sphinxcontrib-bibtex 0.3.6-1 MIGRATED to testing

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r-cran-sfsmisc 1.1-1-1 MIGRATED to testing

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ovito 2.9.0+dfsg1-5 MIGRATED to testing

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armadillo 1:8.200.2+dfsg-1 MIGRATED to testing

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scotch_6.0.4.dfsg1-5_source.changes ACCEPTED into unstable

[Debian FTP Masters]

Accepted:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sun, 26 Nov 2017 10:29:40 +0800
Source: scotch
Binary: scotch ptscotch libscotch-dev libptscotch-dev scotch-dbg ptscotch-dbg 
libscotch-dbg libptscotch-dbg libscotchmetis-dev libscotchparmetis-dev 
libscotch-6.0 libptscotch-6.0
Architecture: source
Version: 6.0.4.dfsg1-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Drew Parsons 
Description:
 libptscotch-6.0 - MPI programs and libraries for graph, mesh and hypergraph 
partiti
 libptscotch-dbg - MPI programs and libraries for graph, mesh and hypergraph 
partiti
 libptscotch-dev - MPI programs and libraries for graph, mesh and hypergraph 
partiti
 libscotch-6.0 - programs and libraries for graph, mesh and hypergraph 
partitionin
 libscotch-dbg - programs and libraries for graph, mesh and hypergraph 
partitionin
 libscotch-dev - programs and libraries for graph, mesh and hypergraph 
partitionin
 libscotchmetis-dev - programs and libraries for graph, mesh and hypergraph 
partitionin
 libscotchparmetis-dev - programs and libraries for graph, mesh and hypergraph 
partitionin
 ptscotch   - MPI programs and libraries for graph, mesh and hypergraph partiti
 ptscotch-dbg - MPI programs and libraries for graph, mesh and hypergraph 
partiti
 scotch - programs and libraries for graph, mesh and hypergraph partitionin
 scotch-dbg - programs and libraries for graph, mesh and hypergraph partitionin
Closes: 865671
Changes:
 scotch (6.0.4.dfsg1-5) unstable; urgency=medium
 .
   * Team upload.
   * debian/rules: apply "set -e" at the build step to halt on build
 error. Closes: #865671.
 - treat tests (make check) as information-only, don't halt on
   check failure
   * improve thread handling with -DSCOTCH_PTHREAD_NUMBER=2 and
 -DSCOTCH_PTHREAD_AFFINITY_LINUX (see INSTALL.txt)
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 568d66fd9cb7df4589ce1e0f6b99d70c6d7a396f 17752 
scotch_6.0.4.dfsg1-5.debian.tar.xz
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scotch_6.0.4.dfsg1-5.debian.tar.xz
Files:
 471cd6114307bdf6b02d72e0078fc1fa 2799 math optional scotch_6.0.4.dfsg1-5.dsc
 39227f03c15bfa1e411a42306ee7eb3c 17752 math optional 
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qhull_2015.2-3_amd64.changes is NEW

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  libqhull-r7-dbgsym_2015.2-3_amd64.deb
  libqhull-r7_2015.2-3_amd64.deb
  libqhull7-dbgsym_2015.2-3_amd64.deb
  libqhull7_2015.2-3_amd64.deb
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Bug#841168: libqhull-dev: Has /usr/include/libqhull_r headers, but no libqhull_r.so

[Barak A. Pearlmutter]

Thanks. Uploading your fix now. Should have done this a while ago,
just slipped between the cracks.
(In general, do feel free to upload unobjectionable fixes to my
packages, I really don't mind. Especially if you also push to the
packaging repo.)

I'm thinking it might make sense to ditch the non-reentrant version of
this library. I doubt there would be any measurable performance loss.
Can you imagine any objections?

--Barak.

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Bug#841168: libqhull-dev: Has /usr/include/libqhull_r headers, but no libqhull_r.so

[Jochen Sprickerhof]

Hi Barak,

the PCL project would like to use the qhull_r version [1], so I had a 
quick look at it and pushed a patch to git [2] to include it. If you are 
ok with it, I would upload the new package as well. As it needs to go 
through new, I would like to do this soon. So if you don't replay within 
the next 10 days, I would assume your are fine with the changes and 
proceed. If you don't agree with the patch, please write me and I will 
revert the commit and leave the package as is.


Cheers Jochen


[1] https://github.com/PointCloudLibrary/pcl/pull/1565
[2] 
https://anonscm.debian.org/cgit/debian-science/packages/qhull.git/commit/?id=c9016569f6961cb07b5a0ba7c3cb95260090986d

* Ian Thomas  [2016-10-18 10:02]:

Package: libqhull-dev
Version: 2015.2-1
Severity: normal
Tags: newcomer

There are two versions of qhull, the original non-reentrant version (libqhull)
and the newer reeentrant version (libqhull_r).  libqhull-dev 2015.2-1 has
include files for both, but only libraries for the non reentrant version.
Hence users cannot link against the reentrant version.

Building the debian package from source indicates that libqhull_r.so is built,
but it is not making its way into libqhull7_2015.2-1_amd64.deb or libqhull-
dev_2015.2-1_amd64.deb



-- System Information:
Debian Release: stretch/sid
 APT prefers xenial-updates
 APT policy: (500, 'xenial-updates'), (500, 'xenial-security'), (500, 
'xenial'), (100, 'xenial-backports')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.4.0-42-generic (SMP w/4 CPU cores)
Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages libqhull-dev depends on:
ii  libqhull7  2015.2-1

libqhull-dev recommends no packages.

libqhull-dev suggests no packages.

