Bug 938273

Summary:	sci-biology/muscle-5.1.0 - Fatal error: cant create Linux/efabestcols.o: No such file or directory
Product:	Gentoo Linux	Reporter:	Toralf Förster <toralf>
Component:	Current packages	Assignee:	Gentoo musl team <musl>
Status:	CONFIRMED ---
Severity:	normal	CC:	sci-biology
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	emerge-info.txt emerge-history.txt.xz environment etc.clang.tar.xz etc.portage.tar.xz qlist-info.txt.xz sci-biology:muscle-5.1.0:20240821-103122.log

Description Toralf Förster gentoo-dev

2024-08-21 12:14:19 UTC

make -j4 
x86_64-pc-linux-musl-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/randomchaintree.o randomchaintree.cpp
x86_64-pc-linux-musl-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/efabestcols.o efabestcols.cpp
x86_64-pc-linux-musl-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/getpairs.o getpairs.cpp
x86_64-pc-linux-musl-g++  -DNDEBUG -pthread -O2 -pipe -march=native -fno-diagnostics-color -fopenmp -ffast-math -c -o Linux/defaulthmmparams.o defaulthmmparams.cpp
Assembler messages:
Fatal error: can't create Linux/efabestcols.o: No such file or directory
Assembler messages:
Fatal error: can't create Linux/randomchaintree.o: No such file or directory

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 23.0_musl_hardened-20240815-231008

  Block bug #35155 if this looks like a parallel build issue.
  Possible reproducer: MAKEOPTS='...  shuffle=29637982'

  The attached etc.portage.tar.xz has all details.
  -------------------------------------------------------------------

GNUMAKEFLAGS="$GNUMAKEFLAGS --shuffle"
gcc-config -l:
 [1] x86_64-pc-linux-musl-14 *
clang/llvm (if any):
clang version 18.1.8
Target: x86_64-pc-linux-musl
Thread model: posix
InstalledDir: /usr/lib/llvm/18/bin
Configuration file: /etc/clang/x86_64-pc-linux-musl-clang.cfg
/usr/lib/llvm/18
18.1.8
Python 3.12.5
Available Ruby profiles:
  [1]   ruby31 (with Rubygems)
  [2]   ruby32 (with Rubygems)
  [3]   ruby33 (with Rubygems) *
Available Rust versions:
  [1]   rust-bin-1.80.1 *
The following VMs are available for generation-2:
php cli (if any):
go version go1.23.0 linux/amd64

  HEAD of ::gentoo
commit 9a05bf02e2af4ca933b28a40847ab9394e8c8c69
Author: Repository mirror & CI <repomirrorci@gentoo.org>
Date:   Wed Aug 21 09:49:44 2024 +0000

    2024-08-21 09:49:43 UTC

emerge -qpvO =sci-biology/muscle-5.1.0
[ebuild  N    ] sci-biology/muscle-5.1.0

Comment 1 Toralf Förster gentoo-dev

2024-08-21 12:14:20 UTC

Created attachment 900863 [details]
emerge-info.txt

Comment 2 Toralf Förster gentoo-dev

2024-08-21 12:14:21 UTC

Created attachment 900864 [details]
emerge-history.txt.xz

Comment 3 Toralf Förster gentoo-dev

2024-08-21 12:14:23 UTC

Created attachment 900865 [details]
environment

Comment 4 Toralf Förster gentoo-dev

2024-08-21 12:14:24 UTC

Created attachment 900866 [details]
etc.clang.tar.xz

Comment 5 Toralf Förster gentoo-dev

2024-08-21 12:14:25 UTC

Created attachment 900867 [details]
etc.portage.tar.xz

Comment 6 Toralf Förster gentoo-dev

2024-08-21 12:14:26 UTC

Created attachment 900868 [details]
qlist-info.txt.xz

Comment 7 Toralf Förster gentoo-dev

2024-08-21 12:14:27 UTC

Created attachment 900869 [details]
sci-biology:muscle-5.1.0:20240821-103122.log