Your message dated Tue, 28 Jul 2020 16:04:26 +0000
with message-id <e1k0s5a-0000nb...@fasolo.debian.org>
and subject line Bug#957783: fixed in seaview 1:5.0.2-3
has caused the Debian Bug report #957783,
regarding seaview: 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.)
--
957783: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957783
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:seaview
Version: 1:4.7-1
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/seaview_4.7-1_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
[...]
g++ -c -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -DUSE_XFT -I/usr/include/freetype2 -DFLTK1 -Dunix
-Icsrc -I. -DNO_PDF -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\"
-DPHYMLNAME=\"phyml\" -fPIC -Dunix -O3 -I. -Icsrc -DNO_PDF
FL/Fl_Native_File_Chooser_FLTK.cxx
gcc -c -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT
-I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF
-DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\"
-fPIC -Dunix -Icsrc csrc/raa_acnuc.c
gcc -c -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT
-I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF
-DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\"
-fPIC -Dunix -Icsrc csrc/parser.c
gcc -c -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT
-I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF
-DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\"
-fPIC -Dunix -Icsrc csrc/md5.c
gcc -c -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT
-I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF
-DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\"
-fPIC -Dunix -Icsrc csrc/zsockr.c
gcc -c -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT
-I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF
-DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\"
-fPIC -Dunix -Icsrc csrc/misc_acnuc.c
gcc -c -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT
-I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF
-DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\"
-fPIC -Dunix -Icsrc csrc/dnapars.c
gcc -c -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT
-I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF
-DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\"
-fPIC -Dunix -Icsrc csrc/protpars.c
gcc -c -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT
-I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF
-DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\"
-fPIC -Dunix -Icsrc csrc/seq.c
gcc -c -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT
-I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF
-DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\"
-fPIC -Dunix -Icsrc csrc/phylip.c
gcc -c -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT
-I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF
-DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\"
-fPIC -Dunix -Icsrc csrc/lwl.c
gcc -c -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT
-I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF
-DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\"
-fPIC -Dunix -Icsrc csrc/bionj.c
gcc -c -O3 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -Wformat -Werror=format-security -DUSE_XFT
-I/usr/include/freetype2 -DFLTK1 -Dunix -Icsrc -I. -DNO_PDF
-DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\"
-fPIC -Dunix -Icsrc csrc/phyml_util.c
g++ -o seaview -Wl,-z,relro -Wl,-z,now -Wl,--as-needed seaview.o custom.o
use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o resource.o
nexus.o viewasprots.o racnuc_fetch.o concatenate.o statistics.o trees.o
treedraw.o addbootstrap.o least_squares_brl.o pseudoterminal.o unrooted.o
pdf_or_ps.o svg.o threads.o tbe.o Fl_Native_File_Chooser_FLTK.o raa_acnuc.o
parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o
bionj.o phyml_util.o `fltk-config --use-images --ldflags` -ldl -lpthread -lz
/usr/bin/ld: dnapars.o:./csrc/dnapars.c:114: multiple definition of `progname';
seaview.o:./seaview.cxx:238: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:109: multiple definition of `chars';
dnapars.o:./csrc/dnapars.c:84: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:112: multiple definition of
`usertree'; dnapars.o:./csrc/dnapars.c:88: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:118: multiple definition of
`threshwt'; dnapars.o:./csrc/dnapars.c:107: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:123: multiple definition of `fsteps';
dnapars.o:./csrc/dnapars.c:103: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:137: multiple definition of `nsteps';
dnapars.o:./csrc/dnapars.c:102: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:133: multiple definition of
`minwhich'; dnapars.o:./csrc/dnapars.c:99: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:116: multiple definition of
`treenode'; dnapars.o:./csrc/dnapars.c:93: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:108: multiple definition of `root';
dnapars.o:./csrc/dnapars.c:83: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:135: multiple definition of
`recompute'; dnapars.o:./csrc/dnapars.c:101: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:127: multiple definition of `temp1';
dnapars.o:./csrc/dnapars.c:110: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:127: multiple definition of `temp';
dnapars.o:./csrc/dnapars.c:110: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:138: multiple definition of `place';
dnapars.o:./csrc/dnapars.c:105: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:135: multiple definition of
`lastrearr'; dnapars.o:./csrc/dnapars.c:101: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:136: multiple definition of `there';