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Bug#882711: segyio: FTBFS on hurd-i386: some *.segy tests still fail

[Aaron M. Ucko]

Source: segyio
Version: 1.3.8-1
Severity: important
Tags: upstream
Justification: fails to build from source
User: debian-h...@lists.debian.org
Usertags: hurd-i386

Thanks again for looking into my previous reports!  Builds of segyio
for most 32-bit architectures now succeed (as do builds for s390x and
sparc64).  However, the build for hurd-i386 (admittedly not a release
architecture) still fails, per the below excerpts from
https://buildd.debian.org/status/fetch.php?pkg=segyio=hurd-i386=1.3.8-1=1511626257=0.

Could you please take a look?

Thanks!



 1/31 Test  #1: c.segy ...***Failed0.01 sec
Assertion failed in file: /<>/lib/test/segy.c on line: 876
starting
interpret file
read inline 4
read inline 22
mod traceh
mod texth
test traceh
test readsubtr(mmap)
test readsubtr(no-mmap)
test writesubtr(no-mmap)
test scan headers(mmap)
test scan headers(no-mmap)

[...]
 3/31 Test  #3: python.segy ..***Failed1.08 sec
test_assign_all_traces (test.segy.TestSegy) ... ok
test_attributes (test.segy.TestSegy) ... ERROR
test_create_from_naught (test.segy.TestSegy) ... ok
test_create_from_naught_prestack (test.segy.TestSegy) ... ok
test_create_sgy (test.segy.TestSegy) ... ok
test_create_sgy_shorter_traces (test.segy.TestSegy) ... ok
test_create_sgy_skip_lines (test.segy.TestSegy) ... ok
test_create_write_lines (test.segy.TestSegy) ... ok
test_depth_slice_reading (test.segy.TestSegy) ... ok
test_depth_slice_writing (test.segy.TestSegy) ... ok
test_fast_slow_dimensions (test.segy.TestSegy) ... ok
test_file_info (test.segy.TestSegy) ... ok
test_fopen_error (test.segy.TestSegy) ... ok
test_gather_mode (test.segy.TestSegy) ... ok
test_header_dict_methods (test.segy.TestSegy) ... ok
test_headers_line_offset (test.segy.TestSegy) ... ok
test_headers_offset (test.segy.TestSegy) ... ok
test_iline_offset (test.segy.TestSegy) ... ok
test_iline_slice_all_offsets (test.segy.TestSegy) ... ok
test_iline_slice_fixed_line (test.segy.TestSegy) ... ok
test_iline_slice_fixed_offset (test.segy.TestSegy) ... ok
test_iline_slicing (test.segy.TestSegy) ... ok
test_inline_4 (test.segy.TestSegy) ... ok
test_line_generators (test.segy.TestSegy) ... ok
test_open_fails_unstructured (test.segy.TestSegy) ... ok
test_open_ignore_geometry (test.segy.TestSegy) ... ok
test_open_nostrict (test.segy.TestSegy) ... ok
test_open_transposed_lines (test.segy.TestSegy) ... ok
test_open_wrong_crossline (test.segy.TestSegy) ... ok
test_open_wrong_inline (test.segy.TestSegy) ... ok
test_read_header (test.segy.TestSegy) ... ok
test_segyio_types (test.segy.TestSegy) ... ok
test_traceaccess_from_array (test.segy.TestSegy) ... ok
test_traces_offset (test.segy.TestSegy) ... ok
test_traces_raw (test.segy.TestSegy) ... ok
test_traces_slicing (test.segy.TestSegy) ... ok
test_wonky_dimensions (test.segy.TestSegy) ... ok
test_write_binary (test.segy.TestSegy) ... ok
test_write_header (test.segy.TestSegy) ... ok
test_wrong_lineno (test.segy.TestSegy) ... ok
test_xline_22 (test.segy.TestSegy) ... ok
test_xline_slicing (test.segy.TestSegy) ... ok

==
ERROR: test_attributes (test.segy.TestSegy)
--
Traceback (most recent call last):
  File "/<>/.pybuild/pythonX.Y_3.6/build/python/test/segy.py", 
line 308, in test_attributes
self.assertListEqual(ils, attrils)
  File "/<>/.pybuild/pythonX.Y_3.6/build/python/segyio/segy.py", 
line 117, in __exit__
self.close()
  File "/<>/.pybuild/pythonX.Y_3.6/build/python/segyio/segy.py", 
line 149, in close
_segyio.close(self.xfd)
OSError: [Errno 1073741902] Function not implemented

--
Ran 42 tests in 0.850s

FAILED (errors=1)

