Accepted dune-grid 2.6.0-1 (source) into unstable

[Ansgar Burchardt]

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Hash: SHA512

Format: 1.8
Date: Wed, 04 Apr 2018 00:08:47 +0200
Source: dune-grid
Binary: libdune-grid-dev libdune-grid-doc
Architecture: source
Version: 2.6.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Ansgar Burchardt 
Description:
 libdune-grid-dev - toolbox for solving PDEs -- grid interface (development 
files)
 libdune-grid-doc - toolbox for solving PDEs -- grid interface (documentation)
Changes:
 dune-grid (2.6.0-1) unstable; urgency=medium
 .
   * New upstream release.
   * d/control: now requires cmake >= 3.1
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dune-grid_2.6.0.orig.tar.xz
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Accepted dune-uggrid 2.6.0-1 (source) into unstable

[Ansgar Burchardt]

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Format: 1.8
Date: Tue, 03 Apr 2018 22:42:23 +0200
Source: dune-uggrid
Binary: libdune-uggrid-dev
Architecture: source
Version: 2.6.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Ansgar Burchardt 
Description:
 libdune-uggrid-dev - software framework for finite element methods 
(development files)
Changes:
 dune-uggrid (2.6.0-1) unstable; urgency=medium
 .
   * New upstream release.
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Accepted dune-localfunctions 2.6.0-1 (source) into unstable

[Ansgar Burchardt]

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Hash: SHA512

Format: 1.8
Date: Tue, 03 Apr 2018 02:09:34 +0200
Source: dune-localfunctions
Binary: libdune-localfunctions-dev libdune-localfunctions-doc
Architecture: source
Version: 2.6.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Ansgar Burchardt 
Description:
 libdune-localfunctions-dev - toolbox for solving PDEs -- local basis 
(development files)
 libdune-localfunctions-doc - toolbox for solving PDEs -- local basis 
(documentation)
Changes:
 dune-localfunctions (2.6.0-1) unstable; urgency=medium
 .
   * New upstream release.
   * d/control: now requires cmake >= 3.1
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Accepted dune-istl 2.6.0-1 (source) into unstable

[Ansgar Burchardt]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Tue, 03 Apr 2018 00:31:44 +0200
Source: dune-istl
Binary: libdune-istl-dev libdune-istl-doc
Architecture: source
Version: 2.6.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Ansgar Burchardt 
Description:
 libdune-istl-dev - toolbox for solving PDEs -- iterative solvers (development 
files)
 libdune-istl-doc - toolbox for solving PDEs -- iterative solvers 
(documentation)
Changes:
 dune-istl (2.6.0-1) unstable; urgency=medium
 .
   * New upstream release.
   * d/control: now requires cmake >= 3.1
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Accepted dune-geometry 2.6.0-1 (source) into unstable

[Ansgar Burchardt]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Tue, 03 Apr 2018 00:30:47 +0200
Source: dune-geometry
Binary: libdune-geometry-dev libdune-geometry-doc
Architecture: source
Version: 2.6.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Ansgar Burchardt 
Description:
 libdune-geometry-dev - toolbox for solving PDEs -- geometry classes 
(development files)
 libdune-geometry-doc - toolbox for solving PDEs -- geometry classes 
(documentation)
Changes:
 dune-geometry (2.6.0-1) unstable; urgency=medium
 .
   * New upstream release.
   * d/control: now requires cmake >= 3.1
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Accepted dune-common 2.6.0-1 (source) into unstable

[Ansgar Burchardt]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Tue, 03 Apr 2018 00:20:33 +0200
Source: dune-common
Binary: libdune-common-dev libdune-common-doc
Architecture: source
Version: 2.6.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Ansgar Burchardt 
Description:
 libdune-common-dev - toolbox for solving PDEs -- basic classes (development 
files)
 libdune-common-doc - toolbox for solving PDEs -- basic classes (documentation)
Changes:
 dune-common (2.6.0-1) unstable; urgency=medium
 .
   * New upstream release.
   * d/control: now requires cmake >= 3.1
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 5484779ec4990123c5a5f8eef570c258b25b68ef2a83f4cf985681de128043c7 8516 
dune-common_2.6.0-1.debian.tar.xz
Files:
 25860da7ed27ee90d4c2d5c16cd472a4 2584 libs optional dune-common_2.6.0-1.dsc
 fb21de7469a2c2cbff6ec7439891c7d6 472127 libs optional 
dune-common_2.6.0.orig.tar.gz
 c80a6a9fd53e5918a3fb7271f97896c2 473 libs optional 
dune-common_2.6.0.orig.tar.gz.asc
 33d61ef87493f7912bc0c3a350da084d 8516 libs optional 
dune-common_2.6.0-1.debian.tar.xz

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Accepted dune-uggrid 2.5.1-2 (source) into unstable

