Accepted yorick 2.2.04+dfsg1-9 (source) into unstable

[Thibaut Paumard]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 19 Mar 2018 20:40:40 +0100
Source: yorick
Binary: yorick yorick-data yorick-dev yorick-mpy-mpich2 yorick-mpy-openmpi 
yorick-mpy-common yorick-doc yorick-full
Architecture: source
Version: 2.2.04+dfsg1-9
Distribution: unstable
Urgency: low
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Thibaut Paumard <thib...@debian.org>
Description:
 yorick - interpreted language and scientific graphics
 yorick-data - interpreted library for the Yorick language
 yorick-dev - development files for the Yorick interpreted language
 yorick-doc - documentation for the Yorick interpreted language
 yorick-full - full installation of the Yorick interpreter and add-ons
 yorick-mpy-common - Message Passing Yorick (common files)
 yorick-mpy-mpich2 - Message Passing Yorick (MPICH2 build)
 yorick-mpy-openmpi - Message Passing Yorick (OpenMPI build)
Changes:
 yorick (2.2.04+dfsg1-9) unstable; urgency=low
 .
   * Reactivate build-time tests with a tweak to only open a window once.
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Files:
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yorick_2.2.04+dfsg1-9.dsc
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yorick_2.2.04+dfsg1-9.debian.tar.xz
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Accepted yorick 2.2.04+dfsg1-8 (source) into unstable

[Thibaut Paumard]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 19 Mar 2018 09:25:08 +0100
Source: yorick
Binary: yorick yorick-data yorick-dev yorick-mpy-mpich2 yorick-mpy-openmpi 
yorick-mpy-common yorick-doc yorick-full
Architecture: source
Version: 2.2.04+dfsg1-8
Distribution: unstable
Urgency: low
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Thibaut Paumard <thib...@debian.org>
Description:
 yorick - interpreted language and scientific graphics
 yorick-data - interpreted library for the Yorick language
 yorick-dev - development files for the Yorick interpreted language
 yorick-doc - documentation for the Yorick interpreted language
 yorick-full - full installation of the Yorick interpreter and add-ons
 yorick-mpy-common - Message Passing Yorick (common files)
 yorick-mpy-mpich2 - Message Passing Yorick (MPICH2 build)
 yorick-mpy-openmpi - Message Passing Yorick (OpenMPI build)
Changes:
 yorick (2.2.04+dfsg1-8) unstable; urgency=low
 .
   * Deactivate build-time test suite on arm64 armhf i386 ppc64el powerpc
 x32 because creating windows sometimes fail within xvfb-run. The
 problem does not seem to occur in a normal X server or in xpra.
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yorick_2.2.04+dfsg1-8.dsc
 98b8e10c1901dd28d071b6e733ba713b 34992 science optional 
yorick_2.2.04+dfsg1-8.debian.tar.xz
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Accepted yorick-av 0.0.4-2 (source) into unstable

[Thibaut Paumard]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 06 Mar 2018 14:01:45 +0100
Source: yorick-av
Binary: yorick-av
Architecture: source
Version: 0.0.4-2
Distribution: unstable
Urgency: low
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Thibaut Paumard <thib...@debian.org>
Description:
 yorick-av  - write movies from Yorick in various formats
Closes: 890880 892176
Changes:
 yorick-av (0.0.4-2) unstable; urgency=low
 .
   * Bug fix: "AVPacket timestamps need to be rescaled for most codecs"
 (Closes: #890880).
   * Bug fix: "Need to set VBV buffer size for MPEG1/2 files", (Closes:
 #892176).
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yorick-av_0.0.4-2.debian.tar.xz
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Bug#892176: yorick-av: Need to set VBV buffer size for MPEG1/2 files

[Thibaut Paumard]

Package: yorick-av
Version: 0.0.4-1
Severity: normal
Tags: patch

Dear self,

FFmpeg complains (warnings) about unset VBV buffer size and buffer overflows
when produgin MPEG 1 (.mpg) or MPEG2 (.vob) files. The resulting files may then
play sluggishly (or not at all, i.e. frozen on first frame) at least in VLC.

This patch sets an appropriate buffer size.

Regards, self.



-- System Information:
Debian Release: 9.3
  APT prefers stable-updates
  APT policy: (900, 'stable-updates'), (900, 'stable'), (500, 'stable-debug'), 
(1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.9.0-5-amd64 (SMP w/8 CPU cores)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), 
LANGUAGE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages yorick-av depends on:
ii  libavcodec57   7:3.2.10-1~deb9u1
ii  libavformat57  7:3.2.10-1~deb9u1
ii  libavutil557:3.2.10-1~deb9u1
ii  libc6  2.24-11+deb9u1
ii  libswscale47:3.2.10-1~deb9u1
ii  yorick 2.2.04+dfsg1-6+b1

yorick-av recommends no packages.

yorick-av suggests no packages.