  Start  4: python.h.segy
 4/31 Test  #4: python.h.segy ***Failed0.24 sec
test_binary_header_size (test.segyio_c._segyioTests) ... ok
test_close_non_existing_file (test.segyio_c._segyioTests) ... ok
test_fread_trace0 (test.segyio_c._segyioTests) ... ok
test_fread_trace0_for_depth (test.segyio_c._segyioTests) ... ok
test_get_and_set_field (test.segyio_c._segyioTests) ... ok
test_indices (test.segyio_c._segyioTests) ... ok
test_line_metrics (test.segyio_c._segyioTests) ... ok
test_metrics (test.segyio_c._segyioTests) ... ok
test_open_and_close_file (test.segyio_c._segyioTests) ... ok
test_open_flush_and_close_file (test.segyio_c._segyioTests) ... ok
test_open_non_existing_file (test.segyio_c._segyioTests) ... ok
test_read_and_write_binary_header (test.segyio_c._segyioTests) ... ok
test_read_and_write_trace (test.segyio_c._segyioTests) ... ok
test_read_and_write_traceheader (test.segyio_c._segyioTests) ... ok
test_read_binary_header_fields (test.segyio_c._segyioTests) ... ok
test_read_line (test.segyio_c._segyioTests) ... ok
test_read_line_mmap (test.segyio_c._segyioTests) ... 

Processing of keras_2.1.1-1_amd64.changes

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Bug#882699: ngspice: Remove build dependency on elyxer to allow for the elyxer removal from Debian

[Sven Hoexter]

Source: ngspice
Version: 26-1.1
Severity: important
Tags: patch

Hello Gudjon, hello Andreas,
I'd like to get elyxer removed from Debian but to allow for that to happen I 
need to get
rid of ngspice dependency on it. The HTML export support in LyX improved a lot 
since
I introduced elyxer to Debian and is nowadays, while not that pretty, on par or 
even better
(as in more complete) then what elyxer has to offer. Also elyxer didn't receive 
any update
for a long time. I see at least some issue when I generate the ngspice 
documentation HTML
export with elyxer.

I've attached the debdiff of a potential NMU I'm willing to upload since I'm 
not sure how
active you're at the moment taking care of ngspice. So if you do not plan to 
upload ngspice
on your own soon and do not object to the elyxer removal itself, I can just 
upload my NMU.

Cheers,
Sven
diff -Nru ngspice-26/debian/changelog ngspice-26/debian/changelog
--- ngspice-26/debian/changelog 2016-04-25 20:51:09.0 +0200
+++ ngspice-26/debian/changelog 2017-11-25 20:12:49.0 +0100
@@ -1,3 +1,13 @@
+ngspice (26-1.2) unstable; urgency=medium
+
+  * Non-maintainer upload.
+  * Remove elyxer from Build-Depends-Indep to allow for the removal of elyxer
+from Debian. The build in HTML export support in LyX improved during the
+last years and is equally usable or even better regarding new LyX file
+formats.
+
+ -- Sven Hoexter   Sat, 25 Nov 2017 20:12:49 +0100
+
 ngspice (26-1.1) unstable; urgency=medium
 
   * Non-maintainer upload.
diff -Nru ngspice-26/debian/control ngspice-26/debian/control
--- ngspice-26/debian/control   2014-07-05 23:49:29.0 +0200
+++ ngspice-26/debian/control   2017-11-25 20:12:23.0 +0100
@@ -7,7 +7,7 @@
 Build-Depends: debhelper (>= 8), automake, libtool, libxaw7-dev, flex,
  bison, gfortran, libedit-dev, libncurses5-dev,
  texinfo, tcl8.6-dev, tcl8.6, tk8.6-dev, tk8.6, blt-dev
-Build-Depends-Indep: lyx, elyxer, texlive, texlive-latex-extra, 
texlive-lang-greek,
+Build-Depends-Indep: lyx, texlive, texlive-latex-extra, texlive-lang-greek,
  texlive-generic-recommended, imagemagick
 Standards-Version: 3.9.5
 Homepage: http://ngspice.sourceforge.net
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Bug#805427: ngspice: FTBFS due to lyx/elyxer problem

[Sven Hoexter]

Hi,
while looking into removing elyxer from Debian I stumpled upon your bugreport.
I just rebuild ngspice with pbuilder without elyxer and can not reproduce
the issue you describe. Either things changed with the current LyX release
(I don't think so, but I did not follow the development closely) or your
issue is not reproducible in my (chroot'ed) environment.

Do you mind providing some more information about the circumstances you
encountered the issue and maybe retest it.

Regards,
Sven

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Bug#882667: hypre: CUDA support: hacks impeded by -W flags

[Drew Parsons]

On Sat, 25 Nov 2017 20:24:50 +0800 Drew Parsons 
wrote:
> 
> Again, the problem is that -W is not recognised by nvcc.  Would have
> to hack the soname patch to encapsulate it inside --compiler-options

Can get further using nvcc --linker-options to carry -Wl options.

But "CC=mpiCC CUDACXX=mpiCC dh_auto_configure" seems better than
"CC=nvcc", together with export OMPI_CXX=g++-5 to set mpiCC.

