openstereogram is marked for autoremoval from testing

[Debian testing autoremoval watch]

openstereogram 0.1+20080921-2 is marked for autoremoval from testing on 
2016-10-21

It (build-)depends on packages with these RC bugs:
837021: openjfx: FTBFS: PosixPlatform.cpp:235:10: error: 'wait' was not 
declared in this scope


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singular is marked for autoremoval from testing

[Debian testing autoremoval watch]

singular 4.0.3-p1+ds-3 is marked for autoremoval from testing on 2016-10-06

It is affected by these RC bugs:
837016: singular: FTBFS: aminclude.am:35: error: DX_COND_doc does not appear in 
AM_CONDITIONAL


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tachyon is marked for autoremoval from testing

[Debian testing autoremoval watch]

tachyon 0.99~b6+dsx-5 is marked for autoremoval from testing on 2016-10-06

It is affected by these RC bugs:
837012: tachyon: FTBFS: ld: tachyon_ogl-glwin.o: undefined reference to symbol 
'XNextEvent'


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aweather is marked for autoremoval from testing

[Debian testing autoremoval watch]

aweather 0.8.1-1 is marked for autoremoval from testing on 2016-10-06

It is affected by these RC bugs:
837002: aweather: FTBFS: gps.h:1905:21: error: field 'real' has incomplete type


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pymca is marked for autoremoval from testing

[Debian testing autoremoval watch]

pymca 5.1.2+dfsg-1 is marked for autoremoval from testing on 2016-10-05

It is affected by these RC bugs:
836850: pymca-doc: fails to upgrade from 'jessie' - trying to overwrite 
/usr/share/doc-base/pymca


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Bug#837869: gnuplot: autoscale on y axis buggy with smooth kdensity

[Celelibi]

Package: gnuplot
Version: 5.0.4+dfsg1-3
Severity: normal

Dear maintainer,

It looks like with "smooth kdensity" gnuplot always take the max of the
weights as yrange-max instead of the real max of the plotted function.
Here is an example:

plot 'file.dat' using 1:(1000) smooth kdensity

With these data:
0
100
200

There's an yrange of [0:1000] while the plot itself doesn't exceed the
value 10. The autoscale seems to be completely off.

This bug seems to apply upstream as well.


Best regards,
Celelibi


-- System Information:
Debian Release: stretch/sid
  APT prefers testing
  APT policy: (990, 'testing'), (500, 'unstable'), (1, 'experimental')
Architecture: i386 (x86_64)

Kernel: Linux 3.10.11 (SMP w/2 CPU cores; PREEMPT)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash
Init: sysvinit (via /sbin/init)

Versions of packages gnuplot depends on:
ii  gnuplot-qt [gnuplot-nox]  5.0.4+dfsg1-3

gnuplot recommends no packages.

Versions of packages gnuplot suggests:
ii  gnuplot-doc  5.0.4+dfsg1-3

-- no debconf information

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Bug#837865: v-sim: (Future) FTBFS due to undeclared build dependencies

[biebl]

Source: v-sim
Version: 3.7.2-1
Severity: important
User: pkg-gnome-maintain...@lists.alioth.debian.org
Usertags: gtk-doc-tools

Hi,

your package v-sim declares a build dependency on gtk-doc-tools.
gtk-doc-tools in turn depends on gnome-common, which in turn pulls in packages
like gettext, intltool or pkg-config.

The dependency on gnome-common was originally added for the GNOME_GTKDOC_CHECK
macro which has been deprecated and replaced by GTK_DOC_CHECK a long time ago.

As gnome-common has been declared deprecated by GNOME upstream [1], we would
like to drop this dependency from gtk-doc-tools.

We did a test of all reverse build dependencies of gtk-doc-tools and v-sim
failed to build due to now missing build dependencies which are no longer
pulled in by gtk-doc-tools.

A complete build log is available at
https://people.debian.org/~biebl/gtk-doc-tools/v-sim.log

We have uploaded that gtk-doc-tools package as 1.25-4 to experimental as well,
so you can test your package against this version.

