R SIG Debian - Jul 2009 - [ANNOUNCEMENT] cran2deb: 1700+ new Debian / R packages

Announcing cran2deb: 1700+ Debian packages from almost all of CRAN
------------------------------------------------------------------

Last Friday's presentation at UseR! 2009 was the first really public mention
of 'cran2deb'. It provides Debian packages of all of CRAN. It started as
Charles' project from last year's Google Summer of Code, was further
extended
by us over the last year.

We currently build for the testing distribution and the i386 and amd64
architectures. This is now publically useable and we welcome wider testing
by Debian users. We hope to extend this to Ubuntu during the summer or fall.

I include what I blogged earlier (which you may have seen via Planet Debian
and/or Planet R).  This also contains the /etc/apt/sources.list entries:


   cran2deb: Would you like 1700+ new Debian / R packages ?

   As I mentioned in my [8]quick write-up of UseR 2009, one of my talks
   was about cran2deb: a system to turn (essentially) all [1]CRAN packages
   into directly apt-get-able binary packages.

   This is essentially a '2.0' version of earlier work with Steffen
   Moeller and David Vernazobres which we had presented in 2007. Then, the
   approach was top-down and monolithic which started to show its limits.
   This time, the idea was to borrow the successful bottom-up approach of
   my [2]CRANberries feed.

   The bulk of the work was done by Charles Blundell as part of his Google
   Summer of Code 2008 project which I had suggested and mentored. After
   that project had concluded, we both felt we should continue with it and
   bring it to 'production'. The CRAN hosts provided us with a (virtual
   Xen) machine to build on, and we are now ready to more publically
   announce the availability of the repositories for i386 and amd64:

      deb http://debian.cran.r-project.org/cran2deb/debian-i386 testing/

   and
  
      deb http://debian.cran.r-project.org/cran2deb/debian-amd64 testing/

   A few more details are provided in [3]our presentation slides. We look
   forward to hearing from folks using; the r-sig-debian list may be a
   good venue for this.


   References
   1. http://cran.r-project.org/
   2. http://dirk.eddelbuettel.com/cranberries
   3. http://dirk.eddelbuettel.com/papers/useR2009cran2deb.pdf


Please direct questions to r-sig-debian (which has subscriber-only posts) or
debian-science. 

Regards,  Dirk and Charles
 
-- 
Three out of two people have difficulties with fractions.

Hi Dirk and Charles,

What a _beautiful_ project! This a giant step forward.

Thanks!

Piet

On Mon, Jul 13, 2009 at 03:44:21PM -0500, Dirk Eddelbuettel
wrote:
> 
> Announcing cran2deb: 1700+ Debian packages from almost all of CRAN
> ------------------------------------------------------------------
> 
> Last Friday's presentation at UseR! 2009 was the first really public
mention
> of 'cran2deb'. It provides Debian packages of all of CRAN. It
started as
> Charles' project from last year's Google Summer of Code, was
further extended
> by us over the last year.
> 
> We currently build for the testing distribution and the i386 and amd64
> architectures. This is now publically useable and we welcome wider testing
> by Debian users. We hope to extend this to Ubuntu during the summer or
fall.
> 
> I include what I blogged earlier (which you may have seen via Planet Debian
> and/or Planet R).  This also contains the /etc/apt/sources.list entries:
> 
> 
>    cran2deb: Would you like 1700+ new Debian / R packages ?
> 
>    As I mentioned in my [8]quick write-up of UseR 2009, one of my talks
>    was about cran2deb: a system to turn (essentially) all [1]CRAN packages
>    into directly apt-get-able binary packages.
> 
>    This is essentially a '2.0' version of earlier work with Steffen
>    Moeller and David Vernazobres which we had presented in 2007. Then, the
>    approach was top-down and monolithic which started to show its limits.
>    This time, the idea was to borrow the successful bottom-up approach of
>    my [2]CRANberries feed.
> 
>    The bulk of the work was done by Charles Blundell as part of his Google
>    Summer of Code 2008 project which I had suggested and mentored. After
>    that project had concluded, we both felt we should continue with it and
>    bring it to 'production'. The CRAN hosts provided us with a
(virtual
>    Xen) machine to build on, and we are now ready to more publically
>    announce the availability of the repositories for i386 and amd64:
> 
>       deb http://debian.cran.r-project.org/cran2deb/debian-i386 testing/
> 
>    and
>   
>       deb http://debian.cran.r-project.org/cran2deb/debian-amd64 testing/
> 
>    A few more details are provided in [3]our presentation slides. We look
>    forward to hearing from folks using; the r-sig-debian list may be a
>    good venue for this.
> 
> 
>    References
>    1. http://cran.r-project.org/
>    2. http://dirk.eddelbuettel.com/cranberries
>    3. http://dirk.eddelbuettel.com/papers/useR2009cran2deb.pdf
> 
> 
> Please direct questions to r-sig-debian (which has subscriber-only posts)
or
> debian-science. 
> 
> Regards,  Dirk and Charles
>  
> -- 
> Three out of two people have difficulties with fractions.
> 
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian

Dirk,

Looks like a lot of work has created a very useful set of packages.
Two questions.