With other sundry hacks, gets to src/struct_mv and stalls at
assumed_part.c, apparently because of inconsistencies in C/C++
standards between nvcc and CC.Depending on whether g++-5 or clang++-3.8 
is used, whether -std=c++11 or c++14 or c++98 is passed to gcc, get
either

 - conflict in multiple definitions of isnan, conflicting between 
CUDA's /usr/include/math_functions.h and /usr/include/x86_64-linux-
gnu/bits/mathcalls.h

 - or similar multiple definitions in abs(float)

 - or  /usr/include/cuda_fp16.h:985:68: error: C does not support default 
arguments
__CUDA_FP16_DECL__ __half2 __shfl(__half2 var, int delta, int width=warpSize);

- or inconsistent C/C++ definitions
./_hypre_struct_mv.h:1464:8: error: expected identifier or '('
extern "C++" {
   ^
./_hypre_struct_mv.h:1488:22: error: unexpected OpenMP directive '#pragma 
omp parallel for'
#pragma omp parallel for schedule(static)

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Processed: notfixed 882421 in 1.3.8-1

[Debian Bug Tracking System]

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

> notfixed 882421 1.3.8-1
Bug #882421 {Done: Jørgen Kvalsvik } [src:segyio] segyio: 
FTBFS on sparc64: test_rotation: AssertionError: 1.571 != 0.0 within 3 places
No longer marked as fixed in versions segyio/1.3.8-1.
> thanks
Stopping processing here.

Please contact me if you need assistance.
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silx_0.6.1+dfsg-1_source.changes ACCEPTED into unstable

[Debian FTP Masters]

Accepted:

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Hash: SHA512

Format: 1.8
Date: Sat, 25 Nov 2017 17:02:19 +0100
Source: silx
Binary: silx python-silx python-silx-dbg python3-silx python3-silx-dbg 
python-silx-doc
Architecture: source
Version: 0.6.1+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Picca Frédéric-Emmanuel 
Description:
 python-silx - Toolbox for X-Ray data analysis - Python2 library
 python-silx-dbg - Toolbox for X-Ray data analysis - Python2 debug
 python-silx-doc - Toolbox for X-Ray data analysis - Documentation
 python3-silx - Toolbox for X-Ray data analysis - Python3
 python3-silx-dbg - Toolbox for X-Ray data analysis - Python3 debug
 silx   - Toolbox for X-Ray data analysis - Executables
Changes:
 silx (0.6.1+dfsg-1) unstable; urgency=medium
 .
   * New upstream version 0.6.1+dfsg
   * update watch file
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silx_0.6.1+dfsg.orig.tar.gz
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silx_0.6.1+dfsg-1.debian.tar.xz
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Thank you for your contribution to Debian.

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Processing of silx_0.6.1+dfsg-1_source.changes

[Debian FTP Masters]

silx_0.6.1+dfsg-1_source.changes uploaded successfully to localhost
along with the files:
  silx_0.6.1+dfsg-1.dsc
  silx_0.6.1+dfsg.orig.tar.gz
  silx_0.6.1+dfsg-1.debian.tar.xz
  silx_0.6.1+dfsg-1_source.buildinfo

Greetings,

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Bug#882421: marked as done (segyio: FTBFS on sparc64: test_rotation: AssertionError: 1.571 != 0.0 within 3 places)

[Debian Bug Tracking System]

Your message dated Sat, 25 Nov 2017 15:11:33 +
with message-id 
and subject line Bug#882421: fixed in segyio 1.3.8-1
has caused the Debian Bug report #882421,
regarding segyio: FTBFS on sparc64: test_rotation: AssertionError: 1.571 != 0.0 
within 3 places
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.)


-- 
882421: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=882421
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: segyio
Version: 1.3.3-1
Severity: important
Tags: upstream
Justification: fails to build from source
User: debian-sp...@lists.debian.org
Usertags: sparc64

The build of segyio for sparc64 (admittedly not a release
architecture) failed per the below excerpts from
https://buildd.debian.org/status/fetch.php?pkg=segyio=sparc64=1.3.3-1=1511256932=0.
1.571 is of course approximately π/2.

Could you please take a look?

Thanks!



16/17 Test  #6: python.tools .***Failed0.61 sec
test_cube_filename (tools.ToolsTest) ... ok
test_cube_identity (tools.ToolsTest) ... ok
test_cube_identity_prestack (tools.ToolsTest) ... ok
test_dt_fallback (tools.ToolsTest) ... ok
test_dt_no_fallback (tools.ToolsTest) ... ok
test_empty_text_header_creation (tools.ToolsTest) ... ok
test_native (tools.ToolsTest) ... ok
test_rotation (tools.ToolsTest) ... FAIL
test_sample_indexes (tools.ToolsTest) ... ok
test_unstructured_rotation (tools.ToolsTest) ... ok
test_values_text_header_creation (tools.ToolsTest) ... ok
test_wrap (tools.ToolsTest) ... ok

==
FAIL: test_rotation (tools.ToolsTest)
--
Traceback (most recent call last):
  File "/<>/.pybuild/pythonX.Y_3.6/build/python/test/tools.py", 
line 128, in test_rotation
close(right, rotation(f, line = 'slow'),  places = 3)
AssertionError: 1.571 != 0.0 within 3 places

--
Ran 12 tests in 0.032s

FAILED (failures=1)
[...]
94% tests passed, 1 tests failed out of 17

Total Test time (real) =   0.92 sec

The following tests FAILED:
  6 - python.tools (Failed)
Errors while running CTest
Makefile:122: recipe for target 'test' failed

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
--- End Message ---
--- Begin Message ---
Source: segyio
Source-Version: 1.3.8-1

We believe that the bug you reported is fixed in the latest version of
segyio, 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 882...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Jørgen Kvalsvik  (supplier of updated segyio 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: SHA256

