Your message dated Thu, 25 Jul 2024 02:35:30 +0000
with message-id <e1swoki-00cxb4...@fasolo.debian.org>
and subject line Bug#1075307: fixed in ncbi-tools6 6.1.20170106+dfsg2-3
has caused the Debian Bug report #1075307,
regarding ncbi-tools6: 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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--
1075307: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075307
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:ncbi-tools6
Version: 6.1.20170106+dfsg2-2
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/ncbi-tools6_6.1.20170106+dfsg2-2_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
[...]
./ln-if-absent ../internal/ideogram/*.dat .
set: No match.
make[3]: [makefile:778: copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/ideochr*.h ../include
set: No match.
make[3]: [makefile:779: copy] Error 1 (ignored)
./ln-if-absent ../internal/ideogram/ideoorgs.h .
make[3]: [makefile:780: copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.c .
set: No match.
make[3]: [makefile:781: copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.dat .
set: No match.
make[3]: [makefile:782: copy] Error 1 (ignored)
./ln-if-absent ../internal/ccap/*.h ../include
set: No match.
make[3]: [makefile:783: copy] Error 1 (ignored)
./ln-if-absent ncbidraw.c ncbidrwg.c
./ln-if-absent ncbithr.c ncbithrs.c
./ln-if-absent ../network/nsclilib/*.h ../include
./ln-if-absent ../network/blast3/client/*.h ../include
./ln-if-absent ../network/id1arch/*.h ../include
./ln-if-absent ../network/id2arch/*.h ../include
mkdir -p ../include/algo/blast/core
./ln-if-absent ../algo/blast/core/*.c .
./ln-if-absent ../algo/blast/core/*.h .
./ln-if-absent ../algo/blast/core/*.inl .
cp -fp ../algo/blast/core/*.h ../include/algo/blast/core
mkdir -p ../include/algo/blast/composition_adjustment
./ln-if-absent ../algo/blast/composition_adjustment/*.c .
cp -fp ../algo/blast/composition_adjustment/*.h \
../include/algo/blast/composition_adjustment
mkdir -p ../include/algo/blast/api
./ln-if-absent ../algo/blast/api/*.c .
cp -fp ../algo/blast/api/*.h ../include/algo/blast/api
chmod -R ug+rw,o+r .
echo Waiting...go
Waiting...go
x86_64-linux-gnu-gcc -c -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall
-Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbithr.c
In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25,
from ../include/ncbilcl.h:150,
from ../include/ncbistd.h:61,
from ncbithr.c:289:
/usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE
are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use
_DEFAULT_SOURCE"
| ^~~~~~~
ncbithr.c: In function ‘s_TlsDestroyAll’:
ncbithr.c:2529:11: warning: variable ‘err_code’ set but not used
[-Wunused-but-set-variable]
2529 | int err_code = 0;
| ^~~~~~~~
cp -p ncbithr.o ../lib
x86_64-linux-gnu-gcc -c -g -O2 -Werror=implicit-function-declaration
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wall
-Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PNG -I../include -DWIN_MOTIF ncbimain.c
In file included from /usr/include/x86_64-linux-gnu/sys/types.h:25,
from ../include/ncbilcl.h:150,
from ../include/ncbi.h:57,
from ncbimain.c:56:
/usr/include/features.h:196:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE
are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
196 | # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use
_DEFAULT_SOURCE"
| ^~~~~~~
ncbimain.c:82:1: error: return type defaults to ‘int’ [-Wimplicit-int]
82 | main(int argc, char *argv[])
| ^~~~
make[3]: *** [makefile:513: ncbimain.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build'
make[2]: *** [debian/rules:83: override_dh_auto_build-arch] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [debian/rules:77: build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:73: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: ncbi-tools6
Source-Version: 6.1.20170106+dfsg2-3
Done: Aaron M. Ucko <u...@debian.org>
We believe that the bug you reported is fixed in the latest version of
ncbi-tools6, 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.
Aaron M. Ucko <u...@debian.org> (supplier of updated ncbi-tools6 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, 24 Jul 2024 21:56:34 -0400
Source: ncbi-tools6
Architecture: source
Version: 6.1.20170106+dfsg2-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Aaron M. Ucko <u...@debian.org>
Closes: 1075307
Changes:
ncbi-tools6 (6.1.20170106+dfsg2-3) unstable; urgency=medium
.
* Fix compilation under GCC 14. (Closes: #1075307.)
- algo/blast/api/hspfilter_queue.c: Cast ersatz virtual function
implementation pointers as appropriate.
- api/asn2ff{2,4}.c, corelib/ncbimain.c, demo/trna2tbl.c,
tools/{ncbisort,pattern1}.c, vibrant/vibmain.c: Stop relying on
implicit int. (In the case of ncbisort.c, take the opportunity to
comment out an occurrence of the deprecated keyword "register.")
- desktop/seqpanel.c: Correct fputs argument order (accidentally left
unswapped when substituting it for printf years ago).
* Standards-Version: 4.7.0 (routine-update)
* Rely on pre-initialized dpkg-architecture variables (routine-update)
Checksums-Sha1:
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ncbi-tools6_6.1.20170106+dfsg2-3.dsc
50da4c067e584698e2d93e5f5a64384a1050f99a 1515436
ncbi-tools6_6.1.20170106+dfsg2-3.debian.tar.xz
Checksums-Sha256:
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ncbi-tools6_6.1.20170106+dfsg2-3.dsc
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ncbi-tools6_6.1.20170106+dfsg2-3.debian.tar.xz
Files:
7877250c48391b6c690318ba56f58ae5 2919 libdevel optional
ncbi-tools6_6.1.20170106+dfsg2-3.dsc
70312c765babe3343d17de1c431650a9 1515436 libdevel optional
ncbi-tools6_6.1.20170106+dfsg2-3.debian.tar.xz
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