Re: Action needed for R-pkg Uploaders

[Joost van Baal-Ilić]

Hi,

Andreas: thanks a lot for this heads-up, and thanks HUGELY for maintaining the
bulk of the r-cran ecosystem in Debian for such a long time.

Op Mon, Mar 11, 2024 at 03:47:42PM +0100 schreef Andreas Tille:
> 

>
> Joost van Baal-Ilić :
>  r-cran-bdgraph
>  r-cran-corpcor
>  r-cran-d3network
>  r-cran-farver
>  r-cran-fdrtool
>  r-cran-formatr
>  r-cran-ggforce
>  r-cran-ggm
>  r-cran-ggrepel
>  r-cran-glasso
>  r-cran-highr
>  r-cran-httpuv
>  r-cran-huge
>  r-cran-hunspell
>  r-cran-knitr
>  r-cran-lavaan
>  r-cran-lisreltor
>  r-cran-markdown
>  r-cran-matrixcalc
>  r-cran-mi
>  r-cran-mime
>  r-cran-nfactors
>  r-cran-qgraph
>  r-cran-rcppparallel
>  r-cran-rockchalk
>  r-cran-sem
>  r-cran-semplot
>  r-cran-semtools
>  r-cran-statcheck
>  r-cran-tweenr
>  r-cran-yaml

I'm afraid I won't have time to take care of those in the near
future.  However, I _do_ plan to keep maintaining:

 r-cran-lavaan
 r-cran-hunspell
 r-cran-markdown
 r-cran-httpuv
 r-cran-statcheck

(And I've just managed to do upload new upstream of r-cran-statcheck;
routine-update indeed makes life much easier :)

So, would it be usefull to do an upload of the 31 - 5 = 26 other packages
dropping my name from Uploaders: so changing:

 Maintainer: Debian R Packages Maintainers 
 Uploaders: Joost van Baal-Ilić 

into

 Maintainer: Debian R Packages Maintainers 

in debian/control?

Thanks, Bye,

Joost

Re: Why was Caffe removed from Debian ?

[Joost van Baal-Ilić]

Hi,

On Sun, Feb 12, 2023 at 08:30:27AM +0100, lemonsqueeze wrote:
> 
> Until bullseye caffe deep learning framework was packaged (cpu-only
> version), however looks like it was removed from testing (likewise it's
> absent in ubuntu jammy).
> 
> I'm wondering why it was removed (was pretty stable and useful), however i
> couldn't find the rationale for it. Could someone point to the removal
> discussion ?

https://tracker.debian.org/news/1285789/caffe-removed-from-testing/

# finish opencv transition (#984284, #1000636, #100637, #1000780)

HTH, Bye,

Joost

Re: We are right before the freeze now - please update anything to latest version that needs updating

[Joost van Baal-Ilić]

Hi Maarten e.a.,

Thanks a lot for investigating!

On Fri, Feb 03, 2023 at 11:52:06AM +0100, Andreas Tille wrote:
> Am Fri, Feb 03, 2023 at 10:55:14AM +0100 schrieb Maarten van Gompel:
> > I'll give it a try today and see how far I can get. Hopefully that's
> > still in time? There will be ABI changes but at least there are no other
> > packages in debian that depend on our stack besides our own packages.
> 
> I guess for ABI changes it is to late since ftpmaster was asked
> to not accept renamed library packages (which you need for an
> ABI change)

Yup.

Otoh, uploading to experimental and getting into unstable/testing later after
the release (my personal ETA: somewhere in april?) is still very useful of
course.  And once stuff is in testing, it can enter backports too.

Bye,

Joost

Re: We are right before the freeze now - please update anything to latest version that needs updating

[Joost van Baal-Ilić]

Hi Andreas e.a.,

[I guess the same is true for debian-science, re-using your -med post here.]

On Wed, Feb 01, 2023 at 03:14:30PM +0100, Andreas Tille wrote to debian-med:
> Hi Maarten and others,
> 
> as subject says we are right before the freeze since packages need some time
> to migrate to testing to reach the next stable release.  We should upload
> what should be in the next release *right now*.  I've explicitly kept Maarten
> in CC since I have no idea how these package interoperate with each other and
> will not touch these.
> 
> Kind regards and thanks to anybody who works hard to make the next stable
> release the best ever.

I feel still responsible for the r-cran stuff @
https://qa.debian.org/developer.php?login=joostvb ; thanks to Andreas and other
debian-science people that is pretty much up to date.

The Debian science-linguistics part I've been working on till about 2016 is
collected at https://qa.debian.org/developer.php?login=ko.vandersloot%40uvt.nl
.  There's quite some work to do there.  Upstream also has commit and upload
access, but I don't expect them to make it in time for the release; the future
of this software in Debian is a bit unclear now.

(These days I'm very busy preparing
https://wiki.debian.org/DebianEvents/be/2023/FOSDEM .)

Bye,

Joost

Re: Help with mcl needed: util/rand.h missing

[Joost van Baal-Ilić]

Hi again Andreas,

[Cc-ing upstream]

On Tue, Oct 25, 2022 at 01:40:19PM +0200, Joost van Baal-Ilić wrote:
> On Tue, Oct 25, 2022 at 09:42:01AM +0200, Andreas Tille wrote:
> > 
> > cimfomfa was quickly accepted in unstable thanks to ftpmaster.  So I
> > wanted to build the latest version of mcl but I stumbled upon
> > 
> > caml/caml_mcl.c:2:10: fatal error: util/rand.h: No such file or 
> > directory
> > 2 | #include "util/rand.h"
> >   |  ^
> > 
> > Do you have any idea where to obtain util/rand.h?
> 
> It came with cimfomfa-18-238/util/rand.h
> 
> does current cimfomfa no longer ship it?

I think you have to patch it: replace

 #include "util/rand.h"

with

 #include 

.

Bye,

Joost

Re: Help with mcl needed: util/rand.h missing

[Joost van Baal-Ilić]

Hi Andreas,

On Tue, Oct 25, 2022 at 09:42:01AM +0200, Andreas Tille wrote:
> Hi Joost,
> 
> cimfomfa was quickly accepted in unstable thanks to ftpmaster.  So I
> wanted to build the latest version of mcl but I stumbled upon
> 
> caml/caml_mcl.c:2:10: fatal error: util/rand.h: No such file or directory
> 2 | #include "util/rand.h"
>   |  ^
> 
> Do you have any idea where to obtain util/rand.h?

It came with cimfomfa-18-238/util/rand.h

does current cimfomfa no longer ship it?

Bye,

Joost




> 
> Kind regards
> 
>  Andreas.
> 
> [1] https://salsa.debian.org/med-team/mcl/-/jobs/3424138
> 
> -- 
> http://fam-tille.de
> 

Re: Uploading cimfomfa

[Joost van Baal-Ilić]

[Cc-ing upstream]

Excellent, yes please, go ahead!