1.  Are there any negatives going from an install.packages("foo")
approach using R then switching to an apt-get install r-cran-foo
method of installing packages?  If I install a deb package on top of
an R installed package, will there be issues?

2.  What will it take to do this for Ubuntu?  Are we going to need a
(virtual) machine for each release or can this be done under chroot
jails on one server?

Excellent work,
Michael

Anna,

On 14 July 2009 at 15:20, Anne Ghisla wrote:
| Hi Dirk, Charles, 
| 
| great work, indeed! Centralisation of packages will surely do a world of
| good.

Thanks!
 
| I just added the line on sources.list, but running aptitude upgrade, it
| asks for gpg key. Where can I obtain it?

I use apt-get directly and it just ignores it / shows a warning. 

We do have a key, we just don't have any webpages yet to show / provide
it. "Soon".  In the meantime, please run 'sudo apt-get update'
etc by hand.

Dirk
 

-- 
Three out of two people have difficulties with fractions.

On 14 July 2009 at 20:24, Markus J?ntti wrote:
| I'd like to second this. While R's install.packages() mechanism is
very good,
| nothing in my experience beats the Debian way of installing packages. Many 
| thanks to Charles and Dirk for providing this service to Debian users.

Thanks!

I also realized after the useR presentation that we didn't really stress the
point that well in the slides: installing using the tools of the operating
system is indeed much more powerful and provides much finer control than the
install.packages() approach.

| I will certainly try to provide feedback once I get behind a decent internet 
| connection and can install package en-masse (rather than from beind my current
| the tethered iPhone provided GPRS connection that I am using to send this
message).

It should become much more fun come next Monday when the masters of CRAN are
back from vacation and we get back to the usual daily flow of packages.  Once
CRAN gets back to daily updates, we should get daily updates for Debian CRAN
Debian packages as well.

Dirk

| Thanks,
| 
| Markus
| 
| Piet Plomp wrote:
| > Hi Dirk and Charles,
| > 
| > What a _beautiful_ project! This a giant step forward.
| > 
| > Thanks!
| > 
| > Piet
| > 
| > On Mon, Jul 13, 2009 at 03:44:21PM -0500, Dirk Eddelbuettel wrote:
| >> Announcing cran2deb: 1700+ Debian packages from almost all of CRAN
| >> ------------------------------------------------------------------
| >>
| >> Last Friday's presentation at UseR! 2009 was the first really
public mention
| >> of 'cran2deb'. It provides Debian packages of all of CRAN. It
started as
| >> Charles' project from last year's Google Summer of Code, was
further extended
| >> by us over the last year.
| >>
| >> We currently build for the testing distribution and the i386 and
amd64
| >> architectures. This is now publically useable and we welcome wider
testing
| >> by Debian users. We hope to extend this to Ubuntu during the summer
or fall.
| >>
| >> I include what I blogged earlier (which you may have seen via Planet
Debian
| >> and/or Planet R).  This also contains the /etc/apt/sources.list
entries:
| >>
| >>
| >>    cran2deb: Would you like 1700+ new Debian / R packages ?
| >>
| >>    As I mentioned in my [8]quick write-up of UseR 2009, one of my
talks
| >>    was about cran2deb: a system to turn (essentially) all [1]CRAN
packages
| >>    into directly apt-get-able binary packages.
| >>
| >>    This is essentially a '2.0' version of earlier work with
Steffen
| >>    Moeller and David Vernazobres which we had presented in 2007.
Then, the
| >>    approach was top-down and monolithic which started to show its
limits.
| >>    This time, the idea was to borrow the successful bottom-up
approach of
| >>    my [2]CRANberries feed.
| >>
| >>    The bulk of the work was done by Charles Blundell as part of his
Google
| >>    Summer of Code 2008 project which I had suggested and mentored.
After
| >>    that project had concluded, we both felt we should continue with
it and
| >>    bring it to 'production'. The CRAN hosts provided us with
a (virtual
| >>    Xen) machine to build on, and we are now ready to more publically
| >>    announce the availability of the repositories for i386 and amd64:
| >>
| >>       deb http://debian.cran.r-project.org/cran2deb/debian-i386
testing/
| >>
| >>    and
| >>   
| >>       deb http://debian.cran.r-project.org/cran2deb/debian-amd64
testing/
| >>
| >>    A few more details are provided in [3]our presentation slides. We
look
| >>    forward to hearing from folks using; the r-sig-debian list may be
a
| >>    good venue for this.
| >>
| >>
| >>    References
| >>    1. http://cran.r-project.org/
| >>    2. http://dirk.eddelbuettel.com/cranberries
| >>    3. http://dirk.eddelbuettel.com/papers/useR2009cran2deb.pdf
| >>
| >>
| >> Please direct questions to r-sig-debian (which has subscriber-only
posts) or
| >> debian-science. 
| >>
| >> Regards,  Dirk and Charles
| >>  
| >> -- 
| >> Three out of two people have difficulties with fractions.
| >>
| >> _______________________________________________
| >> R-SIG-Debian mailing list
| >> R-SIG-Debian at r-project.org
| >> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| > 
| > _______________________________________________
| > R-SIG-Debian mailing list
| > R-SIG-Debian at r-project.org
| > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| > 
| 
| 
| -- 
| Markus Jantti
| Professor of Economics
| Swedish Institute for Social Research
| Stockholm University
| 

-- 
Three out of two people have difficulties with fractions.

