> Oops, it seems that you have misspelled the name :-) You have written
> "mpitch" instead of "mpich". Could you please rename the directory to
> "mpich.git", and the symbolic link to "mpich2.git"?
Done, sorry about that
Fred
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> Thanks, that was very nice of you, Fred. I will wait for a while and
> then verify that the files are accessible through both paths, via the
> git-protocol and the web.
Tell if there is any convenience or cavet and I would revert this move.
Cheers
Frederic
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torquil-guest@wagner:/git/debian-science/packages$ mv mpich2.git mpich.git
mv: cannot move `mpich2.git' to `mpich.git': Read-only file system
ok, I move the rrepository and created the symbolic link
Cheers
Fred
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> So I'd "+1" a "Sage in Debian" GSoC project. It should be mentioned
> here that this is not just a simple packaging job but rather creating a
> small ecosystem which is more sophisticated than packaging a random
> package. In the same manner root comes to mind and I'm pretty sure that
> the Deb
Hello Alexander
> The API is (at least should be) compatible within the PolyBoRi 0.8 series.
to check for all this it would be nice to provide a symbol file.
I know that this is a huge work but as your are the upstream of the project,
this should be not that hard.
look here [1] for the symbol f
Hello
>I thought the flags would be automatically exported to the environment
> using recent versions of debhelper. But it seems, that this is not the
> case. (Unfortunately, lintian didn't complain on my system about this.)
> I fixed that.
this is the case with compat level 9.
So if I am not wr
Hello Alexander,
I just checkout your package and now there is only one lintian complain about
the hardening
N: Processing binary package libpolybori-0.8.2-1 (version 0.8.2-1, arch i386)
...
W: libpolybori-0.8.2-1: hardening-no-relro usr/lib/libpolybori-0.8.2.so.1.0.0
N:
N:This package pro
Good morning,
Yes now it works, but I have plenty of lintian warning or errors.
can you fix them all and explain also the name of the library package ?
thanks
Frederic
N: Using profile debian/main.
N: Setting up lab in /tmp/temp-lintian-lab-yHq5dzKbx6 ...
N:
N: Processing changes file pol
Hello, I did a git clone but when I tryed to build the package with
git-buildpackage, I got this error message
scons: done cleaning targets.
dh_clean
rm -f debian/stamp-scons-build
rm -f stamp-*
rm -rf .sconf_temp/
rm -f .sconsign.dblite
rm -f build-python*
rm -rf build
fatal: Not a valid object
Hello, Radi and Baptiste.
It would be nice to switch from debian-science mailing list to
debian-science-maintainer which seems
much more appropriate for packaging questions.
So please register and continue the discussion on the maintainer one.
thanks for your attention
Fred
PS: posted to de
Hello Radi
> They don't have a 'cctbx.h'. annlib_adaptbx is using ann_adaptor.h to include
> #include
> I investigated this and it looks that only rstbx_integration_ext.so and
> annlib_ext.so are using this header.
ok so nothing else than python extensions are using thoses ann files.
> So you m
> Hi Radi, hi Frédéric,
Hello Baptiste
> I'm going to push my changes tomorrow, if the nightly build test runs well.
> [HEADS UP] I made important changes to the files setup.py and
> sconsutils.py. If you have any changes pending on those two files, it
> might be good to push them now, so that I
mbols, just check
> The same could be done for cbflib. The changes here would be even smaller.
> What is your opinion on that?
yes
See you
Frederic
[1]
http://www.gnu.org/software/automake/manual/automake.html#Libtool-Convenience-Libraries
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> I don't think a python3 package is supported. I'd have to do a 2to3 or
> something
> like that to avoid fixing up everything.
no it was just a "maybe one day the upstream will care about python3". It is
difficult enough like this :)
> I liked a lot to the description of all libraries provided
On Wed, 25 Jul 2012 15:00:07 +0200
Radostan Riedel wrote:
> On Wed, 25. Jul 14:45, Picca Frédéric-Emmanuel wrote:
> > Hello, I am working on this :). I already fortified mmdb and gpp4, still
> > need to do the work for clipper :).
> > you can look for the repository
ill
need to do the work for clipper :).
you can look for the repository on the debian-science repository.
I plan to fortify and multi-arch all of them.
See you
Frederic
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> I know I'd prefer autotools too. Scons is not so bad too. It has some good
> ideas
> but it's a long way to become a drop in replacement for autotools. Maybe in a
> few years it'll be ready. I was searching for shlib versioning and people are
> complaining about it since 2008 and also sended pat
Hello, both of you, I am compiling the current cctbx.
Ijust saw thaht you linkagainst libpython2.x. If I remember correctly this is
wrong for a public extension.