[Ansgar Burchardt]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Tue, 27 Mar 2018 09:53:40 +0200
Source: dune-uggrid
Binary: libdune-uggrid-dev
Architecture: source
Version: 2.5.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Ansgar Burchardt 
Description:
 libdune-uggrid-dev - software framework for finite element methods 
(development files)
Closes: 891151
Changes:
 dune-uggrid (2.5.1-2) unstable; urgency=medium
 .
   * parallel/CMakeLists.txt: use `COMPILE_OPTIONS` instead of
 `COMPILE_DEFINITIONS`.  Fixes build failure with cmake 3.10.
 (Closes: #891151)
 + patch: 0001-cmake-Fix-compatibility-issue-with-CMake-3.10-leadig.patch
Checksums-Sha1:
 912758d2ba85f4885b5bad64628fb24dea1e270f 2196 dune-uggrid_2.5.1-2.dsc
 86dabfdb562f1714e9d08f5f205c487c648fba5a 3888 dune-uggrid_2.5.1-2.debian.tar.xz
Checksums-Sha256:
 57028803fa261ad45489d97d00e1e0a57c088d925989e01d1a4cf302aee383dd 2196 
dune-uggrid_2.5.1-2.dsc
 b3460db96a36826b374f7d9b1a69b14784a6e8b5a6ffb336e4498759805a542c 3888 
dune-uggrid_2.5.1-2.debian.tar.xz
Files:
 cab337f11f3e24d0b1686a73297da5a5 2196 libs optional dune-uggrid_2.5.1-2.dsc
 2df986e19b9c0bdef46ee6fa06b93978 3888 libs optional 
dune-uggrid_2.5.1-2.debian.tar.xz

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Bug#887978: Backtrace

[Ansgar Burchardt]

Hi,

On Thu, 2018-01-25 at 21:43 -0600, John Hasler wrote:
> No symbols package to be found:
> 
> toncho/~ 23 sudo apt-get install solvespace-dbgsym
> [sudo] password for john: 
> Reading package lists... Done
> Building dependency tree   
> Reading state information... Done
> E: Unable to locate package solvespace-dbgsym

The *-dbgsym packages are located in a separate archive.  Please add

  deb https://deb.debian.org/debian-debug unstable-debug main

to your /etc/apt/sources.list and run `apt update`.  The package should
then be found.

Ansgar

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Bug#881612: debian-science: s/libalberta2-dev/libalberta-dev/

[Ansgar Burchardt]

Package: src:debian-science
Version: 1.7
Severity: normal
Control: block 878199 by -1

Please depend on libalberta-dev instead of libalberta2-dev (which is a
transitional package).

Ansgar

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Bug#870203: dune-grid FTBFS on mips: test-ug (Timeout)

[Ansgar Burchardt]

Control: severity -1 important

Adrian Bunk writes:
>   Start 31: test-ug
> 31/60 Test #31: test-ug 
> ...***Timeout 300.02 sec

Yes, saw the same issue also on PowerPC.  I haven't found time to look
at this yet and have asked for dune-grid and rdeps to be removed from
mips and powerpc for now (#869688).  I'm downgrading the bug as the
removal will make this non-RC.

Ansgar

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Bug#864004: dune-grid: FTBFS, and cruft package, on hurd-i386

[Ansgar Burchardt]

retitle 864004 RM: dune-grid [hurd-i386] -- RoM; FTBFS, MPI not working on 
hurd-i386
reassign 864004 ftp.debian.org

Ralf Treinen writes:
> dune-grid fails to build on hurd-i386 (unsatisfiable build-dependency on 
> libdune-common-dev), but did build in the past.
>
> As a consequence, we now have on hurd-i386 a crufty binary package
> libdune-grid-2.3.1, which is not installable. In case you decide not
> to fix the FTBFS, please consider asking for removal of
> libdune-grid-2.3.1:hurd-i386.

MPI does not work on hurd-i386.  I don't have time to fix MPI, so
removal it is.

Ansgar

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Bug#862659: libparmetis-dev: misses dependency on libmetis-dev

[Ansgar Burchardt]

Package: libparmetis-dev
Version: 4.0.3-4+b4
Severity: important

/usr/include/parmetis.h has `#include `, but the
libparmetis-dev binary package has no dependency on a package
providing that include (libmetis-dev).

Ansgar

-- System Information:
Debian Release: 9.0
Architecture: amd64
 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.9.0-2-amd64 (SMP w/8 CPU cores)
Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages libparmetis-dev depends on:
ii  libparmetis4.0   4.0.3-4+b4
ii  mpi-default-dev  1.8

libparmetis-dev recommends no packages.

Versions of packages libparmetis-dev suggests:
pn  parmetis-doc  

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Bug#850229: dune-grid: FTBFS (not enough slots available)

[Ansgar Burchardt]

Control: reassign -1 openmpi-bin 2.0.2~git.20161225-8
Control: severity -1 important
Control: retitle -1 openmpi-bin: default for oversubscription changed

Santiago Vila writes:
> Package: src:dune-grid
> Version: 2.5.0-1
> 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:
[...]
> Status:FAILED
> Output:
>
> --
>There are not enough slots available in the system to satisfy the 
> 2 slots
>that were requested by the application:
>  test-yaspgrid-yaspfactory-1d
>
>Either request fewer slots for your application, or make more 
> slots available
>for use.
>
> --

This looks like OpenMPI changed its default for oversubscription: it
seems to now default to not allowing starting more processes than cores
available (cores, not threads even).  The man page still documents the
`--nooversubscribe` option, though `mpirun --help` shows a
`--oversubscribe` option (which is not understood by older versions).

Other implementations of `mpirun` (mpich) don't seem to understand this
option either, but seem to allow oversubscription by default (like older
versions of OpenMPI).  So one cannot pass the new option to `mpirun`
unconditionally.

I think it is a bug in OpenMPI to just change this default; at least
there should be a way to control this via an environment variable so one
doesn't have to provide OpenMPI-specific options to `mpirun`.

