Bug 721278

Summary:	sci-biology/mcl-14.137 : /.../ld: error: report.o: multiple definition of mclx_n_thread_g
Product:	Gentoo Linux	Reporter:	Toralf Förster <toralf>
Component:	Current packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	RESOLVED DUPLICATE
Severity:	normal
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Bug Depends on:
Bug Blocks:	705764
Attachments:	emerge-info.txt emerge-history.txt environment etc.portage.tbz2 logs.tbz2 sci-biology:mcl-14.137:20200506-142200.log temp.tbz2

Description Toralf Förster gentoo-dev

2020-05-06 14:51:37 UTC

x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../..    -O2 -pipe -march=native  -falign-functions=32:25:16 -fno-common -pthread -c -o report.o report.c
x86_64-pc-linux-gnu-gcc  -O2 -pipe -march=native  -falign-functions=32:25:16 -fno-common -pthread -lm -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o clmformat clmformat.o report.o ../mcl/libmcl.a ../clew/libclew.a  ../gryphon/libgryphon.a ../impala/libimpala.a ../../util/libutil.a -lm 
/usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: error: report.o: multiple definition of mclx_n_thread_g
/usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: clmformat.o: previous definition here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: error: report.o: multiple definition of nu_magic
/usr/lib/gcc/x86_64-pc-linux-gnu/9.3.0/../../../../x86_64-pc-linux-gnu/bin/ld: clmformat.o: previous definition here

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_hardened-abi32+64-20200503-182741

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-9.3.0 *
clang version 10.0.0 
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm/10/bin
/usr/lib/llvm/10
10.0.0
Available Python interpreters, in order of preference:
  [1]   python3.6
  [2]   python3.8 (fallback)
  [3]   python2.7 (fallback)
  [4]   pypy3 (fallback)
Available Ruby profiles:
  [1]   ruby24 (with Rubygems)
  [2]   ruby25 (with Rubygems) *
The following VMs are available for generation-2:
*)	AdoptOpenJDK 8.252_p09 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8  system-vm

The Glorious Glasgow Haskell Compilation System, version 8.0.2

  timestamp(s) of HEAD at this tinderbox image:
/var/db/repos/gentoo	Wed 06 May 2020 01:38:59 PM UTC

emerge -qpvO sci-biology/mcl
[ebuild  N    ] sci-biology/mcl-14.137  USE="blast"

Comment 1 Toralf Förster gentoo-dev

2020-05-06 14:51:40 UTC

Created attachment 636474 [details]
emerge-info.txt

Comment 2 Toralf Förster gentoo-dev

2020-05-06 14:51:43 UTC

Created attachment 636476 [details]
emerge-history.txt

Comment 3 Toralf Förster gentoo-dev

2020-05-06 14:51:45 UTC

Created attachment 636478 [details]
environment

Comment 4 Toralf Förster gentoo-dev

2020-05-06 14:51:48 UTC

Created attachment 636480 [details]
etc.portage.tbz2

Comment 5 Toralf Förster gentoo-dev

2020-05-06 14:51:50 UTC

Created attachment 636482 [details]
logs.tbz2

Comment 6 Toralf Förster gentoo-dev

2020-05-06 14:51:53 UTC

Created attachment 636484 [details]
sci-biology:mcl-14.137:20200506-142200.log

Comment 7 Toralf Förster gentoo-dev

2020-05-06 14:51:56 UTC

Created attachment 636486 [details]
temp.tbz2

Comment 8 Jeroen Roovers (RETIRED) gentoo-dev

2020-05-21 11:50:13 UTC


*** This bug has been marked as a duplicate of bug 706530 ***