Bye, Thanks, Joost

On Thu, Oct 13, 2022 at 09:55:48AM +0200, Andreas Tille wrote:
> Hi Joost,
> 
> thanks to your previous work I was able to get cimfomfa easily built and
> I worked down your list of todo/fixme in d/changelog.  So I'm basically
> ready to upload this package which I would need for the new version of
> mcl.  I hope you don't mind if I do so in a team upload to new.
> 
> Kind regards
>  Andreas.
> 
> -- 
> http://fam-tille.de
> 

Re: adduser claims existing diretory in postinst when running piuparts for shiny-server

[Joost van Baal-Ilić]

Hi Andreas e.a.,

On Fri, May 20, 2022 at 09:43:50AM +0200, Ansgar wrote:
> On Fri, 2022-05-20 at 09:37 +0200, Andreas Tille wrote:
> > the Debian Science team has packaged node-shiny-server[1].
> > It creates a system user in its postinst script.  I've added
> > some debug output to this script[2] since I wanted to debug
> > a piuparts issue which you can see here in salsa CI[3].
> > 
> > This log shows two ways to verify that the home directory
> > of the user does not exist, but adduser fails with
> > 
> >  Stopped: Couldn't create home directory `/home/shiny': File
> > exists.
> > 
> > anyway.
> > 
> > Any idea what's going on here and how to fix this?
> 
> It seems wrong for a system user to use a directory below /home.

Yup, see also 
https://lintian.debian.org/tags/maintainer-script-lacks-home-in-adduser

In
https://wiki.debian.org/AccountHandlingInMaintainerScripts
there are some ideas; I believe there is not yet final consensus in Debian on
how to deal with adduser in maintainer scripts...

Anyway HTH, Bye,

Joost

Re: shiny-server in debian

[Joost van Baal-Ilić]

Hi Eric,

On Wed, Mar 23, 2022 at 10:25:41AM -0400, Eric Brown wrote:
> Thank you Andrius, Andreas et al. for your work in getting
> node-sockjs-client in Debian testing. It appears that shiny-server
> (https://salsa.debian.org/science-team/shiny-server) may now have just
> one dependency left - node-rewire, which I'm not sure is actually
> required to build as it is for CI/development. Also note despite the
> warning for node-stable it appears to be packaged
> (https://packages.debian.org/sid/node-stable).
> 
> There have been many interested parties in packaging shiny-server in
> Debian over the past few years. I wonder if anyone has the time to
> revisit now that (all?) the dependencies are in Debian? I
> unfortunately lack the skills for this.
> 
> $ npm2deb depends -r
> https://github.com/rstudio/shiny-server/raw/master/package.json
> Dependencies:
> NPM   Debian
> shiny-server (1.5.18) None
> ├─ bash (0.0.1)   node-bash (0.0.1-4)
> ├─ client-sessions (^0.8.0)   node-client-sessions 
> (0.8.0-3)


I'm very much interested in getting shiny-server shipped with Debian.  We use
it at $dayjob.  I _might_ have time to take a look and spend some effort on it
soonishlish.  Don't hold your breath though.  I could also help with e.g.
stresstesting pre-release .deb's.

Thanks for your interest, Bye,

Joost

Re: Bug#998244: lists.debian.org: request for debian-math mailing list (was: Re: Debian Math Team)

[Joost van Baal-Ilić]

Hi,

I am interested in the creation of this list.  The Debian Math Team is being
created now; https://salsa.debian.org/math-team was created last week, it
currently has 11 members.  The need for this group (and list) has been
discussed in the thread starting at
https://lists.debian.org/msgid-search/87wnlvn3fg@piedmont.edu ; people
expressed interest there.

Thanks, Bye,

Joost

Re: Debian Math Team

[Joost van Baal-Ilić]

Hi Doug,

On Fri, Oct 29, 2021 at 05:31:20PM +, Torrance, Douglas wrote:
> During the Debian Science BoF at this year's DebConf, there was some
> discussion of creating a team devoted to packaging mathematical software.
> 
> This seemed like a pretty good idea, so I figured that I'd go ahead and
> start working on getting it set up.  I've already created a Salsa group [1]
> and a team on the Debian Package Tracker [2].  If you're interested in
> joining, then you should be able to sign up at these links.
> 
> I figured next would be applying for a mailing list, putting together a team 
> policy, etc.  Any thoughts?
> 
> Doug
> 
> [1] https://salsa.debian.org/math-team
> [2] https://tracker.debian.org/teams/math/

I've just clicked
https://salsa.debian.org/groups/math-team/-/group_members/request_access and
got "Your request for access has been queued for review."  Could you grant me
(user joostvb) access?  In the past I've maintained the mathatical package mcl,
I am interesting in contributing there soonish again.  And I happen to be a
mathematician :)

Thanks, Bye,

Joost

PS: please post here once you've asked for mailing list creation, IIRC
listmasters need public stated support by multiple people before list gets
created.

upstream does not want debian to ship their free software (was: Re: python-cython-blis package)

[Joost van Baal-Ilić]

Just one other example:

On Fri, Mar 05, 2021 at 05:19:01PM +0100, Drew Parsons wrote:
> On 2021-03-05 16:52, Andreas Tille wrote:
> > On Fri, Mar 05, 2021 at 09:52:47AM +0800, Paul Wise wrote:
> > > 
> > > It seems unlikely that upstream will have changed their mind, it

> 
> So there's no legal (or technical) reason to not package, just
> the social reason that doing so will gain the ire of the author.
> 
> There is precedence: the author of cdrtools was extremely hostile to
> packaging,
> https://lists.debian.org/debian-devel/2006/08/msg00113.html
> https://lists.debian.org/debian-devel/2006/08/msg00320.html
> https://lists.debian.org/debian-devel/2006/08/msg00653.html
> 
> Eventually we had to just drop cdrtools (and consequently xcdroast)
> https://lists.debian.org/debian-devel/2006/08/msg00775.html

And there was
https://www.jwz.org/blog/2016/04/i-would-like-debian-to-stop-shipping-xscreensaver/
, 5 years ago.  We decided to ship it anyway.

Bye,

Joost

Re: ycm-cmake-modules / Re: Introduction and joining the debian-science/robotics team

[Joost van Baal-Ilić]

Hi Daniele,

On Mon, Aug 31, 2020 at 11:15:41AM +0200, Daniele E. Domenichelli wrote:
> On 28/08/2020 14:02, Joost van Baal-Ilić wrote:
> > I had a quick look at it and I didn't find any obvious flaws, apart
> > from
> > 
> >  Now running lintian ycm-cmake-modules_0.11.3-3_amd64.changes ...
> >  W: ycm-cmake-modules: embedded-javascript-library 
> > usr/share/doc/ycm-cmake-modules/html/_static/language_data.js please use 
> > sphinx
> >  N: 23 tags overridden (23 info)
> >  Finished running lintian.
> > 
> > .  Could you look into that?
> 
> 
> Thanks for the review.
> The warning should be fixed now.

Nice!


> I was also able to enable salsa-ci, see
> https://salsa.debian.org/science-team/ycm-cmake-modules/-/pipelines/170272/builds
> 
> Unfortunately the "reprotest" (that if I understand it correctly is a
> reproducibility test) is failing, probably for this lintian warning:
> 
> I: ycm-cmake-modules: file-references-package-build-path
> usr/share/doc/ycm-cmake-modules/html/todo.html
> 
> This file contains entries like
> 
> ```
> (The  href="manual/ycm-superbuild.7.html#id2">original entry is
> located in
> /build/ycm-cmake-modules-0.11.3/help/manual/ycm-superbuild.7.rst, line
> 215.)
> ```
> 
> for each `.. todo::` line in the sphinx documentation.
> 
> Unfortunately I don't know what is the proper fix it, since it is a file
> generated by sphinx... Do you have any suggestion?

I think you're right that /build/... in sphinx generated docs causes problems.

