octave won't run

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octave won't run

karl
Octave won't run since a lib is missing.
I can re-emerge it without problems, but the problem still
persist. The lib is there but it has a different version.

Anyone know what this is about ?

$ ldd /usr/bin/octave-cli-4.2.2 | grep not
        liblapack.so.0 => not found
$ ls -l /usr/lib64/liblapack.*
lrwxrwxrwx 1 root root      28 May  9  2019 /usr/lib64/liblapack.a -> lapack/reference/liblapack.a
lrwxrwxrwx 1 root root      14 Nov 29 00:30 /usr/lib64/liblapack.so -> liblapack.so.3
lrwxrwxrwx 1 root root      18 Nov 29 00:30 /usr/lib64/liblapack.so.3 -> liblapack.so.3.8.0
-rwxr-xr-x 1 root root 6886896 Nov 29 00:29 /usr/lib64/liblapack.so.3.8.0

Regards,
/Karl Hammar



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Re: octave won't run

Mick-10
On Thursday, 6 February 2020 08:28:05 GMT [hidden email] wrote:

> Octave won't run since a lib is missing.
> I can re-emerge it without problems, but the problem still
> persist. The lib is there but it has a different version.
>
> Anyone know what this is about ?
>
> $ ldd /usr/bin/octave-cli-4.2.2 | grep not
>         liblapack.so.0 => not found
> $ ls -l /usr/lib64/liblapack.*
> lrwxrwxrwx 1 root root      28 May  9  2019 /usr/lib64/liblapack.a ->
> lapack/reference/liblapack.a lrwxrwxrwx 1 root root      14 Nov 29 00:30
> /usr/lib64/liblapack.so -> liblapack.so.3 lrwxrwxrwx 1 root root      18
> Nov 29 00:30 /usr/lib64/liblapack.so.3 -> liblapack.so.3.8.0 -rwxr-xr-x 1
> root root 6886896 Nov 29 00:29 /usr/lib64/liblapack.so.3.8.0
>
> Regards,
> /Karl Hammar
I don't have these packages on my systems to check, but does 'eselect lapack
list' reveal anything amiss?

Otherwise the latest sci-libs/lapack is 3.8.0, so your links above look
correct as far as I can tell.
--
Regards,

Mick

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Re: octave won't run

karl
Mick:
...
> I don't have these packages on my systems to check, but does 'eselect lapack
> list' reveal anything amiss?
...

$ eselect lapack list
Available LAPACK (lib) candidates:
  (none found)
Available LAPACK (lib64) candidates:
  (none found)
$ eselect blas list
Available BLAS/CBLAS (lib) candidates:
  (none found)
Available BLAS/CBLAS (lib64) candidates:
  (none found)

and after rebuilding lapack with eselect-ldso

$ eselect lapack list
Available LAPACK (lib) candidates:
  (none found)
Available LAPACK (lib64) candidates:
  [1]   reference *
$ eselect blas list
Available BLAS/CBLAS (lib) candidates:
  (none found)
Available BLAS/CBLAS (lib64) candidates:
  [1]   reference *

still same problem.

recompiling octave, same problem.
recompiling octave with  static-libs, same problem.

Regards,
/Karl Hammar


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Re: octave won't run

Mick-10
On Thursday, 6 February 2020 13:44:22 GMT [hidden email] wrote:

> Mick:
> ...
>
> > I don't have these packages on my systems to check, but does 'eselect
> > lapack list' reveal anything amiss?
>
> ...
>
> $ eselect lapack list
> Available LAPACK (lib) candidates:
>   (none found)
> Available LAPACK (lib64) candidates:
>   (none found)
> $ eselect blas list
> Available BLAS/CBLAS (lib) candidates:
>   (none found)
> Available BLAS/CBLAS (lib64) candidates:
>   (none found)
>
> and after rebuilding lapack with eselect-ldso
>
> $ eselect lapack list
> Available LAPACK (lib) candidates:
>   (none found)
> Available LAPACK (lib64) candidates:
>   [1]   reference *
> $ eselect blas list
> Available BLAS/CBLAS (lib) candidates:
>   (none found)
> Available BLAS/CBLAS (lib64) candidates:
>   [1]   reference *
>
> still same problem.
>
> recompiling octave, same problem.
> recompiling octave with  static-libs, same problem.
>
> Regards,
> /Karl Hammar
Unless someone shows up with more knowledge on the specifics it would be worth
posting a bug, or contacting the maintainer for suggestions.
--
Regards,

Mick

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Re: octave won't run

Mark Knecht
Sounds like a ebuild dependency bug, or possibly a bad mix of stable and non-stable packages that haven't been sussed out fully.