-- no debconf information
Description: Set VBV buffer size for MPEG1/2 files
 FFmpeg emits warnings when producing MPEG1/2 files and the VBV buffer
 size has not been set. The output files may then play sluggishly in
 VLC. This backported patch sets a VBV buffer size sufficient to hold
 one frame.
Author: Thibaut Paumard <thib...@debian.org>
Origin: backport
Bug-Debian: coming soon
Forwarded: not-needed
Applied-Upstream: 0.0.5
Last-Update: 2018-03-06 
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- a/yav.c
+++ b/yav.c
@@ -259,6 +259,17 @@
 void yav_opencodec(yav_ctxt *obj, unsigned int width, unsigned int height) {
   obj->video_st->codec->width=width;
   obj->video_st->codec->height=height;
+  if (obj->enc->codec_id == AV_CODEC_ID_MPEG1VIDEO ||
+  obj->enc->codec_id == AV_CODEC_ID_MPEG2VIDEO) {
+AVCPBProperties *props;
+props = (AVCPBProperties*) av_stream_new_side_data
+  (obj->video_st, AV_PKT_DATA_CPB_PROPERTIES, sizeof(*props));
+props->buffer_size = width*height*4;
+props->max_bitrate = 0;
+props->min_bitrate = 0;
+props->avg_bitrate = 0;
+props->vbv_delay = UINT64_MAX;
+  }
   av_dump_format(obj->oc, 0, obj->oc->filename, 1);
 
   if (obj->video_st) {
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Bug#890880: yorick-av: AVPacket timestamps need to be rescaled for most codecs

[Thibaut Paumard]

Package: yorick-av
Version: 0.0.4-1
Severity: important
Tags: upstream

Dear self,

Due to changes in the FFmpeg API, the files produced by yorick-av are
essentially garbage for all but the libtheora codec.

yorick-av should call av_packet_rescale_ts() before
av_interleaved_write_frame().

This is a bug of important severity:
 - it is impossible to use yorick-av to directly produce movies in most popular
formats;
 + however yorick-av can still produce movies in at least one format. Those
movies can then be reencoded using ffmpeg itself, albeit at the cost of
execution time and quality loss.

This is fixed upstream.

Kind regards, self.



-- System Information:
Debian Release: 9.3
  APT prefers stable-updates
  APT policy: (900, 'stable-updates'), (900, 'stable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.9.0-5-amd64 (SMP w/8 CPU cores)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), 
LANGUAGE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages yorick-av depends on:
ii  libavcodec57   7:3.2.10-1~deb9u1
ii  libavformat57  7:3.2.10-1~deb9u1
ii  libavutil557:3.2.10-1~deb9u1
ii  libc6  2.24-11+deb9u1
ii  libswscale47:3.2.10-1~deb9u1
ii  yorick 2.2.04+dfsg1-6+b1

yorick-av recommends no packages.

yorick-av suggests no packages.

-- no debconf information

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Accepted yorick 2.2.04+dfsg1-7 (source all amd64) into unstable

[Thibaut Paumard]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 07 Feb 2018 10:45:31 +0100
Source: yorick
Binary: yorick yorick-data yorick-dev yorick-mpy-mpich2 yorick-mpy-openmpi 
yorick-mpy-common yorick-doc yorick-full
Architecture: source all amd64
Version: 2.2.04+dfsg1-7
Distribution: unstable
Urgency: low
Maintainer: Debian Science Maintainers 
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Thibaut Paumard <thib...@debian.org>
Description:
 yorick - interpreted language and scientific graphics
 yorick-data - interpreted library for the Yorick language
 yorick-dev - development files for the Yorick interpreted language
 yorick-doc - documentation for the Yorick interpreted language
 yorick-full - full installation of the Yorick interpreter and add-ons
 yorick-mpy-common - Message Passing Yorick (common files)
 yorick-mpy-mpich2 - Message Passing Yorick (MPICH2 build)
 yorick-mpy-openmpi - Message Passing Yorick (OpenMPI build)
Changes:
 yorick (2.2.04+dfsg1-7) unstable; urgency=low
 .
   * Move YAO and Spydr from Depends to Suggests of yorick-full, because
 they both depend on python-gtk which is deprecated.
   * Bump debhelper compat version to 10.
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yorick-dev_2.2.04+dfsg1-7_amd64.deb
 565179531b159d8ac23fce6081a62b7ae6096772e1aced4d6475e7767e4a5bfe 853564 
yorick-doc_2.2.04+dfsg1-7_all.deb
 85f1b8e6c3e844df19e78f9b993c3684bbca73afa8c8babbfec54876744ea0df 10504 
yorick-full_2.2.04+dfsg1-7_amd64.deb
 124f48a15bcb3f1494a094eb7122d828e2e8dc3be9c438a32a50f95ce04b323f 32732 
yorick-mpy-common_2.2.04+dfsg1-7_all.deb
 771ee18b030514f02a599ff157de56df47b3fff7be6be5a91400504540c9c188 1100704 
yorick-mpy-mpich2-dbgsym_2.2.04+dfsg1-7_amd64.deb
 b112e3f3458d6c7466f1a5c6e95825b03cb7bf9738a01c72b23e07b55047b778 520404 
yorick-mpy-mpich2_2.2.04+dfsg1-7_amd64.deb
 f8859d85d970dc5fa8284364d409f4e4326941a19a29c37df9a96502707457ba 1102444 
yorick-mpy-openmpi-dbgsym_2.2.04+dfsg1-7_amd64.deb
 aa2646cef96fa5d6c48b2f24d070444389c02cfc0b57f674685e5f01a36754ff 520628 
yorick-mpy-openmpi_2.2.04+dfsg1-7_amd64.deb
 e9ace293dd5f81de9467d0e4c1e2a01be7f01467b24c5e42acd48210169730aa 12272 
yorick_2.2.04+dfsg1-7_amd64.buildinfo
 7c7a77376476c09617a53c13c55a568d20d95ae39c603639a74235bdcd26ee07 690700 
yorick_2.2.04+dfsg1-7_amd64.deb
Files:
 d8b4f93117a105b08b6a786c2e10e11e 3214 science optional 
yorick_2.2.04+dfsg1-7.dsc
 1b4021e07e8b7fdcf385368543e6e2ae 34856 science optional 
yorick_2.2.04+dfsg1-7.debian.tar.xz
 b7eb4e29c55304d933342b846d2e0d8e 495440 science optional 
yorick-data_2.2.04+dfsg1-7_all.deb
 3a7624dd3f9af735e096e8eecabe7832 1490708 debug optional 
yorick-dbgsym_2.2.04+dfsg1-7_amd64.deb
 2481872bb48cf7a1865b8a329aa6789e 19068 debug optional 
yorick-dev-dbgsym_2.2.04+dfsg1-7_amd64.deb
 d240068b0eaa25369db57eb407f7298f 638200 science optional 
yorick-dev_2.2.04+dfsg1-7_amd64.deb
 4684b6ccfbbedf015bbd1a13ad820f6d 853564 doc optional 
yorick-doc_2.2.04+dfsg1-7_all.deb
 e18392be92be4c395f6c060028bb7c84 10504 science optional 
yorick

