Bug#791238: petsc: library transition may be needed when GCC 5 is the default

2015-09-30 Thread Emilio Pozuelo Monfort 
Control: user release.debian@packages.debian.org
Control: usertag -1 - transition

On Wed, 5 Aug 2015 16:17:54 +0200 Martin Pitt  wrote:
> tag 791238 patch
> user release.debian@packages.debian.org
> usertag 791238 + transition
> block 791238 by 790756
> 
> Hello,
> 
> this is a debdiff which we uploaded to Ubuntu (aside from some formal
> debian/changelog differences). As debian/rules is really complex and I
> don't have a good way of testing this, I'd appreciate a second look
> before uploading this.

>From a RT POV, feel free to go ahead with this.

I'm removing the transition tag for now, feel free to add that (and reassign)
once this is uploaded.

[ Note that I haven't actually reviewed the debdiff. ]

Emilio

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Processed: reassign 799493 to kdelibs5-dev, forcibly merging 799520 799493, reassign 799494 to kdelibs5-dev ...

2015-09-30 Thread Debian Bug Tracking System 
Processing commands for cont...@bugs.debian.org:

> reassign 799493 kdelibs5-dev
Bug #799493 [src:k3b] k3b: FTBFS: Missing Build-Depends on libsoprano-dev
Bug reassigned from package 'src:k3b' to 'kdelibs5-dev'.
No longer marked as found in versions k3b/2.0.2-8.
Ignoring request to alter fixed versions of bug #799493 to the same values 
previously set
> forcemerge 799520 799493
Bug #799520 {Done: Felix Geyer } [kdelibs5-dev] 
kdelibs5-dev: Missing dependency on libsoprano-dev
Bug #799360 {Done: Felix Geyer } [kdelibs5-dev] 
dolphin-plugins: FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799362 {Done: Felix Geyer } [kdelibs5-dev] bangarang: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799490 {Done: Felix Geyer } [kdelibs5-dev] cervisia: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799492 {Done: Felix Geyer } [kdelibs5-dev] eqonomize: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799658 {Done: Felix Geyer } [kdelibs5-dev] krecipes: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799493 [kdelibs5-dev] k3b: FTBFS: Missing Build-Depends on libsoprano-dev
Marked Bug as done
Marked as fixed in versions kde4libs/4:4.14.12-2.
Marked as found in versions kde4libs/4:4.14.10-1.
Bug #799360 {Done: Felix Geyer } [kdelibs5-dev] 
dolphin-plugins: FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799362 {Done: Felix Geyer } [kdelibs5-dev] bangarang: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799490 {Done: Felix Geyer } [kdelibs5-dev] cervisia: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799492 {Done: Felix Geyer } [kdelibs5-dev] eqonomize: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799658 {Done: Felix Geyer } [kdelibs5-dev] krecipes: 
FTBFS: Missing Build-Depends on libsoprano-dev
Merged 799360 799362 799490 799492 799493 799520 799658
> reassign 799494 kdelibs5-dev
Bug #799494 [src:kalgebra] kalgebra: FTBFS: Missing Build-Depends on 
libsoprano-dev
Bug reassigned from package 'src:kalgebra' to 'kdelibs5-dev'.
No longer marked as found in versions kalgebra/4:4.14.2-1.
Ignoring request to alter fixed versions of bug #799494 to the same values 
previously set
> forcemerge 799520 799494
Bug #799520 {Done: Felix Geyer } [kdelibs5-dev] 
kdelibs5-dev: Missing dependency on libsoprano-dev
Bug #799360 {Done: Felix Geyer } [kdelibs5-dev] 
dolphin-plugins: FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799362 {Done: Felix Geyer } [kdelibs5-dev] bangarang: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799490 {Done: Felix Geyer } [kdelibs5-dev] cervisia: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799492 {Done: Felix Geyer } [kdelibs5-dev] eqonomize: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799493 {Done: Felix Geyer } [kdelibs5-dev] k3b: FTBFS: 
Missing Build-Depends on libsoprano-dev
Bug #799658 {Done: Felix Geyer } [kdelibs5-dev] krecipes: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799494 [kdelibs5-dev] kalgebra: FTBFS: Missing Build-Depends on 
libsoprano-dev
Marked Bug as done
Marked as fixed in versions kde4libs/4:4.14.12-2.
Marked as found in versions kde4libs/4:4.14.10-1.
Bug #799360 {Done: Felix Geyer } [kdelibs5-dev] 
dolphin-plugins: FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799362 {Done: Felix Geyer } [kdelibs5-dev] bangarang: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799490 {Done: Felix Geyer } [kdelibs5-dev] cervisia: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799492 {Done: Felix Geyer } [kdelibs5-dev] eqonomize: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799493 {Done: Felix Geyer } [kdelibs5-dev] k3b: FTBFS: 
Missing Build-Depends on libsoprano-dev
Bug #799658 {Done: Felix Geyer } [kdelibs5-dev] krecipes: 
FTBFS: Missing Build-Depends on libsoprano-dev
Merged 799360 799362 799490 799492 799493 799494 799520 799658
> reassign 799495 kdelibs5-dev
Bug #799495 [src:kbibtex] kbibtex: FTBFS: Missing Build-Depends on 
libsoprano-dev
Bug reassigned from package 'src:kbibtex' to 'kdelibs5-dev'.
No longer marked as found in versions kbibtex/0.4-4.
Ignoring request to alter fixed versions of bug #799495 to the same values 
previously set
> forcemerge 799520 799495
Bug #799520 {Done: Felix Geyer } [kdelibs5-dev] 
kdelibs5-dev: Missing dependency on libsoprano-dev
Bug #799360 {Done: Felix Geyer } [kdelibs5-dev] 
dolphin-plugins: FTBFS: Missing Build-Depends on libsoprano-dev
Bug #799362 {Done: Felix Geyer } [kdelibs5-dev] bangarang: 
FTBFS: Missing Build-Depends on libsoprano-dev
Bug