Hi Michael,

On 14 July 2009 at 18:44, charles blundell wrote:
| 2009/7/13 Michael Rutter <mar36 at psu.edu>
| > 1.  Are there any negatives going from an
install.packages("foo")
| > approach using R then switching to an apt-get install r-cran-foo
| > method of installing packages?  If I install a deb package on top of
| > an R installed package, will there be issues?
| 
| This should be the same as installing the package twice via R CMD
| INSTALL; I don't expect any issues but I cannot guarantee that I have
| not forgotten something.

Right. R_LIBS aka what you see via .libPaths() in R simply makes it possible
for those in /usr/local/lib/R/site-library [installed via install.packages()]  
to shadow those in /usr/lib/R/site-library. I can't remember if R is now
smart enough to pick the highest version; it may.  At some point in the past
the 'first one found' seemed to win.  So in sum:  no harm, other than
maybe
missing the newest.  We insured that different locations are used which the
man years of co-existence with r-cran-* packages in Debian possible. We
simply extend this now.

Longer term, some real work may need to go to make install.packages() aware
of the OS's package management system. That better work well though...

| > 2.  What will it take to do this for Ubuntu?  Are we going to need a
| > (virtual) machine for each release or can this be done under chroot
| > jails on one server?
| 
| I think, though have never got very far, that differences in package
| naming will be the main technical problem with supporting Ubuntu in a
| similar fashion, assuming re-use of the excellent Debian tools
| (pbuilder, mini-dinstall, etc) with a different set of base packages.
| 
| Each release (i.e., debian i386 testing) requires a chroot
| environment: it could all be done on one machine. We simply use
| pbuilder. Maybe you would not want to do this for too many releases
| (bandwidth, disk space, cpu time).

More details to follow but I may have access to some institutional support
for this. No details yet though.

Cheers, Dirk

-- 
Three out of two people have difficulties with fractions.

Le mardi 14 juillet 2009 ? 14:09 -0500, Dirk Eddelbuettel a ?crit :

[ Snip... ]
> | > 2.  What will it take to do this for Ubuntu?  Are we going to need a
> | > (virtual) machine for each release or can this be done under chroot
> | > jails on one server?
> | 
> | I think, though have never got very far, that differences in package
> | naming will be the main technical problem with supporting Ubuntu in a
> | similar fashion, assuming re-use of the excellent Debian tools
> | (pbuilder, mini-dinstall, etc) with a different set of base packages.
> | 
> | Each release (i.e., debian i386 testing) requires a chroot
> | environment: it could all be done on one machine. We simply use
> | pbuilder. Maybe you would not want to do this for too many releases
> | (bandwidth, disk space, cpu time).
> 
> More details to follow but I may have access to some institutional support
> for this. No details yet though.
Any news on this Ubuntu front ? This announcement *has* seriously
whetted my appetite and almost made me reconsider my decision, a few
years ago, to drop Debian (way too...) unstable in favor of Ubuntu for
everyday work...

					Emmanuel Charpentier

On 19 August 2009 at 11:18, Emmanuel Charpentier wrote:
| Le mardi 14 juillet 2009 ? 14:09 -0500, Dirk Eddelbuettel a ?crit :
| 
| [ Snip... ]
| 
| > | > 2.  What will it take to do this for Ubuntu?  Are we going to need
a
| > | > (virtual) machine for each release or can this be done under
chroot
| > | > jails on one server?
| > | 
| > | I think, though have never got very far, that differences in package
| > | naming will be the main technical problem with supporting Ubuntu in a
| > | similar fashion, assuming re-use of the excellent Debian tools
| > | (pbuilder, mini-dinstall, etc) with a different set of base packages.
| > | 
| > | Each release (i.e., debian i386 testing) requires a chroot
| > | environment: it could all be done on one machine. We simply use
| > | pbuilder. Maybe you would not want to do this for too many releases
| > | (bandwidth, disk space, cpu time).
| > 
| > More details to follow but I may have access to some institutional
support
| > for this. No details yet though.
| 
| Any news on this Ubuntu front ? This announcement *has* seriously

No, sorry. No news.

Dirk

| whetted my appetite and almost made me reconsider my decision, a few
| years ago, to drop Debian (way too...) unstable in favor of Ubuntu for
| everyday work...
| 
| 					Emmanuel Charpentier
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
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