Bug#847974: xmds2: FTBFS in stretch

2017-01-14 Thread Rafael Laboissière 

* Gilles Filippini  [2017-01-14 10:18]:


Control: reassign -1 liboctave-dev
Control: tag -1 + patch

On Sat, 14 Jan 2017 09:57:42 +0100 Gilles Filippini  wrote:


[snip]

Indeed; xmds2 wasn't reported by ben with my hdf5 transition config 
file. Sorry about that. Actually the problem lies in octave where type 
octave_hdf5_id must be adapted to the new hid_t size (int64_t).


Patch proposal coming soon.


Attached.

Raphaël, it has to be fixed before 2016-01-18 to prevent removal of 
xmds2 from testing. I can NMU if needed.


I am taking care of it.

Thanks for the patch,

Rafael

Bug#847974: xmds2: FTBFS in stretch

2017-01-14 Thread Rafael Laboissière 

* Rafael Laboissière  [2017-01-14 12:35]:


* Gilles Filippini  [2017-01-14 10:18]:


Control: reassign -1 liboctave-dev
Control: tag -1 + patch

On Sat, 14 Jan 2017 09:57:42 +0100 Gilles Filippini  wrote:


[snip]

Indeed; xmds2 wasn't reported by ben with my hdf5 transition 
config file. Sorry about that. Actually the problem lies in octave 
where type octave_hdf5_id must be adapted to the new hid_t size 
(int64_t).


Patch proposal coming soon.


Attached.

Raphaël, it has to be fixed before 2016-01-18 to prevent removal of 
xmds2 from testing. I can NMU if needed.


I am taking care of it.

Thanks for the patch,


Sébastien went faster than me.  Great!

Rafael

Bug#847974: xmds2: FTBFS in stretch

2017-01-14 Thread Gilles Filippini 
Control: reassign -1 liboctave-dev
Control: tag -1 + patch

On Sat, 14 Jan 2017 09:57:42 +0100 Gilles Filippini  wrote:
> Control: reassign 847974 octave
> Control: retitle 847974 octave: wrong size for octave_hdf5_id wrt hdf5 1.10
> Control: affects 847974 + src:xmds2
> 
> Adrian Bunk a écrit le 13/01/2017 à 21:48 :
> > On Mon, Dec 12, 2016 at 05:42:37PM +, Santiago Vila wrote:
> >> Package: src:xmds2
> >> Version: 2.2.2+dfsg-2
> >> Severity: serious
> >>
> >> Dear maintainer:
> >>
> >> I tried to build this package in stretch with "dpkg-buildpackage -A"
> >> (which is what the "Arch: all" autobuilder would do to build it)
> >> but it failed:
> >> ...
> >> warning: the size of octave_hdf5_id is smaller than the size of HDF5 hid_t
> >> warning: called from
> >> lorenz.m at line 2 column 3
> >> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140615878277440:
> >>   #000: ../../../src/H5G.c line 464 in H5Gopen2(): not a location
> >> major: Invalid arguments to routine
> >> minor: Inappropriate type
> >>   #001: ../../../src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
> >> major: Invalid arguments to routine
> >> minor: Bad value
> >> ...
> [snip]
> > What happened was the hdf5 transition.
> > 
> > Gilles, you seem to have somehow missed xmds2 in your transition 
> > planning?
> 
> Indeed; xmds2 wasn't reported by ben with my hdf5 transition config file. 
> Sorry about that.
> Actually the problem lies in octave where type octave_hdf5_id must be adapted 
> to the new hid_t size (int64_t).
> 
> Patch proposal coming soon.

Attached.

Raphaël, it has to be fixed before 2016-01-18 to prevent removal of
xmds2 from testing. I can NMU if needed.