Common build-failures and their fixes:

a/ configure.ac:32: error: possibly undefined macro: AC_PROG_INTLTOOL

   make[1]: intltoolize: Command not found

   → Build-Depends: intltool

b/ ./configure: line 5461: syntax error near unexpected token `yes'
   ./configure: line 5461: `GNOME_COMPILE_WARNINGS(yes)'

   ./configure: line 14801: GNOME_CODE_COVERAGE: command not found

   → Build-Depends: gnome-common (for GNOME_* macros)

c/ ./configure: line 17439: syntax error near unexpected token 
`$WARN_CFLAGS_EXTRA,'
   ./configure: line 17439: `AX_APPEND_COMPILE_FLAGS($WARN_CFLAGS_EXTRA, 
WARN_CFLAGS)'

   ./configure: line 2629: syntax error near unexpected token `git-directory'
   ./configure: line 2629: `AX_IS_RELEASE(git-directory)'

   → Build-Depends: autoconf-archive (for AX_* macros)

d/ ./configure: line 12518: intltool-update: command not found
   checking for intltool >= 0.40.0...  found
   ./configure: error: Your intltool is too old.  You need intltool 0.40.0 or 
later.

   → Build-Depends: intltool

e/ make[1]: intltoolize: Command not found

   → Build-Depends: intltool

f/ ./autogen.sh calls gnome-autogen.sh

   → Build-Depends: gnome-common


Please add the required build-dependencies to your package so once we upload
gtk-doc-tools_1.25-4 to unstable your package doesn't FTBFS.

Regards,
Michael


[1] https://wiki.gnome.org/Projects/GnomeCommon/Migration

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Merge the requests for VTK 7.0

[Adrian Bunk]

reassign 810254 src:vtk6
retitle 810254 New release available
severity 826052 wishlist
merge 810254 826052
thanks

New upstream versions of a package are wishlist bugs against the 
package, not WNPP bugs.

And packaging should be done by (or in coordination with) the existing 
maintainer of the old version.

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


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Processed: Merge the requests for VTK 7.0

[Debian Bug Tracking System]

Processing commands for cont...@bugs.debian.org:

> reassign 810254 src:vtk6
Bug #810254 [wnpp] RFP: vtk7 -- Visualization Toolkit (VTK) version 7
Bug reassigned from package 'wnpp' to 'src:vtk6'.
Ignoring request to alter found versions of bug #810254 to the same values 
previously set
Ignoring request to alter fixed versions of bug #810254 to the same values 
previously set
> retitle 810254 New release available
Bug #810254 [src:vtk6] RFP: vtk7 -- Visualization Toolkit (VTK) version 7
Changed Bug title to 'New release available' from 'RFP: vtk7 -- Visualization 
Toolkit (VTK) version 7'.
> severity 826052 wishlist
Bug #826052 [src:vtk6] New release available
Severity set to 'wishlist' from 'normal'
> merge 810254 826052
Bug #810254 [src:vtk6] New release available
Bug #826052 [src:vtk6] New release available
Merged 810254 826052
> thanks
Stopping processing here.

Please contact me if you need assistance.
-- 
810254: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=810254
826052: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=826052
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

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LOAN

[MR]

Greetings to you, are you desperately in need of a loan, you need a loan for 
your business or to pay bills, i can offer you this loan at 1.5% interest rate. 
we have a special and quality service we render to all our customers. we can 
offer you loan ranging from $300  to $1,000,000  depending on how much loan you 
need from us.
Contact us now for more information on our offer.

Thanks and regards

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Bug#837121: marked as done (gazebo: please restrict libkido-dev (build-)dependency to architectures where it is available.)

[Debian Bug Tracking System]

Your message dated Wed, 14 Sep 2016 17:50:16 +
with message-id 
and subject line Bug#837121: fixed in gazebo 7.3.0+dfsg-6
has caused the Debian Bug report #837121,
regarding gazebo: please restrict libkido-dev (build-)dependency to 
architectures where it is available.
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
837121: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=837121
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---

Package: gazebo
Version: 7.3.0+dfsg-3
Severity: serious
Tags: patch

The most recent version of gazebo added a build-dependency on 
libkido-dev to the source package and added a binary on libkido-dev to 
libgazebo7-dev


No mention of this was made in the changelog and no other changes in the 
upload seem to be related but 
https://anonscm.debian.org/git/debian-science/packages/gazebo.git/commit/?id=80f9a218ccebb32258812afdf1cce6b50ab88126 
indicates this was to add support for a new feature.


libkido-dev is only available on a handful of architectures. As a result 
this new (build-)dependency is blocking the migration of the new version 
of the package (and hence the FTBFS fix) to testing.


