bugGNU Octave - Bugs: bug #56171, [octave forge] (control) fails to...

 
 

bug #56171: [octave forge] (control) fails to build and install

Submitted by:  None
Submitted on:  Fri 19 Apr 2019 03:38:36 PM UTC  
 
Category:  Octave Forge Package Severity:  3 - Normal
Priority:  5 - Normal Item Group:  Build Failure
Status:  Need Info Assigned to:  None
Originator Name:  Charles (past) Tolle Originator Email:  -email is unavailable-
Open/Closed:  Open Release:  5.1.0
Operating System:  Mac OS

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( Jump to the original submission)

Sat 04 May 2019 12:55:24 PM UTC, comment #6:

Andrew: yes, they will get email notification if they leave a valid email address.

The following was posted to the mailing list and so did not appear here:

It appears that I had an old path include mistake within my compiler. Still there but it has been patched via CPATH. So the old error has gone away. However a new error has been created within octave's own header files. I tries reinstall octave normally and from source which installed fine. But when I still try to install the -forge packages I now get this error:

the key lines:

Additional info:

My CPATH patch is:

Any idea’s?

John W. Eaton <jwe>
Project Administrator
Sat 20 Apr 2019 05:18:58 PM UTC, comment #5:

Filed bug #56183 for adding tests for building and linking with BLAS, Fortran, etc.

Mike Miller <mtmiller>
Project Administrator
Sat 20 Apr 2019 02:42:57 AM UTC, comment #4:

Do Anonymous submitters get notifications of comments on their posts?

Eh, screw it: here's a downstream Homebrew PR for a revision bump for octave which I think will fix this problem: https://github.com/Homebrew/homebrew-core/pull/39122

Andrew Janke <apjanke>
Sat 20 Apr 2019 02:25:50 AM UTC, comment #3:

This does sound like a local configuration issue or a Homebrew formula definition or "bottling" issue.

On my macOS 10.14.4 box with Xcode 10.2 installed, `pkg install -forge control` succeeds for me in Octave.app 5.1.0 beta 3, which is a customized Homebrew-based installation. (Raises warnings as usual, but the actual build & installation succeeds.) But Octave.app uses customized formulae and builds everything from source, so that doesn't necessarily reflect what's happening with core Homebrew octave installs.

On my vanilla Homebrewed Octave 5.1.0 installation, however, it's busted. Different error message, but definitely busted:

My Homebrew and overall OS installation on this box are pretty well managed imho, so it's less likely to be a local configuration issue here.

gfortran linkage issue? gfortran is provided by gcc.

The gcc Homebrew formula has been updated recently, and the octave formula/bottle has not been updated since:

Often, when a Homebrew formula is updated, its dependencies that have binary linkage to it must also be updated, with a "revision bump" that's just a rebuild to update the bottle to link against the new dependency's build. That may well be what's happening here. Normally, Homebrew's CI infrastructure detects these linkage problems because it runs `brew test` on all the updated formula's dependents. But `brew test` on octave does not involve installing Octave Forge packages, or doing any C/C++/Fortran/mkoctfile compilation. And the Octave installation does not have direct linkage to the gcc libraries (I think). So it may well have missed this.

Reinstalling `octave` from source fixed it for me.

This is consistent with the Homebrew bottle needing a rebuild to account for the gcc update.

Please report this downstream to Homebrew core at https://github.com/Homebrew/homebrew-core/issues. Tell them specifically that "octave may need a revision bump to handle the recent gcc update". Include a link to this Savannah issue so they can see the background of what's going on.

In the meantime, you can run `brew reinstall -s octave` from the shell command line to probably get a working Octave installation.

Also make sure you have run Xcode once and accepted the license agreement it presents, just to make sure.

Also, perhaps Homebrew core should add a trivial usage of `mkoctfile` to the Octave `brew test`, to make sure the development/compilation parts of Octave work. That's a significant component of how Octave is used in the wild. Not sure how you'd set up a trivial mkoctfile that involved Fortran compilation, though. That's probably something Octave itself should ship in its bundled test suite if it wants downstream packagers to exercise it. If this was done, then Homebrew would be able to automatically detect when an Octave rebuild was needed to take care of this case.

Andrew Janke <apjanke>
Fri 19 Apr 2019 04:33:40 PM UTC, comment #2:

Yeah this looks like a local configuration issue. Compiling a C++ source file should naturally be able to find <cstdint>, so I don't think this is a bug in the control package.

Mike Miller <mtmiller>
Project Administrator
Fri 19 Apr 2019 03:56:46 PM UTC, comment #1:

I can just guess that you are using homebrew installing Octave 5.1 on macOS (version?)? You really should add these infos and since this looks like a packaging problem where dependencies aren't installed you might ask the homebrew people

Andreas Weber <andy1978>
Project Member
Fri 19 Apr 2019 03:38:36 PM UTC, original submission:

octave:1> pkg install -forge control
warning: LFLAGS is deprecated and will be removed in a future version of Octave, use LDFLAGS instead
In file included from _control_helper_functions_.cc:1:
In file included from ./is_real_scalar.cc:28:
In file included from /usr/local/Cellar/octave/5.1.0/include/octave-5.1.0/octave/../octave/oct.h:26:
/usr/local/Cellar/octave/5.1.0/include/octave-5.1.0/octave/octave-config.h:64:14: fatal error: 'cstdint' file not found
# include <cstdint>
^
1 error generated.
make: *** [__control_helper_functions__.oct] Error 1
make: *** Waiting for unfinished jobs....
MA02ID.f:188:21:

MA02ID.f:184:72:

DO 90 J = 1, N+1
2
MA02ID.f:188:21:

DWORK(J-1) = DWORK(J-1) + TEMP
1
Warning: Array reference at (1) out of bounds (0 < 1) in loop beginning at (2)
MA02ID.f:188:34:

MA02ID.f:184:72:

DO 90 J = 1, N+1
2
MA02ID.f:188:34:

DWORK(J-1) = DWORK(J-1) + TEMP
1
Warning: Array reference at (1) out of bounds (0 < 1) in loop beginning at (2)
MA02ID.f:230:21:

MA02ID.f:226:72:

DO 160 J = 1, N+1
2
MA02ID.f:230:21:

DWORK(J-1) = DWORK(J-1) + TEMP
1
Warning: Array reference at (1) out of bounds (0 < 1) in loop beginning at (2)
MA02ID.f:230:34:

MA02ID.f:226:72:

DO 160 J = 1, N+1
2
MA02ID.f:230:34:

DWORK(J-1) = DWORK(J-1) + TEMP
1
Warning: Array reference at (1) out of bounds (0 < 1) in loop beginning at (2)
tar -xzf slicot.tar.gz
/usr/local/Cellar/octave/5.1.0/bin/mkoctfile-5.1.0 -Wall -Wno-deprecated-declarations _control_helper_functions_.cc
mkdir sltmp
mv slicot/src/*.f ./sltmp
mv slicot/src_aux/*.f ./sltmp
cp TG04BX.fortran ./sltmp/TG04BX.f
cp TB01ZD.fortran ./sltmp/TB01ZD.f
cd sltmp; /usr/local/Cellar/octave/5.1.0/bin/mkoctfile-5.1.0 -c *.f
ar -rc slicotlibrary.a ./sltmp/*.o
rm -rf sltmp slicot

pkg: error running `make' for the control package.
error: called from
configure_make at line 99 column 9
install at line 184 column 7
pkg at line 441 column 9

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    Follow 2 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2019-04-19 mtmiller StatusNone => Need Info
        SummaryForge control package fails to build and install. => [octave forge] (control) fails to build and install

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