HDF5 I/O broken with integer variables

[Elvis Stansvik]

As described in the upstream report [1], HDF5 I/O using load/save is broken in 4.0.0. This is a regression with the potential for data loss (almost happened to us!).

The bug is fixed upstream with [2], and I plan on asking for an SRU nomination.

[Test Case]

1. Extract the attached .tar.gz, which contains test_hdf5_save.m and test_hdf5_load.m from the upstream report.

2. Run:

2.1. On Octave 3.8:

     octave:1> test_hdf5_save
     x = 123456789

2.2. On Octave 4.0.0:

     octave:1> test_hdf5_load
     x = 255

3. Run (the other way around):

3.1. On Octave 4.0.0:

     octave:2> test_hdf5_save
     x = 123456789

3.2. Octave 3.8:

     octave:1> test_hdf5_load
     x = 21

As you can see, in both cases the result is wrong.

With the updated package installed (see attached debdiff), the result is instead

octave:1> test_hdf5_save
x = 123456789

octave:1> test_hdf5_load
x = 123456789

in both directions (3.8 -> 4.0.0 and 4.0.0 -> 3.8), as expected.

[Regression Potential]

There's really no risk of any regressions. The fix is small and self contained, and the behavior before the fix is completely wrong and could result in data loss.

[1] http://savannah.gnu.org/bugs/?45225
[2] http://hg.savannah.gnu.org/hgweb/octave/rev/d54aa96abadf

[Elvis Stansvik (elvstone)]

Add test case

[Elvis Stansvik (elvstone)]

Attaching debdiff for octave_4.0.0-3ubuntu9 which adds the upstream patch, updating the package to octave_4.0.0-3ubuntu10.

[Mike Miller (mtmiller)]

Instead of cherry-picking this one patch, it might be nice to SRU 4.0.2-1ubuntu2 which fixes many important bugs (see list in bug #1563100).

[Elvis Stansvik (elvstone)]

Attaching debdiff for the wily package as well, since Chris said on IRC he'd be willing to sponsor an SRU for wily.

[Gianfranco Costamagna (costamagnagianfranco)]

@mtmiller there is a library change in 4.0.2, so no-go for xenial.
(unless you ask for single cherry-picks)

@arges, sorry for stealing this fix, I read on ubuntu-devel somebody asking for the new octave and I did the merge.
Looks like the patch is already applied for yakkety, so you should be able to upload on wily and xenial, right?

[Amr Ibrahim (amribrahim1987)]

I guess 4.0.1 could be SRUed to Xenial if it has no new dependencies!

[Elvis Stansvik (elvstone)]

@amribrahim1987, I talked briefly about that with Chris on IRC. The reason I didn't go for 4.0.1 is that it has a boatload of changes, and perhaps not all are SRU-worthy.

[Martin Pitt (pitti)]

Hello Elvis, or anyone else affected,

Accepted octave into xenial-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/octave/4.0.0-3ubuntu9.1 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation how to enable and use -proposed. Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested, and change the tag from verification-needed to verification-done. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed. In either case, details of your testing will help us make a better decision.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance!

[Elvis Stansvik (elvstone)]

@pitti: Thanks! I've tested 4.0.0-3ubuntu9.1 package in xenial-proposed using the test case attached to this report, and the bug is now fixed.

[Brian Murray (brian-murray)]

Hello Elvis, or anyone else affected,

Accepted octave into wily-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/octave/4.0.0-3ubuntu5.1 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation how to enable and use -proposed. Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested, and change the tag from verification-needed to verification-done. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed. In either case, details of your testing will help us make a better decision.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance!

[Elvis Stansvik (elvstone)]

Thanks! I finally got around to testing the package in wily-proposed as well. All looks good. The behavior with integers in HDF5 is now correct with both load/save.

[Launchpad Janitor (janitor)]

This bug was fixed in the package octave - 4.0.0-3ubuntu5.1

---------------
octave (4.0.0-3ubuntu5.1) wily; urgency=medium

  * debian/patches/hdf5-io-integer.patch: Add upstream patch to fix HDF5
    integer I/O. (LP: #1583128)

 -- Elvis Stansvik <email address hidden> Wed, 18 May 2016 13:11:16 -0500

[Brian Murray (brian-murray)]

The verification of the Stable Release Update for octave has completed successfully and the package has now been released to -updates. Subsequently, the Ubuntu Stable Release Updates Team is being unsubscribed and will not receive messages about this bug report. In the event that you encounter a regression using the package from -updates please report a new bug using ubuntu-bug and tag the bug report regression-update so we can easily find any regressions.

[Launchpad Janitor (janitor)]

This bug was fixed in the package octave - 4.0.0-3ubuntu9.1

---------------
octave (4.0.0-3ubuntu9.1) xenial; urgency=medium

  * debian/patches/hdf5-io-integer.patch: Add upstream patch to fix HDF5
    integer I/O. (LP: #1583128)

 -- Elvis Stansvik <email address hidden> Wed, 18 May 2016 10:03:26 -0500