Processed: transition: suitesparse4.4

2015-09-30 Thread Debian Bug Tracking System 
Processing control commands:

> forwarded -1 https://release.debian.org/transitions/html/auto-suitesparse.html
Bug #800556 [release.debian.org] transition: suitesparse4.4
Set Bug forwarded-to-address to 
'https://release.debian.org/transitions/html/auto-suitesparse.html'.
> block -1 by 793762 793765 800101 793764
Bug #800556 [release.debian.org] transition: suitesparse4.4
800556 was not blocked by any bugs.
800556 was not blocking any bugs.
Added blocking bug(s) of 800556: 793764, 793762, 793765, and 800101

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Bug#794736: libvigraimpex: library transition is needed when GCC 5 is the default

2015-09-30 Thread Daniel Stender 
The transition(s) of Vigra (1.10.0 and lib5v5) is just around the corner. We're
checking the reverse-deps, all works/builds fine instead of current 3depict [1],
and I've faced some problems with libreoffice ([2], also not related to 
libvigraimpex-dev,
though). Yet little busy, but this is going to completed soon.

Thanks,
Daniel Stender

[1] https://bugs.debian.org/798858
3depict: FTBFS against mathgl 2.3.3

[2] 
http://www.danielstender.com/vigra/libreoffice_5.0.1-1_amd64-20150911-2300.build

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gpaw_0.11.0.13004-1_amd64.changes ACCEPTED into unstable, unstable

2015-09-30 Thread Debian FTP Masters 


Accepted:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Fri, 14 Aug 2015 18:45:50 -0700
Source: gpaw
Binary: gpaw
Architecture: source amd64
Version: 0.11.0.13004-1
Distribution: unstable
Urgency: low
Maintainer: Debian Science Maintainers 

Changed-By: Marcin Dulak 
Description:
 gpaw   - DFT and beyond within the projector-augmented wave method
Closes: 782543
Changes:
 gpaw (0.11.0.13004-1) unstable; urgency=low
 .
   * Initial release. (Closes: #782543)
Checksums-Sha1:
 ee00e026e43302e60c044f2bdfa167d5d7041959 2101 gpaw_0.11.0.13004-1.dsc
 51e231d4133eba25f9c32fd5f0dab6d32d571da8 1269376 gpaw_0.11.0.13004.orig.tar.gz
 3fbaf32a1e29d7c81135602e667a5b90fe51a367 7248 gpaw_0.11.0.13004-1.debian.tar.xz
 e30834403eb01b00aa15719a62942363ba84dbf3 1026658 gpaw_0.11.0.13004-1_amd64.deb
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gpaw_0.11.0.13004-1_amd64.deb
Files:
 c55435571c501fd0a81b8c42c64dfee8 2101 science optional gpaw_0.11.0.13004-1.dsc
 38e968546590a7ab70a7f818feebe378 1269376 science optional 
gpaw_0.11.0.13004.orig.tar.gz
 f4daf72e8bab30d07289742ea87819dd 7248 science optional 
gpaw_0.11.0.13004-1.debian.tar.xz
 06c0d080bc2637f94f96fafae48e324c 1026658 science optional 
gpaw_0.11.0.13004-1_amd64.deb

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Processed: Re: Bug#800101: libeigen3-dev: CholmodSupport.h uses UF_long which has been removed in SuiteSparse 4.4

2015-09-30 Thread Debian Bug Tracking System 
Processing control commands:

> tags -1 + patch
Bug #800101 [libeigen3-dev] CholmodSupport.h uses UF_long which has been 
removed in SuiteSparse 4.4
Added tag(s) patch.