Thanks,

_g.
diff -Nru octave-4.0.3/debian/changelog octave-4.0.3/debian/changelog
--- octave-4.0.3/debian/changelog   2016-08-18 23:32:15.0 +0200
+++ octave-4.0.3/debian/changelog   2017-01-14 09:34:36.0 +0100
@@ -1,3 +1,11 @@
+octave (4.0.3-2.1) unstable; urgency=medium
+
+  * Non-maintainer upload
+  * New patch octave_hdf5_id.patch to fix octave_hdf5_id type: it should
+be int64_t when building against hdf5 1.10 (closes: #847974)
+
+ -- Gilles Filippini   Sat, 14 Jan 2017 09:34:36 +0100
+
 octave (4.0.3-2) unstable; urgency=medium
 
   [ Rafael Laboissiere ]
diff -Nru octave-4.0.3/debian/patches/octave_hdf5_id.patch 
octave-4.0.3/debian/patches/octave_hdf5_id.patch
--- octave-4.0.3/debian/patches/octave_hdf5_id.patch1970-01-01 
01:00:00.0 +0100
+++ octave-4.0.3/debian/patches/octave_hdf5_id.patch2017-01-13 
23:00:43.0 +0100
@@ -0,0 +1,13 @@
+Index: octave-4.0.3/libinterp/corefcn/oct-hdf5-id.h
+===
+--- octave-4.0.3.orig/libinterp/corefcn/oct-hdf5-id.h
 octave-4.0.3/libinterp/corefcn/oct-hdf5-id.h
+@@ -23,7 +23,7 @@ along with Octave; see the file COPYING.
+ #if !defined (octave_oct_hdf5_id_h)
+ #define octave_oct_hdf5_id_h 1
+ 
+-typedef int octave_hdf5_id;
++typedef int64_t octave_hdf5_id;
+ 
+ extern bool check_hdf5_id_type (bool warn = true);
+ 
diff -Nru octave-4.0.3/debian/patches/series octave-4.0.3/debian/patches/series
--- octave-4.0.3/debian/patches/series  2016-08-18 23:31:10.0 +0200
+++ octave-4.0.3/debian/patches/series  2017-01-13 22:59:38.0 +0100
@@ -9,3 +9,4 @@
 hdf5-mkoctfile.patch
 gcc-6-abs-overload.patch
 gcc-6-include-math-stdlib.patch
+octave_hdf5_id.patch


signature.asc
Description: OpenPGP digital signature

Processed: Re: Bug#847974: xmds2: FTBFS in stretch

2017-01-14 Thread Debian Bug Tracking System 
Processing control commands:

> reassign -1 liboctave-dev
Bug #847974 [octave] octave: wrong size for octave_hdf5_id wrt hdf5 1.10
Bug reassigned from package 'octave' to 'liboctave-dev'.
Ignoring request to alter found versions of bug #847974 to the same values 
previously set
Ignoring request to alter fixed versions of bug #847974 to the same values 
previously set
> tag -1 + patch
Bug #847974 [liboctave-dev] octave: wrong size for octave_hdf5_id wrt hdf5 1.10
Added tag(s) patch.

-- 
847974: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=847974
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

Processed: Re: Bug#847974: xmds2: FTBFS in stretch

2017-01-14 Thread Debian Bug Tracking System 
Processing control commands:

> reassign 847974 octave
Bug #847974 [octave] octave: wrong size for octave_hdf5_id wrt hdf5 1.10
Ignoring request to reassign bug #847974 to the same package
> retitle 847974 octave: wrong size for octave_hdf5_id wrt hdf5 1.10
Bug #847974 [octave] octave: wrong size for octave_hdf5_id wrt hdf5 1.10
Ignoring request to change the title of bug#847974 to the same title
> affects 847974 + src:xmds2
Bug #847974 [octave] octave: wrong size for octave_hdf5_id wrt hdf5 1.10
Ignoring request to set affects of bug 847974 to the same value previously set

-- 
847974: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=847974
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

Bug#847974: xmds2: FTBFS in stretch

2017-01-14 Thread Gilles Filippini 
Control: reassign 847974 octave
Control: retitle 847974 octave: wrong size for octave_hdf5_id wrt hdf5 1.10
Control: affects 847974 + src:xmds2

Adrian Bunk a écrit le 13/01/2017 à 21:48 :
> On Mon, Dec 12, 2016 at 05:42:37PM +, Santiago Vila wrote:
>> Package: src:xmds2
>> Version: 2.2.2+dfsg-2
>> Severity: serious
>>
>> Dear maintainer:
>>
>> I tried to build this package in stretch with "dpkg-buildpackage -A"
>> (which is what the "Arch: all" autobuilder would do to build it)
>> but it failed:
>> ...
>> warning: the size of octave_hdf5_id is smaller than the size of HDF5 hid_t
>> warning: called from
>> lorenz.m at line 2 column 3
>> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140615878277440:
>>   #000: ../../../src/H5G.c line 464 in H5Gopen2(): not a location
>> major: Invalid arguments to routine
>> minor: Inappropriate type
>>   #001: ../../../src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
>> major: Invalid arguments to routine
>> minor: Bad value
>> ...
[snip]
> What happened was the hdf5 transition.
> 
> Gilles, you seem to have somehow missed xmds2 in your transition 
> planning?