Format: 1.8
Date: Sat, 25 Nov 2017 13:02:52 +0100
Source: segyio
Binary: libsegyio1 libsegyio-dev segyio-bin python3-segyio
Architecture: source
Version: 1.3.8-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Jørgen Kvalsvik 
Description:
 libsegyio-dev - SEG-Y read/write library for seismic processing (development)
 libsegyio1 - SEG-Y read/write library for seismic processing (runtime)
 python3-segyio - SEG-Y read/write library for seismic processing (python3 
bindings
 segyio-bin - SEG-Y read/write library for seismic processing (shell utilities)
Closes: 882420 882421
Changes:
 segyio (1.3.8-1) unstable; urgency=medium
 .
   * New upstream release
   * Builds on platforms where long is 32bit (Closes: #882420)
   * Builds on sparc64 (Closes: #882421)
   * Upgrade to Standards-Version 4.1.1
   * Add libc6-dev to tests dependencies
   * Add python3-setuptools and python3-setuptools-scm to build dependencies
   * Remove pycmake licence entry
Checksums-Sha1:
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Bug#882420: marked as done (segyio: FTBFS on s390x: Assertion failed in file: /<>/lib/test/segy.c on line: 547)

[Debian Bug Tracking System]

Your message dated Sat, 25 Nov 2017 15:11:33 +
with message-id 
and subject line Bug#882420: fixed in segyio 1.3.8-1
has caused the Debian Bug report #882420,
regarding segyio: FTBFS on s390x: Assertion failed in file: 
/<>/lib/test/segy.c on line: 547
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.)


-- 
882420: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=882420
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: segyio
Version: 1.3.3-1
Severity: important
Tags: upstream
Justification: fails to build from source
User: debian-s...@lists.debian.org
Usertags: s390x

The build of segyio for s390x failed with a strange error, per the
below excerpt from 
https://buildd.debian.org/status/fetch.php?pkg=segyio=s390x=1.3.3-1=1511256490=0:

   1/17 Test  #1: c.segy ...***Failed0.00 sec
  Assertion failed in file: /<>/lib/test/segy.c on line: 547
  Expected: 4.24, Actual: 4.24, diff: 0.00, eps: 0.00
  starting
  interpret file
  read inline 4

Could you please take a look?

Thanks!

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
--- End Message ---
--- Begin Message ---
Source: segyio
Source-Version: 1.3.8-1

We believe that the bug you reported is fixed in the latest version of
segyio, 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 882...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Jørgen Kvalsvik  (supplier of updated segyio 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: SHA256

Format: 1.8
Date: Sat, 25 Nov 2017 13:02:52 +0100
Source: segyio
Binary: libsegyio1 libsegyio-dev segyio-bin python3-segyio
Architecture: source
Version: 1.3.8-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Jørgen Kvalsvik 
Description:
 libsegyio-dev - SEG-Y read/write library for seismic processing (development)
 libsegyio1 - SEG-Y read/write library for seismic processing (runtime)
 python3-segyio - SEG-Y read/write library for seismic processing (python3 
bindings
 segyio-bin - SEG-Y read/write library for seismic processing (shell utilities)
Closes: 882420 882421
Changes:
 segyio (1.3.8-1) unstable; urgency=medium
 .
   * New upstream release
   * Builds on platforms where long is 32bit (Closes: #882420)
   * Builds on sparc64 (Closes: #882421)
   * Upgrade to Standards-Version 4.1.1
   * Add libc6-dev to tests dependencies
   * Add python3-setuptools and python3-setuptools-scm to build dependencies
   * Remove pycmake licence entry
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Files:
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 6982a71791239ef442434297522ec84c 131190 science optional 
segyio_1.3.8.orig.tar.gz
 3ec1098219e1ac76c087d396af6f8f07 2904 science optional 
segyio_1.3.8-1.debian.tar.xz
 e06e4b35cb1245c84e3a84b43fc13af4 8708 science optional 
segyio_1.3.8-1_amd64.buildinfo

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Bug#882312: marked as done (segyio FTBFS on 32bit: segy_ftell: Assertion `sizeof( long ) == sizeof( long long )' failed)

[Debian Bug Tracking System]

Your message dated Sat, 25 Nov 2017 15:11:33 +
with message-id 
and subject line Bug#882420: fixed in segyio 1.3.8-1
has caused the Debian Bug report #882420,
regarding segyio FTBFS on 32bit: segy_ftell: Assertion `sizeof( long ) == 
sizeof( long long )' failed
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.)


-- 
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Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: segyio
Version: 1.3.3-1
Severity: important

https://buildd.debian.org/status/package.php?p=segyio=sid

...
   dh_auto_test -a -O--buildsystem=pybuild
I: pybuild base:184: dh_auto_test --buildsystem=cmake 
--builddirectory="/<>/.pybuild/pythonX.Y_3.6/build" -- 
cd .pybuild/pythonX.Y_3.6/build && make -j4 test ARGS\+=-j4
make[1]: Entering directory '/<>/.pybuild/pythonX.Y_3.6/build'
Running tests...
/usr/bin/ctest --force-new-ctest-process -j4
Test project /<>/.pybuild/pythonX.Y_3.6/build
  Start  1: c.segy
  Start  2: c.utils
  Start  3: python.segy
  Start  4: python.h.segy
 1/17 Test  #1: c.segy ...***Exception: Other  0.22 sec
testsegy: /<>/lib/src/segy.c:409: segy_ftell: Assertion `sizeof( 
long ) == sizeof( long long )' failed.
starting
interpret file
read inline 4
read inline 22
mod traceh
mod texth
test traceh
test readsubtr(mmap)
test readsubtr(no-mmap)
test writesubtr(no-mmap)
test scan headers(mmap)
test scan headers(no-mmap)