Help neede: yorick_2.2.04+dfsg1-7_amd64.changes REJECTED

[Thibaut Paumard]

Hi guys,

I just tried to update one of my packages to use dbgsym packages but I 
get this error messahe when uploading:


Le 07/02/2018 à 11:22, Debian FTP Masters a écrit :


yorick-dbgsym_2.2.04+dfsg1-7_amd64.deb: trying to install to unstable-debug, 
but could not find source



What have I done wrong?

Regards, Thibaut.


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Bug#848859: FTBFS randomly (failing tests)

[Thibaut Paumard]

Le 04/01/2017 à 19:58, Anton Gladky a écrit :
> 2017-01-04 13:26 GMT+01:00 Santiago Vila :
>> No matter how much glitch-free is the autobuilder you use to build the
>> above package, it will fail to build 1 every 147 times on average,
>> mathematically, because the test is wrongly designed.
> 
> That is not always true. If you look in many tests from numerical
> simulation packages, there is usually a "threshold" for test result
> which should not be exceeded. And the test result varies in
> the limits, which are set by upstream authors. This result
> can be different even on the same machine, running the simulation
> several time. And it is normal.
> 
> The "fix" for such cases is the increasing of the threshold or disabling
> the test completely. Because you can do nothing with it due to the
> nature of numerical simulations.

I addition a build-time test is made to detect potential bugs, which may
themselves be of low severity. What makes the bug RC is that the test
causes FTBFS. Once such a bug has been identified, I tend to fill a bug
with appropriate severity against my own package and disable the test
until the real, low to normal severity bug is fixed.

>> Really, we need more people doing QA, and not stop doing it "because
>> we are near the freeze".
> 
> If you are maintaining the package several years, fixing most of its
> bugs, hoping to see it in release and trying to escape major changes
> several months before the freeze.. Sure, it will actively be defended
> from maintainers if some pseudo-reasons for its removal appear just
> before the freeze. This fact has to be considered as well.

I guess that's a case for a stretch-ignore tag. TBD with the release
team. Regards, Thibaut.

Regards, Thibaut.

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Bug#842817: fixed in yorick-hdf5 0.8.0-7

[Thibaut Paumard]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Thanks for the reminder. The upload is on its way.

Le 02/12/2016 à 11:07, Gilles Filippini a écrit :
> Hi Thibaut,
> 
> On Thu, 03 Nov 2016 11:51:19 +0000 Thibaut Paumard
> <thib...@debian.org> wrote:
>> Source: yorick-hdf5 Source-Version: 0.8.0-7
>> 
>> We believe that the bug you reported is fixed in the latest
>> version of yorick-hdf5, which is due to be installed in the
>> Debian FTP archive.
> [cut]
>> Closes: 842817 Changes: yorick-hdf5 (0.8.0-7) experimental;
>> urgency=medium . * Bug fix: "FTBFS against HDF5 v1.10", thanks to
>> Gilles Filippini (Closes: #842817). * Check against Policy
>> 3.9.8.
> 
> Could you upload this fix to unstable, now that HDF5-1.10
> transition has started?
> 
> Thanks,
> 
> _g.
> 

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Bug#842817: yorick-hdf5: FTBFS against HDF5 v1.10

[Thibaut Paumard]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Le 02/11/2016 à 10:30, Gilles Filippini a écrit :

> 
> Yes, this plan (quick hack + temporarily disabling tests on other
> archs) sounds sensible.

Dear Gilles,

I uploaded the hacked version(0.8.0-6) to experimental
(build-depending on hdf5-dev 1.10). It built successfully on several
architectures, include 64-bit and 32 bit ones.

I guess you can claim this package will not prevent the transition.
https://buildd.debian.org/status/package.php?p=yorick-hdf5=experim
ental

I also started working on the real fix.

Regards, Thibaut.

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Bug#842817: yorick-hdf5: FTBFS against HDF5 v1.10

[Thibaut Paumard]

Thanks Gilles.

This is due to hid_t changing from 32bit to 64bit and mapping that to
the correct integer type in Yorick.

I managed a quick fix, need a little more time to upload it.

Regards, Thibaut.