The attatched patch restricts the (build-)dependencies on libkido-dev to 
the architectures where it is actually available (amd64, arm64, i386, 
ppc64el and alpha)
diff -Nru gazebo-7.3.0+dfsg/debian/changelog gazebo-7.3.0+dfsg/debian/changelog
--- gazebo-7.3.0+dfsg/debian/changelog  2016-08-31 17:57:53.0 +
+++ gazebo-7.3.0+dfsg/debian/changelog  2016-09-07 15:06:23.0 +
@@ -1,3 +1,10 @@
+gazebo (7.3.0+dfsg-3+rpi1) stretch-staging; urgency=medium
+
+  * Restrict (build-)dependency on libkido-dev to architectures where that 
package
+is actually available (amd64, arm64, i386, ppc64el and alpha). 
+
+ -- Peter Michael Green   Wed, 07 Sep 2016 15:06:23 
+
+
 gazebo (7.3.0+dfsg-3) unstable; urgency=medium
 
   [ Jochen Sprickerhof ]
diff -Nru gazebo-7.3.0+dfsg/debian/control gazebo-7.3.0+dfsg/debian/control
--- gazebo-7.3.0+dfsg/debian/control2016-08-30 22:54:59.0 +
+++ gazebo-7.3.0+dfsg/debian/control2016-09-07 15:06:07.0 +
@@ -45,7 +45,7 @@
libbullet-dev,
libsimbody-dev,
libsimbody-dev (<< 4.0.0),
-   libkido-dev,
+   libkido-dev [amd64 arm64 i386 powerpc alpha],
libgdal-dev,
ruby-ronn,
libgtest-dev
@@ -138,7 +138,7 @@
  libignition-math2-dev,
  libbullet-dev,
  libsimbody-dev,
- libkido-dev,
+ libkido-dev [amd64 arm64 i386 powerpc alpha],
  libgazebo7 (= ${binary:Version}),
  gazebo7-common (= ${source:Version}),
  gazebo7-plugin-base (= ${binary:Version}),
--- End Message ---
--- Begin Message ---
Source: gazebo
Source-Version: 7.3.0+dfsg-6

We believe that the bug you reported is fixed in the latest version of
gazebo, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 837...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Jose Luis Rivero  (supplier of updated gazebo 
package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 14 Sep 2016 17:00:37 +
Source: gazebo
Binary: gazebo7-common gazebo7 libgazebo7 libgazebo7-dev gazebo7-plugin-base 
gazebo7-doc
Architecture: source
Version: 7.3.0+dfsg-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Jose Luis Rivero 
Description:
 gazebo7- Open Source Robotics Simulator - Binaries
 gazebo7-common - Open Source Robotics Simulator - Shared files
 gazebo7-doc - Open Source Robotics Simulator - Documentation
 gazebo7-plugin-base - Open Source Robotics Simulator - base plug-ins
 libgazebo7 - Open Source Robotics Simulator - shared library
 libgazebo7-dev - Open Source Robotics Simulator - Development Files
Closes: 837121
Changes:
 gazebo (7.3.0+dfsg-6) unstable; urgency=medium
 .
   * Fix 

gazebo_7.3.0+dfsg-6_source.changes ACCEPTED into unstable

[Debian FTP Masters]

Accepted:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 14 Sep 2016 17:00:37 +
Source: gazebo
Binary: gazebo7-common gazebo7 libgazebo7 libgazebo7-dev gazebo7-plugin-base 
gazebo7-doc
Architecture: source
Version: 7.3.0+dfsg-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Jose Luis Rivero 
Description:
 gazebo7- Open Source Robotics Simulator - Binaries
 gazebo7-common - Open Source Robotics Simulator - Shared files
 gazebo7-doc - Open Source Robotics Simulator - Documentation
 gazebo7-plugin-base - Open Source Robotics Simulator - base plug-ins
 libgazebo7 - Open Source Robotics Simulator - shared library
 libgazebo7-dev - Open Source Robotics Simulator - Development Files
Closes: 837121
Changes:
 gazebo (7.3.0+dfsg-6) unstable; urgency=medium
 .
   * Fix supported arches in libgazebo7-dev package. Thanks to Graham Inggs
 (Closes: #837121)
Checksums-Sha1:
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gazebo_7.3.0+dfsg-6.debian.tar.xz
Checksums-Sha256:
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gazebo_7.3.0+dfsg-6.debian.tar.xz
Files:
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 f9013c5a0f6a57d143aad5a72b6e2a6d 19892 science optional 
gazebo_7.3.0+dfsg-6.debian.tar.xz

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Thank you for your contribution to Debian.