I will sent later the lintian output which is quite huge ;))
See you
Fred
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> mostly two things:
> * there's a bug in squeeze's cdebootstrap, that gets triggered by
> cowbuilder --create, so I had to upgrade cdebootstrap to sid
is it a well known bug or did you fill a bug report ?
> * it was not immediately obvious to me how to make home-built packages
> for the depende
Hello, sorry to answer so late,but I was busy today.
> That's true. By the way, I could write down some of it for the wiki
> (especially the part about setting up cowbuilder, which I found to be a
> little tricky). Is "DebianScience/Tools/InstallingCowbuilder" an
> acceptable page name?
I do not
On Thu, 19 Jul 2012 15:20:04 +0200
Radostan Riedel wrote:
> On Thu, 19. Jul 15:16, Picca Frédéric-Emmanuel wrote:
> > Then it will be possible to polish the patch series and propose them
> > for adoption to the upstream. :))
> I'm a little bit afraid that they might not li
On Thu, 19 Jul 2012 15:05:15 +0200
Radostan Riedel wrote:
> On Thu, 19. Jul 13:50, Picca Frédéric-Emmanuel wrote:
> > In that case no need to bother with this we will remove the pycbf when
> > repacking
> :D Just wrote a patch for that. Anyway I just found a bug in the
Frederic
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Radostan Riedel wrote:
> On Wed, 18. Jul 15:15, Picca Frédéric-Emmanuel wrote:
> > In that case we should work with the cbf maintainer and see if the
> > python binding could be package on its own, do
> > 1) check that both cbf python b
ommit by yourself on the repository.
thanks
Fred
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s-sons.com/software/CBF/
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2] ;)
Cheers
Frederic
[1] http://wiki.debian.org/DebugPackage
[2] http://wiki.debian.org/Multiarch/Implementation
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On Mon, 16 Jul 2012 14:37:55 +0200
Baptiste Carvello wrote:
> Le 16/07/2012 13:04, Picca Frédéric-Emmanuel a écrit :
> >> I just did a:
> >> python$* /usr/bin/scons
> >
> >
> > So we just need to configure with the right python$* version and that&
modules should be called like the upstream
did in other scripts.
Did the graph module represent exactly what is expected ?
>
> But all in all you made some real great progress!
Yes to both of you :)
Cheers
Fred
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> I just solved the boost_python problem. It now builds with system libs and
> checks
> if boost_python-py* is available, if not it uses boost_python. This should
> also work
> with other distro's than Debian. This works completely with Debian's scons
> package. Just tested it and pushed it into
> OK, Nevermind that boost problem was my own stupidity. I was compiling against
> my systems boost lib and the version was actually too low. But it's building
> with 1.49 in sid so no problem here. So I'll push my results later.
pbuilder is your friend :)
> python2.6 and python2.7 both build.
h
> http://blends.alioth.debian.org/blends/ch-sentinel.en.html
> might be what you might look for.
exactly, thanks
> However I *strongly* advise *not* to use the Published-* fields - rather
> use debian/upstream instead!
is there an eplaination of the upstream format ?
> It might be a good ide
> But I think I solved it! I just needed to include the directory in cctbx with
> that
> examples. It's now building with system libs for clipper and boost. I think
> this
> is the best solution. Now I'll see if I can work on the annlib problems.
ok, once you have commited all your work on the g
> OK I think I know what the problem is. This cctbx examples in clipper depend
> on
> cctbx. So we have a clipper depend on cctbx and cctbx depend on clipper
> situation. If I add this directory in clipper the build will fail. I see if I
> can workaround
> this issue in cctbx so we don't need to
On Sat, 14. Jul 13:31, Frédéric-Emmanuel Picca wrote:
> did he answer to your mail about mmdb, clipper and gpp4 ?
No he didn't.
Let's wait at least one more week, maybe he is in holidays.
> I don't think there is an upstream package where this directory is in. So I
> don't think we can fix the wa
> they are using an older clipper version ?
> OK, I think I know what the problem is. I was using the wrong includes but
> when
> I use the systems include I'm missing some header files.
> clipper/cctbx/clipper_cctbx.h
> I quickly searched the web and found this[1]. Looks like it's a header from
Hello,
do we have a link to the list of allowed keyword in the task pages ?
See you
Fred
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Hello
> I don't think we need this, because we are not installing the shlibs into
> /usr/lib during the build I'm using a prefix. This "warning" always happen
> when
> you run "libtool --mode=install", it's more like a reminder then a warning.