I've found some explanation at
https://lintian.debian.org/tags/file-references-package-build-path.html

I'm pretty sure this issue has occured in lots of other packages but
my websearch skills fail it now...

There's also https://tests.reproducible-builds.org/debian/reproducible.html
and lots of documentation supplied @ reproducible-builds.org .

Does this help?  I _might_ have time to search a bit more later.

Thanks, Bye,

Joost

ycm-cmake-modules / Re: Introduction and joining the debian-science/robotics team

[Joost van Baal-Ilić]

Hi Daniele,

On Fri, Aug 28, 2020 at 11:32:48AM +0200, Daniele E. Domenichelli wrote:
> 
> I added the first package to salsa:
> 
>   https://salsa.debian.org/science-team/ycm-cmake-modules/
> 
> This is basically just a collection of CMake modules that is a
> dependency for most of our packages.
> 
> Can anyone review it please?

I had a quick look at it and I didn't find any obvious flaws, apart
from

 Now running lintian ycm-cmake-modules_0.11.3-3_amd64.changes ...
 W: ycm-cmake-modules: embedded-javascript-library 
usr/share/doc/ycm-cmake-modules/html/_static/language_data.js please use sphinx
 N: 23 tags overridden (23 info)
 Finished running lintian.

.  Could you look into that?

Thanks for your work!

Bye,

Joost

RM: dimbl -- ROM; ROM, abandoned upstream (was: Re: Bug#917700: dimbl: FTBFS: build-dependency not installable: libtimbl4-dev)

[Joost van Baal-Ilić]

user debian-rele...@lists.debian.org
usertag 917700 + bsp-2019-01-nl-venlo
thanks

Hi Balint,

Since Maarten "proycon" van Gompel--a collegue of your dimbl comaintainer Ko
van der Sloot--told me he expects no new upstream release of dimbl, I feel it's
best to ask for dimbl's removal from testing and unstable.  Is that OK with
you?

Thanks, Bye,

Joost



Subject: RM: dimbl -- ROM; ROM, abandoned upstream
Package: ftp.debian.org
Severity: normal

Hi,

Please remove dimbl from both testing and unstable: no new upstream release
is expected.  Debian's users are better served without dimbl in the upcoming
stable release.  See also https://bugs.debian.org/917700 "FTBFS:
build-dependency not installable: libtimbl4-dev" for some discussion.

Bye,

Joost

PS:
[11:31] [joostvb(+i)] [5:uvt/#lst(+nt)] [Act: 17,21,25], jan 2019:
> нед 13 11:27 < joostvb> proycon: uit debian verwijderen bedoel je?
> нед 13 11:30 < proycon> ja
> нед 13 11:37 < joostvb> proycon: o, en uh: je verwacht geen nieuwe
>   upstream release?
> нед 13 11:46 < proycon> nope
> нед 13 11:46 < proycon> geen releases, geen gebruikers




On Fri, Jan 11, 2019 at 05:32:11AM +0100, Joost van Baal-Ilić wrote:
> Hi Maarten (upstream),
> 
> Is there no new upstream release expected?  If so, I guess indeed it would be
> best to drop it from Debian.
> 
> Thanks, Bye,
> 
> Joost
> 
> 
> On Thu, Jan 10, 2019 at 08:35:15PM +0100, Maarten van Gompel wrote:
> > Hi Lucas,
> > 
> > We're going to let this package get autoremoved, it's hardly used anyway
> > and not worth the effort to maintain.
> > 
> > Regards,
> > 
> > --
> > 
> > Maarten van Gompel
> > Language Machines research group
> > Centre for Language and Speech Technology
> > Radboud Universiteit Nijmegen
> > 
> > proy...@anaproy.nl
> > https://proycon.anaproy.nl
> > https://github.com/proycon
> > 
> > GnuPG key:  0x39FE11201A31555C
> > XMPP:   proy...@anaproy.nl   Matrix: @proycon:matrix.org
> > Telegram:   proycon  IRC: proycon (freenode)
> > Discord:proycon#8272
> > Mastodon:   https://mastodon.social/@proycon   (@proycon@mastodon.social)
> > Twitter:https://twitter.com/proycon
> > ORCID:  https://orcid.org/-0002-1046-0006
> > Keybase:https://keybase.io/proycon
> > Bitcoin:1BRptZsKQtqRGSZ5qKbX2azbfiygHxJPsd
> 


signature.asc
Description: Digital signature

Re: Debian Maintainer requesting upload permission for selected packages

[Joost van Baal-Ilić]

Hi,

FWIW, I just did

 % dcut --force dm --uid 8AC624881EF2AC30C0E68E2C39FE11201A31555C --allow 
frogdata
 % dcut --force dm --uid 8AC624881EF2AC30C0E68E2C39FE11201A31555C --allow 
mbtserver

granting Maarten "proycon" van Gompel upload permissions for those 2 source
packages.

Bye,

Joost



signature.asc
Description: Digital signature

Re: Moving remaining Debian Science packages from SVN to Git

[Joost van Baal-Ilić]

Hi Andreas,

On Wed, Jan 24, 2018 at 01:37:25PM +0100, Andreas Tille wrote:
> Hi,
> 
> I'm currently moving the last remaining packages from SVN to Git
> (salsa.d.o) and remove the according SVN dir.  I'm also removing
> the SVN dirs of just moved packages as well as from packages that
> were removed from Debian.
> 
> This went fine so far but I stumbled upon one issue with dimbl where
> some Git repository was created and afterwards development in SVN
> continued (involved people in CC).  I now merged everything "somehow"
> into the existing Git repository and hope that's fine for you.
> 
> In case there might be somebody who is not happy about the move please
> let me know.


Thanks a lot for this work!

I don't have time to investigate the dimbl-situation soonish.  Possibly Maarten
(CC-ed) is interested.

Bye,

Joost

Re: Export of alioth mailing list archive not working

[Joost van Baal-Ilić]

Hi Tobias,

On Wed, Jan 10, 2018 at 11:43:25AM +0100, Tobias Hansen wrote:
> 
> due to the deprecation of Alioth I now want to ask for a replacement of 
> debian-science-sagem...@lists.alioth.debian.org on lists.debian.org. I would 
> like the archive to be imported and followed the instructions on [1] to 
> export the mbox file, but it didn't work:
> 
> thansen@moszumanska:~$ sudo /usr/local/bin/export-list 
> debian-science-sagemath > output.tar.gz
> Mailbox 
> (/var/lib/mailman/archives/public//debian-science-sagemath.mbox/debian-science-sagemath.mbox)
>  not found or empty - continuing anyway (trying to export subscribers)
> 
> I got a file containing the list of subscribers. Does anybody know how to do 
> it? Am I missing permissions?
> 

maybe being added to group 'list' would fix it indeed.  however, i am not quite 
sure how
this is supposed to work:

joostvb@moszumanska:~% ls -l 
/var/lib/mailman/archives/public/debian-science-sagemath
lrwxrwxrwx 1 root list 69 авг  9  2016 
/var/lib/mailman/archives/public/debian-science-sagemath -> 
/srv/lists.alioth.debian.org/archives/private/debian-science-sagemath

joostvb@moszumanska:~% ls -ld 
/srv/lists.alioth.debian.org/archives/private/debian-science-sagemath
ls: cannot access 
/srv/lists.alioth.debian.org/archives/private/debian-science-sagemath: 
Permission denied
joostvb@moszumanska:~% ls -ld /srv/lists.alioth.debian.org/archives/private
drwxrws--- 2787 www-data list 131072 нов 13 20:08 
/srv/lists.alioth.debian.org/archives/private/

'public' symlinking to 'private' feels wrong to me.

better contact listmaster@d.o i guess, or file a bug.