Ansgar

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Bug#850229: dune-grid: FTBFS (not enough slots available)

[Ansgar Burchardt]

On Thu, 2017-01-05 at 12:59 +0200, Graham Inggs wrote:
> On 05/01/2017 12:05, Santiago Vila wrote:
> > Status:FAILED
> > Output:
> >    --
> > 
> >    There are not enough slots available in the system to
> > satisfy the 2 slots
> >    that were requested by the application:
> >  test-yaspgrid-yaspfactory-1d
> > 
> >    Either request fewer slots for your application, or make
> > more slots available
> >    for use.
> >    --
> > 
> 
> I started seeing similar errors in other MPI applications since the 
> upload of openmpi 2.0.2~ to unstable.
> 
> The solution was to add --oversubscribe to the mpirun command line, 

Yes, it looks like OpenMPI changed the default :-/

> The bug should be reproducible with sbuild on a single CPU virtual
> > machine.
> > It always fail for me (I tried 10 times in different autobuilders).
> 
> If I understand correctly, --oversubscribe should be needed in your
> case where you have fewer CPUs than the number of processes
> requested, but I was seeing the errors even when there were more than
> enough CPUs available.

On my laptop with 4 cores + HT (so 8 threads), I see `mpirun` complain
once I start more than 4 processes, i.e. more processes than real
cores.  Did you count threads or cores when you tried?

Ansgar

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Bug#845539: Avoid building documentation on arch-dep-only builds

[Ansgar Burchardt]

I don't maintain the package, but I was wondering:

With both override_dh_auto_configure-arch and -indep, what happens when
 building both arch-indep and arch-dep packages?

Ansgar

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Bug#838327: dune-pdelab: FTBFS in testing (error: cannot convert 'mem_usage_t*' to 'GlobalLU_t*')

[Ansgar Burchardt]

Santiago Vila writes:
> /usr/include/dune/istl/superlu.hh: In static member function 'static void 
> Dune::SuperLUSolveChooser::solve(superlu_options_t*, SuperMatrix*, 
> int*, int*, int*, char*, double*, double*, SuperMatrix*, SuperMatrix*, void*, 
> int, SuperMatrix*, SuperMatrix*, double*, double*, double*, double*, 
> mem_usage_t*, SuperLUStat_t*, int*)':
> /usr/include/dune/istl/superlu.hh:172:34: error: cannot convert 
> 'mem_usage_t*' to 'GlobalLU_t*' for argument '19' to 'void 
> dgssvx(superlu_options_t*, SuperMatrix*, int*, int*, int*, char*, double*, 
> double*, SuperMatrix*, SuperMatrix*, void*, int, SuperMatrix*, SuperMatrix*, 
> double*, double*, double*, double*, GlobalLU_t*, mem_usage_t*, 
> SuperLUStat_t*, int*)'
>   memusage, stat, info);
>   ^

That looks like an API change in SuperLU.  The following changelog entry
for SuperLU 5.0 looks related:

+---
|  Remove 'static' variable 'Glu' in *gstrf.c, instead, pass it as an argument.
+---[ http://crd-legacy.lbl.gov/~xiaoye/SuperLU/changes.html ]

I wouldn't be surprised if `GlobalLU_t` and `Glu` were related; will try
to look at this.

Ansgar

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Bug#820455: paraview: User Manual missing

[Ansgar Burchardt]

Package: paraview
Version: 5.0.1+dfsg1-2
Severity: normal

Opening the User Manual via "Help -> Help (F1)" shows the "ParaView
User Manual" with four subsections (Source, Filters, Readers,
Writers).  However trying to open any of them just gives an error message:

+---
| QTextBrowser: No document for qthelp://paraview.org/paraview/Filters.html 
(:0, )
| QTextBrowser: No document for qthelp://paraview.org/paraview/Readers.html 
(:0, )
| QTextBrowser: No document for qthelp://paraview.org/paraview/Writers.html 
(:0, )
| QTextBrowser: No document for qthelp://paraview.org/paraview/Sources.html 
(:0, )
+---

The paraview-doc package is installed here.

Ansgar

-- System Information:
Debian Release: stretch/sid
  APT prefers testing
  APT policy: (500, 'testing'), (300, 'buildd-unstable'), (300, 'unstable'), 
(1, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 4.4.0-1-amd64 (SMP w/8 CPU cores)
Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages paraview depends on:
ii  libavcodec-ffmpeg56   7:2.8.6-1+b2
ii  libavformat-ffmpeg56  7:2.8.6-1+b2
ii  libavutil-ffmpeg547:2.8.6-1+b2
ii  libc6 2.22-5
ii  libexpat1 2.1.1-1
ii  libfreetype6  2.6.3-3
ii  libgcc1   1:5.3.1-13
ii  libgl1-mesa-glx [libgl1]  11.1.2-1
ii  libgl2ps0 1.3.8-1.2
ii  libhdf5-101.8.16+docs-6
ii  libjpeg62-turbo   1:1.4.2-2
ii  libjsoncpp1   1.7.2-1
ii  libnetcdf-c++44.2-6
ii  libnetcdf11   1:4.4.0-1
ii  libogg0   1.3.2-1
ii  libopenmpi1.101.10.2-11
ii  libpng16-16   1.6.21-2
ii  libpython2.7  2.7.11-7
ii  libqt5core5a  5.5.1+dfsg-16
ii  libqt5gui55.5.1+dfsg-16
ii  libqt5help5   5.5.1-3
ii  libqt5network55.5.1+dfsg-16
ii  libqt5widgets55.5.1+dfsg-16
ii  libstdc++65.3.1-13
ii  libswscale-ffmpeg37:2.8.6-1+b2
ii  libtheora01.1.1+dfsg.1-8
ii  libtiff5  4.0.6-1
ii  libx11-6  2:1.6.3-1
ii  libxml2   2.9.3+dfsg1-1
ii  libxt61:1.1.5-1
ii  python-autobahn   0.10.3+dfsg1-5
ii  python-matplotlib 1.5.1-1+b1
ii  python-mpi4py 1.3.1+hg20131106-2+b2
ii  python-six1.10.0-2
ii  python-twisted16.0.0-1
ii  tcl [tclsh]   8.6.0+9
ii  tcl8.58.5.19-2
ii  zlib1g1:1.2.8.dfsg-2+b1

