Bug 688074 – sci-chemistry/gromacs-2019.3 : ninja: build stopped: subcommand failed.

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Toralf Förster 2019-06-14 17:23:26 UTC]

Output written on gromacs.pdf (558 pages, 12352527 bytes).
Transcript written on gromacs.log.
ninja: build stopped: subcommand failed.
 * ERROR: sci-chemistry/gromacs-2019.3::gentoo failed (compile phase):
 *   ninja -v -j1 -l0 manual failed
 * 

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1-desktop-gnome-systemd_20190608-211904

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-9.1.0 *

Available Python interpreters, in order of preference:
  [1]   python3.6
  [2]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby24 (with Rubygems) *
Available Rust versions:
  [1]   rust-1.35.0 *
java-config:
The following VMs are available for generation-2:
1)	IcedTea JDK 3.12.0 [icedtea-8]
*)	IcedTea JDK 3.12.0 [icedtea-bin-8]
Available Java Virtual Machines:
  [1]   icedtea-8 
  [2]   icedtea-bin-8  system-vm

emerge -qpvO sci-chemistry/gromacs
[ebuild     U ] sci-chemistry/gromacs-2019.3 [2018.7] USE="X doc fftw gmxapi%* hwloc lmfit%* offensive openmp single-precision threads tng -blas -cuda -double-precision -lapack -mkl -mpi -opencl -test" CPU_FLAGS_X86="avx avx2 sse2 sse4_1 -fma4" PYTHON_TARGETS="python2_7%*"

[Comment 1 Toralf Förster 2019-06-14 17:23:29 UTC]

according to last comment in bug #673340 this is another issue then?

[Comment 2 Toralf Förster 2019-06-14 17:23:32 UTC]

Created attachment 579780 [details]
emerge-info.txt

[Comment 3 Toralf Förster 2019-06-14 17:23:35 UTC]

Created attachment 579782 [details]
emerge-history.txt

[Comment 4 Toralf Förster 2019-06-14 17:23:37 UTC]

Created attachment 579784 [details]
environment

[Comment 5 Toralf Förster 2019-06-14 17:23:40 UTC]

Created attachment 579786 [details]
etc.portage.tbz2

[Comment 6 Toralf Förster 2019-06-14 17:23:43 UTC]

Created attachment 579788 [details]
logs.tbz2

[Comment 7 Toralf Förster 2019-06-14 17:23:45 UTC]

Created attachment 579790 [details]
sci-chemistry:gromacs-2019.3:20190614-155922.log.bz2

[Comment 8 Toralf Förster 2019-06-14 17:23:48 UTC]

Created attachment 579792 [details]
temp.tbz2

[Comment 9 Alexey Shvetsov 2019-06-19 08:48:05 UTC]

Looks like i missing some deps... So i'll try to check it with pure stage3 lxc container

[Comment 10 Larry the Git Cow 2019-07-07 14:30:58 UTC]

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c89206b88338218fcfd234e0977940c24e526ae6

commit c89206b88338218fcfd234e0977940c24e526ae6
Author:     Alexey Shvetsov <[e-mail]>
AuthorDate: 2019-07-07 14:30:15 +0000
Commit:     Alexey Shvetsov <[e-mail]>
CommitDate: 2019-07-07 14:30:15 +0000

    sci-chemistry/gromacs: Add missing dep for docs
    
    GROMACS need graphviz to build doc
    
    Closes: https://bugs.gentoo.org/688074
    Package-Manager: Portage-2.3.68, Repoman-2.3.16
    Signed-off-by: Alexey Shvetsov <[e-mail]>

 sci-chemistry/gromacs/gromacs-2019.2.ebuild    | 1 +
 sci-chemistry/gromacs/gromacs-2019.3.ebuild    | 1 +
 sci-chemistry/gromacs/gromacs-2019.9999.ebuild | 1 +
 3 files changed, 3 insertions(+)