Bye,

Joost

Re: new iproposal: a specific OS for psychologist

[Joost van Baal-Ilić]

Hi Fran,

On Mon, Oct 09, 2017 at 01:43:19PM -0400, Franps wrote:
> Hi, My name is Francisco Montero, I would like to ask you if it is possible 
> to develop an OS based on Debian (similar to SkoleLinux/DebianEdu) specific 
> for psychologist (both applied psychologist and researcher psychologist) 
> built with a set of predetermine tools such as pspp (data analysis), 
> neurodebian, zotero (citation manager), bibus (connection to data base 
> provider) pgp tools for confidential reports about patients,...
> I am psychologist and professor at University. I don't know about 
> programming, but I would help to search for the appropiate tools for an 
> specific OS for psychologist (asking partners, testing tools in debian 
> packages...).
> Psychologists as other researchers usually depend on privative software to 
> research and to improve the knowledge about human behavior and mind. We would 
> love a new Free Software OS based on Debian.
> Currently I am user of Debian Stretch and I think this would be a very useful 
> OS to built an specific OS for psyhologist. I offer myself to contribute of 
> topics related to psychology during the development process and the spread of 
> the new OS if this is released.
> Please, let me know your opinion about my proposal.
> Thank you very much for yor attention.

Your message will more likely get a reply when it's posted at
debian-science@lists.debian.org; the debian-publicity list is used to discuss
how to deal with and manage publicity for Debian.

I here do post your message at debian-science; you'll likely get a more useful
reply one of these days.

Bye,

Joost

upstream and "obsolete"-ness of debian supplied software (was: Re: Is theano worth saving?)

[Joost van Baal-Ilić]

Hi,

On Wed, Feb 08, 2017 at 11:31:10AM +, Ghislain Vaillant wrote:
> On Wed, 2017-02-08 at 10:58 +0100, Joost van Baal-Ilić wrote:
> > On Wed, Feb 08, 2017 at 09:47:08AM +, Ghislain Vaillant wrote:
> > > On Wed, 2017-02-08 at 10:17 +0100, Daniel Stender wrote:
> > > > On 08.02.2017 09:13, Rebecca N. Palmer wrote:
> > > > > I have patches for #848764 and #831540; I haven't yet found the cause
> > > > > of #831541, but as it only affects big-endian systems, partial
> > > > > removal is an option.
> > > > > 
> > > > > However, one of these bugs is a point where upstream plan to make an
> > > > > incompatible change (though my fix doesn't), and upstream aren't sure
> > > > > whether having Theano in a long-release-cycle distribution such as
> > > > > Debian is a good idea: https://github.com/Theano/Theano/issues/5494
> > > 
> > > On first read, it sounds to me that upstream is failing to understand
> > > that having theano in the archive does not replace or substitute
> > > traditional development workflow via pip if users want to.
> > 
> > And/or maybe upstream feels anybody using an "obsolete" version of theano
> > is doing something wrong.  And/or maybe upstream would feel some kind of
> > obligation/duty to support users of "obsolete" versions of Debian-shipped
> > theano on Debian systems, if Debian were to ship with those.  See also the
> > xscreensaver debacle, some months ago.  I'm just guessing here,
> > extrapolating from other upstreams.
> 
> xscreensaver is an application, so upstream's anger was justified since
> users had no other (simple) alternative to using the outdated packaged
> version.

The xscreensaver situation indeed has some different aspects.

> theano is a library, and libraries provided in Debian should be
> packaged as redepends for other frameworks / applications . That's why
> you are invited to provide a justification in your ITPs as to why
> packaging the library for Debian is necessary.
> 
> Unlike with xscreensaver, users do have an alternative for using the
> latest theano: fire a virtualenv and use the latest theano there via
> `pip install`.
> 
> Same comment for numpy, scipy and the rest of the scientific Python
> ecosystem. Anyone using for instance jessie + the system numpy for
> serious development is clearly missing out, and should get to know
> modern development tools (i.e. venv, pip, anaconda...).

Indeed, true, but there's software developers; but there's also people merely
_using_ applications depending upon the libraries we're talking about.

> > > Our packages are here to support future applications / frameworks,
> > > which may require an appropriately packaged theano. Considering the
> > > success of deep-learning these days, this prospect is quite likely.
> > > 
> > > > > (Note that their suggested alternative of using pip will involve
> > > > > manually installing libblas-dev, as pip only knows about Python
> > > > > dependencies.)
> > 
> > Anyway, it would be good to make clear what Debian expects of upstream, and
> > how shipping theano with Debian might even be _beneficial_ for upstream.
> 
> Indeed, in the form of dynamic CI (with autopkgtest) and testing on a
> variety of architectures they might not have access to otherwise.
> Whether they care or not is a different story.
> 
> I believe the easiness of `apt install` which Daniel brought in is no
> longer so much of a *strong* argument, now that pip + wheels has become
> quite mature. That's my personal opinion though.

Thanks for your extra arguments.

The for me personally (system administrator at a university) most convincing
argument in https://wiki.debian.org/AdvantagesForUpstream is: "Administrators
of larger installations can install your software from the official archive and
don't need to make special effort to provision your software."  And
administrators automagically benefit from debian-supplied security upgrades for
the software, with zero extra cost.

(And then there's also the worth reading https://wiki.debian.org/UpstreamGuide
, 'though slightly less applicable for this discussion.)

Thanks, Bye,

Joost

Re: Is theano worth saving?

[Joost van Baal-Ilić]

Hi,

On Wed, Feb 08, 2017 at 09:47:08AM +, Ghislain Vaillant wrote:
> On Wed, 2017-02-08 at 10:17 +0100, Daniel Stender wrote:
> > On 08.02.2017 09:13, Rebecca N. Palmer wrote:
> > > I have patches for #848764 and #831540; I haven't yet found the cause of
> > > #831541, but as it only affects big-endian systems, partial removal is an
> > > option.
> > > 
> > > However, one of these bugs is a point where upstream plan to make an
> > > incompatible change (though my fix doesn't), and upstream aren't sure
> > > whether having Theano in a long-release-cycle distribution such as Debian
> > > is a good idea: https://github.com/Theano/Theano/issues/5494
> 
> On first read, it sounds to me that upstream is failing to understand
> that having theano in the archive does not replace or substitute
> traditional development workflow via pip if users want to.

And/or maybe upstream feels anybody using an "obsolete" version of theano is
doing something wrong.  And/or maybe upstream would feel some kind of
obligation/duty to support users of "obsolete" versions of Debian-shipped
theano on Debian systems, if Debian were to ship with those.  See also the
xscreensaver debacle, some months ago.  I'm just guessing here, extrapolating
from other upstreams.

> Our packages are here to support future applications / frameworks,
> which may require an appropriately packaged theano. Considering the
> success of deep-learning these days, this prospect is quite likely.
> 
> > > (Note that their suggested alternative of using pip will involve manually
> > > installing libblas-dev, as pip only knows about Python dependencies.)

Anyway, it would be good to make clear what Debian expects of upstream, and how
shipping theano with Debian might even be _beneficial_ for upstream.