  Start  5: python.enum.segy
 2/17 Test  #2: c.utils ..   Passed0.84 sec
 3/17 Test  #4: python.h.segy    Passed1.01 sec
  Start  6: python.tools
  Start  7: python.context
 4/17 Test  #5: python.enum.segy .   Passed0.94 sec
  Start  8: python.example.about
 5/17 Test  #7: python.context ...   Passed0.50 sec
  Start  9: python.example.write
 6/17 Test  #6: python.tools .   Passed1.03 sec
  Start 10: python.example.makefile
 7/17 Test  #3: python.segy ..   Passed2.09 sec
  Start 11: python.example.makepsfile
 8/17 Test  #8: python.example.about .   Passed1.13 sec
  Start 12: python.example.subcube
 9/17 Test  #9: python.example.write .   Passed1.17 sec
  Start 13: python.example.rotate
10/17 Test #10: python.example.makefile ..   Passed1.25 sec
  Start 14: python.example.scan_min_max
11/17 Test #11: python.example.makepsfile    Passed0.93 sec
  Start 15: applications.catr
12/17 Test #12: python.example.subcube ...   Passed0.92 sec
  Start 16: applications.catb
13/17 Test #13: python.example.rotate    Passed1.07 sec
14/17 Test #15: applications.catr    Passed0.59 sec
  Start 17: applications.cath
15/17 Test #14: python.example.scan_min_max ..   Passed1.11 sec
16/17 Test #16: applications.catb    Passed0.70 sec
17/17 Test #17: applications.cath    Passed0.57 sec

94% tests passed, 1 tests failed out of 17

Total Test time (real) =   4.79 sec

The following tests FAILED:
  1 - c.segy (OTHER_FAULT)
Errors while running CTest
Makefile:120: recipe for target 'test' failed
make[1]: *** [test] Error 8
--- End Message ---
--- Begin Message ---
Source: segyio
Source-Version: 1.3.8-1

We believe that the bug you reported is fixed in the latest version of
segyio, 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 882...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Jørgen Kvalsvik  (supplier of updated segyio 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: SHA256

Format: 1.8
Date: Sat, 25 Nov 2017 13:02:52 +0100
Source: segyio
Binary: libsegyio1 libsegyio-dev segyio-bin python3-segyio
Architecture: source
Version: 1.3.8-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Jørgen Kvalsvik 
Description:
 

segyio_1.3.8-1_source.changes ACCEPTED into unstable

[Debian FTP Masters]

Accepted:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 25 Nov 2017 13:02:52 +0100
Source: segyio
Binary: libsegyio1 libsegyio-dev segyio-bin python3-segyio
Architecture: source
Version: 1.3.8-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Jørgen Kvalsvik 
Description:
 libsegyio-dev - SEG-Y read/write library for seismic processing (development)
 libsegyio1 - SEG-Y read/write library for seismic processing (runtime)
 python3-segyio - SEG-Y read/write library for seismic processing (python3 
bindings
 segyio-bin - SEG-Y read/write library for seismic processing (shell utilities)
Closes: 882420 882421
Changes:
 segyio (1.3.8-1) unstable; urgency=medium
 .
   * New upstream release
   * Builds on platforms where long is 32bit (Closes: #882420)
   * Builds on sparc64 (Closes: #882421)
   * Upgrade to Standards-Version 4.1.1
   * Add libc6-dev to tests dependencies
   * Add python3-setuptools and python3-setuptools-scm to build dependencies
   * Remove pycmake licence entry
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segyio_1.3.8-1_source.changes uploaded successfully to localhost
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  segyio_1.3.8-1.dsc
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Processed: closing 861369

[Debian Bug Tracking System]

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

> close 861369 7.8.1+dfsg-2
Bug #861369 [gazebo7] gazebo7: Please do not depend on transitional dummy pkg 
ttf-liberation
Marked as fixed in versions gazebo/7.8.1+dfsg-2.
Bug #861369 [gazebo7] gazebo7: Please do not depend on transitional dummy pkg 
ttf-liberation
Marked Bug as done
> thanks
Stopping processing here.

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Processed: forcibly merging 882420 882312

[Debian Bug Tracking System]

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

> forcemerge 882420 882312
Bug #882420 [src:segyio] segyio: FTBFS on s390x: Assertion failed in file: 
/<>/lib/test/segy.c on line: 547
Bug #882312 [src:segyio] segyio FTBFS on 32bit: segy_ftell: Assertion `sizeof( 
long ) == sizeof( long long )' failed
Added tag(s) upstream.
Merged 882312 882420
> thanks
Stopping processing here.

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Bug#876411: marked as done (admesh: autopkgtests fail since 0.98.3-1 upload)

[Debian Bug Tracking System]

Your message dated Sat, 25 Nov 2017 13:33:37 +
with message-id 
and subject line Bug#876411: fixed in admesh 0.98.3-2
has caused the Debian Bug report #876411,
regarding admesh: autopkgtests fail since 0.98.3-1 upload
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.

