| 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 packages | Assignee: | 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 |
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Created attachment 606850 [details]
emerge-info.txt
Created attachment 606852 [details]
emerge-history.txt
Created attachment 606854 [details]
environment
Created attachment 606856 [details]
etc.portage.tbz2
Created attachment 606858 [details]
sci-biology:clustalw-mpi-0.13-r2:20200128-142727.log
Created attachment 606860 [details]
temp.tbz2
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(-) |
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"