dnapars.o:./csrc/dnapars.c:104: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:124: multiple definition of
`bestrees'; dnapars.o:./csrc/dnapars.c:106: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:139: multiple definition of `names';
dnapars.o:./csrc/dnapars.c:112: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:112: multiple definition of `trout';
dnapars.o:./csrc/dnapars.c:89: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:109: multiple definition of `col';
dnapars.o:./csrc/dnapars.c:84: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:120: multiple definition of
`enterorder'; dnapars.o:./csrc/dnapars.c:94: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:112: multiple definition of `jumble';
dnapars.o:./csrc/dnapars.c:88: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:109: multiple definition of
`njumble'; dnapars.o:./csrc/dnapars.c:84: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:109: multiple definition of `jumb';
dnapars.o:./csrc/dnapars.c:84: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:119: multiple definition of `seed';
dnapars.o:./csrc/dnapars.c:92: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:130: multiple definition of
`progname'; seaview.o:./seaview.cxx:238: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:126: multiple definition of
`garbage'; dnapars.o:./csrc/dnapars.c:109: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:113: multiple definition of
`mulsets'; dnapars.o:./csrc/dnapars.c:89: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:109: multiple definition of `msets';
dnapars.o:./csrc/dnapars.c:84: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:113: multiple definition of
`firstset'; dnapars.o:./csrc/dnapars.c:89: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:112: multiple definition of `thresh';
dnapars.o:./csrc/dnapars.c:88: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:112: multiple definition of
`weights'; dnapars.o:./csrc/dnapars.c:88: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:112: multiple definition of
`progress'; dnapars.o:./csrc/dnapars.c:89: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:112: multiple definition of
`stepbox'; dnapars.o:./csrc/dnapars.c:89: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:113: multiple definition of `ancseq';
dnapars.o:./csrc/dnapars.c:89: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:107: multiple definition of
`outtreename'; dnapars.o:./csrc/dnapars.c:80: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:109: multiple definition of `ith';
dnapars.o:./csrc/dnapars.c:84: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:113: multiple definition of
`justwts'; dnapars.o:./csrc/dnapars.c:89: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:117: multiple definition of
`threshold'; dnapars.o:./csrc/dnapars.c:87: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:111: multiple definition of
`inseed0'; dnapars.o:./csrc/dnapars.c:86: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:111: multiple definition of `inseed';
dnapars.o:./csrc/dnapars.c:86: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:107: multiple definition of
`weightfilename'; dnapars.o:./csrc/dnapars.c:81: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:107: multiple definition of
`intreename'; dnapars.o:./csrc/dnapars.c:80: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:107: multiple definition of
`outfilename'; dnapars.o:./csrc/dnapars.c:80: first defined here
/usr/bin/ld: protpars.o:./csrc/protpars.c:107: multiple definition of
`infilename'; dnapars.o:./csrc/dnapars.c:80: first defined here
/usr/bin/ld: protpars.o:./csrc/phylip.h:366: multiple definition of
`firstplotblock'; dnapars.o:./csrc/phylip.h:366: first defined here
/usr/bin/ld: protpars.o:./csrc/phylip.h:345: multiple definition of `javarun';
dnapars.o:./csrc/phylip.h:345: first defined here
/usr/bin/ld: seq.o:./csrc/phylip.h:366: multiple definition of
`firstplotblock'; dnapars.o:./csrc/phylip.h:366: first defined here
/usr/bin/ld: seq.o:./csrc/phylip.h:345: multiple definition of `javarun';
dnapars.o:./csrc/phylip.h:345: first defined here
/usr/bin/ld: phylip.o:./csrc/phylip.h:345: multiple definition of `javarun';
dnapars.o:./csrc/phylip.h:345: first defined here
/usr/bin/ld: phylip.o:./csrc/phylip.h:366: multiple definition of
`firstplotblock'; dnapars.o:./csrc/phylip.h:366: first defined here
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:46: seaview] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" returned
exit code 2
make: *** [debian/rules:18: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: seaview
Source-Version: 1:5.0.2-3
Done: Nilesh Patra <npatra...@gmail.com>
We believe that the bug you reported is fixed in the latest version of
seaview, 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.
Nilesh Patra <npatra...@gmail.com> (supplier of updated seaview 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: Tue, 28 Jul 2020 19:47:08 +0530
Source: seaview
Architecture: source
Version: 1:5.0.2-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Nilesh Patra <npatra...@gmail.com>
Closes: 957783
Changes:
seaview (1:5.0.2-3) unstable; urgency=medium
.
* Team Upload.
* Fix gcc-10 FTBFS (Closes: #957783)
* compat version: 13
Checksums-Sha1:
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6024fa796c5737eca66217a1e45be9c32a0c5d24 8108 seaview_5.0.2-3_amd64.buildinfo
Checksums-Sha256:
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Files:
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15eec030a83538bca275bd6639ce6347 17588 science optional
seaview_5.0.2-3.debian.tar.xz
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