mkdir -p /var/tmp/portage/sci-biology/hmmer-2.3.2-r5/image/usr/share/man/man1 for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch ; do\ cp src/$file /var/tmp/portage/sci-biology/hmmer-2.3.2-r5/image/usr/bin/;\ done cp: cannot stat 'src/hmmalign': No such file or directory cp: cannot stat 'src/hmmbuild': No such file or directory cp: cannot stat 'src/hmmcalibrate': No such file or directory ------------------------------------------------------------------- This is an unstable amd64 chroot image at a tinderbox (==build bot) name: 17.1_no_multilib_systemd-j4-20221028-160004 ------------------------------------------------------------------- gcc-config -l: [1] x86_64-pc-linux-gnu-12 * clang/llvm (if any): clang version 15.0.3 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/lib/llvm/15/bin Configuration file: /etc/clang/clang.cfg /usr/lib/llvm/15 15.0.3 Python 3.10.8 Available Ruby profiles: [1] ruby27 (with Rubygems) [2] ruby31 (with Rubygems) * Available Rust versions: [1] rust-bin-1.64.0 * The following VMs are available for generation-2: 1) Eclipse Temurin JDK 17.0.4.1_p1 [openjdk-bin-17] *) Eclipse Temurin JDK 8.345_p01 [openjdk-bin-8] Available Java Virtual Machines: [1] openjdk-bin-8 system-vm [2] openjdk-bin-17 The Glorious Glasgow Haskell Compilation System, version 9.0.2 php cli (if any): GNU Make 4.3 HEAD of ::gentoo commit 7cd1beeccdd8ae4cb750e44548665dd91a53826f Author: Repository mirror & CI <repomirrorci@gentoo.org> Date: Fri Oct 28 23:01:59 2022 +0000 2022-10-28 23:01:58 UTC emerge -qpvO sci-biology/hmmer [ebuild N ] sci-biology/hmmer-3.1_beta2-r1 USE="-gsl -mpi -test" CPU_FLAGS_X86="sse"
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Okay, it fails because it's not including pthread in the hmmcalibrate.c It sets in config.h #define HMMER_THREADS 1 so it should include pthread.h I can't reproduce this and I can't understand how this situation is even possible barring very damaged system or libc with bad implementation of pthreads.
Can't reproduce