> We could run that command at the end but I don't th
Hello
De : Radostan Riedel [raybu...@googlemail.com]
Date d'envoi : jeudi 12 juillet 2012 16:39
À : debian-science@lists.debian.org
Objet : Re: RE : RE : RE : RE : RE : cctbx debian package
On Thu, 12. Jul 09:51, Baptiste Carvello wrote:
> I'd rather propos
> I have no idea whether this is somehow related to the really wide scope
> of Debian Science. Since some time I have the gut feeling that we
> should split some more focussed Blends from the large Debian Science
> umbrella which would create some more focussed teams and it might
> enhance the com
> > if we got a working setup.py all this comes for free ;)
> You're right but I need to call their scons system to build the extensions and
> shlibs.
ok when overriding the auto_build target we can
step1: build the shared libraries with scons
step2 use dh_python2 with setup.py to build all exten
Hello,
> Install target is not ready to use. We need to figure out how the package
> structure will look like first
In fact the recommended way to package python modules is to use dh_python2 [1]
> > One small difficulty though: the extensions need to be built for all the
> > supported python ve
found by argument-dependent lookup at the point of instantiation [-fpermissive]
> In file included from
> /tmp/buildd/cctbx-2012.05.08.2305/cctbx_sources/mmtbx/bulk_solvent/bulk_solvent_ext.cpp:7:0:
> /tmp/buildd/cctbx-2012.05.08.2305/cctbx_sources/mmtbx/bulk_solvent/bulk_solvent.h:935:1:
> note:
> > can you add these informations into the wiki page. so I will avoid to ask
> > again and again.
> > I know myself ;). then it would be possible to point upstream to the wiki
> > page.
> I'll update the wiki page.
thanks
> > all this to avoid building a build system on our own.
> Yeah I know
just for the record, I got this error now that I added the right build-dep
/tmp/buildd/cctbx-2012.05.08.2305/cctbx_sources/mmtbx/bulk_solvent/bulk_solvent_ext.cpp:108:33:
required from here
/tmp/buildd/cctbx-2012.05.08.2305/cctbx_sources/mmtbx/bulk_solvent/bulk_solvent.h:395:9:
error: 'r_facto
> Yeah I know shame on me :)! I was just working on other problems first...
> Seriously I don't think the rules file is in a shape where it can be used
> yet. A
> lot of cctbx packages were added and others got thrown out since last year.
> Also
> there is a bug in fftw3tbx were also header files
Hello
ok I added
build: build-py
but now I got this error :), it seems that a build-dep is missing :)
libgl1-mesa-dev ?
you should always build your package with pbuilder or cowbuilder to check that
it will build in the buildd.
git-buildpackage --git-pbuilder is your friend :)
g++ -o gltbx
just for information, the .la are useless, look at here [1]
So the important point is to build the the .so files and there links the same
way it is done with autotools.
We need also to take into account that these libraries should be installed with
the multi-arch-triplet on day [2]
exemple
lrwx
straints.so
See you
Fred
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g/debian-devel/2002/07/msg02030.html
[2]
http://www.gnu.org/software/libtool/manual/html_node/Updating-version-info.html
[3] http://www.scons.org/wiki/SconsRecipes
[4]
http://us.generation-nt.com/answer/bug-357023-pyspf-debian-control-generated-during-build-clean-help-166422011.html
[5] http://collab-ma
s is another story :)
[1] http://wiki.debian.org/DebianScience/cctbx
Cheers
Frederic
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Hello both of you, I created the gpp4 and clipper git repositories from the
Ubuntu packages
I would refresh them using dh, fixing the watch files to check if we have the
latest version of the libraries etc...
enjoy.
> Hello Baptiste,
> Great! Yeah some of the patches don't apply completely or
> Hello,
> thanks to both of you for your answers. I subscribed to the ITP bug. I
> will write to Carlo Segre tomorrow.
great
> I also cloned the git repo. From a quick look at the commit messages, it
> looks like some of the original patches don't apply on latest cctbx. If
> it is so, I will fi
se parties
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Hello Andreas
> Hello,
> I would like to inform you about one result of the "Debian packaging
> hands-on tutorial" which was integrated into the Debian Science
> sprint[1] kindly hosted by ESFR[2] (thanks to the organisers). In the
> tutorial session I was busy with Rainer Wilcke and a colleague
-science/svn-commit.3.tmp'
I will try this evening from my house to check thaht this is not a port problem.
See you
Frédéric
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svn line
4970
what is wrong ?
thanks
Frédéric
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mounting dev/pts filesystem
I: unmounting proc filesystem
-> Cleaning COW directory
forking: rm -rf /var/cache/pbuilder/build//cow.18320
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Hello
I am in vacation until the end of the mounth
already started to package 4.6.0 version_
De : Jerome Kieffer [jerome.kief...@esrf.fr]
Date d'envoi : jeudi 17 mai 2012 12:20
À : debian-science@lists.debian.org
Objet : issue on backporting pymca
Hello,
I wou
Hello Gudjon
If I where you, I would separate th eRC bug fix and your attempt to add the
symbol file.