Not a good long-term solution, especially if you're forgetful like me, but as a test you might try creating a symlink for libapack.so.0 pointing to libapack.so.3 and see if octave runs. 

Best to remove that more or less right away but it might get you through a test period waiting for the ebuild to get fixed.

- Mark

On Thu, Feb 6, 2020 at 6:59 AM Mick <[hidden email]> wrote:
On Thursday, 6 February 2020 13:44:22 GMT [hidden email] wrote:
> Mick:
> ...
>
> > I don't have these packages on my systems to check, but does 'eselect
> > lapack list' reveal anything amiss?
>
> ...
>
> $ eselect lapack list
> Available LAPACK (lib) candidates:
>   (none found)
> Available LAPACK (lib64) candidates:
>   (none found)
> $ eselect blas list
> Available BLAS/CBLAS (lib) candidates:
>   (none found)
> Available BLAS/CBLAS (lib64) candidates:
>   (none found)
>
> and after rebuilding lapack with eselect-ldso
>
> $ eselect lapack list
> Available LAPACK (lib) candidates:
>   (none found)
> Available LAPACK (lib64) candidates:
>   [1]   reference *
> $ eselect blas list
> Available BLAS/CBLAS (lib) candidates:
>   (none found)
> Available BLAS/CBLAS (lib64) candidates:
>   [1]   reference *
>
> still same problem.
>
> recompiling octave, same problem.
> recompiling octave with  static-libs, same problem.
>
> Regards,
> /Karl Hammar

Unless someone shows up with more knowledge on the specifics it would be worth
posting a bug, or contacting the maintainer for suggestions.
--
Regards,

Mick
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Re: octave won't run

karl
In reply to this post by Mick-10
Mick:
...
> Unless someone shows up with more knowledge on the specifics it would be worth
> posting a bug, or contacting the maintainer for suggestions.
...

Since octave compiles/emerges successfully, there are no log files left.
Can I tell emerge to not remove the build directory ?

Regards,
/Karl Hammar


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Re: octave won't run

karl
In reply to this post by Mark Knecht
Mark:
> Sounds like a ebuild dependency bug, or possibly a bad mix of stable and
> non-stable packages that haven't been sussed out fully.
>
> Not a good long-term solution, especially if you're forgetful like me, but
> as a test you might try creating a symlink for libapack.so.0 pointing to
> libapack.so.3 and see if octave runs.
>
> Best to remove that more or less right away but it might get you through a
> test period waiting for the ebuild to get fixed.

Yes, that short term solution works.

Regards,
/Karl Hammar


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Re: octave won't run

Neil Bothwick
In reply to this post by karl
On Thu,  6 Feb 2020 17:33:25 +0100 (CET), [hidden email] wrote:

> > Unless someone shows up with more knowledge on the specifics it would
> > be worth posting a bug, or contacting the maintainer for suggestions.
> >  
> ...
>
> Since octave compiles/emerges successfully, there are no log files left.
> Can I tell emerge to not remove the build directory ?

FEATURES=keepwork will do that, but don't leave it enabled. However, it
shouldn't be necessary since logs are saved in /var/log/portage unless
configured otherwise in make.conf.


--
Neil Bothwick

"I need your clothes, your boots, and your tagline!"

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Re: octave won't run

Ian Zimmerman-3
In reply to this post by Mick-10
On 2020-02-06 09:56, Mick wrote:

> Otherwise the latest sci-libs/lapack is 3.8.0, so your links above look
> correct as far as I can tell.

Note that sci-libs/lapack and sci-libs/lapack-reference are 2 distinct
packages.  The OP presumably has the latter.

Both of them existing may be the real bug here.

