Bug 755818 – [science overlay] sci-physics/atompaw-4.0.0.14 : configure: error: no working linear algebra libraries have been found

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Toralf Förster 2020-11-20 15:57:39 UTC]

checking how to hardcode library paths into programs... immediate
checking whether linear algebra libraries work... no
configure: error: no working linear algebra libraries have been found

!!! Please attach the following file when seeking support:
!!! /var/tmp/portage/sci-physics/atompaw-4.0.0.14/work/atompaw-4.0.0.14_build/config.log

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

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_no-multilib-libressl_science-20201116-220441

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

gcc-config -l:
 [1] x86_64-pc-linux-gnu-10.2.0 *
/usr/lib/llvm/11
11.0.0
Available Python interpreters, in order of preference:
  [1]   python3.7
  [2]   python3.9 (fallback)
  [3]   python3.8 (fallback)
  [4]   python2.7 (fallback)
The following VMs are available for generation-2:
*)	AdoptOpenJDK 8.272_p10 [openjdk-bin-8]
Available Java Virtual Machines:
  [1]   openjdk-bin-8  system-vm

The Glorious Glasgow Haskell Compilation System, version 8.8.4

  timestamp(s) of HEAD at this tinderbox image:
/var/db/repos/gentoo	Fri Nov 20 02:35:36 AM UTC 2020
/var/db/repos/libressl	Sat Nov  7 03:06:11 PM UTC 2020

emerge -qpvO sci-physics/atompaw
[ebuild  N    ] sci-physics/atompaw-4.0.0.14  USE="-doc -libxc -longplot -test"

[Comment 1 Toralf Förster 2020-11-20 15:57:40 UTC]

Created attachment 673852 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2020-11-20 15:57:42 UTC]

Created attachment 673855 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2020-11-20 15:57:43 UTC]

Created attachment 673858 [details]
environment

[Comment 4 Toralf Förster 2020-11-20 15:57:44 UTC]

Created attachment 673861 [details]
etc.portage.tbz2

[Comment 5 Toralf Förster 2020-11-20 15:57:45 UTC]

Created attachment 673864 [details]
logs.tbz2

[Comment 6 Toralf Förster 2020-11-20 15:57:47 UTC]

Created attachment 673867 [details]
sci-physics:atompaw-4.0.0.14:20201120-035015.log

[Comment 7 Toralf Förster 2020-11-20 15:57:48 UTC]

Created attachment 673870 [details]
temp.tbz2

[Comment 8 Honza Macháček 2020-12-03 12:32:46 UTC]

Created attachment 676414 [details, diff]
Ask pkgconfig for both LAPACK and BLAS

This bug is easy. Once upon a time the pkgconfig for LAPACK used to report the necessary parameters for BLAS as well. Some time ago, I don't remember when and why, the pkgconfig data for LAPACK were narrowed strictly to LAPACK, so asking pkgconfig for BLAS too is now necessary.

[Comment 9 Honza Macháček 2020-12-03 12:36:58 UTC]

Created attachment 676417 [details, diff]
Update atompaw to the latest version, 4.1.0.6

Since the time I lost track of the development in the science overlay, dropped off contributing and started to update my ebuilds only in my personal overlay, atompaw got several updates. One important is its adaptation to the new API of the libxc, that was changed between its versions 2.1 and 2.2. The curent libxc version is 5.0.0, so its high time to update.

[Comment 10 Sam James 2020-12-03 12:37:48 UTC]

(In reply to Honza Macháček from comment #9)
> Created attachment 676417 [details, diff] [details, diff]
> Update atompaw to the latest version, 4.1.0.6
> 
> Since the time I lost track of the development in the science overlay,
> dropped off contributing and started to update my ebuilds only in my
> personal overlay, atompaw got several updates. One important is its
> adaptation to the new API of the libxc, that was changed between its
> versions 2.1 and 2.2. The curent libxc version is 5.0.0, so its high time to
> update.

Could you give the GCO sign off in a comment here so we can use these (both patches)?

[Comment 11 Aisha Tammy 2020-12-03 12:51:41 UTC]

Hmm, might be easier on everyone to make a PR in ::science?
Of course, if you don't want to use github, here is fine too.

[Comment 12 Honza Macháček 2020-12-04 07:32:27 UTC]

(In reply to Sam James from comment #10)
> Could you give the GCO sign off in a comment here so we can use these (both
> patches)?

I had to first look up what GCO is. As long as this form is acceptable I hereby sign off the Gentoo Certificate of Origin for both my patches. Jan Macháček <[e-mail]>

[Comment 13 Honza Macháček 2020-12-04 07:42:22 UTC]

(In reply to Aisha Tammy from comment #11)
> Hmm, might be easier on everyone to make a PR in ::science?
> Of course, if you don't want to use github, here is fine too.

Thats what I'm planning to start doing since I've found out my old access to contributing to the science overlay no longer works, and I've recalled reading somwhere something about a migration to Github. Somehow I've never yet found enough time to look for the information how to use Github, to read that information, and to start contributing the new way.

Maybe sometimes in the future, while cleaning my various past debts.

[Comment 14 Larry the Git Cow 2020-12-11 18:55:09 UTC]

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

https://gitweb.gentoo.org/proj/sci.git/commit/?id=38fa02c8cc33f0dfc7dc8fe9788b583e9dd22d3b

commit 38fa02c8cc33f0dfc7dc8fe9788b583e9dd22d3b
Author:     Aisha Tammy <[e-mail]>
AuthorDate: 2020-12-09 21:42:30 +0000
Commit:     Aisha Tammy <[e-mail]>
CommitDate: 2020-12-11 18:55:04 +0000

    sci-physics/atompaw: fix linking to blas
    
    Closes: https://bugs.gentoo.org/755818
    
    Jan Macháček <[e-mail]>
    Package-Manager: Portage-3.0.11, Repoman-3.0.2
    Signed-off-by: Aisha Tammy <[e-mail]>

 sci-physics/atompaw/Manifest                | 4 ++--
 sci-physics/atompaw/atompaw-4.0.0.14.ebuild | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)