I already tryed to add a symbol file for one of my c++ library and it took me a
few iteration to fix this symbol file for all debian supporter arch, then I
gave up.
so to me, you should
1) re
Hello,
> Hi list
> Is anyone interested in uploading qwtplot3d for me. It closes two RC bugs and
> I need it uploaded to fix ftbs > in one of my other packages pyqwt3d.
Yes I am, but your package does not build on my i386 laptop.
You did the "mistake" to add a symbol file for a c++ library [
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etcdf package.
what is the difference with python-netCDF4 ?
Regards
Fred
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rds,
Frederic
[1] http://tango-controls.org/
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Le Mon, 26 Sep 2011 16:06:10 +0200,
Picca Frédéric-Emmanuel a écrit
:
> I think this is what you want.
>
> Data files contained in the PDB archive (ftp://ftp.wwpdb.org) are free of
> all copyright restrictions and made fully and freely available for both
> non-commercial and
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Le Mon, 26 Sep 2011 15:53:46 +0200,
Teemu Ikonen a écrit :
> 2011/9/26 Picca Frédéric-Emmanuel
> :
> > so for you the .pdb files are DFSGfree ?
>
> There have been PDB-files from the Protein Data Bank in the Debian
> archive since at least 1998 (rasmol source packag
hange a pdb file but to obtain a PDB ID you
need to ask for to the database guyes.
so for you the .pdb files are DFSGfree ?
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déric-Emmanuel
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find some time to send a
mail explaining this efforts. Nevertheless I started a page about this
on the wiki [2].
[1] http://www.synchrotron-soleil.fr/
[2] http://wiki.debian.org/SynchrotronRadiationSoftware
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> debian-science-maintainers-comm...@lists.alioth.debian.org ???
isn't it debian-science-commits ?
> Either this or status quo is fine with me.
same here for me.
Fred
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> The wiki is manually edited and I really hope it will NOT be updated.
> Why should it? We should really stop manually editing those Wiki pages
> because in contrary what people keep on telling you about Wikis: It just
> is outdated. The tasks pages of the Blends web sentinel[1] will be
> update
opriate to put my reply
in
the #592701 bug history, and I forgot to CC the debian-science list.
> On Thu, Aug 12, 2010 at 10:53:18AM +0200, Picca Frédéric-Emmanuel wrote:
> > Is it possible to add the source hkl package [1] in the physics task
> > and also in the data-acquisition.
> Commited in data acquisition!
> Sylvestre
thanks a lot :)
Frederic
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GPG public key 1024D/A59B1171 2009-08-11
fingerprint = 1688 A3D6 F0BD E4DF 2E6B 06AA B6A9 BA6A A59B 1171
uid Picca Frédéric-Emmanuel
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Dear mentors,
I am looking for a sponsor for my package "hkl".
It provides a diffractometer calculation library and a GUI (ghkl).
I would like also to add it in the debian science repository
thanks for your advices.
* Package name: hkl
Version : 4.0.2-1
Upstream Author : pi...@sy
> Bonjour,
Bonjour ;)
> If nobody started to work on it, I will have a look on this during the
> week.
thanks for your help
Frederic
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ht
In fact the object of the mail was wrong sorry for that.
Message d'origine
De: PICCA Frédéric-Emmanuel
[mailto:frederic-emmanuel.pi...@synchrotron-soleil.fr]
Date: sam. 13/03/2010 20:44
À: debian-science@lists.debian.org
Objet : review of the tango package
Hello
I am lo
Hello
I am looking for someone to review my package "tango".
This package provide three services for the tango control system used
by a few synchrotron facilities in europe. (ESRF, SOLEIL, ALBA, PETRAIII,
MAXLAb IV)
and also some smaller laboratories for their how experiment.
This control system
Hello
I am working with the upstream of the Tango control system [1] fo provide a
correct
debian package of their software. But the usptream is using ubuntu
(jantry/karmic) instead
of debian.
now that this software is not yet part of debian I am asking for the right to
create
two (ubuntu branch
Le Mon, 17 Aug 2009 12:44:48 +0200,
PICCA Frédéric-Emmanuel a écrit
:
Sorry I miss spell the name of the repository
tanog.git -> tango.git
I hope someone will give me good advices for this package.
thanks
Frederic
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GPG public key 1024D/A59B1171 2009-08-11
fingerprint = 1688 A
Hello
I have just created the debian-science/packages/tango.git repository on
git.debian.org to work on the Tango Control-System http://tango-controls.org
which is part of the data-acquisition
meta package. This software is not yet part of the official debian (it already
needs some work to be "
Le Thu, 12 Feb 2009 15:31:30 +0100 (CET),
Andreas Tille a écrit :
> On Thu, 12 Feb 2009, Picca Frédéric-Emmanuel wrote:
>
> > Do you thing that it could be possible to move this repository into
> > the debian-science git repository.
>
> Sure, why not?
As I am pa
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