NetBSD Problem Report #48272

From prlw1@inf.phy.cam.ac.uk  Fri Oct  4 13:02:36 2013
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Date: Fri, 04 Oct 2013 14:02:27 +0100
From: prlw1@cam.ac.uk
Reply-To: prlw1@cam.ac.uk
To: gnats-bugs@NetBSD.org
Subject: octave and blas build failure
X-Send-Pr-Version: 3.95

>Number:         48272
>Category:       pkg
>Synopsis:       octave and blas fail to build
>Confidential:   no
>Severity:       serious
>Priority:       medium
>Responsible:    pkg-manager
>State:          closed
>Class:          sw-bug
>Submitter-Id:   net
>Arrival-Date:   Fri Oct 04 13:05:00 +0000 2013
>Closed-Date:    Mon Jul 20 07:44:51 +0000 2020
>Last-Modified:  Mon Jul 20 07:44:51 +0000 2020
>Originator:     Patrick Welche
>Release:        NetBSD 6.99.24
>Organization:
>Environment:
NetBSD-current/amd64 with base GCC
>Description:
Building octave gets stuck with:

  /usr/lib/libstdc++.so.7: undefined reference to `_Unwind_GetIPInfo@GCC_4.2.0'

Thinking this may have something to do with fortran being built with a
different compiler to the one which build libstdc++, I tried rebuilding
g95 and libtool-fortran. Now octave fails on its dependency blas with:

--- libblas.la ---
libtool-fortran  --mode=link --tag=F77 g95 -o libblas.la caxpy.lo ...
   ztrsv.lo   -rpath /usr/pkg/lib -version-info 1:1
libtool-fortran: link: g77 -shared   .libs/caxpy.o ...  .libs/ztrsv.o
   -L/usr/obj/pkgsrc/math/blas/work.x86_64/.buildlink/lib
   -soname libblas.so.1 -o .libs/libblas.so.1.0.1
g95: libblas.so.1: No such file or directory
g95: unrecognized option '-soname'
*** [libblas.la] Error code 1 
>How-To-Repeat:
Try to build octave.
>Fix:

>Release-Note:

>Audit-Trail:
From: Joerg Sonnenberger <joerg@britannica.bec.de>
To: gnats-bugs@NetBSD.org
Cc: pkg-manager@netbsd.org, gnats-admin@netbsd.org, pkgsrc-bugs@netbsd.org
Subject: Re: pkg/48272: octave and blas build failure
Date: Sun, 6 Oct 2013 05:31:42 +0200

 On Fri, Oct 04, 2013 at 01:05:00PM +0000, prlw1@cam.ac.uk wrote:
 > >Number:         48272
 > >Category:       pkg
 > >Synopsis:       octave and blas fail to build
 > >Confidential:   no
 > >Severity:       serious
 > >Priority:       medium
 > >Responsible:    pkg-manager
 > >State:          open
 > >Class:          sw-bug
 > >Submitter-Id:   net
 > >Arrival-Date:   Fri Oct 04 13:05:00 +0000 2013
 > >Originator:     Patrick Welche
 > >Release:        NetBSD 6.99.24
 > >Organization:
 > >Environment:
 > NetBSD-current/amd64 with base GCC
 > >Description:
 > Building octave gets stuck with:
 > 
 >   /usr/lib/libstdc++.so.7: undefined reference to `_Unwind_GetIPInfo@GCC_4.2.0'

 Well, the problem here is that the libgcc from g95 is picked up, which
 doesn't support the (newer) interface system libstdc++ expects. Not sure
 how to fix this, not providing a shared Fortran RTL also breaks things.

 Joerg

From: Thomas Klausner <wiz@NetBSD.org>
To: NetBSD bugtracking <gnats-bugs@NetBSD.org>
Cc: 
Subject: Re: pkg/48272: octave and blas build failure
Date: Tue, 5 May 2015 11:33:59 +0200

 I've just successfully built math/octave on 7.99.15/amd64.
  Thomas

From: Patrick Welche <prlw1@cam.ac.uk>
To: gnats-bugs@NetBSD.org
Cc: 
Subject: Re: pkg/48272: octave and blas build failure
Date: Tue, 5 May 2015 23:52:24 +0100

 >  I've just successfully built math/octave on 7.99.15/amd64.

 Did you set PKGSRC_FORTRAN=gfortran or somesuch?

From: Thomas Klausner <wiz@NetBSD.org>
To: NetBSD bugtracking <gnats-bugs@NetBSD.org>
Cc: 
Subject: Re: pkg/48272: octave and blas build failure
Date: Wed, 6 May 2015 09:15:05 +0200

 On Tue, May 05, 2015 at 10:55:00PM +0000, Patrick Welche wrote:
 >  Did you set PKGSRC_FORTRAN=gfortran or somesuch?

 No.
  Thomas

From: Aleksej Saushev <asau@inbox.ru>
To: gnats-bugs@netbsd.org
Cc: 
Subject: Re: pkg/48272: octave and blas build failure
Date: Wed, 06 May 2015 23:55:07 +0300

 Thomas Klausner <wiz@NetBSD.org> writes:

 > The following reply was made to PR pkg/48272; it has been noted by GNATS.
 >
 > From: Thomas Klausner <wiz@NetBSD.org>
 > To: NetBSD bugtracking <gnats-bugs@NetBSD.org>
 > Cc: 
 > Subject: Re: pkg/48272: octave and blas build failure
 > Date: Wed, 6 May 2015 09:15:05 +0200
 >
 >  On Tue, May 05, 2015 at 10:55:00PM +0000, Patrick Welche wrote:
 >  >  Did you set PKGSRC_FORTRAN=gfortran or somesuch?
 >  
 >  No.

