Your message dated Thu, 23 Jul 2020 20:50:45 +0000
with message-id <e1jyiav-0007nc...@fasolo.debian.org>
and subject line Bug#957681: fixed in phylip 1:3.697+dfsg-2
has caused the Debian Bug report #957681,
regarding phylip: ftbfs with GCC-10
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.)
--
957681: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957681
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:phylip
Version: 1:3.697+dfsg-1
Severity: normal
Tags: sid bullseye
User: debian-...@lists.debian.org
Usertags: ftbfs-gcc-10
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-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/phylip_3.697+dfsg-1_unstable_gcc10.log
The last lines of the build log are at the end of this report.
To build with GCC 10, either set CC=gcc-10 CXX=g++-10 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-10/porting_to.html
[...]
dh build --with javahelper --no-parallel
dh_update_autotools_config -O--no-parallel
dh_autoreconf -O--no-parallel
dh_auto_configure -O--no-parallel
jh_linkjars -O--no-parallel
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build --sourcedirectory=src --buildsystem=makefile -- -f Makefile.unx
all
cd src && make -j1 "INSTALL=install --strip-program=true" -f
Makefile.unx all
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
Building PHYLIP version 3.696
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -DUNX -fomit-frame-pointer -Wdate-time
-D_FORTIFY_SOURCE=2 -c -o clique.o clique.c
clique.c: In function ‘getoptions’:
clique.c:219:5: warning: ignoring return value of ‘scanf’ declared with
attribute ‘warn_unused_result’ [-Wunused-result]
219 | scanf("%c%*[^\n]", &ch);
| ^~~~~~~~~~~~~~~~~~~~~~~
clique.c:249:15: warning: ignoring return value of ‘scanf’ declared with
attribute ‘warn_unused_result’ [-Wunused-result]
249 | scanf("%ld%*[^\n]", &Cliqmin);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
clique.c:273:15: warning: ignoring return value of ‘scanf’ declared with
attribute ‘warn_unused_result’ [-Wunused-result]
273 | scanf("%c%*[^\n]", &ch2);
| ^~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -DUNX -fomit-frame-pointer -Wdate-time
-D_FORTIFY_SOURCE=2 -c -o disc.o disc.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -DUNX -fomit-frame-pointer -Wdate-time
-D_FORTIFY_SOURCE=2 -c -o phylip.o phylip.c
In file included from /usr/include/stdio.h:867,
from phylip.c:32:
In function ‘fgets’,
inlined from ‘getstryng’ at phylip.c:234:11,
inlined from ‘readlong’ at phylip.c:464:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:263:9: warning: call to
‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger
size than length of destination buffer [-Wattribute-warning]
263 | return __fgets_chk_warn (__s, __bos (__s), __n, __stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘fgets’,
inlined from ‘getstryng’ at phylip.c:234:11,
inlined from ‘initcategs’ at phylip.c:600:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:263:9: warning: call to
‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger
size than length of destination buffer [-Wattribute-warning]
263 | return __fgets_chk_warn (__s, __bos (__s), __n, __stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘fgets’,
inlined from ‘getstryng’ at phylip.c:234:11,
inlined from ‘initprobcat’ at phylip.c:631:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:263:9: warning: call to
‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger
size than length of destination buffer [-Wattribute-warning]
263 | return __fgets_chk_warn (__s, __bos (__s), __n, __stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘fgets’,
inlined from ‘getstryng’ at phylip.c:234:11,
inlined from ‘initfreqs’ at phylip.c:1018:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:263:9: warning: call to
‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger
size than length of destination buffer [-Wattribute-warning]
263 | return __fgets_chk_warn (__s, __bos (__s), __n, __stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘fgets’,
inlined from ‘getstryng’ at phylip.c:234:11,
inlined from ‘readlong’ at phylip.c:464:5,
inlined from ‘initnumlines’ at phylip.c:1123:20:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:263:9: warning: call to
‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger
size than length of destination buffer [-Wattribute-warning]
263 | return __fgets_chk_warn (__s, __bos (__s), __n, __stream);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-Wformat -Werror=format-security -O3 -DUNX -fomit-frame-pointer clique.o disc.o
phylip.o -lm -Wl,-z,relro -Wl,-z,now -o clique
/usr/bin/ld: disc.o:./src/phylip.h:354: multiple definition of
`firstplotblock'; clique.o:./src/phylip.h:354: first defined here
/usr/bin/ld: disc.o:./src/phylip.h:334: multiple definition of `javarun';
clique.o:./src/phylip.h:334: first defined here
/usr/bin/ld: phylip.o:./src/phylip.h:334: multiple definition of `javarun';
clique.o:./src/phylip.h:334: first defined here
/usr/bin/ld: phylip.o:./src/phylip.h:354: multiple definition of
`firstplotblock'; clique.o:./src/phylip.h:354: first defined here
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile.unx:280: clique] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
dh_auto_build: error: cd src && make -j1 "INSTALL=install --strip-program=true"
-f Makefile.unx all returned exit code 2
make[1]: *** [debian/rules:18: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:15: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: phylip
Source-Version: 1:3.697+dfsg-2
Done: Shayan Doust <he...@shayandoust.me>
We believe that the bug you reported is fixed in the latest version of
phylip, 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 957...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Shayan Doust <he...@shayandoust.me> (supplier of updated phylip 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: SHA256
Format: 1.8
Date: Thu, 23 Jul 2020 16:37:36 +0000
Source: phylip
Architecture: source
Version: 1:3.697+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Shayan Doust <he...@shayandoust.me>
Closes: 957681
Changes:
phylip (1:3.697+dfsg-2) unstable; urgency=medium
.
* Team upload
.
[ Steffen Möller ]
* Added ref to conda
* d/u/metadata: yamllint
.
[ Shayan Doust ]
* Fix gcc-10 multiple definition errors (Closes: #957681)
* Standards-Version: 4.5.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Trim trailing whitespace.
* Use secure URI in Homepage field.
Checksums-Sha1:
dfdaec4f9fadcaab3934d6e95d7df429eed4b0ff 2175 phylip_3.697+dfsg-2.dsc
ee555e983a1a7fd841ca2d53ae11b145a3ba0f79 13388
phylip_3.697+dfsg-2.debian.tar.xz
8fd425223be921e710593b94bc728b8a11a8b502 11665
phylip_3.697+dfsg-2_amd64.buildinfo
Checksums-Sha256:
7e2784afc31c9674d0b3968f2d01f8d56bfe807f889e6bbbf0f9ee6ad872bad9 2175
phylip_3.697+dfsg-2.dsc
3e5f542b15b921408c4a1a6721273a120f84d8f1b4c5e12f0fc44f6e303ebd47 13388
phylip_3.697+dfsg-2.debian.tar.xz
f5414e3f134ff6ebf482b882fdffec48559d356435cd2477316fbf678f958af4 11665
phylip_3.697+dfsg-2_amd64.buildinfo
Files:
ea8899bf78e22e1cf4945eaae0c7246d 2175 science optional phylip_3.697+dfsg-2.dsc
8bfef23c473727161490bf32e14c6168 13388 science optional
phylip_3.697+dfsg-2.debian.tar.xz
d64d6cab4b605e5dc343bf156112eea2 11665 science optional
phylip_3.697+dfsg-2_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=56gP
-----END PGP SIGNATURE-----
--- End Message ---