Le 01/11/2016 à 14:16, Gilles Filippini a écrit :
> Source: yorick-hdf5
> Version: 0.8.0-5
> Severity: important
> 
> Hi,
> 
> yorick-hdf5 FTBFS againt HDF5 v1.10 currently in experimental:
> 
>dh_auto_test
> make -j1 check
> make[1]: Entering directory '/<>'
> /usr/lib/yorick/bin/yorick -batch check.i
>  Creating data.h5 with data
> ERROR (h5write) Unable to create group
>   LINE: 785  FILE: /<>/hdf5.i
> yorick: quitting on error in batch mode
> /usr/lib/yorick/Makepkg:159: recipe for target 'check-dll' failed
> make[1]: *** [check-dll] Error 1
> make[1]: Leaving directory '/<>'
> dh_auto_test: make -j1 check returned exit code 2
> debian/rules:9: recipe for target 'build' failed
> make: *** [build] Error 2
> dpkg-buildpackage: error: debian/rules build gave error exit status 2
> 
> Full build log attached.
> 
> Thanks,
> 
> _g.
> 
> 
> -- System Information:
> Debian Release: stretch/sid
>   APT prefers testing
>   APT policy: (500, 'testing')
> Architecture: amd64 (x86_64)
> Foreign Architectures: i386
> 
> Kernel: Linux 4.7.0-1-amd64 (SMP w/2 CPU cores)
> Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
> 
> 
> 
> 

-- 
* Dr Thibaut Paumard   | LESIA/CNRS - Table équatoriale (bât. 5)   *
* Tel: +33 1 45 07 78 60   | Observatoire de Paris - Section de Meudon *
* Fax: +33 1 45 07 79 17   | 5, Place Jules Janssen*
* thibaut.paum...@obspm.fr | 92195 MEUDON CEDEX (France)   *



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Bug#831442: mpich: Broken /usr/lib/libmpich.so.12 symlink, depending on installation order

[Thibaut Paumard]

Control: severity -1 normal

Dear all,

I have been able to work around this bug in yorick by adding a file
debian/shlibs.local in the source tree with this single line:

libmpich 12 libmpich12

Le 08/08/2016 12:12, Thibaut Paumard a écrit :
> Hi have open a new bug against libc-bin (ldconfig) to follow that up on
> that side: 833728

The libc-bin maintainers think that the proper fix would be to also
convert openmpi to multiarch and move the alternative main link also to
the multiarch directory.

I'm downgrading the severity since a workaround exists to avoid FTBFS.

Kind regards, Thibaut.

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Bug#831442: mpich: Broken /usr/lib/libmpich.so.12 symlink, depending on installation order

[Thibaut Paumard]

Hi have open a new bug against libc-bin (ldconfig) to follow that up on
that side: 833728

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Bug#831442: mpich: Broken /usr/lib/libmpich.so.12 symlink, depending on installation order

[Thibaut Paumard]

Control: severity -1 serious

Dear Nicholas,

Le 16/07/2016 07:23, Nicholas Breen a écrit :
> A symlink /usr/lib/libmpich.so.12 is created only depending on what order the
> packages libmpich12 and libmpich-dev are installed in, apparently requiring
> libmpich-dev to be unpacked before libmpich12 is configured.

Thanks, it's actually due to a very old and known bug in ldconfig and
honestly I don't think that it is going to be fixed anytime soon:

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=249122
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=224450

What happens is that if libmpich is installed before libopenmpi, then
libmpi.so (indirectly) points to
/usr/lib/x86_64-linux-gnu/libmpich.so.12.1.0
So the SONAME of libmpi.so is libmpich.so.12, and ldconfig creates the
corresponding symlink.

When libopenmpi is then installed, libmpi.so ceases to point to
libmpich, but the libmpich.so.12 link continues to exist, and indirectly
points to /usr/lib/openmpi/lib/libmpi.so!

I don't know how to do it, but the mpich package (and the openmpi
package?) should attempt to make sure that this link is not created or
is removed whenever libmpi.so stops pointing to libmpich.

As already mentioned, the autobuilders now default to installing
libmpich first. A workaround (for the autobuilders!) would be to
forcibly remove the /usr/lib/libmpich.so.12 symlink upon installation of
libopenmpi.

I think this bug is potentially very harmful (with wrongly link binaries
and FTBFSes) and warrants a serious severity.

Kind regards, Thibaut.

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Bug#814943: mpi-default-dev: provide the list of architectures for each MPI implementation

[Thibaut Paumard]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Dear Mattia,

Le 27/02/2016 12:29, Mattia Rizzolo a écrit :
>> The feature that I would need for e.g. the yorick package is the
>> list of architectures on which each implementation is available.
>> This is what I currently check and hardcode by hand. I guess this
>> is also what other people do when they provide packages with
>> distinct names for each flavour.

Yes, it is certainly loosing of its usefulness...

> Guess I can do that too. I personally think it's kind of pointless
> as of now, where mpich is available everywhere and openmpi is
> available on all but m68k (not considering powerpcspe that
> yesterday has been resurrected from ashes…)
> 
> Anyway, What about:
> 
> https://anonscm.debian.org/cgit/debian-science/packages/mpi-defaults.g
it/commit/?id=57d37c200258e7512733d7ee36aade8bf806ffea
>
>  ?

Perfect, thanks.

> I do think this is a bigger improvment than hardcoding this in a
> donzen of packages, everyone with its own data source.
> 

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Bug#814943: mpi-default-dev: provide the list of architectures for each MPI implementation

[Thibaut Paumard]

Package: mpi-default-dev
Version: 1.2
Severity: wishlist

It has been discussed in
  https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=813128
that some MPI packages build in two flavours (openmpi and mpich) and
need to know at upload time for which architecture each implementation
is available.

It has been proposed to add two variables to
/usr/share/mpi-default-dev/debian_defaults for this purpose.

Last iteration of this discussion below.

Mattia, it looks like there is a misunderstanding: in your commit,
OPENMPI_ARCHITECTURES and MPICH_ARCHITECTURES only list the
architectures for which each implementation is the default. The
feature that I would need for e.g. the yorick package is the list of
architectures on which each implementation is available. This is what
I currently check and hardcode by hand. I guess this is also what
other people do when they provide packages with distinct names for
each flavour.