Indeed; xmds2 wasn't reported by ben with my hdf5 transition config file. Sorry 
about that.
Actually the problem lies in octave where type octave_hdf5_id must be adapted 
to the new hid_t size (int64_t).

Patch proposal coming soon.

Thanks,

_g.




signature.asc
Description: OpenPGP digital signature

Processed: Re: Bug#847974: xmds2: FTBFS in stretch

2017-01-14 Thread Debian Bug Tracking System 
Processing control commands:

> reassign 847974 octave
Bug #847974 [src:xmds2] xmds2: FTBFS in stretch
Bug reassigned from package 'src:xmds2' to 'octave'.
No longer marked as found in versions xmds2/2.2.2+dfsg-2.
Ignoring request to alter fixed versions of bug #847974 to the same values 
previously set
> retitle 847974 octave: wrong size for octave_hdf5_id wrt hdf5 1.10
Bug #847974 [octave] xmds2: FTBFS in stretch
Changed Bug title to 'octave: wrong size for octave_hdf5_id wrt hdf5 1.10' from 
'xmds2: FTBFS in stretch'.
> affects 847974 + src:xmds2
Bug #847974 [octave] octave: wrong size for octave_hdf5_id wrt hdf5 1.10
Added indication that 847974 affects src:xmds2

-- 
842177: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=842177
847974: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=847974
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

Bug#847974: xmds2: FTBFS in stretch

2017-01-13 Thread Adrian Bunk 
On Mon, Dec 12, 2016 at 05:42:37PM +, Santiago Vila wrote:
> Package: src:xmds2
> Version: 2.2.2+dfsg-2
> Severity: serious
> 
> Dear maintainer:
> 
> I tried to build this package in stretch with "dpkg-buildpackage -A"
> (which is what the "Arch: all" autobuilder would do to build it)
> but it failed:
>...
> warning: the size of octave_hdf5_id is smaller than the size of HDF5 hid_t
> warning: called from
> lorenz.m at line 2 column 3
> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140615878277440:
>   #000: ../../../src/H5G.c line 464 in H5Gopen2(): not a location
> major: Invalid arguments to routine
> minor: Inappropriate type
>   #001: ../../../src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140615878277440:
>   #000: ../../../src/H5Gdeprec.c line 796 in H5Gget_num_objs(): not a 
> location ID
> major: Invalid arguments to routine
> minor: Inappropriate type
>   #001: ../../../src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
> major: Invalid arguments to routine
> minor: Bad value
> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140615878277440:
>   #000: ../../../src/H5G.c line 725 in H5Gclose(): not a group
> major: Invalid arguments to routine
> minor: Inappropriate type
>...
> The build history I keep is like this:
> 
> Status: successful  xmds2_2.2.2+dfsg-2_amd64-20161118T125207Z
> Status: successful  xmds2_2.2.2+dfsg-2_amd64-20161123T025916Z
> Status: successful  xmds2_2.2.2+dfsg-2_amd64-20161128T001945Z
> Status: successful  xmds2_2.2.2+dfsg-2_amd64-20161202T231309Z
> Status: failed  xmds2_2.2.2+dfsg-2_amd64-20161207T065906Z
> Status: failed  xmds2_2.2.2+dfsg-2_amd64-20161208T214652Z
> Status: failed  xmds2_2.2.2+dfsg-2_amd64-20161208T214639Z
> Status: failed  xmds2_2.2.2+dfsg-2_amd64-20161208T214702Z
> 
> Something happened in stretch between 2016-12-02 and 2016-12-07
> that made this package to FTBFS.

What happened was the hdf5 transition.

Gilles, you seem to have somehow missed xmds2 in your transition 
planning?

