Your message dated Mon, 21 Sep 2020 17:03:32 +0000
with message-id <[email protected]>
and subject line Bug#966127: fixed in embassy-phylip 3.69.660-4
has caused the Debian Bug report #966127,
regarding embassy-phylip: FTBFS with GCC 10: multiple definition of ... due to
-fno-common
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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--
966127: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=966127
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: embassy-phylip
Version: 3.69.660-3
Severity: serious
Tags: ftbfs sid bullseye
Justification: fails to build from source
User: [email protected]
Usertags: ftbfs-gcc-10
Hi,
embassy-phylip started to FTBFS when GCC 10 was made the default compiler:
/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2
-fdebug-prefix-map=/build/embassy-phylip-3.69.660=. -fstack-protector-strong
-Wformat -Werror=format-security -I/usr/lib/emboss/include
-I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplo
t -L/usr/lib/emboss/lib -Wl,--rpath,/usr/lib/emboss/lib -O2 -Wl,-z,relro
-Wl,--as-needed -o fclique clique.o disc.o phylip.o -L/usr/lib -lnucleus -lacd
-lajaxdb -lensembl -lajaxg -lajax -lepcre -leplplot -lX11 -lXaw -lXt -lm
-lgd -lpng -lz -lm
/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2
-fdebug-prefix-map=/build/embassy-phylip-3.69.660=. -fstack-protector-strong
-Wformat -Werror=format-security -I/usr/lib/emboss/include
-I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplot
-L/usr/lib/emboss/lib -Wl,--rpath,/usr/lib/emboss/lib -O2 -Wl,-z,relro
-Wl,--as-needed -o fconsense consense.o cons.o phylip.o -L/usr/lib -lnucleus
-lacd -lajaxdb -lensembl -lajaxg -lajax -lepcre -leplplot -lX11 -lXaw -lXt
-lm -lgd -lpng -lz -lm
/bin/bash ../libtool --tag=CC --mode=link gcc -g -O2
-fdebug-prefix-map=/build/embassy-phylip-3.69.660=. -fstack-protector-strong
-Wformat -Werror=format-security -I/usr/lib/emboss/include
-I/usr/lib/emboss/include/epcre -I/usr/lib/emboss/include/eplplot
-L/usr/lib/emboss/lib -Wl,--rpath,/usr/lib/emboss/lib -O2 -Wl,-z,relro
-Wl,--as-needed -o fcontml contml.o cont.o phylip.o -L/usr/lib -lnucleus -lacd
-lajaxdb -lensembl -lajaxg -lajax -lepcre -leplplot -lX11 -lXaw -lXt -lm
-lgd -lpng -lz -lm
libtool: link: gcc -g -O2 -fdebug-prefix-map=/build/embassy-phylip-3.69.660=.
-fstack-protector-strong -Wformat -Werror=format-security
-I/usr/lib/emboss/include -I/usr/lib/emboss/include/epcre
-I/usr/lib/emboss/include/eplplot -Wl,--rpath -Wl,/usr/lib/emboss/lib -O2
-Wl,-z -Wl,relro -Wl,--as-needed -o fclique clique.o disc.o phylip.o
-L/usr/lib/emboss/lib -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg
-lajax -lepcre -leplplot -lX11 -lXaw -lXt -lgd -lpng -lz -lm
/usr/bin/ld: disc.o:./src/disc.c:4: multiple definition of `phylostates';
clique.o:./src/clique.c:12: first defined here
/usr/bin/ld: phylip.o:./src/phylip.c:43: multiple definition of
`embossouttree'; clique.o:./src/clique.c:76: first defined here
/usr/bin/ld: phylip.o:./src/phylip.c:40: multiple definition of
`embossoutfile'; clique.o:./src/clique.c:75: first defined here
libtool: link: gcc -g -O2 -fdebug-prefix-map=/build/embassy-phylip-3.69.660=.
-fstack-protector-strong -Wformat -Werror=format-security
-I/usr/lib/emboss/include -I/usr/lib/emboss/include/epcre
-I/usr/lib/emboss/include/eplplot -Wl,--rpath -Wl,/usr/lib/emboss/lib -O2
-Wl,-z -Wl,relro -Wl,--as-needed -o fconsense consense.o cons.o phylip.o
-L/usr/lib/emboss/lib -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg
-lajax -lepcre -leplplot -lX11 -lXaw -lXt -lgd -lpng -lz -lm
/usr/bin/ld: phylip.o:./src/phylip.c:43: multiple definition of
`embossouttree'; consense.o:./src/consense.c:23: first defined here
/usr/bin/ld: phylip.o:./src/phylip.c:40: multiple definition of
`embossoutfile'; consense.o:./src/consense.c:22: first defined here
libtool: link: gcc -g -O2 -fdebug-prefix-map=/build/embassy-phylip-3.69.660=.
-fstack-protector-strong -Wformat -Werror=format-security
-I/usr/lib/emboss/include -I/usr/lib/emboss/include/epcre
-I/usr/lib/emboss/include/eplplot -Wl,--rpath -Wl,/usr/lib/emboss/lib -O2
-Wl,-z -Wl,relro -Wl,--as-needed -o fcontml contml.o cont.o phylip.o
-L/usr/lib/emboss/lib -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg
-lajax -lepcre -leplplot -lX11 -lXaw -lXt -lgd -lpng -lz -lm
/usr/bin/ld: phylip.o:./src/phylip.c:43: multiple definition of
`embossouttree'; contml.o:./src/contml.c:73: first defined here
/usr/bin/ld: phylip.o:./src/phylip.c:40: multiple definition of
`embossoutfile'; contml.o:./src/contml.c:72: first defined here
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:1193: fclique] Error 1
make[3]: *** Waiting for unfinished jobs....
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:1197: fconsense] Error 1
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:1201: fcontml] Error 1
make[3]: Leaving directory '/build/embassy-phylip-3.69.660/src'
make[2]: *** [Makefile:1093: all] Error 2
make[2]: Leaving directory '/build/embassy-phylip-3.69.660/src'
make[1]: *** [Makefile:425: all-recursive] Error 1
make[1]: Leaving directory '/build/embassy-phylip-3.69.660'
dh_auto_build: error: make -j3 returned exit code 2
make: *** [debian/rules:7: build] Error 25
More information about the corresponding GCC change can be found here:
https://gcc.gnu.org/gcc-10/porting_to.html
"Default to -fno-common"
Andreas
--- End Message ---
--- Begin Message ---
Source: embassy-phylip
Source-Version: 3.69.660-4
Done: Shayan Doust <[email protected]>
We believe that the bug you reported is fixed in the latest version of
embassy-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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Shayan Doust <[email protected]> (supplier of updated embassy-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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 21 Sep 2020 15:38:28 +0000
Source: embassy-phylip
Architecture: source
Version: 3.69.660-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Shayan Doust <[email protected]>
Closes: 966127
Changes:
embassy-phylip (3.69.660-4) unstable; urgency=medium
.
* Team upload.
* Use old behaviour of gcc (via -fcommon) There are a lot of variables
to sort so simply use -fcommon for now (Closes: #966127)
* Standards-Version: 4.5.0 (routine-update)
* debhelper-compat 13 (routine-update)
* Remove trailing whitespace in debian/changelog (routine-update)
* Remove trailing whitespace in debian/copyright (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Set field Upstream-Name in debian/copyright.
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