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Processing of gazebo_7.3.0+dfsg-6_source.changes

[Debian FTP Masters]

gazebo_7.3.0+dfsg-6_source.changes uploaded successfully to localhost
along with the files:
  gazebo_7.3.0+dfsg-6.dsc
  gazebo_7.3.0+dfsg-6.debian.tar.xz

Greetings,

Your Debian queue daemon (running on host franck.debian.org)

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Processing of gazebo_7.3.0+dfsg-6_source.changes

[Debian FTP Masters]

gazebo_7.3.0+dfsg-6_source.changes uploaded successfully to 
ftp-master.debian.org
along with the files:
  gazebo_7.3.0+dfsg-6.dsc
  gazebo_7.3.0+dfsg-6.debian.tar.xz

Greetings,

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urdfdom_1.0.0-2_source.changes ACCEPTED into unstable

[Debian FTP Masters]

Accepted:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 14 Sep 2016 19:02:02 +0200
Source: urdfdom
Binary: liburdfdom-model liburdfdom-model-state liburdfdom-sensor 
liburdfdom-world liburdfdom-dev liburdfdom-tools
Architecture: source
Version: 1.0.0-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Jochen Sprickerhof 
Description:
 liburdfdom-dev - URDF DOM - development files
 liburdfdom-model - URDF DOM - model library
 liburdfdom-model-state - URDF DOM - model state library
 liburdfdom-sensor - URDF DOM - sensor library
 liburdfdom-tools - URDF DOM - tools
 liburdfdom-world - URDF DOM - world library
Changes:
 urdfdom (1.0.0-2) unstable; urgency=medium
 .
   [ Jose Luis Rivero ]
   * Include Google copyright for gtest
 .
   [ Jochen Sprickerhof ]
   * Install cmake files again
   * Team upload.
Checksums-Sha1:
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Files:
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 b01e622573f8c8ac88f6e3c9c548cddf 4280 libs optional 
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Thank you for your contribution to Debian.

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python-hdf5storage_0.1.14-1_source.changes ACCEPTED into unstable

[Debian FTP Masters]

Accepted:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 13 Sep 2016 18:29:58 +0100
Source: python-hdf5storage
Binary: python-hdf5storage python3-hdf5storage python-hdf5storage-doc
Architecture: source
Version: 0.1.14-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Ghislain Antony Vaillant 
Description:
 python-hdf5storage - high-level utilities to read from and write to HDF5 
(Python 2)
 python-hdf5storage-doc - documentation for hdf5storage
 python3-hdf5storage - high-level utilities to read from and write to HDF5 
(Python 3)
Changes:
 python-hdf5storage (0.1.14-1) unstable; urgency=medium
 .
   * New upstream release.
   * Remove extra arguments for nose.
   * Simplify the packaging testsuite.
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python-hdf5storage_0.1.14-1.debian.tar.xz
Files:
 084f7388c58b55601e68e8c4943054b6 2533 python optional 
python-hdf5storage_0.1.14-1.dsc
 be528d121673a046dc1fe37e3e047efc 98621 python optional 
python-hdf5storage_0.1.14.orig.tar.gz
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python-hdf5storage_0.1.14-1.debian.tar.xz

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Bug#837796: paraview: segfaults when performing query-based selections

[Francesco Poli (wintermute)]

Package: paraview
Version: 5.1.2+dfsg1-1
Severity: important

Hello!

First of all, thanks for maintaining ParaView in Debian.

I noticed a segfault that can be obtained reproducibly.
It happens with query-based selections.

The steps to reproduce the segfaults are the ones detailed
in _Exercise 2.27 Performing Query-Based Selections_
of The ParaView Tutorial version 5.1 [1] (see page 59 or
pdfpage 67 [2]), which uses the can.ex2 example data file [3].

[1] http://www.paraview.org/Wiki/The_ParaView_Tutorial
[2] http://www.paraview.org/Wiki/images/f/f7/ParaViewTutorial51.pdf
[3] http://www.paraview.org/Wiki/images/5/5d/ParaViewTutorialData.tar.gz

I get a segfault as soon as I execute step 6 (click the Run Selection
Query button).

Please investigate and fix this bug and/or forward my bug report
upstream.

Thanks for your time!
Bye.


-- System Information:
Debian Release: stretch/sid
  APT prefers testing
  APT policy: (800, 'testing'), (500, 'unstable')
Architecture: amd64 (x86_64)

Kernel: Linux 4.6.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: sysvinit (via /sbin/init)