Versions of packages paraview recommends:
ii  mpi-default-bin  1.4
ii  paraview-doc 5.0.1+dfsg1-2
ii  paraview-python  5.0.1+dfsg1-2

Versions of packages paraview suggests:
pn  h5utils 
pn  hdf5-tools  

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Bug#820453: paraview: "Help -> ParaView Guide" gives error

[Ansgar Burchardt]

Package: paraview
Version: 5.0.1+dfsg1-2
Severity: normal

When choosing "Help -> ParaView Guide" in the menu, I get this error:

+---
| File ( "/usr/doc/ParaViewGuide-CE.pdf" ) does not exist
| on your installation. (:0, )
+---

paraview-doc is installed, but doesn't contain the guide (also not in
a different location).

Ansgar

-- System Information:
Debian Release: stretch/sid
  APT prefers testing
  APT policy: (500, 'testing'), (300, 'buildd-unstable'), (300, 'unstable'), 
(1, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 4.4.0-1-amd64 (SMP w/8 CPU cores)
Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages paraview depends on:
ii  libavcodec-ffmpeg56   7:2.8.6-1+b2
ii  libavformat-ffmpeg56  7:2.8.6-1+b2
ii  libavutil-ffmpeg547:2.8.6-1+b2
ii  libc6 2.22-5
ii  libexpat1 2.1.1-1
ii  libfreetype6  2.6.3-3
ii  libgcc1   1:5.3.1-13
ii  libgl1-mesa-glx [libgl1]  11.1.2-1
ii  libgl2ps0 1.3.8-1.2
ii  libhdf5-101.8.16+docs-6
ii  libjpeg62-turbo   1:1.4.2-2
ii  libjsoncpp1   1.7.2-1
ii  libnetcdf-c++44.2-6
ii  libnetcdf11   1:4.4.0-1
ii  libogg0   1.3.2-1
ii  libopenmpi1.101.10.2-11
ii  libpng16-16   1.6.21-2
ii  libpython2.7  2.7.11-7
ii  libqt5core5a  5.5.1+dfsg-16
ii  libqt5gui55.5.1+dfsg-16
ii  libqt5help5   5.5.1-3
ii  libqt5network55.5.1+dfsg-16
ii  libqt5widgets55.5.1+dfsg-16
ii  libstdc++65.3.1-13
ii  libswscale-ffmpeg37:2.8.6-1+b2
ii  libtheora01.1.1+dfsg.1-8
ii  libtiff5  4.0.6-1
ii  libx11-6  2:1.6.3-1
ii  libxml2   2.9.3+dfsg1-1
ii  libxt61:1.1.5-1
ii  python-autobahn   0.10.3+dfsg1-5
ii  python-matplotlib 1.5.1-1+b1
ii  python-mpi4py 1.3.1+hg20131106-2+b2
ii  python-six1.10.0-2
ii  python-twisted16.0.0-1
ii  tcl [tclsh]   8.6.0+9
ii  tcl8.58.5.19-2
ii  zlib1g1:1.2.8.dfsg-2+b1

Versions of packages paraview recommends:
ii  mpi-default-bin  1.4
ii  paraview-doc 5.0.1+dfsg1-2
ii  paraview-python  5.0.1+dfsg1-2

Versions of packages paraview suggests:
pn  h5utils 
pn  hdf5-tools  

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Bug#813691: make openmpi the default on s390x

[Ansgar Burchardt]

Control: tag -1 moreinfo

On Thu, 2016-02-04 at 12:59 +0100, Matthias Klose wrote:
> Package: src:mpi-defaults
> Version: 1.0.2+nmu2
> Tags: patch
> 
> please make openmpi the default on s390x. while mpi itself is not
> used that much 
> on s390x, it may be better to go with the implementation which is
> used for most 
> architectures.
> 
> patch at
> https://launchpad.net/ubuntu/+source/mpi-defaults/1.0.2+nmu2ubuntu1

OpenMPI is currently not built on s390x: it is not listed in the source
packages Architecture: field.

Ansgar

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Bug#798024: typo in clblas-ppc64el patch ?