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Bug#800101: libeigen3-dev: CholmodSupport.h uses UF_long which has been removed in SuiteSparse 4.4

2015-09-30 Thread Sébastien Villemot 
Control: tags -1 + patch

Le samedi 26 septembre 2015 à 21:45 +0200, Sébastien Villemot a écrit :
> On Mon, 27 Jul 2015 10:55:40 +0200 Sébastien Villemot wrote:
> > Package: src:yade
> > Version: 1.14.0-5
> 
> > Your package fails to build against suitesparse 4.4, which is
> > available in
> > experimental.
> > 
> > A full build log is attached. The relevant part seems to be:
> > 
> >  /usr/include/eigen3/Eigen/src/CholmodSupport/CholmodSupport.h: In
> > function 'cholmod_sparse
> > Eigen::viewAsCholmod(Eigen::SparseMatrix<_Scalar, _Options,
> > _Index>&)':
> >  /usr/include/eigen3/Eigen/src/CholmodSupport/CholmodSupport.h:81:3
> > 7: error: 'UF_long' was not declared in this scope
> > else if (internal::is_same<_Index,UF_long>::value)
> > 
> > Note that UF_long has been replaced by SuiteSparse_long in recent 
> > versions of
> > suitesparse.
> 
> I now realize that the bug lies in eigen3. Cloning accordingly.

I attach a patch for this issue. It should work with both suitesparse
4.2 (currently in sid) and 4.4 (to be uploaded soon).

Cheers,

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Description: Compatibility fix with suitesparse >= 4.4
 The UF_long type has been replaced by SuiteSparse_long in recent versions of
 SuiteSparse.
Author: Sébastien Villemot 
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=800101
Forwarded: no
Last-Update: 2015-09-30
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/Eigen/src/CholmodSupport/CholmodSupport.h
+++ b/Eigen/src/CholmodSupport/CholmodSupport.h
@@ -78,7 +78,7 @@ cholmod_sparse viewAsCholmod(SparseMatri
   {
 res.itype = CHOLMOD_INT;
   }
-  else if (internal::is_same<_StorageIndex,UF_long>::value)
+  else if (internal::is_same<_StorageIndex,SuiteSparse_long>::value)
   {
 res.itype = CHOLMOD_LONG;
   }


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Bug#799284: debian-science: Stop recommending python-pyke in science-machine-learning

2015-09-30 Thread Daniele Tricoli 
Hello Barry,

On Thursday 17 September 2015 10:32:26 Barry Warsaw wrote:
> python-pyke (source package pyke) hasn't been modified upstream since
> at least 2013 if not earlier.  pyke is no longer compatible with the
> newer versions of ply which are in unstable.  science-machine-learning
> is the only reverse-dependency on python-pyke, as a Recommends, so
> this should probably be removed.

I was going to work on the RC bug of pyke about unsatisfiable dependencies in 
sid (#799577) (I'm not using pyke anymore so unfortunately I did not 
discovered this before: thanks Barry for spotting this!) and I discovered what 
you already explained here: pyke is no longer compatible with ply and it seems 
to be death upstream (although upstream seems still active on the Sourceforge 
forums).

I wrote to upstream asking if there is a plan for a new version of pyke:

https://sourceforge.net/p/pyke/discussion/77/thread/fe27b26a/

but I agree with Barry: it should be removed from the archive. It is already 
on the autoremoval list for testing and after the upload of science-machine-
learning it can be removed from unstable

Maybe we should wait a bit to see if upstream will reply.

I can fill the RM bug, for the ftp-team should be easier to handle the RM if 
the request came from the maintainer, right?

Please tell me what do you think about!

Kind regards,

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lhapdf 5.9.1-4 MIGRATED to testing

2015-09-30 Thread Debian testing watch 
FYI: The status of the lhapdf source package
in Debian's testing distribution has changed.