Bye,

Joost

Bug#843328: O: dimbl - Distributed Memory Based Learner for Natural Language Processing

[Joost van Baal-Ilić]

Package: wnpp
Severity: normal

Hi,

I am no longer interested in maintaining dimbl.  Upstream (Maarten van Gompel)
feels shipping dimbl with Debian is of very limited use: people interested in
dimbl likely are better served always using the very latest version of it.

I'll request for removal of dimbl from unstable and testing, soonish.

Unless someone else steps up RSN, that is.  Be aware there is serious/RC/FTBFS
Bug #833905 open (which is relatively easy to fix).)

(From the description: The Dimbl Distributed Memory Based Learner is a wrapper
around the k-nearest neighbor classifier in TiMBL, offering parallel
classification on multi-CPU machines. Dimbl splits the original training set,
builds separate TiMBL classifiers per training subset, and merges their
nearest-neighbor sets per classified instance.  If you do scientific research
in Natural Language Processing using the Memory-Based Learning technique, Dimbl
will likely be of use to you.)

Bye,

Joost



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Description: Digital signature

Re: statistics: who maintains R packages in Debian (was: Re: Debhelper for R packages)

[Joost van Baal-Ilić]

On Sat, Oct 08, 2016 at 01:59:14PM -0500, Dirk Eddelbuettel wrote:
> 
> On 8 October 2016 at 20:32, Joost van Baal-Ilić wrote:
> | On Sat, Oct 08, 2016 at 12:08:50PM -0500, Dirk Eddelbuettel wrote:
> | > On 8 October 2016 at 17:45, Joost van Baal-Ilić wrote:
> | > | Otoh: currently R stuff is mainly maintained within debian-science and
> | > | debian-med.  
> | > 
> | > Well: the R package itself, addons like ess, rpy2, rkward, ... , and 
> several
> | > dozen r-cran-packages maintained are not.
> | 
> | You're right, and I knew that.  The word "mainly" might have been not the 
> right
> | one; sorry about that.  
> | 
> | I got curious about who exactly maintains how many r-cran packages 
> currently in
> | testing/stretch, came up with this quick and (very!) crude hack:
> | 
> | joostvb@banach:~% for p in $( apt-cache search --names-only r-cran | \
> |  cut -d' ' -f1 ); do echo -n "$p "; apt-cache show $p | grep Maintainer; 
> done | \
> |  cut -d' ' -f3- | cut -d\< -f2 | sed 's/^/ | 
> |   1 <harry.southwo...@gmail.com>
> |   1 <i...@maintz.de>
> |   1 <lifong...@gmail.com>
> |   1 <ond...@debian.org>
> |   2 <j...@debian.org>
> |   7 <debichem-de...@lists.alioth.debian.org>
> |  19 <lawre...@debian.org>
> | 105 <debian-science-maintain...@lists.alioth.debian.org>
> | 130 <e...@debian.org>
> | 137 <debian-med-packag...@lists.alioth.debian.org>
> 
> That's a very good start; you may also want to look at 'apt-cache rdepends
> r-base-core' (and maybe r-base) to get the r-bioc-* and r-other-* packages.

Thanks for the hint; turns out I missed some packages maintained by
debian-med-packaging and debichem-devel:

Who exactly maintains how many r-cran, r-bioc and r-other packages currently in
testing/stretch:

joostvb@banach:~% for p in \
 $( apt-cache search --names-only 'r-cran-|r-bioc-|r-other-' | cut -d' ' -f1 ); 
\
  do echo -n "$p "; apt-cache show $p | grep Maintainer; done | \
  cut -d' ' -f3- | cut -d\< -f2 | sed 's/^/
  1 <i...@maintz.de>
  1 <lifong...@gmail.com>
  1 <ond...@debian.org>
  2 <j...@debian.org>
 11 <debichem-de...@lists.alioth.debian.org>
 19 <lawre...@debian.org>
105 <debian-science-maintain...@lists.alioth.debian.org>
130 <e...@debian.org>
187 <debian-med-packag...@lists.alioth.debian.org>

Bye,

Joost

Re: Debhelper for R packages

[Joost van Baal-Ilić]

Hi,

On Sun, Oct 09, 2016 at 02:20:07PM +0200, Andreas Tille wrote:
> On Sat, Oct 08, 2016 at 05:45:16PM +0200, Joost van Baal-Ilić wrote:
> > > IMHO that's not matter of personal preference but a matter of how to
> > > work together in a Debian maintainers team.  There are tools working on
> > > git.debian.org but not elsewhere.  I keep on thinking that a Debian R
> > > maintainers group would make a lot of sense and R packages should be
> > > maintained on alioth.
> > 
> > Yup.  Otoh: currently R stuff is mainly maintained within debian-science and
> > debian-med.  Scaling benefits are there; I don't think moving to a new 
> > debian-r
> > would improve stuff _that_ much.
> 
> I was not speaking about those packages that are just team maintained.
> There are a lot of others that are not - for these a Debian R team would
> make sense ... and for r-base for sure.

I'm sorry but to me it's not clear what problem would be solved by having
r-base being team maintained.  I just checked
http://metadata.ftp-master.debian.org/changelogs//main/r/r-base/r-base_3.3.1-1_changelog
and https://bugs.debian.org/cgi-bin/pkgreport.cgi?pkg=r-base;dist=unstable and
couldn't find any problem which would clearly benefit from team maintenance.

Bye,

Joost

-- 
Always gonna keep in touch // Never want to use a crutch
 × MacKaye, Preslar, Baker, Nelson  1982

statistics: who maintains R packages in Debian (was: Re: Debhelper for R packages)

[Joost van Baal-Ilić]

On Sat, Oct 08, 2016 at 12:08:50PM -0500, Dirk Eddelbuettel wrote:
> On 8 October 2016 at 17:45, Joost van Baal-Ilić wrote:
> | Otoh: currently R stuff is mainly maintained within debian-science and
> | debian-med.  
> 
> Well: the R package itself, addons like ess, rpy2, rkward, ... , and several
> dozen r-cran-packages maintained are not.

You're right, and I knew that.  The word "mainly" might have been not the right
one; sorry about that.  

I got curious about who exactly maintains how many r-cran packages currently in
testing/stretch, came up with this quick and (very!) crude hack:

joostvb@banach:~% for p in $( apt-cache search --names-only r-cran | \
 cut -d' ' -f1 ); do echo -n "$p "; apt-cache show $p | grep Maintainer; done | 
\
 cut -d' ' -f3- | cut -d\< -f2 | sed 's/^/
  1 <i...@maintz.de>
  1 <lifong...@gmail.com>
  1 <ond...@debian.org>
  2 <j...@debian.org>
  7 <debichem-de...@lists.alioth.debian.org>
 19 <lawre...@debian.org>
105 <debian-science-maintain...@lists.alioth.debian.org>
130 <e...@debian.org>
137 <debian-med-packag...@lists.alioth.debian.org>


Bye,

Joost

-- 
For that which befalleth the sons of men befalleth beasts; even one thing
befalleth them: as the one dieth, so dieth the other; yea, they have all one
breath; so that a man hath no preeminence above a beast --  Ecc 3:19 (KJV)


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Re: Debhelper for R packages

[Joost van Baal-Ilić]