Kind regards, Thibaut.

Le 16/02/2016 19:37, Mattia Rizzolo a écrit :
> On Tue, Feb 16, 2016 at 11:37:19AM +0100, Thibaut Paumard wrote:
>>> then mpi-defaults would need a sourceful uploads every single
>>> time a new architecture is added (and we want to support MPI
>>> there and openmpi builds), and also suddenly file a dozen RC
>>> bugs (as all packages using such a system would start to fail).
>>> Yes, we can do it, though.
>
> See
> https://anonscm.debian.org/cgit/debian-science/packages/mpi-defaults.g
it/commit/?id=07ef8a6
>
>
https://anonscm.debian.org/cgit/debian-science/packages/mpi-defaults.git
/commit/?id=4fa28c2
> https://anonscm.debian.org/cgit/debian-science/packages/mpi-defaults.g
it/commit/?id=d9656b2
>
>
>> So, what we want if to render RC buggy some packages that need a
>> source upload whenever OPENMPI_ARCHITECTURES or
>> MPICH_ARCHITECTURES change.
>
> Somebody needs to do that.  I can also have mpi-defaults provide a
> script to be called by the packages at build time, if somebody
> provides it.
>
>> An easier way would be for those packages to have a versioned
>> dependency on mpi-default-dev and bump this version when either
>> variable changes, e.g.
>>
>> Build-Depends: mpi-default-dev (>= 1.3), mpi-default-dev (<<
>> 1.4~)
>
> umh, looks messy.
>
>> This is assuming the minor part of the version of
>> mpi-default-dev changes when either variable changes. The version
>> can then have also a micro digit, to allow for new versions that
>> don't change these variables
>
> in the past mpi-defaults was binNMUed to change defaults; don't
> rely on that.
>
>> Actually a versioned dependency seems required anyway since you
>> know your new package will FTBFS with earlier versions of
>> mpi-default-dev.
>
> *shrugs*
>
>> The only thing is that you can also predict that later versions
>> of mpi-default-dev will break your package.
>>
>> This discussion getting off-topic for this bug, should we move
>> somewhere else?
>
> indeed. probably better suited for a mpi-defaults bug; feel free to
> open one and report a summary of what said here.
>

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Bug#812995: yorick-ynfft: FTBFS with libnfft version 3.3

[Thibaut Paumard]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Thanks,

I forwarded this bug report to upstream.

Kind regards, Thibaut.

Le 08/02/2016 20:19, Gianfranco Costamagna a écrit :
> Hi Thibaut and Debian Science maintainers,
> 
> I did a little patch to fix the build failure, but now there is a 
> testsuite failure:
> 
> here the patch
> 
> --- yorick-ynfft-1.0.2.orig/yor_nfft.c +++
> yorick-ynfft-1.0.2/yor_nfft.c @@ -312,7 +312,7 @@ struct _op { 
> #define GET_INP_DIMS(op)((op)->plan.N) #define
> GET_OVR_DIMS(op)((op)->plan.n) #define GET_OVR_FACT(op)
> ((op)->plan.sigma) -#define GET_NFFT_FLAGS(op)
> ((op)->plan.nfft_flags) +#define GET_NFFT_FLAGS(op)
> ((op)->plan.flags) #define GET_FFTW_FLAGS(op)
> ((op)->plan.fftw_flags) #define GET_CUTOFF(op)
> ((op)->plan.m) #define GET_NEVALS(op)  ((op)->nevals) @@
> -1013,7 +1013,7 @@ static void make_nfft_plan(nfft_plan *pl }
> 
> /* Precompute interpolation weights. */ -  if ((plan->nfft_flags &
> PRE_ONE_PSI) != 0) { +  if ((plan->flags & PRE_ONE_PSI) != 0) { 
> nfft_precompute_one_psi(plan); } return;
> 
> basically nfft_flags has been renamed in flags.
> 
> the testsuite failure is: make[1]: Entering directory
> '/build/yorick-ynfft-1.0.2' /usr/bin/make tests make[2]: Entering
> directory '/build/yorick-ynfft-1.0.2' /usr/lib/yorick/bin/yorick
> -batch nfft-tests.i 1-D transform (A0 vs. A1): SUCCESS - absolute
> error: max. = 1.9e-14, RMS = 3.9e-15 1-D transform (A1 vs. A2):
> SUCCESS - absolute error: max. = 1.2e-15, RMS = 2.8e-16
> 
> ERROR (nfft_full_matrix) length must be a strictly positive even
> number LINE: 272  FILE: /build/yorick-ynfft-1.0.2/nfft.i yorick:
> quitting on error in batch mode Makefile:97: recipe for target
> 'tests' failed make[2]: *** [tests] Error 1 make[2]: Leaving
> directory '/build/yorick-ynfft-1.0.2' debian/rules:27: recipe for
> target 'override_dh_auto_test' failed
> 
> 
> and I'm not sure what does it mean.
> 
> do you have any clue?
> 
> cheers,
> 
> Gianfranco
> 
> On Thu, 28 Jan 2016 12:37:48 + Ghislain Antony Vaillant 
>  wrote:
>> Package: yorick-ynfft Version: 1.0.2-2 Severity: important
> 
>> Dear Maintainer,
> 
>> This source package fails to build with the latest release of 
>> libnfft available in experimental. The relevant portion of the 
>> build log is available below.
> 
>> Version 3.3 introduced some API breaking changes in the
>> signature of the public structures.
> 
>> ``` cc -I. -DVERSION=\"1.0.2\" -Wdate-time -D_FORTIFY_SOURCE=2
>> -g -O2 -fstack-protector-strong -Wformat -Werror=format-security 
>> -Wdate-time -D_FORTIFY_SOURCE=2  -fPIC -DPLUG_IN -I. 
>> -I/usr/lib/yorick/include -o yor_nfft.o -c yor_nfft.c
>> yor_nfft.c: In function 'op_eval': yor_nfft.c:380:12: warning:
>> assignment from incompatible pointer type
>> [-Wincompatible-pointer-types] inp_dims = GET_INP_DIMS(op); ^
>> yor_nfft.c: In function 'op_extract': yor_nfft.c:313:33: warning:
>> initialization from incompatible pointer type
>> [-Wincompatible-pointer-types] #define GET_OVR_DIMS(op)
>> ((op)->plan.n) ^ yor_nfft.c:448:22: note: in expansion of macro
>> 'GET_OVR_DIMS' const int *src = GET_OVR_DIMS(op); ^
>> yor_nfft.c:312:33: warning: initialization from incompatible
>> pointer type [-Wincompatible-pointer-types] #define 
>> GET_INP_DIMS(op)((op)->plan.N) ^ yor_nfft.c:459:22:
>> note: in expansion of macro 'GET_INP_DIMS' const int *src = 
>> GET_INP_DIMS(op); ^ yor_nfft.c:315:44: error: 'nfft_plan {aka 
>> struct }' has no member named 'nfft_flags' #define 
>> GET_NFFT_FLAGS(op)  ((op)->plan.nfft_flags) ^ 
>> yor_nfft.c:500:27: note: in expansion of macro 'GET_NFFT_FLAGS'
>> int value = get_flags(GET_NFFT_FLAGS(op), GET_FFTW_FLAGS(op)); ^
>>  yor_nfft.c:315:44: error: 'nfft_plan {aka struct }'
>> has no member named 'nfft_flags' #define GET_NFFT_FLAGS(op) 
>> ((op)->plan.nfft_flags) ^ yor_nfft.c:503:17: note: in expansion
>> of macro 'GET_NFFT_FLAGS' int value = GET_NFFT_FLAGS(op); ^ 
>> yor_nfft.c: In function 'make_nfft_plan': yor_nfft.c:1016:12: 
>> error: 'nfft_plan {aka struct }' has no member named 
>> 'nfft_flags' if ((plan->nfft_flags & PRE_ONE_PSI) != 0) { ```
> 
>> -- System Information: Debian Release: stretch/sid APT prefers 
>> testing APT policy: (500, 'testing'), (2, 'unstable'), (1, 
>> 'experimental') Architecture: amd64 (x86_64) Foreign
>> Architectures: i386
> 
>> Kernel: Linux 4.3.0-1-amd64 (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)
> 