[Ansgar Burchardt]

Ghislain Vaillant  writes:
> In the patch you provided, d/rules is modified with:
>
>  # Uncomment this to turn on verbose mode.
>  #export DH_VERBOSE=1
>
> +DEB_HOST_ARCH=$(shell dpkg-architecture -qDEB_HOST_ARCH)
> +
>  export DEB_BUILD_MAINT_OPTIONS = hardening=+all
>  export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
>  export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
>
> +ifeq ($(DEB_BUILD_ARCH), ppc64el)
> +DEB_CFLAGS_MAINT_APPEND += -mno-altivec
> +endif
> +
>  %:
>   dh $@ --sourcedirectory=src \
>   --buildsystem=cmake \
>
> Isn't it s/DEB_HOST_ARCH/DEB_BUILD_ARCH at the beginning?

I think it should be DEB_HOST_ARCH (also below).
>From man:dpkg-architecture(1):

| build machine: The machine the package is built on.
| host machine: The machine the package is built for.

and I assume this is not for some helper programs intended to be run as
part of the build (on the build machine), but for the binaries that
should end up in the package.

Ansgar

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Bug#795963: dune-istl: FTBFS: bcrsimplicitbuild.cc:269:51: error: no match for 'operator<<'

[Ansgar Burchardt]

Control: tag -1 upstream fixed-upstream
Control: fixed -1 2.4~20150506gee6e5f6-1

> dune-istl fails to build from source on unstable/amd64:
>
>   [..]
>
>   bcrsimplicitbuild.cc: In function 'int testEntryConsistency()':
>   bcrsimplicitbuild.cc:269:51: error: no match for 'operator<<' (operand
>   types are 'std::basic_ostream' and 'std::ostream {aka
>   std::basic_ostream}')
>std::cerr<<"ERROR: Entries are not consistent"<
Date:   Sat Nov 29 07:59:44 2014 +0100

Fix wrong std::cerr at end of output.

It should be std::endl.
Courtesy of GCC 5-svn, it refuses to compile these.

Ansgar

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Bug#795242: incomplete copyright information

[Ansgar Burchardt]

Package: src:coin3
Version: 3.1.4~abc9f50-9
Severity: serious

debian/copyright is incomplete. At least the license and copyright
information for the embedded copy of expat that lintian warns about is
missing.

Ansgar

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Bug#795241: source package contains *.exe without source

[Ansgar Burchardt]

Package: src:coin3
Version: 3.1.4~abc9f50-9
Severity: serious

The source package contains *.exe files for which the source seems to
be missing. Please make sure the source is included or exclude them
from the upstream tarball.

  coin3-3.1.4~abc9f50/cfg/*.exe

Ansgar

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Packaging certain libraries as "end-user software"

[Ansgar Burchardt]

Hi,

I'm wondering about the shared library packaging requirements in Policy
for the special case of scientific libraries that are not intended to be
used by applications, but are to be used by end-users directly, and that
do not have a stable ABI.

In particular does splitting out the shared library package provide
anything useful here? It means additional work for no benefit I can see
as parallel installation of multiple versions would require having
multiple -dev packages as well to be useful...

I'm considering to move the shared libraries into the -dev package, have
lib*-dev Provides: lib*-x.y.z and shlibs generate dependencies on the
provided virtual package. While no applications depend on the shared
libraries, the virtual packages are needed as the entire framework is
split over multiple source packages providing shared libraries with
dependencies between them. I'm thinking of dune-* / libdune-*-dev here,
but the same probably applies to other packages like deal.ii as well.

Does anyone see any problems with this plan?

Ansgar

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Bug#624349: libmpich2-dev: Activates debugging compiler option -g

[Ansgar Burchardt]

Control: reopen -1
Control: found -1 3.1-5+b2
Control: fixed -1 1.4~rc2-2

It looks like there was a regression and mpich started to pass compiler
options via mpicxx.mpich again:

  $ mpicxx.mpich -show
  g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security 
-Wl,-z,relro -I/usr/include/mpich -L/usr/lib/x86_64-linux-gnu -lmpichcxx 
-lmpich -lopa -lmpl -lrt -lcr -lpthread

Flags like -g, -O2, -fstack-protector-strong, -Wformat,
-Werror=format-security and -Wl,-z,relro should not be passed to
programs compiled with mpi*.mpich; doing so might break building with
different compilers that do not understand the same set of flags as used
to build the Debian package. See also [1].

Ansgar

  [1] 

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Bug#773424: vtk6 has the wrong library paths for vt libraries; using full paths to dlopen instead of library names

[Ansgar Burchardt]

Hi,

Don Armstrong  writes:
> $ echo 'package require vtk'|vtk6
> couldn't load file "/usr/lib/libvtkCommonCoreTCL-6.1.so":
> /usr/lib/libvtkCommonCoreTCL-6.1.so: cannot open shared object file:
> No such file or directory
[...]
> I suspect that something is giving a full path to dlopen instead of a
> library name, and fixing that will solve this problem.

I think the problem is in /usr/lib/tcltk/vtk-6.1/pkgIndex.tcl:

+---
|   namespace eval ::vtk::init {
| proc load_library_package {libName libPath {libPrefix {lib}}} {
|   #first try to load a static package, then try the shared package.
|   if {[catch "load {} $libName"]} {
| set libExt [info sharedlibextension]
| set currentDirectory [pwd]
| set libFile [file join $libPath "$libPrefix$libName-6.1$libExt"]
| if {[catch "cd {$libPath}; load {$libFile}" errorMessage]} {
+---

So load_library_package is looking in a specific location for the shared
libraries, and later:

+---
| ::vtk::init::load_library_package {vtk${kit}TCL} {[file dirname [file 
dirname [file dirname [info script}
+---

I assume `[info script]' refers to /usr/lib/tcltk/vtk-6.1/pkgIndex.tcl,
so this should look in /usr/lib and not the correct (multi-arch)
location.