Versions of packages paraview depends on:
ii  libavcodec57  7:3.1.3-1+b3
ii  libavformat57 7:3.1.3-1+b3
ii  libavutil55   7:3.1.3-1+b3
ii  libc6 2.23-5
ii  libexpat1 2.2.0-1
ii  libfreetype6  2.6.3-3+b1
ii  libgcc1   1:6.1.1-11
ii  libgl1-mesa-glx [libgl1]  12.0.2-1
ii  libgl2ps1 1.3.9-4
ii  libhdf5-101.8.16+docs-8
ii  libjpeg62-turbo   1:1.5.0-1
ii  libjsoncpp1   1.7.4-3
ii  libnetcdf-c++44.2-6
ii  libnetcdf11   1:4.4.1-2
ii  libogg0   1.3.2-1
ii  libopenmpi1.101.10.3-3
ii  libpng16-16   1.6.24-2
ii  libpython2.7  2.7.12-3
ii  libqt4-help   4:4.8.7+dfsg-8
ii  libqt4-network4:4.8.7+dfsg-8
ii  libqtcore44:4.8.7+dfsg-8
ii  libqtgui4 4:4.8.7+dfsg-8
ii  libstdc++66.1.1-11
ii  libswscale4   7:3.1.3-1+b3
ii  libtheora01.1.1+dfsg.1-14
ii  libtiff5  4.0.6-2
ii  libx11-6  2:1.6.3-1
ii  libxml2   2.9.4+dfsg1-1+b1
ii  libxt61:1.1.5-1
ii  python-autobahn   0.10.3+dfsg1-7
ii  python-matplotlib 1.5.2-1
ii  python-mpi4py 1.3.1+hg20131106-2+b2
ii  python-six1.10.0-3
ii  python-twisted16.3.0-1
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  1.7
ii  paraview-doc 5.1.2+dfsg1-1
ii  paraview-python  5.1.2+dfsg1-1

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

-- no debconf information

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python-hdf5storage_0.1.14-1_source.changes uploaded successfully to localhost
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  python-hdf5storage_0.1.14-1.dsc
  python-hdf5storage_0.1.14.orig.tar.gz
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fcl_0.5.0-4_source.changes ACCEPTED into unstable

[Debian FTP Masters]

Accepted:

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Format: 1.8
Date: Wed, 14 Sep 2016 10:56:37 +0200
Source: fcl
Binary: libfcl0.5 libfcl-dev
Architecture: source
Version: 0.5.0-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Jochen Sprickerhof 
Description:
 libfcl-dev - Flexible Collision Library - development files
 libfcl0.5  - Flexible Collision Library - shared library
Changes:
 fcl (0.5.0-4) unstable; urgency=medium
 .
   * Team upload.
   * Enable octomap support on armel and armhf again.
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fcl_0.5.0-4_source.changes uploaded successfully to localhost
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forge_0.9.0-1_amd64.changes is NEW

[Debian FTP Masters]

binary:forge-doc is NEW.
binary:libforge-dev is NEW.
binary:libforge0 is NEW.
source:forge is NEW.

Your package has been put into the NEW queue, which requires manual action
from the ftpteam to process. The upload was otherwise valid (it had a good
OpenPGP signature and file hashes are valid), so please be patient.

Packages are routinely processed through to the archive, and do feel
free to browse the NEW queue[1].

If there is an issue with the upload, you will receive an email from a
member of the ftpteam.

If you have any questions, you may reply to this email.

[1]: https://ftp-master.debian.org/new.html

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fcl_0.5.0-4_source.changes REJECTED

[Debian FTP Masters]

fcl_0.5.0-4.dsc: Invalid size hash for fcl_0.5.0.orig.tar.gz:
According to the control file the size hash should be 5588803,
but fcl_0.5.0.orig.tar.gz has 5760425.

If you did not include fcl_0.5.0.orig.tar.gz in your upload, a different version
might already be known to the archive software.

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dune-functions_2.4~20160825g0fd5975-1_multi.changes ACCEPTED into unstable

[Debian FTP Masters]

Accepted:

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Format: 1.8
Date: Wed, 14 Sep 2016 09:59:56 +0200
Source: dune-functions
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Architecture: all source
Version: 2.4~20160825g0fd5975-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Ansgar Burchardt 
Description: 
 libdune-functions-dev - toolbox for solving PDEs -- interface for functions 
(development
 libdune-functions-doc - toolbox for solving PDEs -- interface for functions 
(documentatio
Changes:
 dune-functions (2.4~20160825g0fd5975-1) unstable; urgency=medium
 .
   * New upstream snapshot.
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Files: 
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fcl_0.5.0-4_source.changes uploaded successfully to localhost
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Re: dolfin_2016.1.0-4_source.changes ACCEPTED into unstable

[Drew Parsons]

On Wed, 2016-09-14 at 09:56 +0200, Johannes Ring wrote:
> Hi Drew,
> Changes:
> >  dolfin (2016.1.0-4) unstable; urgency=medium
> >  .
> >    * Disable HDF5 support.
> > 
> Can you give more details about the error? I think this might be a
> bug
> in the FindHDF5.cmake file in CMake. Did you see this problem with
> version 3.6.1 or 3.6.2 of CMake? Or both? There was a regression in
> version 3.6.1 that was fixed in 3.6.2 as can be seen here:
> 
> https://cmake.org/gitweb?p=cmake.git;a=commit;h=b61eab249f6d119e6353c
> 02c4c79ccb15a3825b9
> https://blog.kitware.com/cmake-3-6-2-available-for-download/
> 
> It would be good if we can re-enable HDF5 support again once this is
> fixed.

