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Bug 706414 - sci-biology/embassy-phylipnew-3.69.660 : fails to build with -fno-common or gcc-10
Summary: sci-biology/embassy-phylipnew-3.69.660 : fails to build with -fno-common or g...
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
: 720988 (view as bug list)
Depends on:
Blocks: -fno-common
  Show dependency tree
 
Reported: 2020-01-26 10:09 UTC by Toralf Förster
Modified: 2020-05-21 11:49 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


Attachments
emerge-info.txt (emerge-info.txt,15.11 KB, text/plain)
2020-01-26 10:09 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,84.17 KB, text/plain)
2020-01-26 10:09 UTC, Toralf Förster
Details
environment (environment,101.51 KB, text/plain)
2020-01-26 10:10 UTC, Toralf Förster
Details
etc.portage.tbz2 (etc.portage.tbz2,11.77 KB, application/x-bzip)
2020-01-26 10:10 UTC, Toralf Förster
Details
logs.tbz2 (logs.tbz2,11.27 KB, application/x-bzip)
2020-01-26 10:10 UTC, Toralf Förster
Details
sci-biology:embassy-phylipnew-3.69.660:20200126-094738.log (sci-biology:embassy-phylipnew-3.69.660:20200126-094738.log,13.16 KB, text/plain)
2020-01-26 10:10 UTC, Toralf Förster
Details
temp.tbz2 (temp.tbz2,28.44 KB, application/x-bzip)
2020-01-26 10:10 UTC, Toralf Förster
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Toralf Förster gentoo-dev 2020-01-26 10:09:53 UTC
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.  -I../include -I/usr/include  -I/usr/include/plplot  -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64    -O2 -pipe -march=native -fno-common  -O2 -c -o disc.o disc.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I.  -I../include -I/usr/include  -I/usr/include/plplot  -I/usr/include/emboss -DAJ_LinuxLF -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64    -O2 -pipe -march=native -fno-common  -O2 -c -o phylip.o phylip.c
/bin/sh ../libtool  --tag=CC   --mode=link x86_64-pc-linux-gnu-gcc    -O2 -pipe -march=native -fno-common  -O2  -Wl,-O1 -Wl,--as-needed -o fclique clique.o disc.o phylip.o -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax   -lm 
libtool: link: x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -O2 -Wl,-O1 -o fclique clique.o disc.o phylip.o  -Wl,--as-needed -L/usr/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -lm
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: disc.o:(.bss+0x38): multiple definition of `phylostates'; clique.o:(.bss+0x4a0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: phylip.o:(.bss+0x50): multiple definition of `embossouttree'; clique.o:(.bss+0xf8): first defined here

  -------------------------------------------------------------------

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_no-multilib-20200124-204141

  -------------------------------------------------------------------

  Please see the tracker bug for details.

gcc-config -l:
 [1] x86_64-pc-linux-gnu-9.2.0 *


llvm:
9.0.1
Available Python interpreters, in order of preference:
  [1]   python3.7
  [2]   python3.6
  [3]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby24 (with Rubygems)
  [2]   ruby25 (with Rubygems) *
Available Rust versions:
  [1]   rust-1.40.0 *



repository:
==> /var/db/repos/gentoo/metadata/timestamp.chk <==
Sun, 26 Jan 2020 08:26:14 +0000

emerge -qpvO sci-biology/embassy-phylipnew
[ebuild  N    ] sci-biology/embassy-phylipnew-3.69.660  USE="-X -mysql -pdf -png -postgres -static-libs"
Comment 1 Toralf Förster gentoo-dev 2020-01-26 10:09:56 UTC
Created attachment 604564 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2020-01-26 10:09:59 UTC
Created attachment 604566 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2020-01-26 10:10:02 UTC
Created attachment 604568 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2020-01-26 10:10:05 UTC
Created attachment 604570 [details]
etc.portage.tbz2
Comment 5 Toralf Förster gentoo-dev 2020-01-26 10:10:07 UTC
Created attachment 604572 [details]
logs.tbz2
Comment 6 Toralf Förster gentoo-dev 2020-01-26 10:10:10 UTC
Created attachment 604574 [details]
sci-biology:embassy-phylipnew-3.69.660:20200126-094738.log
Comment 7 Toralf Förster gentoo-dev 2020-01-26 10:10:13 UTC
Created attachment 604576 [details]
temp.tbz2
Comment 8 Jeroen Roovers gentoo-dev 2020-05-21 11:49:21 UTC
*** Bug 720988 has been marked as a duplicate of this bug. ***