As an alternative to changing this and if lib*TCL-6.1.so are not used
otherwise, one could move the shared objects out of the multi-arch
location to /usr/lib and into the tcl-vtk6 package.

Ansgar

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Re: taurus_3.3.0+dfsg-2_i386.changes REJECTED

[Ansgar Burchardt]

Hi,

PICCA Frederic-Emmanuel writes:
>> Signature for changes file was already seen at 2014-08-06 12:18:56.774195.
>> Please refresh the signature of the changes file if you want to upload it 
>> again.
>
> Hello, I refresh the signature 3 times, and each time I got a REJECT.
> I do not understand what's going on Someone can explain ?

If dak finds errors with an upload in the first run, it may try to
process a .changes file again. That breaks with the new code that
disallows reuploading already seen .changes files.

I could find the real reject reason in the log files:

| taurus_3.3.0+dfsg-2.dsc: Invalid size hash for
| taurus_3.3.0+dfsg.orig.tar.gz:
| According to the control file the size hash should be 15675932,
| but taurus_3.3.0+dfsg.orig.tar.gz has 15773769.
|
| If you did not include taurus_3.3.0+dfsg.orig.tar.gz in you upload, a
| different version might already be known to the archive software.

I'll try to fix the bug in dak itself soon.

Ansgar

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Bug#752069: RM: libalberta2 -- ROM; superseded by alberta

[Ansgar Burchardt]

Package: ftp.debian.org
Severity: normal

Please remove libalberta2 from the archive. The alberta source package
provides a newer version (3.0).

Ansgar

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Bug#751464: gmsh: Merge "..." + Translate gives wrong mesh

[Ansgar Burchardt]

Package: gmsh
Version: 2.8.4+dfsg-1+b1
Severity: normal

Merging a .geo file and then translating the volume in it results in a
wrong mesh.

I've attached an example: the unit cube (0,0,0) to (1,1,1) is
translated along the z-axis. The translated cube is defined by the
corners (0,0,1) and (1,1,2). However the resulting mesh has a node on
the z=0 plane (where z should be 1) and another on the z=1 plane that
belongs on the z=2 plane.

Run "gmsh -3 cube1.geo" or choose Mesh->3D in the GUI to reproduce the
problem. One has to rotate the cube to see the problem. Or look at
these nodes in the .msh file:

9 0.5 0.5 0
10 0.5 0.5 1

The problem does not happen when using Include instead of Merge or
when including the contents of unit-cube.geo directly.

Ansgar

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Debian Release: jessie/sid
  APT prefers testing
  APT policy: (500, 'testing'), (100, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 3.14-1-amd64 (SMP w/8 CPU cores)
Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages gmsh depends on:
ii  libann0  1.1.2+doc-5
ii  libblas3 [libblas.so.3]  1.2.20110419-7
ii  libc62.19-1
ii  libfltk-gl1.31.3.2-5
ii  libfltk-images1.31.3.2-5
ii  libfltk1.3   1.3.2-5
ii  libgcc1  1:4.9.0-5
ii  libgl1-mesa-glx [libgl1] 10.1.4-1
ii  libgl2ps01.3.8-1
ii  libglu1-mesa [libglu1]   9.0.0-2
ii  libjpeg8 8d-2
ii  liblapack3 [liblapack.so.3]  3.5.0-2
ii  libmed1  3.0.6-5
ii  liboce-foundation8   0.15-4
ii  liboce-modeling8 0.15-4
ii  libopenmpi1.61.6.5-8
ii  libpng12-0   1.2.50-1
ii  libstdc++6   4.9.0-5
ii  libtet1.51.5.0-3
ii  libx11-6 2:1.6.2-2
ii  mpi-default-bin  1.0.2+nmu1

Versions of packages gmsh recommends:
pn  gmsh-doc  

gmsh suggests no packages.

-- no debconf information
Merge "unit-cube.geo";
Translate{0,0,1}{
  Volume{1};
}
Mesh.CharacteristicLengthMin = 1;
Point(1) = {0, 0, 0};
Point(2) = {1, 0, 0};
Point(3) = {1, 1, 0};
Point(4) = {0, 1, 0};
Point(5) = {0, 0, 1};
Point(6) = {1, 0, 1};
Point(7) = {1, 1, 1};
Point(8) = {0, 1, 1};

Line(1) = {1,2};
Line(2) = {2,3};
Line(3) = {3,4};
Line(4) = {4,1};
Line(5) = {5,6};
Line(6) = {6,7};
Line(7) = {7,8};
Line(8) = {8,5};
Line(9) = {1,5};
Line(10) = {2,6};
Line(11) = {3,7};
Line(12) = {4,8};

Line Loop(1) = {1,2,3,4};
Line Loop(2) = {5,6,7,8};
Line Loop(3) = {1,10,-5,-9};
Line Loop(4) = {2,11,-6,-10};
Line Loop(5) = {3,12,-7,-11};
Line Loop(6) = {4,9,-8,-12};

Plane Surface(1) = {1};
Plane Surface(2) = {2};
Plane Surface(3) = {3};
Plane Surface(4) = {4};
Plane Surface(5) = {5};
Plane Surface(6) = {6};

Surface Loop(1) = {1,2,3,4,5,6};