Hi Johannes,  I agree, it would be good to have HDF5 support. 
Note that we've never actually had it. It was enabled in the configure
line but got disabled during configure.  Historical build logs are at 
https://buildd.debian.org/status/logs.php?pkg=dolfin=amd64
and
https://buildd.debian.org/status/package.php?p=dolfin

The problem seems to be come from the 2 versions of hdf5,
libhdf5-mpi-dev (parallel) and libhdf5-dev (serial).  We want dolfin to
use libhdf5-mpi-dev but libhdf5-dev is pulled in by libarmadillo-dev
via libvtk6-dev.

So both versions of hdf5 are installed simultaneously. dolfin detects
the serial version and complains that it's not consistent with the
parallel CXX that it found.  Previously dolfin just disabled HDF5 at
that point.  But now (possibly due to updates in the hdf5 packages)
it's started keeping HDF5 enabled. But then it's confused about the
parallel version. It wants to access H5Pset_dxpl_mpio which is only
defined in parallel HDF5, but it's using the serial HDF5 libraries. So
the build now fails against H5Pset_dxpl_mpio (at least, until I
disabled HDF5).

I've put some more detail into the git commit, 
https://anonscm.debian.org/git/debian-science/packages/fenics/dolfin.git/commit/?id=5ccf048ccb4fd7f98aff26fd072787cbe750afea

Another nuance is that parallel HDF5 provides parallel-aware compiler
wrappers, h5pcc (C) and h5pfc (fortran), but there is no h5pc++ or
h5pcxx for C++.

Part of the problem is that FindHDF5.cmake currently looks for h5pc++
or h5c++, which breaks discovery of parallel HDF5 since there is no
h5pc++.

Perhaps it could help if FindHDF5.cmake used the HDF5 pkgconfig files.
 The default is /usr/lib//pkgconfig/hdf5.pc
which doesn't help since it could be either hdf5-serial.pc or
hdf5-openmpi.pc (or hdf5-mpich.pc), controlled by update-alternatives.
But FindHDF5.cmake could look for the mpi or the serial version, or
have the .pc file provided as a configure option.

hdf5-openmpi.pc gives Cflags but no CXXflags. I'm not certain if that
would be enough, but "-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi -lhdf5"
would fix the build failure I think.






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forge_0.9.0-1_amd64.changes uploaded successfully to localhost
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  forge_0.9.0-1.dsc
  forge_0.9.0.orig.tar.gz
  forge_0.9.0-1.debian.tar.xz
  forge-doc_0.9.0-1_all.deb
  libforge-dev_0.9.0-1_amd64.deb
  libforge0-dbgsym_0.9.0-1_amd64.deb
  libforge0_0.9.0-1_amd64.deb

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dune-functions_2.4~20160825g0fd5975-1_multi.changes uploaded successfully to 
localhost
along with the files:
  dune-functions_2.4~20160825g0fd5975-1.dsc
  dune-functions_2.4~20160825g0fd5975.orig.tar.xz
  dune-functions_2.4~20160825g0fd5975-1.debian.tar.xz
  libdune-functions-dev_2.4~20160825g0fd5975-1_all.deb
  libdune-functions-doc_2.4~20160825g0fd5975-1_all.deb

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Re: dolfin_2016.1.0-4_source.changes ACCEPTED into unstable

[Johannes Ring]

Hi Drew,

On Wed, Sep 14, 2016 at 8:33 AM, Debian FTP Masters
 wrote:
> Changes:
>  dolfin (2016.1.0-4) unstable; urgency=medium
>  .
>* Disable HDF5 support.
>  HDF5 was never actually enabled previously due to a discrepant
>  configuration between serial and parallel HDF5, but that now
>  causes dolfin to fail to build.

Can you give more details about the error? I think this might be a bug
in the FindHDF5.cmake file in CMake. Did you see this problem with
version 3.6.1 or 3.6.2 of CMake? Or both? There was a regression in
version 3.6.1 that was fixed in 3.6.2 as can be seen here:

https://cmake.org/gitweb?p=cmake.git;a=commit;h=b61eab249f6d119e6353c02c4c79ccb15a3825b9
https://blog.kitware.com/cmake-3-6-2-available-for-download/

It would be good if we can re-enable HDF5 support again once this is fixed.