On Sat, Oct 08, 2016 at 12:12:12PM -0500, Dirk Eddelbuettel wrote:
> 
> On 7 October 2016 at 22:24, Dylan wrote:
> | 2016-10-07 16:25 GMT+02:00 Gordon Ball :
> | > On 07/10/16 15:33, Dirk Eddelbuettel wrote:
> | >> On 7 October 2016 at 15:09, Andreas Tille wrote:
> | >> | I'm fine with these changes.  If you want to let this propagate to all
> | >> | R+BioConductor packages probably a lintian warning makes sense.  May be
> | >>
> | >> Really?  We don't have an officially sanctioned policy that _mandates_ 
> this.
> [...]
> | There is the same thing on the Bioconductor page: "Canonical url for
> | use in publications, etc., will always redirect to current release
> | version (or devel if package is not in release yet)."
> 
> I wasn't clear here. I obviously have no issue with checks for the canonical
> URL which CRAN now mandates and checks for in uploads to CRAN; I fixed many
> of my (R upstream) packages already. So sure, that check is helpful.
> 
> I was gently objecting to making dh-r a mandate.  It's a new tool, so let's
> give people a chance to try and use / improve it. Or not to if they prefer.
> It's better if this evolves naturally than per fiat.
> 
> We may well all use it.  Time will tell.

I couldn't agree more.  I'm a cdbs fan, and some of my packages I maintain with
neither cdbs nor dh.  So I was _very_ happy to find out cdbs was the tool used
by many r-cran packages, when I started packaging r-cran stuff.  Don't get me
wrong: I am happy we now can use dh to build r-cran packages: more choice is
always welcome.  So: thanks a lot Gordon and Dylan for your work.  I however
won't immediately start converting my r-cran packages from cdbs to dh-r.

Bye,

Joost

-- 
Debian is essentially an eclectic anarchy. We do not practise the
tyranny of the masses around here.  --Andrew Suffield
http://mdcc.cx/   ※  Tilburg, Низоземска   ★   http://ad1810.com/


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Re: Debhelper for R packages

[Joost van Baal-Ilić]

On Sat, Oct 08, 2016 at 08:05:36AM +0200, Andreas Tille wrote:
> On Fri, Oct 07, 2016 at 04:25:40PM +0200, Gordon Ball wrote:
> > 
> > > Sure, and some people prefer GitHub or Gitlab or their own git server.
> > > Different strokes for different folks.
> > 
> > They should in any case be in sync, providing I remember to keep them
> > so. The Vcs-Url in d/control will remain the git.debian.org one.
> 
> IMHO that's not matter of personal preference but a matter of how to
> work together in a Debian maintainers team.  There are tools working on
> git.debian.org but not elsewhere.  I keep on thinking that a Debian R
> maintainers group would make a lot of sense and R packages should be
> maintained on alioth.

Yup.  Otoh: currently R stuff is mainly maintained within debian-science and
debian-med.  Scaling benefits are there; I don't think moving to a new debian-r
would improve stuff _that_ much.

Also, R packages is not exactly dh-r.  Having all R packages semi-centrally
maintained would be nice.  I am not quite sure wether having dh-r in the same
group would bring very huge benefits.

Bye,

Joost

Re: Looking for sponsors to upload various updated packages

[Joost van Baal-Ilić]

Hi Maarten,

And while you're at it, please remove my name from debian/control
of python-pynlpl libfolia uctodata ucto frogdata frog; since I lack the
time for maintaining those.

Thanks, Bye,

Joost

PS: Anton: thanks a lot for the review!


On Sun, Sep 04, 2016 at 08:35:13PM +0200, Anton Gladky wrote:
> Hi Maarten,
> 
> short notes about python-pynlpl.
> - VCS-fields are missing, please add them
> - pristine-tar branch is missing. Please refer Debian Science policy about 
> that.
> - It looks like the 1.0 version of this package is released by upstream
>   please consider to package it instead of 0.9.3
> - Apply "cme fix dpkg" or {"cme fix dpkg-control", "cme fix dpkg-copyright"}
> - Move debian/*.1 to something like "debian/manpages" not to overcrowd
> debian-folder.
> - Drop autogenerated unneeded commented lines in d/rules
> - Consider adding autopkgtests, DEP-8. If you need examples for that,
> please let me know.
> 
> If these notes are relevant to another packages, please apply
> them also. When you are ready please let me know.
> 
> Best regards
> 
> Anton
> 
> 
> 2016-08-07 10:06 GMT+02:00 Maarten van Gompel :
> > Hi,
> >
> > Thanks for the quick upload of libticcutils, timbl, timblserver, mbt and 
> > mbtserver!
> > The only remaining packages for upload are now:
> >
> >   python-pynlpl libfolia uctodata ucto frogdata frog
> >
> > Regards,
> >
> > --
> >
> > Maarten van Gompel
> > Centre for Language Studies
> > Radboud Universiteit Nijmegen
> >
> > proy...@anaproy.nl
> > http://proycon.anaproy.nl
> > http://github.com/proycon
> >
> > GnuPG key:  0x1A31555C  XMPP: proy...@anaproy.nl
> > Telegram:   proycon IRC: proycon (freenode)
> > Twitter:https://twitter.com/proycon
> > Bitcoin:1BRptZsKQtqRGSZ5qKbX2azbfiygHxJPsd
> >
> 

Re: Looking for sponsors to upload various updated packages

[Joost van Baal-Ilić]

Hi,

On Fri, Aug 05, 2016 at 11:42:58AM +0200, Maarten van Gompel wrote:
> 
> I have prepared updated debian packages for a significant portion of our
> research group's software stack of Natural Language Processing tools, with 
> help
> also from Joost van Baal-Ilić. I am currently looking for sponsors to upload
> this all to debian.
> 
> It concerns the following packages, all have been updated to the latest
> upstream sources:
> 
>  * git://anonscm.debian.org/debian-science/packages/python-pynlpl.git
>  * git://anonscm.debian.org/debian-science/packages/libticcutils.git
>  * git://anonscm.debian.org/debian-science/packages/libfolia.git
>  * git://anonscm.debian.org/debian-science/packages/uctodata.git
> * new package (split from ucto)
>  * git://anonscm.debian.org/debian-science/packages/ucto.git
>  * git://anonscm.debian.org/debian-science/packages/timbl.git
>  * git://anonscm.debian.org/debian-science/packages/timblserver.git
>  * git://anonscm.debian.org/debian-science/packages/mbt.git
>  * git://anonscm.debian.org/debian-science/packages/mbtserver.git
>  * git://anonscm.debian.org/debian-science/packages/frogdata.git
>  * git://anonscm.debian.org/debian-science/packages/frog.git

I'll take

 mbt mbtserver libticcutils timbl timblserver dimbl

which leaves

 python-pynlpl libfolia uctodata ucto frogdate frog

for anybody else interested. Some of those have recently been removed from
testing, btw.

> All packages were verified to build and install with no or minimal (and
> in that case ignorable) lintian warnings. These releases also close various 
> existing bugs.
> 
> The packages are heavily inter-dependent. When testing, the order layed out 
> above should
> result in no dependency problems.
> 
> I'm not sure what the proper or most convenient procedure is to get uploaded 
> to
> debian. Is it sufficient to link the git repositories as I did or should I 
> rather
> send all the relevant source packages?

I guess debian-science members are ok with these pointers to the relevant git
repo's.  For sure _I_ am :)

Thanks for your work!