--
Ian

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Re: octave won't run

Marc Joliet
Am Donnerstag, 6. Februar 2020, 18:45:12 CET schrieb Ian Zimmerman:
> On 2020-02-06 09:56, Mick wrote:
> > Otherwise the latest sci-libs/lapack is 3.8.0, so your links above look
> > correct as far as I can tell.
>
> Note that sci-libs/lapack and sci-libs/lapack-reference are 2 distinct
> packages.  The OP presumably has the latter.
>
> Both of them existing may be the real bug here.

You motivated me to look this up on my system, and I don't think that's right:

- octave depends on virtual/lapack, and
- virtual/lapack does *not* depend on lapack-reference:

  RDEPEND="
       >=sci-libs/lapack-3.8.0[eselect-ldso?]
       eselect-ldso? ( || (
           >=sci-libs/lapack-3.8.0[eselect-ldso]
           sci-libs/openblas[eselect-ldso] ) )
  "
  DEPEND="${RDEPEND}"

Note also that lapack-reference has no eselect-ldso USE flag, which Karl
changed as per one of his other emails.

Karl, what exactly is the error message you get?  Can you find anything
related on bugs.gentoo.org?  FWIW, my octave installation starts just fine,
but I use openblas:

% eselect lapack list
Available LAPACK (lib) candidates:
  (none found)
Available LAPACK (lib64) candidates:
  [1]   openblas *
  [2]   reference
% eselect blas list
Available BLAS/CBLAS (lib) candidates:
  (none found)
Available BLAS/CBLAS (lib64) candidates:
  [1]   openblas *
  [2]   reference

HTH
--
Marc Joliet
--
"People who think they know everything really annoy those of us who know we
don't" - Bjarne Stroustrup

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Re: octave won't run

Philip Webb-2
In reply to this post by Ian Zimmerman-3
200206 Ian Zimmerman wrote:
> On 2020-02-06 09:56, Mick wrote:
>> Otherwise the latest sci-libs/lapack is 3.8.0,
> so your links above look correct as far as I can tell.
> Note that sci-libs/lapack and sci-libs/lapack-reference
> are 2 distinct packages.  The OP presumably has the latter.
> Both of them existing may be the real bug here.

FWIW my own set-up seems to support that.

  872: ~> ls -l /usr/lib64/liblapack.*
  lrwxrwxrwx 1 root root      14 Nov 16 17:11 /usr/lib64/liblapack.so -> liblapack.so.3
  lrwxrwxrwx 1 root root      18 Nov 16 17:11 /usr/lib64/liblapack.so.3 -> liblapack.so.3.8.0
  -rwxr-xr-x 1 root root 6637008 Nov 16 17:11 /usr/lib64/liblapack.so.3.8.0
  873: ~>

When I checked earlier today, there were broken symlinks to  lapack-reference ,
but deleting them made no difference : the pkg isn't installed.
Octave opens & calculates '1+1' without any problems.

So the solution to the OP's problem mb simply to unmerge  lapack-reference .

--
========================,,============================================
SUPPORT     ___________//___,   Philip Webb
ELECTRIC   /] [] [] [] [] []|   Cities Centre, University of Toronto
TRANSIT    `-O----------O---'   purslowatchassdotutorontodotca


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Re: octave won't run

karl
In reply to this post by Ian Zimmerman-3
Ian:
> On 2020-02-06 09:56, Mick wrote:
>
> > Otherwise the latest sci-libs/lapack is 3.8.0, so your links above look
> > correct as far as I can tell.
>
> Note that sci-libs/lapack and sci-libs/lapack-reference are 2 distinct
> packages.  The OP presumably has the latter.
>
> Both of them existing may be the real bug here.

 The refrence one isn't installed:

# emerge --search sci-libs/lapack-reference
 
[ Results for search key : sci-libs/lapack-reference ]
Searching...

*  sci-libs/blas-reference
      Latest version available: 20070226-r4
      Latest version installed: [ Not Installed ]
      Size of files: 5208 KiB
      Homepage:      http://www.netlib.org/blas/
      Description:   Basic Linear Algebra Subprograms F77 reference implementations
      License:       BSD

*  sci-libs/lapack-reference
      Latest version available: 3.2.1-r4
      Latest version installed: [ Not Installed ]
      Size of files: 4694 KiB
      Homepage:      http://www.netlib.org/lapack/index.html
      Description:   FORTRAN reference implementation of LAPACK Linear Algebra PACKage
      License:       BSD

Regards,
/Karl Hammar