Volume (1) = {1};
$MeshFormat
2.2 0 8
$EndMeshFormat
$Nodes
14
1 0 0 1
2 1 0 1
3 1 1 1
4 0 1 1
5 0 0 2
6 1 0 2
7 1 1 2
8 0 1 2
9 0.5 0.5 0
10 0.5 0.5 1
11 0.5 0 1.5
12 1 0.5 1.5
13 0.5 1 1.5
14 0 0.5 1.5
$EndNodes
$Elements
64
1 15 2 0 1 1
2 15 2 0 2 2
3 15 2 0 3 3
4 15 2 0 4 4
5 15 2 0 5 5
6 15 2 0 6 6
7 15 2 0 7 7
8 15 2 0 8 8
9 1 2 0 1 1 2
10 1 2 0 2 2 3
11 1 2 0 3 3 4
12 1 2 0 4 4 1
13 1 2 0 5 5 6
14 1 2 0 6 6 7
15 1 2 0 7 7 8
16 1 2 0 8 8 5
17 1 2 0 9 1 5
18 1 2 0 10 2 6
19 1 2 0 11 3 7
20 1 2 0 12 4 8
21 2 2 0 1 2 3 9
22 2 2 0 1 1 2 9
23 2 2 0 1 3 4 9
24 2 2 0 1 1 9 4
25 2 2 0 2 6 10 5
26 2 2 0 2 10 8 5
27 2 2 0 2 7 10 6
28 2 2 0 2 8 10 7
29 2 2 0 3 6 11 2
30 2 2 0 3 2 11 1
31 2 2 0 3 11 6 5
32 2 2 0 3 11 5 1
33 2 2 0 4 3 12 2
34 2 2 0 4 12 6 2
35 2 2 0 4 7 12 3
36 2 2 0 4 12 7 6
37 2 2 0 5 4 13 3
38 2 2 0 5 13 7 3
39 2 2 0 5 8 13 4
40 2 2 0 5 13 8 7
41 2 2 0 6 4 14 8
42 2 2 0 6 1 14 4
43 2 2 0 6 5 8 14
44 2 2 0 6 1 5 14
45 4 2 0 1 10 7 12 3
46 4 2 0 1 10 1 5 14
47 4 2 0 1 10 6 2 12
48 4 2 0 1 4 10 8 14
49 4 2 0 1 10 7 3 13
50 4 2 0 1 10 6 11 2
51 4 2 0 1 10 4 8 13
52 4 2 0 1 1 10 5 11
53 4 2 0 1 1 10 2 9
54 4 2 0 1 1 4 10 9
55 4 2 0 1 4 3 10 9
56 4 2 0 1 10 3 2 9
57 4 2 0 1 11 1 10 2
58 4 2 0 1 1 4 14 10
59 4 2 0 1 3 12 10 2
60 4 2 0 1 13 4 3 10
61 4 2 0 1 8 10 13 7
62 4 2 0 1 6 5 10 11
63 4 2 0 1 7 6 10 12
64 4 2 0 1 10 5 8 14
$EndElements
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Bug#751395: Do not compress perl scripts

[Ansgar Burchardt]

On 06/12/2014 14:48, Mathieu Malaterre wrote:
> Package: vtk6-doc
> Version: 6.1.0+dfsg-5
> Severity: important
> 
> This is sort of a duplicate of 610964. Third party app expect the perl
> scripts to not be compressed. Marking as important, but should be
> grave since it will make package such as GDCM FTBFS.

That would be a bug in GDCM:

+--
| Packages must not require the existence of any files in
| /usr/share/doc/ in order to function [114].
|
| [114] The system administrator should be able to delete files in
| /usr/share/doc/ without causing any programs to break.
+--[ Debian Policy, 12.3 Additional documentation ]

Ansgar

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Bug#749920: libvtk6: improper SOVERSION

[Ansgar Burchardt]

On 05/30/2014 18:11, Mathieu Malaterre wrote:
> libvtk6 package is a bad copy/paste from libvtk5 package. It does not
> use proper SOVERSION naming as required by debian policy
> 
> https://www.debian.org/doc/debian-policy/ch-sharedlibs.html#s-sharedlibs-runtime
> [...]
> The run-time shared library must be placed in a package whose name
> changes whenever the SONAME of the shared library changes.

That is possible even when the package name doesn't include the full
soversion as long as it changes with the next ABI break, for example
libvtk6 -> libvtk6.2.  There is no need to rename libvtk6 to libvtk6.1
(and rebuild rdeps) just for the sake of giving it a different name.

> Please rename package to libvtk6.1, I believe this also affects
> libvtk6-dev package.

-dev package names really shouldn't depend on the ABI version (except in
very care cases). It just cases unneccessary work on transitions as one
needs sourceful uploads to update the Build-Depends field in all rdeps.

Ansgar

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Re: VTK6 bugs

[Ansgar Burchardt]

On 06/02/2014 14:59, Mathieu Malaterre wrote:
> On Mon, Jun 2, 2014 at 2:53 PM, Anton Gladky  wrote:
>> Hi Mathieu,
>>
>> thanks for your help for maintaining VTK6 and filing those bugs,
>> Please do not forget to file appropriate bugs against VTK5.8 and
>> VTK5.10 as well.
> 
> My pleasure.
> 
> None of those I reported apply to vtk5.8 AFAIK. Do you think of anyone
> in particular ?

