R-repo

[Pierre-Yves Chibon]

Dear all,

To the great despair of spot, I have started to build CRAN and
Bioconductor :-)
This time, I am trying to make things cleaner and more accessible.

I just uploaded all the spec files on github:
https://github.com/pypingou/R-repo-spec
and the scripts on:
https://github.com/pypingou/R-repo-utility

The whole project is hosted at http://r-repo.org

At the moment everything is still in a early stage (for example, the
r-repo-release rpm is not even done yet), but if you configure the repo
by hand, you should be able to get RPMs.

At least this time, if work becomes overwhelming again, what has been
done will remain accessible :-)

I would prefer to not announce this officially just yet, but some
feedback be nice (thus this email). So if you feel like testing and are
facing problem, let me know!

Hope this helps,
Best regards,
Pierre

[Adam Huffman]

On Wed, Jan 4, 2012 at 8:43 AM, Pierre-Yves Chibon <pingou(a)pingoured.fr&gt; wrote:
>  Dear all,
>
>  To the great despair of spot, I have started to build CRAN and
>  Bioconductor :-)
>  This time, I am trying to make things cleaner and more accessible.
>
>  I just uploaded all the spec files on github:
>  https://github.com/pypingou/R-repo-spec
>  and the scripts on:
>  https://github.com/pypingou/R-repo-utility
>
>  The whole project is hosted at http://r-repo.org
>
>  At the moment everything is still in a early stage (for example, the
>  r-repo-release rpm is not even done yet), but if you configure the repo
>  by hand, you should be able to get RPMs.
>
>  At least this time, if work becomes overwhelming again, what has been
>  done will remain accessible :-)
>
>  I would prefer to not announce this officially just yet, but some
>  feedback be nice (thus this email). So if you feel like testing and are
>  facing problem, let me know!
>
>  Hope this helps,
>  Best regards,
>  Pierre
>  
Pierre,

Many thanks for this.  I've been working on some of the Bioinformatics
R packages off and on and it will be very helpful.  I'll send you any
useful changes I already have.

Cheers,
Adam

[José Abílio Matos]

On 01/04/2012 08:43 AM, Pierre-Yves Chibon wrote:
>  Dear all,
>
>  To the great despair of spot, I have started to build CRAN and
>  Bioconductor :-)
>  This time, I am trying to make things cleaner and more accessible.
>
>  I just uploaded all the spec files on github:
>  https://github.com/pypingou/R-repo-spec
>  and the scripts on:
>  https://github.com/pypingou/R-repo-utility
>
>  The whole project is hosted at http://r-repo.org
>
>  At the moment everything is still in a early stage (for example, the
>  r-repo-release rpm is not even done yet), but if you configure the repo
>  by hand, you should be able to get RPMs.
>
>  At least this time, if work becomes overwhelming again, what has been
>  done will remain accessible :-)
>
>  I would prefer to not announce this officially just yet, but some
>  feedback be nice (thus this email). So if you feel like testing and are
>  facing problem, let me know!
>
>  Hope this helps,
>  Best regards,
>  Pierre 
After almost two months going on what is the outcome of this project?

Back in September I wanted to package some R libraries and it took some
time to get all the packages due to the build requirement of each
package, I had to unravel the dependencies while deciding what was
necessary to bootstrap the process, and not even speaking about circular
references. Clearly a fun project... :-)

So this always makes a fun read. :-)

-- 
José Matos

[Pierre-Yves Chibon]

On Wed, 2012-02-29 at 19:21 +0000, José Matos wrote:
>  
>  After almost two months going on what is the outcome of this project? 
Well the structure is there and a number of rpms available.
I have started on the update mechanism but I have only got around the
first round.
The spec are on github and I have no problem giving the rights to commit
if people are interested (<hint>, <hint> ;-)).

>  Back in September I wanted to package some R libraries and it took
>  some time to get all the packages due to the build requirement of each
>  package, I had to unravel the dependencies while deciding what was
>  necessary to bootstrap the process, and not even speaking about
>  circular references. Clearly a fun project... :-)  
<irony>hm R ? circular dependencies? I think I've heard about that once
or twice </irony>

Pierre

[José Abílio Matos]

On 2012-02-29 21:21, Pierre-Yves Chibon wrote:
>  On Wed, 2012-02-29 at 19:21 +0000, José Matos wrote:
> > After almost two months going on what is the outcome of this project?
>  Well the structure is there and a number of rpms available.
>  I have started on the update mechanism but I have only got around the
>  first round.
>  The spec are on github and I have no problem giving the rights to commit
>  if people are interested (<hint>, <hint> ;-)). 
After June 11th sure, until there I have 18h of classes per week for
undergrads, master and phd students and with a seven months old lovely
daughter there is not much of free time, oh and surely the scouts
work... :-)

My last surge for build R packages for Fedora is due to the academic work.
I have several students doing their master thesis using stochastic
differential equations in several domains and for that I suggested them
to use R packages since R is a language they learn in the course.

One of the packages that is appropriate is the Sim.DiffProc package. For
that package the chain dependency is relatively simple.

