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Bug 706960 - sci-biology/clustalw-mpi-0.13-r2 : fails to build with -fno-common or gcc-10
Summary: sci-biology/clustalw-mpi-0.13-r2 : 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: 2020-01-28 18:49 UTC by Toralf Förster
Modified: 2020-01-28 18:49 UTC (History)
0 users

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


Attachments
emerge-info.txt (emerge-info.txt,15.33 KB, text/plain)
2020-01-28 18:49 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,90.55 KB, text/plain)
2020-01-28 18:49 UTC, Toralf Förster
Details
environment (environment,46.29 KB, text/plain)
2020-01-28 18:49 UTC, Toralf Förster
Details
etc.portage.tbz2 (etc.portage.tbz2,12.64 KB, application/x-bzip)
2020-01-28 18:49 UTC, Toralf Förster
Details
sci-biology:clustalw-mpi-0.13-r2:20200128-142727.log (sci-biology:clustalw-mpi-0.13-r2:20200128-142727.log,12.51 KB, text/plain)
2020-01-28 18:49 UTC, Toralf Förster
Details
temp.tbz2 (temp.tbz2,13.89 KB, application/x-bzip)
2020-01-28 18:49 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2020-01-28 18:49:17 UTC
stupid.c:402:3: warning: implicit declaration of function ‘preverse_pass’ [-Wimplicit-function-declaration]
  402 |   preverse_pass(midi, A, B, M, N, go2, RR, SS, gS);
      |   ^~~~~~~~~~~~~
mpicc  -Wl,-O1 -Wl,--as-needed -o clustalw-mpi clustalw-mpi.o interface.o sequence.o showpair.o malign.o malign_mpi_progressive.o malign_mpi_pdiff.o util.o trees.o gcgcheck.o prfalign_mpi_pdiff.o prfalign_mpi_progressive.o pairalign_new.o calcgapcoeff.o calcprf1.o calcprf2.o calctree.o readmat.o alnscore.o random.o parallel_compare.o prfalign.o stupid.o -lm 
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x2c): multiple definition of `ktup'; showpair.o:(.bss+0x34): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: parallel_compare.o:(.bss+0x0): multiple definition of `zzd'; showpair.o:(.bss+0x0): first defined here

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_systemd-20200126-201521

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

  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]   python3.6
  [3]   python3.7 (fallback)
  [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 <==
Tue, 28 Jan 2020 12:46:19 +0000

emerge -qpvO sci-biology/clustalw-mpi
[ebuild  N    ] sci-biology/clustalw-mpi-0.13-r2  USE="-mpi_njtree -static_pairalign"
Comment 1 Toralf Förster gentoo-dev 2020-01-28 18:49:20 UTC
Created attachment 606850 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2020-01-28 18:49:23 UTC
Created attachment 606852 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2020-01-28 18:49:26 UTC
Created attachment 606854 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2020-01-28 18:49:29 UTC
Created attachment 606856 [details]
etc.portage.tbz2
Comment 5 Toralf Förster gentoo-dev 2020-01-28 18:49:32 UTC
Created attachment 606858 [details]
sci-biology:clustalw-mpi-0.13-r2:20200128-142727.log
Comment 6 Toralf Förster gentoo-dev 2020-01-28 18:49:35 UTC
Created attachment 606860 [details]
temp.tbz2