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Bug 707166 - sci-biology/meme-4.11.2_p2 : fails to build with -fno-common or gcc-10
Summary: sci-biology/meme-4.11.2_p2 : fails to build with -fno-common or gcc-10
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:
Depends on:
Blocks: -fno-common
  Show dependency tree
 
Reported: 2020-01-29 17:51 UTC by Toralf Förster
Modified: 2020-01-29 17:52 UTC (History)
0 users

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


Attachments
emerge-info.txt (emerge-info.txt,16.13 KB, text/plain)
2020-01-29 17:52 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,215.69 KB, text/plain)
2020-01-29 17:52 UTC, Toralf Förster
Details
environment (environment,117.98 KB, text/plain)
2020-01-29 17:52 UTC, Toralf Förster
Details
etc.portage.tbz2 (etc.portage.tbz2,15.95 KB, application/x-bzip)
2020-01-29 17:52 UTC, Toralf Förster
Details
logs.tbz2 (logs.tbz2,12.15 KB, application/x-bzip)
2020-01-29 17:52 UTC, Toralf Förster
Details
sci-biology:meme-4.11.2_p2:20200129-020308.log (sci-biology:meme-4.11.2_p2:20200129-020308.log,137.11 KB, text/plain)
2020-01-29 17:52 UTC, Toralf Förster
Details
temp.tbz2 (temp.tbz2,39.43 KB, application/x-bzip)
2020-01-29 17:52 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2020-01-29 17:51:57 UTC
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..   -DUNIX -D__USE_FIXED_PROTOTYPES__  -DMAIN  -I/usr/include/libxml2  -std=gnu89 -Wall -Wno-unused -O2 -pipe -march=native -fno-common   -c -o ame-ramen_scan.o `test -f 'ramen_scan.c' || echo './'`ramen_scan.c
x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I..   -DUNIX -D__USE_FIXED_PROTOTYPES__  -DMAIN  -I/usr/include/libxml2  -std=gnu89 -Wall -Wno-unused -O2 -pipe -march=native -fno-common   -c -o ame-fisher_exact.o `test -f 'fisher_exact.c' || echo './'`fisher_exact.c
/bin/sh ../libtool  --tag=CC   --mode=link x86_64-pc-linux-gnu-gcc -DMAIN  -I/usr/include/libxml2  -std=gnu89 -Wall -Wno-unused -O2 -pipe -march=native -fno-common    -Wl,-O1 -Wl,--as-needed -o ame ame-ame.o ame-ramen_scan.o ame-fisher_exact.o libcommon.la -lxml2  -lm  -lmpi -lz -lm 
libtool: link: x86_64-pc-linux-gnu-gcc -DMAIN -I/usr/include/libxml2 -std=gnu89 -Wall -Wno-unused -O2 -pipe -march=native -fno-common -Wl,-O1 -o ame ame-ame.o ame-ramen_scan.o ame-fisher_exact.o  -Wl,--as-needed ./.libs/libcommon.a -lexslt -lxslt -lgcrypt -lgpg-error -lxml2 -lmpi -lz -lm
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ame-fisher_exact.o:(.bss+0x20): multiple definition of `log_factorial'; ame-ame.o:(.bss+0x0): first defined here
collect2: error: ld returned 1 exit status

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

  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 *

clang:
clang version 9.0.1 
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm/9/bin
llvm:
9.0.1
Available Python interpreters, in order of preference:
  [1]   python3.8
  [2]   python3.7
  [3]   python3.6
  [4]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby24 (with Rubygems)
  [2]   ruby25 (with Rubygems) *
Available Rust versions:
  [1]   rust-1.40.0 *
java-config:
The following VMs are available for generation-2:
*)	AdoptOpenJDK 8.242_p08 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8  system-vm

repository:
==> /var/db/repos/gentoo/metadata/timestamp.chk <==
Wed, 29 Jan 2020 00:26:22 +0000

emerge -qpvO sci-biology/meme
[ebuild  N    ] sci-biology/meme-4.11.2_p2  USE="-debug -doc -examples -mpi" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7"
Comment 1 Toralf Förster gentoo-dev 2020-01-29 17:52:00 UTC
Created attachment 607630 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2020-01-29 17:52:02 UTC
Created attachment 607632 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2020-01-29 17:52:05 UTC
Created attachment 607634 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2020-01-29 17:52:08 UTC
Created attachment 607636 [details]
etc.portage.tbz2
Comment 5 Toralf Förster gentoo-dev 2020-01-29 17:52:10 UTC
Created attachment 607638 [details]
logs.tbz2
Comment 6 Toralf Förster gentoo-dev 2020-01-29 17:52:13 UTC
Created attachment 607640 [details]
sci-biology:meme-4.11.2_p2:20200129-020308.log
Comment 7 Toralf Förster gentoo-dev 2020-01-29 17:52:16 UTC
Created attachment 607642 [details]
temp.tbz2