> Please tell me if you need a full build log, and I will attach it.
> 
> (Using sbuild on a single CPU virtual machine, it always fails for me,
> on different machines, so it should be easy to reproduce).
> 
> Thanks.

cu
Adrian

-- 

   "Is there not promise of rain?" Ling Tan asked suddenly out
of the darkness. There had been need of rain for many days.
   "Only a promise," Lao Er said.
   Pearl S. Buck - Dragon Seed

Bug#847974: xmds2: FTBFS in stretch

2016-12-12 Thread Santiago Vila 
Package: src:xmds2
Version: 2.2.2+dfsg-2
Severity: serious

Dear maintainer:

I tried to build this package in stretch with "dpkg-buildpackage -A"
(which is what the "Arch: all" autobuilder would do to build it)
but it failed:


[...]
 debian/rules build-indep
dh build-indep --with python2
   dh_testdir -i
   dh_update_autotools_config -i
   dh_auto_configure -i
   dh_auto_build -i
make -j1
make[1]: Entering directory '/<>/xmds2-2.2.2+dfsg'
make[2]: Entering directory '/<>/xmds2-2.2.2+dfsg/xpdeint'
Setting top to   : 
/<>/xmds2-2.2.2+dfsg/xpdeint 
Setting out to   : 
/<>/xmds2-2.2.2+dfsg/xpdeint 
Setting top == out (remember to use "update_outputs")
Checking for the Cheetah python module   : ok 

[... snipped ...]

Copyright 2000-2014 Graham Dennis, Joseph Hope, Mattias Johnsson
and the xmds team
Generating source code...
... done
Compiling simulation...
... done. Type './lorenz' to run.
Segment 1: minimum timestep: 1.296096e-05 maximum timestep: 4.00e-03
  Attempted 9669 steps, 0.00% steps failed.
Generating output for lorenz
xsil2graphics2 from xmds2 version 2.2.2 "XMDS2 is a game of two halves" (Debian 
package 2.2.2+dfsg-2)
Generating output for MATLAB/Octave.
Writing import script for 'lorenz.xsil' to 'lorenz.m'.
octave: X11 DISPLAY environment variable not set
octave: disabling GUI features
warning: the size of octave_hdf5_id is smaller than the size of HDF5 hid_t
warning: called from
lorenz.m at line 2 column 3
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140615878277440:
  #000: ../../../src/H5G.c line 464 in H5Gopen2(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
  #001: ../../../src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140615878277440:
  #000: ../../../src/H5Gdeprec.c line 796 in H5Gget_num_objs(): not a location 
ID
major: Invalid arguments to routine
minor: Inappropriate type
  #001: ../../../src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 140615878277440:
  #000: ../../../src/H5G.c line 725 in H5Gclose(): not a group
major: Invalid arguments to routine
minor: Inappropriate type
error: structure has no member 't'
error: called from
lorenz.m at line 3 column 8

error: writing file '/sbuild-nonexistent/.octave_hist': No such file or 
directory
error: ignoring octave_execution_exception while preparing to exit
debian/rules:15: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1
make[1]: Leaving directory '/<>/xmds2-2.2.2+dfsg'
debian/rules:9: recipe for target 'build-indep' failed
make: *** [build-indep] Error 2
dpkg-buildpackage: error: debian/rules build-indep gave error exit status 2


The build history I keep is like this:

Status: successful  xmds2_2.2.2+dfsg-2_amd64-20161118T125207Z
Status: successful  xmds2_2.2.2+dfsg-2_amd64-20161123T025916Z
Status: successful  xmds2_2.2.2+dfsg-2_amd64-20161128T001945Z
Status: successful  xmds2_2.2.2+dfsg-2_amd64-20161202T231309Z
Status: failed  xmds2_2.2.2+dfsg-2_amd64-20161207T065906Z
Status: failed  xmds2_2.2.2+dfsg-2_amd64-20161208T214652Z
Status: failed  xmds2_2.2.2+dfsg-2_amd64-20161208T214639Z
Status: failed  xmds2_2.2.2+dfsg-2_amd64-20161208T214702Z

Something happened in stretch between 2016-12-02 and 2016-12-07
that made this package to FTBFS.

Please tell me if you need a full build log, and I will attach it.

(Using sbuild on a single CPU virtual machine, it always fails for me,
on different machines, so it should be easy to reproduce).

Thanks.