Some do, for example #750200:

   Package: vtk
   Version: 5.8.0-17.2
   ...
   Build-Depends: ... tcl8.5-dev, tk8.5-dev ...

Ansgar


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Bug#746772: dune-grid: FTBFS on mipsel

[Ansgar Burchardt]

On 05/03/2014 14:11, Ivo De Decker wrote:
> The binnmu of dune-grid on mipsel failed twice:
> 
> https://buildd.debian.org/status/logs.php?pkg=dune-grid&arch=mipsel

mayer.debian.org has only 1 GB RAM (+ 0.5 GB swap), but is configured to
build in parallel with 2 processes. dune-grid however needs more RAM per
core to build sccessfully.

The package is now blacklisted on that buildd and built successfully on
eysler.debian.org[1].

  [1]


Ansgar

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Bug#742013: ALBERTA: old license in demo/COPYING and a small patch

[Ansgar Burchardt]

Hi,

I just wanted to confirm if my mail arrived. Besides a missing feature
in Debian's pkg-config package[1] this is the only thing blocking me
from updating the ALBERTA package for Debian.

Regards,
Ansgar

  [1] Which should be addressed soon.

On 04/11/2014 09:02, Ansgar Burchardt wrote:
> I'm working on preparing Debian packages for the new ALBERTA 3.0.0
> release (thanks for that). While taking a quick look I noticed that
> there is still a reference to an (old?) license in demo/COPYING:
> 
> ALBERTA is freely distributed for research and education,
> but you have to sign a license agreement; download the license
> agreement from
> 
> Is this only a left-over from some older version or does this apply
> anywhere, for example for the demo package?
> 
> I also found another small problem: alberta-utilities.pc.in contains
> "-lalberta-utilities!SUFFIX!", but the shared library itself uses an
> underscore instead of a dash (patch attached).




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Bug#742013: ALBERTA: old license in demo/COPYING and a small patch

[Ansgar Burchardt]

Hi,

I'm working on preparing Debian packages for the new ALBERTA 3.0.0
release (thanks for that). While taking a quick look I noticed that
there is still a reference to an (old?) license in demo/COPYING:

ALBERTA is freely distributed for research and education,
but you have to sign a license agreement; download the license
agreement from

Is this only a left-over from some older version or does this apply
anywhere, for example for the demo package?

I also found another small problem: alberta-utilities.pc.in contains
"-lalberta-utilities!SUFFIX!", but the shared library itself uses an
underscore instead of a dash (patch attached).

Regards,
Ansgar
--- a/alberta-utilities.pc.in
+++ b/alberta-utilities.pc.in
@@ -11,5 +11,5 @@
 Description: The ALBERTA utilities library.
 URL: http://www.alberta-fem.de
 Requires: ${DEPENDENCIES}
-Libs: -L${libdir} -lalberta-utilities!SUFFIX!
+Libs: -L${libdir} -lalberta_utilities!SUFFIX!
 Cflags: -I${includedir}
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Bug#742013: alberta: new upstream release (3.0) available

[Ansgar Burchardt]

Source: libalberta2
Version: 2.0.1-6
Control: block 740285 with -1

A new upstream release (3.0) is available[1]. It would be nice if the
Debian package could be updated to allow fixing #740285.

  [1]


I might take a look at it myself in the next weeks, although I do not
use ALBERTA myself.

Ansgar

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Bug#740285: src:dune-pdelab: FTBFS against libsuperlu-dev >= 4.3

[Ansgar Burchardt]

On 02/27/2014 22:05, Sébastien Villemot wrote:
> There is a name clash between headers from libalberta2-dev and libsuperlu-dev.
> 
> According to the upstream bug report, alberta has renamed the function in
> recent source snapshots (and maybe in 3.0-rc7 available for download, this
> needs to be checked). So the right solution is probably to update alberta in
> Debian.

Alterta-3.0 was released upstream[1]. So once the alberta package in
Debian is fixed, I can take a look at fixing this issue.

  [1]


Ansgar

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Bug#741778: dune-localfunctions: FTBFS: ! LaTeX Error: File `xcolor.sty' not found.

[Ansgar Burchardt]

Control: reassign -1 texlive-pictures 2013.20140314-1
Control: severity -1 important
Control: retitle -1 texlive-pictures: pgf needs latex-xcolor

David Suárez  writes:
> During a rebuild of all packages in sid, your package failed to build on
> amd64.
>
> Relevant part (hopefully):
[...]
>> (./dune-localfunctions-manual.tex
[...]
>> ! LaTeX Error: File `xcolor.sty' not found.

pgf moved from the pgf package (which has Depends: latex-xcolor) to
texlive-pictures which no longer mentions latex-xcolor (neither in
Depends nor in Recommends).

A trivial example no longer works in a clean unstable chroot with only
texlive-latex-extra and texlive-latex-recommended installed:

\documentclass{article}
\usepackage{pgf}
\begin{document}
Bla.
\end{document}

It gives the same error as above:

! LaTeX Error: File `xcolor.sty' not found.

This looks like a bug in the TeX package to me, therefore reassigning
it there.

Ansgar

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Bug#736402: netgen: depends on development package (tix-dev)

[Ansgar Burchardt]

Package: netgen
Version: 4.9.13.dfsg-8
Severity: normal

The netgen binary package depends on a development package (tix-dev)
in addition to the runtime package (tix).

Ansgar

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