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Bug#803876: yorick-av: FTBFS with FFmpeg 2.9

[Thibaut Paumard]

Le 08/01/2016 00:10, Andreas Cadhalpun a écrit :
> Dear Maintainer,
> 
> the next version of FFmpeg is planned to be released this month
> (and it might be called 3.0 instead of 2.9).
> 

Dear Andreas,

thanks for the heads up. The package is on its way, thanks for the patch.

I initially wanted to include it directly upstream but I realise that I
don't have the time to do so right know.

Kind regards, Thibaut.

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Bug#786694: FFTW FTBFS

[Thibaut Paumard]

Control: tag -1 + pending

For the record, I have committed my patch to svn (revision 47058).

Kind regards, Thibaut.

Le 23/06/2015 12:13, Thibaut Paumard a écrit :
 Control: tag -1 + patch
 
 On Sun, 24 May 2015 16:03:44 +0200 Reiner Herrmann rei...@reiner-h.de
 wrote:

 I think this could be related to an issue we already faced with automake 
 [1][2].
 Depending on the timezone, .info files are sometimes not (re)generated from 
 source (example [3]).
 This could explain why it doesn't happen in your local setup, when you are 
 not varying
 the timezone (the .info files are not regenerated with makeinfo), but on 
 jenkins it does.
 
 Hi,
 
 it's even worse: fftw.info is FTBFS.
 
 I have prepared a patch, I would appreciate if someone could ack before
 I upload it, which I will do before the bunch of reverse dependencies
 are removed from testing on 2015-07-21.
 
 Kind regards, Thibaut.
 
 
 

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Bug#786694: [Reproducible-builds] Bug#786694: rcs and fftw fail to build with makeinfo: command not found

[Thibaut Paumard]

Control: tag -1 + patch

On Sun, 24 May 2015 16:03:44 +0200 Reiner Herrmann rei...@reiner-h.de
wrote:
 
 I think this could be related to an issue we already faced with automake 
 [1][2].
 Depending on the timezone, .info files are sometimes not (re)generated from 
 source (example [3]).
 This could explain why it doesn't happen in your local setup, when you are 
 not varying
 the timezone (the .info files are not regenerated with makeinfo), but on 
 jenkins it does.

Hi,

it's even worse: fftw.info is FTBFS.

I have prepared a patch, I would appreciate if someone could ack before
I upload it, which I will do before the bunch of reverse dependencies
are removed from testing on 2015-07-21.

