bugGNU Octave - Bugs: bug #58466, [MXE Octave] could not build netcdf

 
 

bug #58466: [MXE Octave] could not build netcdf

Submitter:  Avinoam Kalma <avinoam>
Submitted:  Sun 31 May 2020 04:37:32 AM UTC
   
 
Category:  Configuration and Build System Severity:  3 - Normal
Priority:  5 - Normal Item Group:  Build Failure
Status:  Invalid / Not an Octave Bug Assigned to:  None
Originator Name:  Avinoam Open/Closed:  * Closed
Release:  * dev Operating System:  * GNU/Linux
Fixed Release:  None Planned Release:  None
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Thu 04 Jun 2020 03:45:28 AM UTC, comment #13: 

Thanks for checking.

Closed as Invalid

Avinoam Kalma <avinoam>
Group Member
Wed 03 Jun 2020 07:12:52 PM UTC, comment #12: 

BTW I think this bug can be closed now.

Philip Nienhuis <philipnienhuis>
Group Member
Wed 03 Jun 2020 07:12:19 PM UTC, comment #11: 

Same here.
BTW I discovered I didn't have ccache installed, that usually makes for a factor of two or so in building time.

I grepped through the .mk files to see which packages depend on hdf5; but that didn't shed any light on the issue.

BTW I did note that there's a vtk.mk, but vtk doesn't appear in the installed-packages/ subdir so doesn't seem to be built at all. Is this a stale dependency?

Philip Nienhuis <philipnienhuis>
Group Member
Wed 03 Jun 2020 04:01:25 AM UTC, comment #10: 

After deleting the mxe-octave tree and rebuild it (which takes a lot of time, as Philip commented), netcdf building succeded.

(BTW, rebuilding only HDF did not help)

Avinoam Kalma <avinoam>
Group Member
Tue 02 Jun 2020 03:32:57 PM UTC, comment #9: 

Rebuilding now, but I saw the hdf5 libs have been rebuilt yesterday in the course of building what I tested today.
So it looks like a few more dependencies are affected.

Philip Nienhuis <philipnienhuis>
Group Member
Tue 02 Jun 2020 02:24:29 PM UTC, comment #8: 

Turns out that on Win10 Octave (dev) also crashes while running __run_test_suite__.m in bug45969.tst at the statement:

%!   save ("-hdf5", hdf5_filename, "f2");

in the %testif HDF5 test stanza.
So you're right, it must be the hdf5 libs.
I'll try your suggestion.

Philip Nienhuis <philipnienhuis>
Group Member
Tue 02 Jun 2020 06:27:25 AM UTC, comment #7: 

I'm guessing, it might be the hdf libraries.
It might be enough to find and delete all files in usr/[target]/lib that contain hdf and re-build hdf5 (touch src/hdf5.mk).
No guarantees this will work though.
Also I'm typing this from memory. So please check if the file and folder names are correct.

Markus Mützel <mmuetzel>
Group administrator
Tue 02 Jun 2020 05:28:28 AM UTC, comment #6: 

What outdated libraries could that be?

Same issue here with a fairly up-to-date mxe-octave build tree.
I'd like to avoid rebuilding the entire lot as that takes > 20 hours on my box.

Philip Nienhuis <philipnienhuis>
Group Member
Mon 01 Jun 2020 07:59:52 AM UTC, comment #5: 

There are probably some outdated libraries in your build tree.
Does the error persist in a fresh build tree?

Markus Mützel <mmuetzel>
Group administrator
Mon 01 Jun 2020 03:18:20 AM UTC, comment #4: 

It was running configure/make on an existing build

Avinoam Kalma <avinoam>
Group Member
Sun 31 May 2020 11:58:22 PM UTC, comment #3: 

Was that with a new build or just running configure/make on an existing build ?

John Donoghue <lostbard>
Group Member
Sun 31 May 2020 04:59:02 PM UTC, comment #2: 

Indeed, it fails after this change.

I have used


./configure --enable-octave=stable --enable-windows-64 --enable-64 --disable-system-opengl --enable-binary-packages --with-ccache



Avinoam Kalma <avinoam>
Group Member
Sun 31 May 2020 07:16:28 AM UTC, comment #1: 

Does it still fail at hg id 6dc7dff06550?
https://hg.octave.org/mxe-octave/rev/6dc7dff06550

Which configure flags did you use?

Markus Mützel <mmuetzel>
Group administrator
Sun 31 May 2020 04:37:32 AM UTC, original submission:  


netcdf build fails after https://hg.octave.org/mxe-octave/rev/440ce30431c2

last line in log file:


ome/avinoam/mxe-octave/usr/bin/x86_64-w64-mingw32-ld: ../libhdf5/.libs/libnchdf5.a(libnchdf5_la-hdf5open.o):hdf5open.c:(.text+0x4731): undefined reference to `H5Literate2'


Avinoam Kalma <avinoam>
Group Member

 

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    Follow 6 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2020-06-04 avinoam StatusNeed Info Invalid / Not an Octave Bug
        Open/ClosedOpen Closed
    2020-06-03 philipnienhuis Carbon-Copy- Added philipnienhuis
    2020-05-31 mmuetzel StatusNone Need Info
    2020-05-31 avinoam Carbon-Copy- Added lostbard
        Carbon-Copy- Added mmuetzel

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