-25) unstable; urgency=medium
.
* Team upload.
* gcc-14.patch: fix multiple build failures with gcc 14.
Note that the patch alone is not sufficient as such as motifmatrix.c
is still affected by a case of assignment to integer from pointer
without a cast which feels like a compiler bug. See #1075638.
* d/control: build depends on the libfl-dev.
Apparently the missing libl.a went below the radar for building dyc.
* d/rules: build and provide the dyc compiler to the rest of the build.
* d/rules: work around weird compiler behavior. (Closes: #1075638)
* d/control: declare compliance to standards version 4.7.0.
Checksums-Sha1:
f62fdd1c2a90e9b9d12c47ab437ad6baec4eb5ac 2305 wise_2.4.1-25.dsc
97c02fec57cc662f7cf6aba621da09971dc009fa 39944 wise_2.4.1-25.debian.tar.xz
Checksums-Sha256:
4050ccd2fc9cf8272f9fa446adb7a10790d1b72b0cff9fdfc6f000284a625f95 2305
wise_2.4.1-25.dsc
1d5eafd21cab385e75f51f6b1c869e8be80e7845a21d7f1653d200704e80768c 39944
wise_2.4.1-25.debian.tar.xz
Files:
57f62a245e9d4373f5fb39f33342ad03 2305 science optional wise_2.4.1-25.dsc
15f80c4850dd04e2edc1c09c2fbeb7e2 39944 science optional
wise_2.4.1-25.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=XytS
-----END PGP SIGNATURE-----
pgp9xsRpQHrpS.pgp
Description: PGP signature
--- End Message ---
