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Bug 955075 - sci-chemistry/pymol-3.0.0-r1 - [gcc-15] x86_64-pc-linux-gnu-g++: fatal error: cannot read spec file libgomp.spec: No such file or directory
Summary: sci-chemistry/pymol-3.0.0-r1 - [gcc-15] x86_64-pc-linux-gnu-g++: fatal error:...
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal
Assignee: Gentoo Chemistry-Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2025-04-29 16:58 UTC by Toralf Förster
Modified: 2025-04-29 16:58 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


Attachments
emerge-info.txt (emerge-info.txt,20.71 KB, text/plain)
2025-04-29 16:58 UTC, Toralf Förster
Details
emerge-history.txt.xz (emerge-history.txt.xz,68.34 KB, application/x-xz)
2025-04-29 16:58 UTC, Toralf Förster
Details
environment (environment,168.37 KB, text/plain)
2025-04-29 16:58 UTC, Toralf Förster
Details
etc.clang.tar.xz (etc.clang.tar.xz,1.61 KB, application/x-xz)
2025-04-29 16:58 UTC, Toralf Förster
Details
etc.portage.tar.xz (etc.portage.tar.xz,55.36 KB, application/x-xz)
2025-04-29 16:58 UTC, Toralf Förster
Details
logs.tar.xz (logs.tar.xz,252 bytes, application/x-xz)
2025-04-29 16:58 UTC, Toralf Förster
Details
qlist-info.txt.xz (qlist-info.txt.xz,77.48 KB, application/x-xz)
2025-04-29 16:58 UTC, Toralf Förster
Details
sci-chemistry:pymol-3.0.0-r1:20250429-003615.log.xz (sci-chemistry:pymol-3.0.0-r1:20250429-003615.log.xz,15.73 KB, application/x-xz)
2025-04-29 16:58 UTC, Toralf Förster
Details
temp.tar.xz (temp.tar.xz,49.89 KB, application/x-xz)
2025-04-29 16:58 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2025-04-29 16:58:36 UTC
too long lines were shrinked:

2025-04-29 00:37:46,378 root INFO x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -std=c++17 -DNDEBUG -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_U
2025-04-29 00:37:50,191 root INFO x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -std=c++17 -DNDEBUG -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_U
2025-04-29 00:37:50,477 root INFO x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -std=c++17 -DNDEBUG -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_U
2025-04-29 00:37:53,868 root INFO x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -std=c++17 -DNDEBUG -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_U
2025-04-29 00:37:56,690 root INFO x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -std=c++17 -DNDEBUG -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_U
2025-04-29 00:37:59,071 root INFO x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-diagnostics-color -Werror=lto-type-mismatch -Werror=strict-aliasing -Werror=odr -flto -std=c++17 -DNDEBUG -shared -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0 -Werror
x86_64-pc-linux-gnu-g++: fatal error: cannot read spec file libgomp.spec: No such file or directory
compilation terminated.
error: command '/usr/bin/x86_64-pc-linux-gnu-g++' failed with exit code 1

  -------------------------------------------------------------------
  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 23.0_desktop_systemd-20250423-205002

  KEYWORDED/UNMASKED

  [gcc-15] Requested by sam
  <sys-devel/gcc-15.0.9999:15

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-14
 [2] x86_64-pc-linux-gnu-15 *
clang version 20.1.3
llvm-config: 20.1.3
Python 3.12.10
go version go1.24.2 linux/amd64
Available Ruby profiles:
  [1]   ruby32 (with Rubygems) *
Available Rust versions:
  [1]   rust-bin-1.86.0 *
The following VMs are available for generation-2:
1)	Eclipse Temurin JDK 11.0.26_p4 [openjdk-bin-11]
2)	Eclipse Temurin JDK 17.0.14_p7 [openjdk-bin-17]
*)	Eclipse Temurin JDK 21.0.7_p6 [openjdk-bin-21]
4)	Eclipse Temurin JDK 8.442_p06 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8 
  [2]   openjdk-bin-11 
  [3]   openjdk-bin-17 
  [4]   openjdk-bin-21  system-vm

  HEAD of ::gentoo
commit f7e19435026db92aaba1c15e4b5fa161f2d33fc4
Author: Repository mirror & CI <repomirrorci@gentoo.org>
Date:   Mon Apr 28 22:50:19 2025 +0000

    2025-04-28 22:50:19 UTC

The tinderbox task was: sci-chemistry/pymol

emerge -qpvO =sci-chemistry/pymol-3.0.0-r1
[ebuild  N    ] sci-chemistry/pymol-3.0.0-r1  USE="netcdf -debug -test -web" PYTHON_TARGETS="python3_12 -python3_11 -python3_13"
Comment 1 Toralf Förster gentoo-dev 2025-04-29 16:58:36 UTC
Created attachment 927007 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2025-04-29 16:58:38 UTC
Created attachment 927008 [details]
emerge-history.txt.xz
Comment 3 Toralf Förster gentoo-dev 2025-04-29 16:58:40 UTC
Created attachment 927009 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2025-04-29 16:58:41 UTC
Created attachment 927010 [details]
etc.clang.tar.xz
Comment 5 Toralf Förster gentoo-dev 2025-04-29 16:58:42 UTC
Created attachment 927011 [details]
etc.portage.tar.xz
Comment 6 Toralf Förster gentoo-dev 2025-04-29 16:58:43 UTC
Created attachment 927012 [details]
logs.tar.xz
Comment 7 Toralf Förster gentoo-dev 2025-04-29 16:58:44 UTC
Created attachment 927013 [details]
qlist-info.txt.xz
Comment 8 Toralf Förster gentoo-dev 2025-04-29 16:58:45 UTC
Created attachment 927014 [details]
sci-chemistry:pymol-3.0.0-r1:20250429-003615.log.xz
Comment 9 Toralf Förster gentoo-dev 2025-04-29 16:58:46 UTC
Created attachment 927015 [details]
temp.tar.xz