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

Bug 707150

Summary: sci-biology/phylip-3.696-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:phylip-3.696-r2:20200129-000011.log

Description Toralf Förster gentoo-dev 2020-01-29 17:42:46 UTC
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result   -c -o clique.o clique.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result   -c -o disc.o disc.c
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wno-unused-result   -c -o phylip.o phylip.c
x86_64-pc-linux-gnu-gcc -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -fno-common -Wno-unused-result clique.o disc.o phylip.o -lm -o clique
/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 `firstplotblock'; clique.o:(.bss+0x628): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: disc.o:(.bss+0x39): multiple definition of `javarun'; clique.o:(.bss+0x629): first defined here

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_desktop-libressl-20200125-232521

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

  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:
*)	IcedTea JDK 3.14.0 [icedtea-bin-8]
Available Java Virtual Machines:
  [1]   icedtea-bin-8  system-vm

repository:
==> /var/db/repos/gentoo/metadata/timestamp.chk <==
Tue, 28 Jan 2020 23:06:26 +0000

emerge -qpvO sci-biology/phylip
[ebuild  N    ] sci-biology/phylip-3.696-r2
Comment 1 Toralf Förster gentoo-dev 2020-01-29 17:42:49 UTC
Created attachment 607528 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2020-01-29 17:42:52 UTC
Created attachment 607530 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2020-01-29 17:42:55 UTC
Created attachment 607532 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2020-01-29 17:42:58 UTC
Created attachment 607534 [details]
etc.portage.tbz2
Comment 5 Toralf Förster gentoo-dev 2020-01-29 17:43:00 UTC
Created attachment 607536 [details]
sci-biology:phylip-3.696-r2:20200129-000011.log
Comment 6 Larry the Git Cow gentoo-dev 2020-10-27 20:56:35 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1f16dff22517a1d448e3d40e44621f2dd62c5c10

commit 1f16dff22517a1d448e3d40e44621f2dd62c5c10
Author:     David Seifert <soap@gentoo.org>
AuthorDate: 2020-10-27 20:56:18 +0000
Commit:     David Seifert <soap@gentoo.org>
CommitDate: 2020-10-27 20:56:18 +0000

    sci-biology/phylip: Remove old
    
    Closes: https://bugs.gentoo.org/707150
    Closes: https://bugs.gentoo.org/727982
    Package-Manager: Portage-3.0.8, Repoman-3.0.2
    Signed-off-by: David Seifert <soap@gentoo.org>

 sci-biology/phylip/Manifest               |  2 --
 sci-biology/phylip/phylip-3.69-r1.ebuild  | 51 ----------------------------
 sci-biology/phylip/phylip-3.696-r1.ebuild | 54 ------------------------------
 sci-biology/phylip/phylip-3.696-r2.ebuild | 55 -------------------------------
 4 files changed, 162 deletions(-)

Additionally, it has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fb89f8f6053ab2d65cd1c7b1604aa0a1df8bf216

commit fb89f8f6053ab2d65cd1c7b1604aa0a1df8bf216
Author:     David Seifert <soap@gentoo.org>
AuthorDate: 2020-10-27 20:56:15 +0000
Commit:     David Seifert <soap@gentoo.org>
CommitDate: 2020-10-27 20:56:15 +0000

    sci-biology/phylip: Version bump to 3.698
    
    Bug: https://bugs.gentoo.org/707150
    Bug: https://bugs.gentoo.org/727982
    Package-Manager: Portage-3.0.8, Repoman-3.0.2
    Signed-off-by: David Seifert <soap@gentoo.org>

 sci-biology/phylip/Manifest                        |   1 +
 .../phylip/files/phylip-3.698-fno-common.patch     |  70 ++++++
 .../phylip/files/phylip-3.698-makefile.patch       | 266 +++++++++++++++++++++
 sci-biology/phylip/phylip-3.698.ebuild             |  60 +++++
 4 files changed, 397 insertions(+)