So if you do not mind I have several questions regarding this issue.

1) Why is r-repo.org not available for Fedora? Lack of time is a fair
answer. :-)

2) I noticed that you have R-xlsxjars packaged in r-repo, from a quick
glance it looks like it just packages a set of jar files. I am clueless
when it comes to java but are not those some kind of binary files that
could be replaced using dependencies for system libraries? I am aware
that jars can have different purposes but I am asking anyway.


> > Back in September I wanted to package some R libraries and it
> took
> > some time to get all the packages due to the build requirement of each
> > package, I had to unravel the dependencies while deciding what was
> > necessary to bootstrap the process, and not even speaking about
> > circular references. Clearly a fun project... :-) 
>  <irony>hm R ? circular dependencies? I think I've heard about that once
>  or twice </irony> 
Do you have any idea of how R install.packages deals with these cases?

While searching for further information I noticed that the corresponding
effort on the debian side is cran2deb
http://r-forge.r-project.org/scm/?group_id=247

and the active repository is available at http://debian-r.debian.net/

> From the available discussion and from my previous work I know that
there are several issues to be tracked. One of them is the package
license and the other are the external (system libraries) dependencies.
Is this information stored in any central place (database)?

>  Pierre 
Thank for all your hard work and regards,

-- 
José Matos

[Pierre-Yves Chibon]

On Sat, 2012-05-12 at 13:45 +0100, José Matos wrote:
>  On 2012-02-29 21:21, Pierre-Yves Chibon wrote:
>  > On Wed, 2012-02-29 at 19:21 +0000, José Matos wrote:
>  >> After almost two months going on what is the outcome of this project?
>  > Well the structure is there and a number of rpms available.
>  > I have started on the update mechanism but I have only got around the
>  > first round.
>  > The spec are on github and I have no problem giving the rights to commit
>  > if people are interested (<hint>, <hint> ;-)).
>  
>  After June 11th sure, until there I have 18h of classes per week for
>  undergrads, master and phd students and with a seven months old lovely
>  daughter there is not much of free time, oh and surely the scouts
>  work... :-)
>  
>  My last surge for build R packages for Fedora is due to the academic work.
>  I have several students doing their master thesis using stochastic
>  differential equations in several domains and for that I suggested them
>  to use R packages since R is a language they learn in the course.
>  
>  One of the packages that is appropriate is the Sim.DiffProc package. For
>  that package the chain dependency is relatively simple.
>  
>  So if you do not mind I have several questions regarding this issue.
>  
>  1) Why is r-repo.org not available for Fedora? Lack of time is a fair
>  answer. :-) 
Time is definitively part of the answer the other part being the
challenge of rebuilding the repo once in a while when necessary.

>  2) I noticed that you have R-xlsxjars packaged in r-repo, from a
> quick
>  glance it looks like it just packages a set of jar files. I am clueless
>  when it comes to java but are not those some kind of binary files that
>  could be replaced using dependencies for system libraries? I am aware
>  that jars can have different purposes but I am asking anyway. 
R can be coupled with java as it can be with C/C++/fortran &so on, I
*assume* that this is what was done in this package (again, *assumed*).
If it is not the case, then for sure it should not be this way and it
should rely on system libraries.

R-repo is/was aiming at automatically generated RPM which mean that a
number of them are not 100% valid. At least it gives us a basis for
further improvement.

I have to say that from my side time is truly limiting and the situation
won't change (it will even get worse) with the fact that I am starting
the last year of my PhD but at least this time everything is publicly
available on github if there are people interested in the
maintenance/development of the project.

>  >> Back in September I wanted to package some R libraries and
> it took
>  >> some time to get all the packages due to the build requirement of each
>  >> package, I had to unravel the dependencies while deciding what was
>  >> necessary to bootstrap the process, and not even speaking about
>  >> circular references. Clearly a fun project... :-) 
>  > <irony>hm R ? circular dependencies? I think I've heard about that once
>  > or twice </irony>
>  
>  Do you have any idea of how R install.packages deals with these cases? 
To be honest, I do not know, but I am not sure install.packages runs the
tests and thus it likely doesn't run into the circular dependency
problem which are most of the time of the type: A requires B which
suggests A (or similar).

>  While searching for further information I noticed that the
> corresponding
>  effort on the debian side is cran2deb
>  http://r-forge.r-project.org/scm/?group_id=247
>  
>  and the active repository is available at http://debian-r.debian.net/
>  
>  From the available discussion and from my previous work I know that
>  there are several issues to be tracked. One of them is the package
>  license and the other are the external (system libraries) dependencies.
>  Is this information stored in any central place (database)? 
There are no form of license check done atm in R-repo and it doesn't
rely on a central database.
The dependency tree is built by parsing the PACKAGES files from the
different repository. 
The R-repo-utility [1] contains the script doing the work (building the
tree, building the RPMs, checking for updates and so on).


Let me know if I can be of any help.

Regards,
Pierre

[1] https://github.com/pypingou/R-repo-utility