Kind regards, Thibaut.
diff -Nru fftw-2.1.5/debian/changelog fftw-2.1.5/debian/changelog
--- fftw-2.1.5/debian/changelog	2011-11-29 01:48:33.0 +0100
+++ fftw-2.1.5/debian/changelog	2015-06-23 11:48:52.0 +0200
@@ -1,3 +1,13 @@
+fftw (2.1.5-2) unstable; urgency=low
+
+  * Team upload.
+  * Bug fix: FTBFS with TZ=GMT-14, thanks to Holger Levsen (Closes:
+#786694).
+  * Fix fftw.texi and make sure it is always rebuilt.
+  * Check against Policy 3.9.6
+
+ -- Thibaut Paumard thib...@debian.org  Tue, 23 Jun 2015 11:48:16 +0200
+
 fftw (2.1.5-1) unstable; urgency=low
 
   * Team upload.
diff -Nru fftw-2.1.5/debian/control fftw-2.1.5/debian/control
--- fftw-2.1.5/debian/control	2011-11-29 01:55:44.0 +0100
+++ fftw-2.1.5/debian/control	2015-06-23 11:47:43.0 +0200
@@ -4,8 +4,8 @@
 Maintainer: Debian Science Team debian-science-maintainers@lists.alioth.debian.org
 Uploaders: Paul Brossier p...@debian.org
 Build-Depends: debhelper (= 4.0.0), autotools-dev, autoconf, automake, libtool,
- mpi-default-dev, gfortran
-Standards-Version: 3.9.2
+ mpi-default-dev, gfortran, texinfo
+Standards-Version: 3.9.6
 Vcs-Svn: svn://svn.debian.org/svn/debian-science/packages/fftw/
 Vcs-Browser: http://svn.debian.org/viewsvn/debian-science/packages/fftw/
 Homepage: http://fftw.org
diff -Nru fftw-2.1.5/debian/patches/info-syntax fftw-2.1.5/debian/patches/info-syntax
--- fftw-2.1.5/debian/patches/info-syntax	1970-01-01 01:00:00.0 +0100
+++ fftw-2.1.5/debian/patches/info-syntax	2015-06-23 11:43:46.0 +0200
@@ -0,0 +1,36 @@
+Description: Fix doc/fftw.info syntax
+ title, subtitle and author commands to use {}
+Author: Thibaut Paumard
+Origin: vendor
+Forwarded: no
+Last-Update: 20015-06-23
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/doc/fftw.texi
 b/doc/fftw.texi
+@@ -5,6 +5,11 @@
+ @settitle FFTW
+ @c %**end of header
+ 
++@dircategory Science
++@direntry
++* FFTW: (fftw).FFTW User's Manual
++@end direntry
++
+ @include version.texi
+ @setchapternewpage odd
+ @c define constant index (ct)
+@@ -46,10 +51,10 @@
+ @titlepage
+ @sp 10
+ @comment The title is printed in a large font.
+-@title{FFTW User's Manual}
++@title FFTW User's Manual
+ @subtitle For version @value{VERSION}, @value{UPDATED}
+-@author{Matteo Frigo}
+-@author{Steven G. Johnson}
++@author Matteo Frigo
++@author Steven G. Johnson
+ 
+ @c The following two commands start the copyright page.
+ @page
diff -Nru fftw-2.1.5/debian/patches/series fftw-2.1.5/debian/patches/series
--- fftw-2.1.5/debian/patches/series	2011-11-29 02:20:21.0 +0100
+++ fftw-2.1.5/debian/patches/series	2015-06-23 11:33:59.0 +0200
@@ -2,3 +2,4 @@
 #03_fix_doc.dpatch
 #04_configure.dpatch
 05_ac_define_syntax.diff
+info-syntax
diff -Nru fftw-2.1.5/debian/rules fftw-2.1.5/debian/rules
--- fftw-2.1.5/debian/rules	2011-11-29 02:06:06.0 +0100
+++ fftw-2.1.5/debian/rules	2015-06-23 11:33:59.0 +0200
@@ -48,6 +48,7 @@
 build-indep-stamp: autoreconf-stamp
 	# docs
 	F77=gfortran CFLAGS=$(CFLAGS) ./configure $(CONFFLAGS) --enable-float --enable-type-prefix $(ARCHCONFFLAGS)
+	rm -f doc/fftw.info
 	$(MAKE) -C doc
 	$(MAKE) -C doc html 
 	$(MAKE) -C FAQ 
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Bug#787837: yorick-data: unowned directories in /usr/local after purge (policy 6.8 and 9.1.2): /usr/local/lib/yorick/

[Thibaut Paumard]

Control: clone -1 -2
Control: reassign -2 debhelper
Control: retitle -2 dh_usrlocal leaves directories behind
Control: severity -2 normal

Le 05/06/2015 16:06, Andreas Beckmann a écrit :
 during a test with piuparts I noticed your package left unowned files on
 the system after purge, which is a violation of policy 6.8:

Hi,

Yorick uses dh_usrlocal to manage a tree of directories in /usr/local:
  /usr/local/lib/yorick
  /usr/local/lib/yorick/bin
  /usr/local/lib/yorick/lib
  /usr/local/lib/yorick/share
  ...

The problem is that dh_usrlocal attempts to remove the trunk directory
(/usr/local/lib/yorick) before the branches. At that point, the trunk is
not empty *yet*. Therefore, this directory remains.

I'll work around the problem in Yorick, but a bug is left in
dh_usrlocal, which should remove a tree in depth first, so the trunk is
removed too. I don't code in Perl (yet), so I can't provide a patch
efficiently.

Kind regards, Thibaut.

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Bug#785692: SEGFAULT at startup if not in the first PATH directory

[Thibaut Paumard]

Package: yorick
Version: 2.2.04+dfsg-1
Severity: important

Hi self,

when launching Yorick simply as 'yorick', if it is not in the first directory
of PATH, then it segfaults.

