Bug 706348 – sci-biology/bwa-0.7.16a : fails to build with -fno-common or gcc-10

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Toralf Förster 2020-01-25 19:07:06 UTC]

x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  fastmap.c -o fastmap.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_pair.c -o bwtsw2_pair.o
x86_64-pc-linux-gnu-gcc -c -O2 -pipe -march=native -fno-common -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  main.c -o main.o
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ./libbwa.a(rope.o):(.rodata+0x30): multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):(.rodata+0x58): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ./libbwa.a(rle.o):(.rodata+0x0): multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):(.rodata+0x58): first defined here

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

  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 *


llvm:
9.0.1
Available Python interpreters, in order of preference:
  [1]   python3.7
  [2]   python3.6
  [3]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby24 (with Rubygems)
  [2]   ruby25 (with Rubygems) *
Available Rust versions:
  [1]   rust-1.40.0 *



repository:
==> /var/db/repos/gentoo/metadata/timestamp.chk <==
Sat, 25 Jan 2020 17:46:40 +0000

emerge -qpvO sci-biology/bwa
[ebuild  N    ] sci-biology/bwa-0.7.16a

[Comment 1 Toralf Förster 2020-01-25 19:07:08 UTC]

Created attachment 604356 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2020-01-25 19:07:11 UTC]

Created attachment 604358 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2020-01-25 19:07:14 UTC]

Created attachment 604360 [details]
environment

[Comment 4 Toralf Förster 2020-01-25 19:07:16 UTC]

Created attachment 604362 [details]
etc.portage.tbz2

[Comment 5 Toralf Förster 2020-01-25 19:07:19 UTC]

Created attachment 604364 [details]
sci-biology:bwa-0.7.16a:20200125-182142.log

[Comment 6 Toralf Förster 2020-01-25 19:07:22 UTC]

Created attachment 604366 [details]
temp.tbz2

[Comment 7 Sergei Trofimovich (RETIRED) 2020-01-25 19:29:26 UTC]

Created attachment 604382 [details, diff]
bwa-0.7.16a-gcc-10.patch

[Comment 8 Larry the Git Cow 2020-01-25 19:38:52 UTC]

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=71f83be9beeb1ed4c39d0e0ad442a8aba54a2c8c

commit 71f83be9beeb1ed4c39d0e0ad442a8aba54a2c8c
Author:     David Seifert <[e-mail]>
AuthorDate: 2020-01-25 19:38:35 +0000
Commit:     David Seifert <[e-mail]>
CommitDate: 2020-01-25 19:38:35 +0000

    sci-biology/bwa: Fix -fno-common bug
    
    Closes: https://bugs.gentoo.org/706348
    Package-Manager: Portage-2.3.85, Repoman-2.3.20
    Signed-off-by: David Seifert <[e-mail]>

 sci-biology/bwa/bwa-0.7.16a.ebuild             | 10 ++++++----
 sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch |  7 +++++++
 2 files changed, 13 insertions(+), 4 deletions(-)