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-- 
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Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: admesh
Version: 0.98.3-1
Tags: patch
User: ubuntu-de...@lists.ubuntu.com
Usertags: origin-ubuntu artful autopkgtest

Hi Anton

ADMesh's autopkgtests have been failing since the 0.98.3-1 upload [1].
Output of the 'regression' test changed because it includes the
version.

If you are happy with the attached patch, I can do a team upload.

Regards
Graham


[1] https://ci.debian.net/packages/a/admesh/unstable/amd64/
--- a/debian/tests/regression
+++ b/debian/tests/regression
@@ -98,7 +98,6 @@
 EOF
 
 cat < regression_test_output_etalon
-ADMesh version 0.98.2, Copyright (C) 1995, 1996 Anthony D. Martin
 ADMesh comes with NO WARRANTY.  This is free software, and you are welcome to
 redistribute it under certain conditions.  See the file COPYING for details.
 Opening block.stl
@@ -111,7 +110,6 @@
 Calculating volume...
 Verifying neighbors...
 
-= Results produced by ADMesh version 0.98.2 
 Input file : block.stl
 File type  : ASCII STL file
 Header : SOLID  Untitled1
@@ -137,6 +135,8 @@
 EOF
 
 admesh block.stl > regression_test_output_current
+# delete lines containing the ADMesh version
+sed -i '/version/d' regression_test_output_current
 DIFFRESULT=`diff regression_test_output_current regression_test_output_etalon`
 if [ "$DIFFRESULT" != "" ]; then
   rm regression_test_output_current
--- End Message ---
--- Begin Message ---
Source: admesh
Source-Version: 0.98.3-2

We believe that the bug you reported is fixed in the latest version of
admesh, 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 876...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Anton Gladky  (supplier of updated admesh 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: Sat, 25 Nov 2017 14:16:13 +0100
Source: admesh
Binary: admesh libadmesh-dev libadmesh1
Architecture: source
Version: 0.98.3-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Anton Gladky 
Description:
 admesh - Tool for processing triangulated solid meshes. Binary
 libadmesh-dev - Tool for processing triangulated solid meshes. Development 
files
 libadmesh1 - Tool for processing triangulated solid meshes. Shared library
Closes: 876411
Changes:
 admesh (0.98.3-2) unstable; urgency=medium
 .
   [ Graham Inggs ]
   * [deb03ba] Fix autopkgtests. (Closes: #876411)
 .
   [ Anton Gladky ]
   * [7706a6b] Set Standards-Version: 4.1.1
   * [6beb46f] Remove obsolete Testsuite-field in d/control
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gap-io_4.5.0+ds-1_source.changes ACCEPTED into unstable

[Debian FTP Masters]

Accepted:

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Hash: SHA512

Format: 1.8
Date: Sat, 25 Nov 2017 13:11:29 +
Source: gap-io
Binary: gap-io
Architecture: source
Version: 4.5.0+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Jerome Benoit 
Description:
 gap-io - low level C library IO bindings for GAP
Changes:
 gap-io (4.5.0+ds-1) unstable; urgency=medium
 .
   * New upstream minor version.
   * Debianization:
 - debian/copyright:
   - Files-Excluded field, refresh;
   - update;
 - debian/watch:
   - version, bump to version 4;
   - repack policy, revisit;
 - debian/control:
   - debhelper, bump to 10;
   - Standards Version, bump to 4.1.1 (no change);
   - Depends field, bump to gap 4r8p8;
 - debian/patches/*:
   - d/p/debianization.patch, update;
 - debian/rules:
   - debhelper, bump to 10;
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 - debian/clean, refresh;
 - debian/makedoc.g, refresh;
 - debian/tests/*, introduce.
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gap-io_4.5.0+ds-1_source.changes uploaded successfully to localhost
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  gap-io_4.5.0+ds-1.dsc
  gap-io_4.5.0+ds.orig.tar.xz
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Bug#882667: hypre: CUDA support: hacks impeded by -W flags

[Drew Parsons]

Source: hypre
Version: 2.13.0-1exp1
Severity: normal

With some hacking, we can start attempting to build hypre with CUDA
support (private build, or perhaps a separate hypre package in contrib).

Brief notes:

- The version of nvcc (nvidia-cuda-toolkit) in debian non-free is 8.0.61-3
nvcc does not yet support gcc 7, and nvcc 8 does not support gcc 6
To also use mpiCC (so mpi.h is known, etc), need OMPI_CXX
So need 
  CC=nvcc CUDACXX=mpiCC dh_auto_configure -- $(extra_flags) --enable-shared

- nvcc does not recognise dpkg-buildflags flags (-W flags in
particular), so need to set an empty LDFLAGS and friends

- must hack src/config/configure.in where nvcc flags are defined,
replace -fPIC with --compiler-options '-fPIC'