Bye,

Joost

Bug#831889: ITP: r-cran-lavaan -- GNU R package for latent variable analysis -- lavaan

[Joost van Baal-Ilić]

Package: wnpp
Severity: wishlist

* Package name: r-cran-lavaan
* URL : https://cran.r-project.org/web/packages/lavaan
* License : GPL-2+
  Description : GNU R package for latent variable analysis -- lavaan
   This package supplies latent variable analysis for R.  One can
   use lavaan to estimate a large variety of multivariate statistical models,
   including path analysis, confirmatory factor analysis, structural equation
   modeling and growth curve models.

I am working on the packaging using debian-science's git at Alioth
https://anonscm.debian.org/cgit/debian-science/packages/r-cran-lavaan.git

See also https://lists.debian.org/<20151110083253.gb6...@dijkstra.uvt.nl>
"running RStudio's Shiny Server the Debian way" for background.

Bye,

Joost

-- 
http://mdcc.cx/


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Bug#831883: ITP: r-cran-corpcor -- GNU R for Estimation of Covariance and Correlation -- corpcor

[Joost van Baal-Ilić]

Package: wnpp
Severity: wishlist

* Package name: r-cran-corpcor
* URL : https://cran.r-project.org/web/packages/corpcor ,
  http://strimmerlab.org/software/corpcor/
* License : GPL-2
  Description : GNU R for Estimation of Covariance and Correlation

The R corpcor package is a dependency for semPlot, which I intend to package as
r-cran-semplot.

I am working on the packaging using debian-science's git at Alioth
https://anonscm.debian.org/cgit/debian-science/packages/r-cran-corpcor.git

See also https://lists.debian.org/<20151110083253.gb6...@dijkstra.uvt.nl>
"running RStudio's Shiny Server the Debian way" for background.

Bye,

Joost



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Bug#831880: ITP: r-cran-matrixcalc -- GNU R functions for matrix calculations -- matrixcalc

[Joost van Baal-Ilić]

Package: wnpp
Severity: wishlist

* Package name: r-cran-matrixcalc
* URL : https://cran.r-project.org/web/packages/matrixcalc
* License : GPL-2+
  Description : GNU R functions for matrix calculations -- matrixcalc

 GNU R package supplying functions to support matrix calculations
 for probability, econometric and numerical analysis. There are
 additional functions that are comparable to APL functions which
 are useful for actuarial models such as pension mathematics.

The R matrixcalc package is a dependency for sem, which I intend to package as
r-cran-sem.

I am working on the packaging using debian-science's git at Alioth
https://anonscm.debian.org/cgit/debian-science/packages/r-cran-matrixcalc.git

See also https://lists.debian.org/<20151110083253.gb6...@dijkstra.uvt.nl>
"running RStudio's Shiny Server the Debian way" for background.

Bye,

Joost



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Bug#813815: ITP: r-cran-nfactors -- GNU R package for Parallel Analysis and Non Graphical Solutions to the Cattell Scree Test -- nFactors

[Joost van Baal-Ilić]

Package: wnpp
Severity: wishlist

* Package name: r-cran-nfactors
  Upstream Author : Gilles Raiche (Universite du Quebec a Montreal)
* URL : https://cran.r-project.org/web/packages/nFactors/
* License : GPL
  Programming Lang: R
  Description : GNU R package for Parallel Analysis and Non Graphical 
Solutions to the Cattell Scree Test -- nFactors

 This package supplies Parallel Analysis and Non Graphical Solutions to the
 Cattell Scree Test for R.

Bye,

Joost

Bug#813481: ITP: r-cran-markdown -- GNU R package providing R bindings to the Sundown Markdown rendering library

[Joost van Baal-Ilić]

Package: wnpp
Severity: wishlist

* Package name: r-cran-markdown
  Version : 0.7.7
  Upstream Author : Yihui Xie 
* URL : https://cran.r-project.org/web/packages/markdown/
* License : GPL e.a.
  Programming Lang: R, C
  Description : GNU R package providing R bindings to the Sundown Markdown 
rendering library

 Provides R bindings to the Sundown Markdown rendering library by Vicent Marti 
e.a.,
 based upon work by Natacha Porté.  Markdown is a plain-text formatting syntax 
that can
 be converted to XHTML or other formats.
 .
 The R function `markdownToHTML` renders a markdown file to HTML. Options
 controlling HTML output and supported markdown extensions can be optionally
 specified.
 .
 The package also exports the underlying Sundown C extension API which
 enables creating and calling custom renderers using the `renderMarkdown`
 function.


The R markdown package is a dependency for r-cran-knitr (ITP Bug#808155);
r-cran-knitr is needed for RStudio's Shiny Server.

I'll work on the packaging using debian-science's git at Alioth, at
http://anonscm.debian.org/gitweb/?p=debian-science/packages/r-cran-markdown.git 
.

See also https://lists.debian.org/<20151110083253.gb6...@dijkstra.uvt.nl>
"running RStudio's Shiny Server the Debian way".

Bye,

Joost



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Re: engrid in debian

[Joost van Baal-Ilić]

Hi Mauro,

Thanks for your interest in making Debian better!

On Tue, Jan 12, 2016 at 03:11:50PM +0100, Mauro Darida wrote:
> On Wednesday 13 January 2016 00:37:53 Jonathon Love wrote:
> > excellent. the git servers are accessed by ssh, and you have not added
> > your public key to alioth (presumably). try this:
> > 
> > https://wiki.debian.org/Alioth/SSH
> > 
> > but you probably should put a little more effort into researching how to
> > do this stuff yourself. getting a good grasp of things like SSH, git,
> > public keys, etc. will put you in a better place to contribute.
> > 
> That one is a good link, thanks. I would suggest, from my (newbie) point of 
> view, to update the docs adding that alioth ssh connection is done via keys 
> only

Yes, that's a good suggestion.

> (and putting the above link in the same page would help too).

You and everyone can edit these wiki pages after creating an account on
wiki.debian.org.

> One more question: after publishing the git repository on alioth:
> $ cd /git/debian-science/packages/
> $ mkdir engrid.git && cd engrid.git
> $ git --bare init --shared=all
> 
> how can you debian people can access to the source package ? That it is not 
> clear to me...

The stuff on alioth is publicly available.

I, and others having read/write access to debian-science, should be able to
access is running:

 joostvb@nusku:~/git% git clone 
ssh://git.debian.org/git/debian-science/packages/engrid.git

However, it seems something went wrong when you created your repo on alioth:

 fatal: '/git/debian-science/packages/engrid.git' does not appear to be a git 
repository

Indeed, there is no git.debian.org:/git/debian-science/packages/engrid.git .

You can also check at https://anonscm.debian.org/cgit/ ; your repo should show 
up there
once you've succesfully created it.

> Do I need more git commands to end the procedure and the above 
> is just a preliminary start on alioth ?

Yes, it seems so.

Bye,

Joost

Bug#808159: ITP: r-cran-yaml -- Methods to convert R data to YAML and back

[Joost van Baal-Ilić]

Package: wnpp
Severity: wishlist

* Package name: r-cran-yaml
  Version : 2.1.13
  Upstream Author : Jeremy Stephens 
* URL : https://cran.r-project.org/web/packages/yaml
* License : BSD_3_clause
  Programming Lang: R, C
  Description : Methods to convert R data to YAML and back

 This package implements the libyaml YAML 1.1 parser and emitter for R.


The R yaml package is needed for RStudio's Shiny Server.