Johannes

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Bug#835284: marked as done (urdfdom: FTBFS: Could not find a configuration file for package "urdfdom_headers" that is 367 compatible with requested version "0.4".)

[Debian Bug Tracking System]

Your message dated Wed, 14 Sep 2016 09:42:42 +0200
with message-id 
and subject line urdfdom: FTBFS: Could not find a configuration file for 
package "urdfdom_headers" that is 367 compatible with requested version "0.4".
has caused the Debian Bug report #835284,
regarding urdfdom: FTBFS: Could not find a configuration file for package 
"urdfdom_headers" that is 367 compatible with requested version "0.4".
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
835284: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=835284
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: urdfdom
Version: 0.4.1-1
Severity: serious
Justification: fails to build from source
User: reproducible-bui...@lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org

Dear Maintainer,

urdfdom fails to build from source in unstable/amd64:

  [..]

  CMAKE_INSTALL_LIBDIR:PATH=lib/x86_64-linux-gnu
  
  //program executables (libexec)
  CMAKE_INSTALL_LIBEXECDIR:PATH=libexec
  
  //locale-dependent data (DATAROOTDIR/locale)
  CMAKE_INSTALL_LOCALEDIR:PATH=
  
  //No help, variable specified on the command line.
  CMAKE_INSTALL_LOCALSTATEDIR:UNINITIALIZED=/var
  
  //man documentation (DATAROOTDIR/man)
  CMAKE_INSTALL_MANDIR:PATH=
  
  //C header files for non-gcc (/usr/include)
  CMAKE_INSTALL_OLDINCLUDEDIR:PATH=/usr/include
  
  //Install path prefix, prepended onto install directories.
  CMAKE_INSTALL_PREFIX:PATH=/usr
  
  //system admin executables (sbin)
  CMAKE_INSTALL_SBINDIR:PATH=sbin
  
  //modifiable architecture-independent data (com)
  CMAKE_INSTALL_SHAREDSTATEDIR:PATH=com
  
  //No help, variable specified on the command line.
  CMAKE_INSTALL_SYSCONFDIR:UNINITIALIZED=/etc
  
  //Path to a program.
  CMAKE_LINKER:FILEPATH=/usr/bin/ld
  
  //Path to a program.
  CMAKE_MAKE_PROGRAM:FILEPATH=/usr/bin/make
  
  //Flags used by the linker during the creation of modules.
  CMAKE_MODULE_LINKER_FLAGS:STRING= -Wl,-z,relro
  
  //Flags used by the linker during debug builds.
  CMAKE_MODULE_LINKER_FLAGS_DEBUG:STRING=
  
  //Flags used by the linker during release minsize builds.
  CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL:STRING=
  
  //Flags used by the linker during release builds.
  CMAKE_MODULE_LINKER_FLAGS_RELEASE:STRING=
  
  //Flags used by the linker during Release with Debug Info builds.
  CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO:STRING=
  
  //Path to a program.
  CMAKE_NM:FILEPATH=/usr/bin/nm
  
  //Path to a program.
  CMAKE_OBJCOPY:FILEPATH=/usr/bin/objcopy
  
  //Path to a program.
  CMAKE_OBJDUMP:FILEPATH=/usr/bin/objdump
  
  //Value Computed by CMake
  CMAKE_PROJECT_NAME:STATIC=urdfdom
  
  //Path to a program.
  CMAKE_RANLIB:FILEPATH=/usr/bin/ranlib
  
  //Flags used by the linker during the creation of dll's.
  CMAKE_SHARED_LINKER_FLAGS:STRING= -Wl,-z,relro
  
  //Flags used by the linker during debug builds.
  CMAKE_SHARED_LINKER_FLAGS_DEBUG:STRING=
  
  //Flags used by the linker during release minsize builds.
  CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL:STRING=
  
  //Flags used by the linker during release builds.
  CMAKE_SHARED_LINKER_FLAGS_RELEASE:STRING=
  
  //Flags used by the linker during Release with Debug Info builds.
  CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO:STRING=
  
  //If set, runtime paths are not added when installing shared libraries,
  // but are added when building.
  CMAKE_SKIP_INSTALL_RPATH:BOOL=NO
  
  //If set, runtime paths are not added when using shared libraries.
  CMAKE_SKIP_RPATH:BOOL=NO
  
  //Flags used by the linker during the creation of static libraries.
  CMAKE_STATIC_LINKER_FLAGS:STRING=
  
  //Flags used by the linker during debug builds.
  CMAKE_STATIC_LINKER_FLAGS_DEBUG:STRING=
  
  //Flags used by the linker during release minsize builds.
  CMAKE_STATIC_LINKER_FLAGS_MINSIZEREL:STRING=
  