 You're using clang, that's why.
 (My guess.)

From: Thomas Klausner <wiz@NetBSD.org>
To: NetBSD bugtracking <gnats-bugs@NetBSD.org>
Cc: 
Subject: Re: pkg/48272: octave and blas build failure
Date: Wed, 6 May 2015 23:30:13 +0200

 On Wed, May 06, 2015 at 09:20:01PM +0000, Aleksej Saushev wrote:
 >  You're using clang, that's why.
 >  (My guess.)

 I'm pretty sure that I use gcc. I do have clang installed, but
 PKGSRC_COMPILER, CLANGBASE, and HAVE_LLVM are not set. I use modular
 xorg in case it makes a difference.
  Thomas

From: David Holland <dholland-pbugs@netbsd.org>
To: gnats-bugs@NetBSD.org
Cc: 
Subject: Re: pkg/48272: octave and blas build failure
Date: Thu, 9 Jul 2015 17:26:47 +0000

 On Tue, May 05, 2015 at 09:35:01AM +0000, Thomas Klausner wrote:
  >  I've just successfully built math/octave on 7.99.15/amd64.

 fwiw, I've been able to build blas just fine lately, although I
 haven't tried octave.

 -- 
 David A. Holland
 dholland@netbsd.org

From: Patrick Welche <prlw1@cam.ac.uk>
To: gnats-bugs@netbsd.org
Cc: 
Subject: Re: pkg/48272: octave and blas build failure
Date: Fri, 4 Sep 2015 14:47:28 +0100

 octave and friends now build successfully with g95. The problem is that
 the binary it generates doesn't behave e.g.:

 make test
 ...
   src/DLD-FUNCTIONS/besselj.cc ........................... PASS  180/180 
   src/DLD-FUNCTIONS/betainc.cc ........................... PASS    6/6   
   src/DLD-FUNCTIONS/bsxfun.cc ............................terminate called after throwing an instance of 'octave_execution_exception'
 panic: Abort trap -- stopping myself...
 Makefile:2127: recipe for target 'check' failed
 gmake[1]: *** [check] Abort trap (core dumped)
 gmake[1]: Leaving directory '/tmp/obj/math/octave/work/octave-3.6.4/test'
 Makefile:2549: recipe for target 'check' failed

 note the .cc => c++ and Joerg's comment.

 Simply quitting octave:

 octave:1> quit
 terminate called after throwing an instance of 'octave_interrupt_exception'
 panic: Abort trap -- stopping myself...
 attempting to save variables to 'octave-core'...
 save to 'octave-core' complete
 [1]   Abort trap (core dumped) octave


 A blas, lapack and octave built with PKGSRC_FORTRAN=gfortran is OK:

   src/DLD-FUNCTIONS/besselj.cc ........................... PASS  180/180 
   src/DLD-FUNCTIONS/betainc.cc ........................... PASS    6/6   
   src/DLD-FUNCTIONS/bsxfun.cc ............................ PASS   73/73  
   src/DLD-FUNCTIONS/cellfun.cc ........................... PASS  122/122 
   src/DLD-FUNCTIONS/chol.cc .............................. PASS   27/27  
   src/DLD-FUNCTIONS/conv2.cc ............................. PASS   23/23  
   src/DLD-FUNCTIONS/convhulln.cc ......................... PASS    4/4   
   src/DLD-FUNCTIONS/dassl.cc ............................. PASS    4/4   
 ...
 Summary:

   PASS   9863
   FAIL      6

State-Changed-From-To: open->feedback
State-Changed-By: maya@NetBSD.org
State-Changed-When: Wed, 04 Sep 2019 21:58:06 +0000
State-Changed-Why:
this should be fixed by joerg:Be a good citizen and try using the libgcc from the C compiler.
(commit to g95).
Is it still having problems at runtime?


From: Patrick Welche <prlw1@cam.ac.uk>
To: gnats-bugs@netbsd.org
Cc: 
Subject: Re: pkg/48272 (octave and blas fail to build)
Date: Fri, 6 Sep 2019 12:07:09 +0100

 On Wed, Sep 04, 2019 at 09:58:06PM +0000, maya@NetBSD.org wrote:
 > Is it still having problems at runtime?

 Yes. I commented out

 #PKGSRC_FORTRAN=gfortran
 #GFORTRAN_VERSION=7

 zapped my packages and did a pbulk build.

 $ octave
 XDM authorization key matches an existing client![1]   Abort trap (core dumped) 

 This is after logging out, rm .Xauthority .tmw?????? .xsm?????? .prx??????,
 restarting xdm, and logging back in.

 It's different to the earlier report, but still doesn't work.

 I'll try putting GFORTRAN back and recheck just in case.

State-Changed-From-To: feedback->closed
State-Changed-By: prlw1@NetBSD.org
State-Changed-When: Mon, 20 Jul 2020 07:44:51 +0000
State-Changed-Why:
PKGSRC_FORTRAN=gfortran is now the default


>Unformatted:

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