Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!

Bug 706960

Summary: sci-biology/clustalw-mpi-0.13-r2 : fails to build with -fno-common or gcc-10
Product: Gentoo Linux Reporter: Toralf Förster <toralf>
Component: Current packagesAssignee: Gentoo Science Biology related packages <sci-biology>
Status: RESOLVED FIXED    
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
sci-biology:clustalw-mpi-0.13-r2:20200128-142727.log
temp.tbz2

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
Comment 7 Larry the Git Cow gentoo-dev 2020-11-01 18:36:49 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c76141a9ed378795deac9e8fdd8f9ff5e6b1b91b

commit c76141a9ed378795deac9e8fdd8f9ff5e6b1b91b
Author:     David Seifert <soap@gentoo.org>
AuthorDate: 2020-11-01 18:36:24 +0000
Commit:     David Seifert <soap@gentoo.org>
CommitDate: 2020-11-01 18:36:24 +0000

    sci-biology/clustalw-mpi: Port to EAPI 7
    
    * Rename USE flags to avoid underscore
    * Fix building against GCC 10 / -fno-common
    
    Closes: https://bugs.gentoo.org/695122
    Closes: https://bugs.gentoo.org/706960
    Package-Manager: Portage-3.0.8, Repoman-3.0.2
    Signed-off-by: David Seifert <soap@gentoo.org>

 ...mpi-0.13-r2.ebuild => clustalw-mpi-0.13-r3.ebuild} | 19 +++++++++++--------
 .../files/clustalw-mpi-0.13-fno-common.patch          | 13 +++++++++++++
 ...-gentoo.patch => clustalw-mpi-0.13-makefile.patch} |  0
 sci-biology/clustalw-mpi/metadata.xml                 | 18 ++++++++----------
 4 files changed, 32 insertions(+), 18 deletions(-)