  //Flags used by the linker during release builds.
  CMAKE_STATIC_LINKER_FLAGS_RELEASE:STRING=
  
  //Flags used by the linker during Release with Debug Info builds.
  CMAKE_STATIC_LINKER_FLAGS_RELWITHDEBINFO:STRING=
  
  //Path to a program.
  CMAKE_STRIP:FILEPATH=/usr/bin/strip
  
  //If this value is on, makefiles will be generated without the
  // .SILENT directive, and all commands will be echoed to the console
  // during the make.  This is useful for debugging only. With Visual
  // Studio IDE projects all commands are done without /nologo.
  CMAKE_VERBOSE_MAKEFILE:BOOL=ON
  
  //Path to a file.
  TinyXML_INCLUDE_DIR:PATH=/usr/include
  
  //Path to a library.
  

Processed: gazebo: please restrict libkido-dev (build-)dependency to architectures where it is available

[Debian Bug Tracking System]

Processing control commands:

> reopen -1
Bug #837121 {Done: Jose Luis Rivero } [gazebo] 
gazebo: please restrict libkido-dev (build-)dependency to architectures where 
it is available.
'reopen' may be inappropriate when a bug has been closed with a version;
all fixed versions will be cleared, and you may need to re-add them.
Bug reopened
No longer marked as fixed in versions gazebo/7.3.0+dfsg-5.

-- 
837121: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=837121
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

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Bug#837121: gazebo: please restrict libkido-dev (build-)dependency to architectures where it is available

[Graham Inggs]

Control: reopen -1


Hi Maintainer

I see you updated gazebo's build-dependencies in 7.3.0+dfsg-5.
Please do the same for libgazebo7-dev's binary dependencies, i.e.


--- a/debian/control
+++ b/debian/control
@@ -137,7 +138,7 @@
  libignition-math2-dev,
  libbullet-dev,
  libsimbody-dev,
- libkido-dev [amd64 arm64 i386 powerpc alpha],
+ libkido-dev [amd64 arm64 i386 ppc64el alpha mipsel],
  libgazebo7 (= ${binary:Version}),
  gazebo7-common (= ${source:Version}),
  gazebo7-plugin-base (= ${binary:Version}),


Regards
Graham

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dolfin_2016.1.0-4_source.changes ACCEPTED into unstable

[Debian FTP Masters]

Accepted:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 14 Sep 2016 12:52:59 +0800
Source: dolfin
Binary: libdolfin-dev libdolfin2016.1 libdolfin2016.1-dbg python-dolfin 
python-dolfin-dbg dolfin-doc dolfin-bin
Architecture: source
Version: 2016.1.0-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Team 

Changed-By: Drew Parsons 
Description:
 dolfin-bin - Executable scripts for DOLFIN
 dolfin-doc - Documentation and demo programs for DOLFIN
 libdolfin-dev - Shared links and header files for DOLFIN
 libdolfin2016.1 - Shared libraries for DOLFIN
 libdolfin2016.1-dbg - Shared libraries with debugging symbols for DOLFIN
 python-dolfin - Python interface for DOLFIN
 python-dolfin-dbg - Python extension modules for DOLFIN with debugging symbols
Changes:
 dolfin (2016.1.0-4) unstable; urgency=medium
 .
   * Disable HDF5 support.
 HDF5 was never actually enabled previously due to a discrepant
 configuration between serial and parallel HDF5, but that now
 causes dolfin to fail to build.
Checksums-Sha1:
 08c22f3da34154c832207f2a4cd2dedd6b2f44d1 2956 dolfin_2016.1.0-4.dsc
 9267b4881c966570b5c4b327823ecc86c37346d8 37472 dolfin_2016.1.0-4.debian.tar.xz
Checksums-Sha256:
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dolfin_2016.1.0-4.dsc
 b9da83ca47b6f52309cd7da3af02e5587516092bc0a14a7c9c7dda9ce658e9d5 37472 
dolfin_2016.1.0-4.debian.tar.xz
Files:
 44e44cc98b53c7a968ecf73de8d04882 2956 math extra dolfin_2016.1.0-4.dsc
 37eca7429fdaf26dce36f9b67ece8746 37472 math extra 
dolfin_2016.1.0-4.debian.tar.xz

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Thank you for your contribution to Debian.

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Processing of dolfin_2016.1.0-4_source.changes

[Debian FTP Masters]

dolfin_2016.1.0-4_source.changes uploaded successfully to localhost
along with the files:
  dolfin_2016.1.0-4.dsc
  dolfin_2016.1.0-4.debian.tar.xz

Greetings,

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