I'm working on the mime packaging using debian-science's git at Alioth, at
http://anonscm.debian.org/gitweb/?p=debian-science/packages/r-cran-yaml.git .

See also Bug#808142: ITP: r-cran-httpuv, Bug#808148: ITP: r-cran-jsonlite,
#808155: ITP: r-cran-knitr, #808156: ITP: r-cran-mime and
https://lists.debian.org/<20151110083253.gb6...@dijkstra.uvt.nl> "running
RStudio's Shiny Server the Debian way".

This is today's last ITP from me. :)

Bye,

Joost

-- 
Le premier qui, ayant enclos un terrain, s'avisa de dire « Ceci est à moi »,
et trouva des gens assez simples pour le croire, fut le vrai fondateur de la
société civile.  Que de crimes, que de guerres, de meurtres, que de misères
et d'horreurs n'eût point épargnés au genre humain celui qui, arrachant les
pieux ou comblant le fossé, eût crié à ses semblables : Gardez-vous
d'écouter cet imposteur; vous êtes perdus, si vous oubliez que les fruits
sont à tous, et que la terre n'est à personne.
  —-Jean-Jacques Rousseau, De l'Inégalité parmi les hommes, 1755


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running RStudio's Shiny Server the Debian way

[Joost van Baal-Ilić]

Hi,

If you're insterested in helping packaging GNU R software, you might like
this: I plan to run RStudio's Shiny Server (
https://www.rstudio.com/products/shiny/shiny-server/ ) the Debian way, using
Debian packages for as many components as possible.  My time is limited
though.  Help is welcome :)

I've just started the effort, up to now I've made some very rough packages of
'r-cran-shiny' and 'r-cran-rmarkdown'.  You can fetch them via

 deb http://non-gnu.uvt.nl/debian jessie uvt

or view at

 http://non-gnu.uvt.nl/debian/jessie/r-cran-shiny/
 http://non-gnu.uvt.nl/debian/jessie/r-cran-rmarkdown/

.  I'll post proper ITP's and maintain packaging via debian-science's git
soonish.

Still needed is, at least, packaging of

 knitr, R6, mime, evaluate, highr, htmltools, formatR, markdown, yaml,
 jsonlite, httpuv, stringr, stringi ( ITP #801085 )

.  Likely licensing issues will pop up.  We'll see...

Help, ideas, tips welcome.

Bye,

Joost

-- 
Joost van Baal-Ilić   http://abramowitz.uvt.nl/
 Tilburg University
mailto:joostvb.uvt.nl   The Netherlands


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Re: Bug#617296: RFP: rstudio -- IDE for GNU R

[Joost van Baal-Ilić]

Hi,

On Mon, Sep 21, 2015 at 08:41:39AM +0100, Iain R. Learmonth wrote:
> On Mon, Sep 21, 2015 at 08:25:26AM +0200, Andreas Tille wrote:
> > I hope we could settle with RStudio maintained in Debian Science
> > repository.

> 
> Does this RFP include the web-based frontend? I've been looking at getting a
> service set up at my University and it would be great if I can do it on a
> Pure Debian system.

FWIW: Same here in Tilburg, .nl.

Bye,

Joost

-- 
http://abramowitz.uvt.nl/  http://mdcc.cx/  http://ad1810.com/

Re: Last call before metapackage creation for Wheezy

[Joost van Baal-Ilić]

Hi again,

On Wed, Apr 10, 2013 at 09:28:16AM +0200, Andreas Tille wrote:
 On Wed, Apr 10, 2013 at 09:07:40AM +0200, Joost van Baal-Ilić wrote:
  
  The package mcl should get added to
  http://blends.alioth.debian.org/science/tasks/mathematics  and/or
 
 Added.

Thanks.

  http://blends.alioth.debian.org/science/tasks/biology .
 
 H, we do have it in med-bio-dev.

A OK.  No need for adding to biology then.

 Currently science-biology depends
 from med-bio and med-bio-dev.  I admit that the plan to resolve such
 dependencies on the tasks pages is now h at least six years old
 (born in the good old days of Extremadura meetings and inspired by
 Frederic Lehobey) but was not implemented yet.  The good news is that
 there is some movement in this direction which is that Blends metadata
 will be moved into UDD to resolve #703402 and which turns the task into
 simply enhancing a SQL query compared to a way more complex parsing
 algorithm.  The other positive move is that there might be a GSoC
 project at horizont - at least one student replied to my project
 suggestion to enhance the tasks pages.

Yep, saw the GSoC announcement, very nice!

  http://blends.alioth.debian.org/science/tasks/linguistics
snip
  ( Likely python-timbl (https://github.com/proycon/python-timbl) should get 
  added
  to linguistics soonish.  Maarten van Gompel is gonna package it.  No ITP 
  filed
  yet, there however is https://bugs.launchpad.net/ubuntu/+bug/618884 .  It 
  won't
  enter wheezy; likely will get shipped with jessie.  No hurry here for the
  metapackages. )
 
 OK, for no hurry for the metapackages.  However, it is always a good
 idea to inject the packaging into Debian Science VCS.  Once the machine
 readable data are there we can list the project as prospective package
 by simply adding a Depends: packagename into the tasks file.  This
 helps others to notice / join.  If you have no idea what I'm talking
 about just look here[1].  So injecting your code into VCS and adding the
 package to the tasks files has two advantages:
 
   1. It will be made popular
   2. You will not forget to mention it once it is uploaded

 [1] http://debian-med.alioth.debian.org/tasks/bio#pkgvcs-debs

Yes, of course, that's the plan.  Just like e.g. the timbl package.  Alioth
user proycon-guest has already been granted commit access.  We'd like to use
SVN, not git. Rationale: all other related linguistics packages are in SVN, and
Ko van der Sloot, our other linguistics hacker, has no experience in using git
(and is not really interested in acquiring it either).  I am fine with that,
and so is Maarten proycon.

Bye,

Joost

-- 
Laziness:  (1) the mental alertness to avoid hard work.  (2) there
is no such thing. Everyone works hard at whatever they want to do.
http://mdcc.cx/The Thinking Man's Dictionary, Kevin Solway


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Re: ITP: python-timbl -- Python bindings for the Tilburg Memory Based Learner (Timbl)

[Joost van Baal-Ilić]

Hi,

Some background info: python-timbl (https://github.com/proycon/python-timbl)
will get maintained under the debian-science umbrella, using this groups
SVN-repo at Alioth (user proycon-guest).  I'll co-maintain the package.  See
also https://bugs.launchpad.net/ubuntu/+bug/618884 .

Bye,

Joost



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Re: Cannot commit to alioth anymore

[Joost van Baal-Ilić]

Try to ssh directly to svn.debian.org.  You might get a host-key changed
message.

Bye,

Joost

Op Tue  6 Sep 2011 om 01:20:34 +0200 schreef Yann Pouillon:
 Hi,
 
 I would like to commit a few changes to the nanoscale-physics-dev task.
 
 In the past, everything has always gone very smoothly using svn+ssh, but
 now I systematically get:
 
   svn: Network connection closed unexpectedly
 
 Other protocols (https, svn) fail as well.
 
 The URL I've been using all the time is the following:
 
   svn+ssh://svn.debian.org/svn/blends/projects/science/trunk/debian-science
 
 Did I miss something important?
 
 Best regards,
 
 Yann.
 
 -- 
 Free Software is good for you.



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