Your message dated Wed, 07 Aug 2024 10:38:56 +0000
with message-id <e1sbe4g-00b7ra...@fasolo.debian.org>
and subject line Bug#1075617: fixed in velvet 1.2.10+dfsg1-9
has caused the Debian Bug report #1075617,
regarding velvet: 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
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--
1075617: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075617
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:velvet
Version: 1.2.10+dfsg1-8
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/velvet_1.2.10+dfsg1-8_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
[...]
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’
declared but never defined
174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’
declared but never defined
173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker *
marker);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c
src/passageMarker.c -o obj/passageMarker.o
In file included from src/passageMarker.c:29:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’
declared but never defined
178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
| ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’
declared but never defined
177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker *
marker);
| ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’
declared but never defined
174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’
declared but never defined
173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker *
marker);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c
src/graphStats.c -o obj/graphStats.o
In file included from src/graphStats.c:28:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’
declared but never defined
178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
| ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’
declared but never defined
177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker *
marker);
| ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’
declared but never defined
174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’
declared but never defined
173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker *
marker);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c
src/correctedGraph.c -o obj/correctedGraph.o
In file included from src/correctedGraph.c:26:
src/graph.h:178:20: warning: inline function ‘setShortReadMarkerOffset’
declared but never defined
178 | extern inline void setShortReadMarkerOffset(ShortReadMarker * marker,
| ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:177:27: warning: inline function ‘getShortReadMarkerOffset’
declared but never defined
177 | extern inline ShortLength getShortReadMarkerOffset(ShortReadMarker *
marker);
| ^~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:174:20: warning: inline function ‘setShortReadMarkerPosition’
declared but never defined
174 | extern inline void setShortReadMarkerPosition(ShortReadMarker * marker,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
src/graph.h:173:26: warning: inline function ‘getShortReadMarkerPosition’
declared but never defined
173 | extern inline Coordinate getShortReadMarkerPosition(ShortReadMarker *
marker);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c src/dfib.c
-o obj/dfib.o
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c
src/dfibHeap.c -o obj/dfibHeap.o
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c
src/recycleBin.c -o obj/recycleBin.o
gcc -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D LONGSEQUENCES -c
src/readSet.c -o obj/readSet.o
src/readSet.c: In function ‘readFastXFile’:
src/readSet.c:641:21: error: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’}
from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types]
641 | file.gzFile = file.autoFile = NULL;
| ^
src/readSet.c: In function ‘readFastXPair’:
src/readSet.c:680:22: error: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’}
from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types]
680 | file1.gzFile = file1.autoFile = NULL;
| ^
src/readSet.c:681:22: error: assignment to ‘gzFile’ {aka ‘struct gzFile_s *’}
from incompatible pointer type ‘AutoFile *’ [-Wincompatible-pointer-types]
681 | file2.gzFile = file2.autoFile = NULL;
| ^
make[2]: *** [Makefile:109: obj/readSet.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j1 "INSTALL=install --strip-program=true"
LONGSEQUENCES=Y OPENMP=Y velveth velvetg OPENMP=1 "CPPFLAGS=-Wdate-time
-D_FORTIFY_SOURCE=2" "CFLAGS=-g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection"
LDFLAGS=-Wl,-z,relro returned exit code 2
make[1]: *** [debian/rules:25: build_long_versions] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:7: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: velvet
Source-Version: 1.2.10+dfsg1-9
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
velvet, 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 velvet 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 11:51:33 +0200
Source: velvet
Architecture: source
Version: 1.2.10+dfsg1-9
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1075617
Changes:
velvet (1.2.10+dfsg1-9) unstable; urgency=medium
.
* Team upload.
* gcc-14.patch: new: fix incompatible pointer types. (Closes: #1075617)
* d/control: declare compliance to standards version 4.7.0.
* hardening.patch: also propagate CPPFLAGS.
This allows fortifying the source where applicable.
Checksums-Sha1:
75fc71ea02e7cec0f886eee2795b6a0d307bceed 2393 velvet_1.2.10+dfsg1-9.dsc
a90ae2c99b8e907d21ea487acced5450df59e5ec 18476
velvet_1.2.10+dfsg1-9.debian.tar.xz
Checksums-Sha256:
94082ab4475c68a3acc783f349fdc172c0b6114f0883b9eb6b5335060d537f2b 2393
velvet_1.2.10+dfsg1-9.dsc
6d34641dd5a1fec20bb47508d3e2e045cd06a0e73dbeda44e38c90be0b135183 18476
velvet_1.2.10+dfsg1-9.debian.tar.xz
Files:
e7e1c2672fcdd52e65edad9630fa1bbb 2393 science optional
velvet_1.2.10+dfsg1-9.dsc
a40a683daca2441b5ded8972fbe1508b 18476 science optional
velvet_1.2.10+dfsg1-9.debian.tar.xz
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--- End Message ---