- build with g++-5  fails at src/utilities/gpuMem.c:
$nvcc -O --compiler-options '-fPIC' -DUSE_NVTX -DHYPRE_USE_GPU 
-DHYPRE_USE_MANAGED  -ccbin=mpiCC -expt-extended-lambda -arch compute_35 
--std=c++11 -Xcompiler -fopenmp -Xcompiler   -DHYPRE_USE_CUDA  -DUSE_NVTX 
-DHYPRE_USE_GPU  -DHYPRE_USE_MANAGED -I /usr/local/cuda/include  
-DHAVE_CONFIG_H -I.. -I./.. -I.-c gpuMem.c
  gpuMem.c: In function ‘getstreamOlde’:
  gpuMem.c:335:23: error: storage size of ‘s’ isn’t constant
 static cudaStream_t s[MAXSTREAMS];
 ^
  gpuMem.c: In function ‘getdomain’:
  gpuMem.c:351:31: error: storage size of ‘h’ isn’t constant
   static nvtxDomainHandle_t h[MAXDOMAINS];
 ^
  gpuMem.c: In function ‘getevent’:
  gpuMem.c:364:22: error: storage size of ‘s’ isn’t constant
 static cudaEvent_t s[MAXEVENTS];


This gpuMem.c does compile cleanly under OMPI_CXX=clang++-3.8
Pass through using export OMPI_CXX=clang++-3.8 in debian/rules.

Finally then, using 
  export OMPI_CXX=clang++-3.8
  CC=nvcc CUDACXX=mpiCC dh_auto_configure -- $(extra_flags) --with-cuda 
--enable-unified-memory --with-nvcc --enable-shared

the libHYPRE_utilities.so build proceeds but fails at link time
providing the soname, 
  nvcc -shared -o libHYPRE_utilities-2.13.0.so amg_linklist.o binsearch.o 
exchange_data.o fortran_matrix.o hypre_ap.o hypre_complex.o hypre_memory.o 
hypre_printf.o hypre_qsort.o memory_dmalloc.o mpistubs.o qsplit.o random.o 
threading.o timer.o timing.o umalloc_local.o hypre_mpi_comm_f2c.o hypre_error.o 
F90_HYPRE_error.o hypre_prefix_sum.o hypre_merge_sort.o hypre_hopscotch_hash.o 
gpuErrorCheck.o gpuMem.o -lmpi -lm -Wl,-soname,libHYPRE_utilities-2.13.0.so 
-Wl,-z,defs
  nvcc fatal   : Unknown option 'Wl,-soname,libHYPRE_utilities-2.13.0.so'

Again, the problem is that -W is not recognised by nvcc.  Would have
to hack the soname patch to encapsulate it inside --compiler-options

Is it worth it?




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Bug#882591: marked as done (gazebo FTBFS: /usr/include/boost/predef/language/stdc.h:52: Parse error at "defined")

[Debian Bug Tracking System]

Your message dated Sat, 25 Nov 2017 11:53:56 +
with message-id 
and subject line Bug#882591: fixed in gazebo 7.8.1+dfsg-3
has caused the Debian Bug report #882591,
regarding gazebo FTBFS: /usr/include/boost/predef/language/stdc.h:52: Parse 
error at "defined"
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.)


-- 
882591: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=882591
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: gazebo
Version: 7.8.1+dfsg-2
Severity: serious

Some recent change in unstable makes gazebo FTBFS:

https://tests.reproducible-builds.org/debian/history/gazebo.html
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/gazebo.html

...
/usr/include/boost/predef/language/stdc.h:52: Parse error at "defined"
gazebo/gui/CMakeFiles/gazebo_gui.dir/build.make:75: recipe for target 
'gazebo/gui/moc_ApplyWrenchDialog.cxx' failed
make[3]: *** [gazebo/gui/moc_ApplyWrenchDialog.cxx] Error 1
--- End Message ---
--- Begin Message ---
Source: gazebo
Source-Version: 7.8.1+dfsg-3

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 882...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Jochen Sprickerhof  (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)


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Hash: SHA512

Format: 1.8
Date: Sat, 25 Nov 2017 12:35:51 +0100
Source: gazebo
Binary: gazebo7-common gazebo7 libgazebo7 libgazebo7-dev gazebo7-plugin-base 
gazebo7-doc
Architecture: source
Version: 7.8.1+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Jochen Sprickerhof 
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: 882591
Changes:
 gazebo (7.8.1+dfsg-3) unstable; urgency=medium
 .
   * Team upload.
   * Move dependency according to links file.
   * Add patch for Q_MOC_RUN (Closes: #882591)
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-- 

gazebo_7.8.1+dfsg-3_source.changes ACCEPTED into unstable

[Debian FTP Masters]

Accepted:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sat, 25 Nov 2017 12:35:51 +0100
Source: gazebo
Binary: gazebo7-common gazebo7 libgazebo7 libgazebo7-dev gazebo7-plugin-base 
gazebo7-doc
Architecture: source
Version: 7.8.1+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Jochen Sprickerhof 
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: 882591
Changes:
 gazebo (7.8.1+dfsg-3) unstable; urgency=medium
 .
   * Team upload.
   * Move dependency according to links file.
   * Add patch for Q_MOC_RUN (Closes: #882591)
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Thank you for your contribution to Debian.

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Processing of gazebo_7.8.1+dfsg-3_source.changes

[Debian FTP Masters]

gazebo_7.8.1+dfsg-3_source.changes uploaded successfully to localhost
along with the files:
  gazebo_7.8.1+dfsg-3.dsc
  gazebo_7.8.1+dfsg-3.debian.tar.xz
  gazebo_7.8.1+dfsg-3_source.buildinfo

Greetings,

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

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Dear friend

[Curtis Scaparrotti]

Dear friend

My name is Curtis Scaparrotti, I have a Business proposal for you, contact me 
for more information

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