  Previous version: 5.9.1-3.1
  Current version:  5.9.1-4

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ompl REMOVED from testing

2015-09-30 Thread Debian testing watch 
FYI: The status of the ompl source package
in Debian's testing distribution has changed.

  Previous version: 0.14.2+dfsg-1
  Current version:  (not in testing)
  Hint: 
#20150929
Bug #794458: release.debian.org: boost1.58/icu/gcc5 transition

The script that generates this mail tries to extract removal
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were not originally meant to be machine readable, so if the
reason for removing your package seems to be nonsense, it is
probably the reporting script that got confused. Please check the
actual hints file before you complain about meaningless removals.

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Bug#800466: FTBFS: 4 failed tests with ValueError: could not broadcast input array

2015-09-30 Thread Emilio Pozuelo Monfort 
On Tue, 29 Sep 2015 21:28:07 +0200 Gilles Filippini  wrote:
> On Tue, 29 Sep 2015 20:46:42 +0200 Gilles Filippini  wrote:
> > Source: pytables
> > Version: 3.2.1-1
> > Severity: serious
> > Justification: FTBFS
> > 
> > -BEGIN PGP SIGNED MESSAGE-
> > Hash: SHA256
> > 
> > Hi,
> > 
> > pytables FTBFS on a clean amd64 sid chroot. 4 tests fail with similar
> > error messages:
> > ==
> > ERROR: None (tables.tests.test_tables.RecArrayRangeTestCase)
> > - --
> > Traceback (most recent call last):
> >   File 
> > "/tmp/buildd/pytables-3.2.1/build/lib.linux-x86_64-2.7/tables/tests/test_tables.py",
> >  line 2169, in test01a_range
> > self.check_range()
> >   File 
> > "/tmp/buildd/pytables-3.2.1/build/lib.linux-x86_64-2.7/tables/tests/test_tables.py",
> >  line 2042, in check_range
> > recarray = table.read(self.start, self.stop, self.step)
> >   File 
> > "/tmp/buildd/pytables-3.2.1/build/lib.linux-x86_64-2.7/tables/table.py", 
> > line 1965, in read
> > arr = self._read(start, stop, step, field, out)
> >   File 
> > "/tmp/buildd/pytables-3.2.1/build/lib.linux-x86_64-2.7/tables/table.py", 
> > line 1887, in _read
> > self.row._fill_col(result, start, stop, step, field)
> >   File "tables/tableextension.pyx", line 1272, in 
> > tables.tableextension.Row._fill_col (tables/tableextension.c:15021)
> > ValueError: could not broadcast input array from shape (2) into shape (0)
> 
> This is upstream issue #481 [1] which was fixed by commit 44dba04 [2].
> 
> [1] 
> [2] 
> 
> 
> I've successfully tested this patch, but then a python3.5 related error 
> occurs:
> 
> Ran 5734 tests in 147.360s
> 
> OK (skipped=42)
> + cd /tmp/buildd/pytables-3.2.1/build/lib.linux-x86_64-3.5
> + env PYTHONPATH=. LOCPATH=/tmp/buildd/pytables-3.2.1/tmp-locales 
> LC_ALL=en_US.UTF-8 python3.5 tables/tests/test_all.py -vvv
> Traceback (most recent call last):
>   File "tables/tests/test_all.py", line 10, in 
> import tables
>   File 
> "/tmp/buildd/pytables-3.2.1/build/lib.linux-x86_64-3.5/tables/__init__.py", 
> line 123, in 
> from tables.file import File, open_file, copy_file, openFile, copyFile
>   File 
> "/tmp/buildd/pytables-3.2.1/build/lib.linux-x86_64-3.5/tables/file.py", line 
> 31, in 
> import numexpr
>   File "/usr/lib/python3/dist-packages/numexpr/__init__.py", line 40, in 
> 
> from numexpr.expressions import E
>   File "/usr/lib/python3/dist-packages/numexpr/expressions.py", line 45, in 
> 
> from numexpr import interpreter
> ImportError: cannot import name 'interpreter'
> debian/rules:58: recipe for target 'override_dh_install' failed
> make[1]: *** [override_dh_install] Error 1
> make[1]: Leaving directory '/tmp/buildd/pytables-3.2.1'
> debian/rules:26: recipe for target 'binary' failed
> make: *** [binary] Error 2

That's just because numexpr hasn't been rebuilt for the python 3.5 transition
yet, see:

https://release.debian.org/transitions/html/python3.5.html

It should work once that's done.

Emilio

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