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
Created attachment 604356 [details] emerge-info.txt
Created attachment 604358 [details] emerge-history.txt
Created attachment 604360 [details] environment
Created attachment 604362 [details] etc.portage.tbz2
Created attachment 604364 [details] sci-biology:bwa-0.7.16a:20200125-182142.log
Created attachment 604366 [details] temp.tbz2
Created attachment 604382 [details, diff] bwa-0.7.16a-gcc-10.patch
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 <soap@gentoo.org> AuthorDate: 2020-01-25 19:38:35 +0000 Commit: David Seifert <soap@gentoo.org> 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 <soap@gentoo.org> 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(-)