Yorick works fine if it is in the first directory of the PATH and if started
with its full path.

Regards, self.



-- System Information:
Debian Release: 8.0
  APT prefers stable
  APT policy: (990, 'stable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 3.16.0-4-amd64 (SMP w/8 CPU cores)
Locale: LANG=fr_FR.utf8, LC_CTYPE=fr_FR.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages yorick depends on:
ii  debconf  1.5.56
ii  libc62.19-18
ii  libx11-6 2:1.6.2-3
ii  yorick-data  2.2.04+dfsg-1

Versions of packages yorick recommends:
ii  rlwrap0.41-1
ii  yorick-z  1.2.0+cvs20080115-5+b1

Versions of packages yorick suggests:
ii  curl7.38.0-4+deb8u2
ii  emacs23 [emacsen]   23.4+1-4.1+b1
ii  emacs24 [emacsen]   24.4+1-5
ii  yorick-dbg  2.2.04+dfsg-1
pn  yorick-full none
pn  yorick-mpy-openmpi | yorick-mpy-mpich2  none

-- no debconf information

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Re: Bug#764993: yorick-spydr: please create spydr48.png icon without build timestamp

[Thibaut Paumard]

Thanks, we'll apply the patch in the next upload.




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Bug#761932: yorick: linking with libpthread fixes FTBFS of yorick-av and yorick-hdf5

[Thibaut Paumard]

Le 17/09/2014 00:06, Svante Signell a écrit :
  The attached patch adds a link directive
 on libpthread for Hurd in debian/rules.

Thanks for researching this, I'll upload the fix whenever I find the
time to do so.

Kind regards, Thibaut.



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Bug#756703: yorick-hdf5: [hdf5 transition] please support hdf5 1.8.13 new packaging layout

[Thibaut Paumard]

Le 01/08/2014 00:55, Gilles Filippini a écrit :
 Source: yorick-hdf5
 Version: 0.8.0-4
 Severity: important
 Tags: patch
 User: p...@debian.org
 Usertags: HDF5-transition
 
 Hi,
 
 The hdf5 1.8.13 package in experimental features a new layout for
 headers and libraries, so that all the binary packages are now
 co-installable.
 
 Please find attached a patch proposal to support both the current
 and the new layouts.
 

Dear Gilles,

I'm busy nursing right now. Please go ahead.

Kind regards, Thibaut.


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* Tel: +33 1 45 07 78 60   | Observatoire de Paris - Section de Meudon *
* Fax: +33 1 45 07 79 17   | 5, Place Jules Janssen*
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Re: Excessive bounces in this mailing list

[Thibaut Paumard]

Le 20/07/2014 08:22, Tollef Fog Heen a écrit :
 ]] Anton Gladky 
 
 I have the same problem and need to reactivate mailing list membership
 often. It can be because of gmail-account CC-ing alioth`s admins.
 
 Well, stop bouncing list emails then.  List emails should be dropped,
 not bounced, according to current best practice.
 

The user does not have this choice. Many e-mail providers bounce spam.
That's how it is. Debian should not discriminate against users who don't
run there own mail server.

Kind regards, Thibaut.



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Re: Excessive bounces in this mailing list

[Thibaut Paumard]

Le 17/07/2014 15:29, Jose Luis Rivero a écrit :
 Hi all:
 
 I'm periodically receiving this message in my mailbox:
 
 
 Your membership in the mailing list debian-science-maintainers has
 been disabled due to excessive bounces 

Metoo, on many Debian mailing lists.

I've tried several providers (free.fr, gmail). Finally, I've setteld for
using my professional address, which doesn't seem to bounce e-mail.

I believe that many public providers try to bounce SPAM, and that the
Debian administrators think that it is bad practice. However in practice
I think we have to live with providers bouncing spam, so the bouncing
barrier should be dropped.

Kind regards, Thibaut.




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Bug#747976: yorick-av: FTBFS on kfreebsd-i386

[Thibaut Paumard]

Control: severity -1 normal
Control: retitle -1 yorick-av: some codecs SIGFPE on kfreebsd-i386

Le 13/05/2014 14:20, Sebastian Ramacher a écrit :
 When rebuilt for the libav transition, yorick-av failed to build 
 kfreebsd-i386:
 |dh_auto_test -a
 | make[1]: Entering directory '/«PKGBUILDDIR»'
 | /usr/lib/yorick/bin/yorick -batch check.i
 | ==
 |  testing extension: 'mpg'
 | ==
 | Output #0, mpeg, to 'libavcheck.mpg':
 | Stream #0.0: Video: mpeg1video, yuv420p, 704x288, q=2-31, 400 kb/s, 90k 
 tbn, 24 tbc
 | ERROR (*main*) Floating point interrupt (SIGFPE)
 | WARNING detailed line number information unavailable
 | now at pc= 177 (of 225), failed at pc= 183
 |   LINE: 53  FILE: /«PKGBUILDDIR»/check.i
 | yorick: quitting on error in batch mode
 | make[1]: *** [check-dll] Error 1

Hi,

I have checked that some codecs work. As a temporary fix, I have
disabled the test suite on kfreebsd-i386 and decreased the severity.

This is the only architecture with this failure. All the tests pass
correctly on similar architectures: kfreebsd-amd64 and on i386. In my
experience, this usually means that the bug is actually in the
architecture itself (in the libc or in the kernel).

I have tracked the SIGFPE down to strtod() which is called by
av_expr_parse() with the string tex^qComp inside avcodec_open2(). Of
course SIGFPE is asynchronous and I can't be certain strdtod() is the
actual culprit.

Kind regards, Thibaut.



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