[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Launchpad Bug Tracker]

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   Wed, 18 May 2016 10:03:26 -0500

** Changed in: octave (Ubuntu Xenial)
   Status: Fix Committed => Fix Released

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  HDF5 I/O broken with integer variables

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Launchpad Bug Tracker]

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   Wed, 18 May 2016 13:11:16 -0500

** Changed in: octave (Ubuntu Wily)
   Status: Fix Committed => Fix Released

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Title:
  HDF5 I/O broken with integer variables

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Elvis Stansvik]

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.

** Tags removed: verification-done-xenial verification-needed
** Tags added: verification-done

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Title:
  HDF5 I/O broken with integer variables

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[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!

** Changed in: octave (Ubuntu Wily)
   Status: New => Fix Committed

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Title:
  HDF5 I/O broken with integer variables

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Elvis Stansvik]

** Tags removed: verification-done
** Tags added: verification-done-xenial verification-needed

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Title:
  HDF5 I/O broken with integer variables

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Elvis Stansvik]

@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.

** Tags removed: verification-needed
** Tags added: verification-done

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Title:
  HDF5 I/O broken with integer variables

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Martin Pitt]

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!

** Changed in: octave (Ubuntu Xenial)
   Status: New => Fix Committed

** Tags added: verification-needed

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Title:
  HDF5 I/O broken with integer variables

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Elvis Stansvik]

@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.

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  HDF5 I/O broken with integer variables

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Amr Ibrahim]

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

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Title:
  HDF5 I/O broken with integer variables

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[LocutusOfBorg]

@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?

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Elvis Stansvik]

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

** Patch added: "debdiff for the wily package"
   
https://bugs.launchpad.net/ubuntu/+source/octave/+bug/1583128/+attachment/4665708/+files/octave_4.0.0-3ubuntu6.debdiff

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Chris J Arges]

** Also affects: octave (Ubuntu Wily)
   Importance: Undecided
   Status: New

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Chris J Arges]

** Changed in: octave (Ubuntu)
   Status: New => Fix Released

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Mike Miller]

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).

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Chris J Arges]

** Also affects: octave (Ubuntu Xenial)
   Importance: Undecided
   Status: New

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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Elvis Stansvik]

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

** Patch added: "debdiff for octave_4.0.0-3ubuntu9 source package"
   
https://bugs.launchpad.net/ubuntu/+source/octave/+bug/1583128/+attachment/4665484/+files/octave_4.0.0-3ubuntu10.debdiff

** Description changed:

  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 nominating this bug
- for an SRU request and attach a debdiff.
+ 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, which includes the patch, the result
- is instead
+ 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

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Title:
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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Elvis Stansvik]

Add test case

** Description changed:

  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 nominating this bug
  for an SRU request and attach a debdiff.
  
  [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, which includes the patch, 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

** Attachment removed: "Test case for saving/loading HDF5 with integer data"
   
https://bugs.launchpad.net/ubuntu/+source/octave/+bug/1583128/+attachment/4665399/+files/test_hdf5.tar.gz

** Attachment added: "Test case for saving/loading HDF5 with integer data"
   
https://bugs.launchpad.net/ubuntu/+source/octave/+bug/1583128/+attachment/4665441/+files/test_hdf5.tar.gz

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Title:
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[Bug 1583128] Re: HDF5 I/O broken with integer variables

[Elvis Stansvik]

** Description changed:

- As described in the upstream report [1], HDF I/O using load/save is
+ 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 making an SRU request
- with an updated octave package that includes this patch (will be my
- first SRU).
+ The bug is fixed upstream with [2], and I plan on nominating this bug
+ for an SRU request and to attach a debdiff.
  
- To reproduce:
  
- * Extract the attached .tar.gz, which contains test_hdf5_save.m and
+ [Test Case]
+ 
+ 1. Extract the attached .tar.gz, which contains test_hdf5_save.m and
  test_hdf5_load.m from the upstream report.
  
- * Run:
+ 2. Run:
  
- [Octave 3.8]
+ 2.1. On Octave 3.8:
  
- octave:1> test_hdf5_save
- x = 123456789
+  octave:1> test_hdf5_save
+  x = 123456789
  
- [Octave 4.0.0]
+ 2.2. On Octave 4.0.0:
  
- octave:1> test_hdf5_load
- x = 255
+  octave:1> test_hdf5_load
+  x = 255
  
- And the other way around:
+ 3. Run (the other way around):
  
- [Octave 4.0.0]
+ 3.1. On Octave 4.0.0:
  
- octave:2> test_hdf5_save
- x = 123456789
+  octave:2> test_hdf5_save
+  x = 123456789
  
- [Octave 3.8]
+ 3.2. Octave 3.8:
  
- octave:1> test_hdf5_load
- x = 21
+  octave:1> test_hdf5_load
+  x = 21
  
  As you can see, in both cases the result is wrong.
  
+ 
+ [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

** Description changed:

  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 nominating this bug
- for an SRU request and to attach a debdiff.
- 
+ for an SRU request and attach a debdiff.
  
  [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
+  octave:1> test_hdf5_save
+  x = 123456789
  
  2.2. On Octave 4.0.0:
  
-  octave:1> test_hdf5_load
-  x = 255
+  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
+  octave:2> test_hdf5_save
+  x = 123456789
  
  3.2. Octave 3.8:
  
-  octave:1> test_hdf5_load
-  x = 21
+  octave:1> test_hdf5_load
+  x = 21
  
  As you can see, in both cases the result is wrong.
- 
  
  [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

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  HDF5 I/O broken with integer variables

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