R SIG Debian - Feb 2015 - Suggestions to improve the info page of /bin/linux/debian

After Johannes set up the CRAN repository for Jessie, I had quite some 
trouble figuring out what any user should do to have a running and 
up-to-date R in Debian (particularly Testing). Part of the problem is, I 
think, the overwhelming documentation on the page "DEBIAN PACKAGES OF R 
SOFTWARE" which is provided on CRAN at /bin/linux/debian. Some information 
is also lacking in places.

So here are a few suggestions to try to arrange this page. The main one is 
actually a reorganization of the whole page, which should make it easier 
from a user perspective. Note that I think all information I added is 
correct, but it might not be entirely accurate.

I think the page in itself would benefit largely from the inclusion of a 
table of contents (with links to sections). With the page reorganized, that 
would follow this:

INSTALLATION
    ADMINISTRATION AND MAINTENANCE
    PATHWAYS TO R PACKAGES
BACKPORTS ON CRAN
    SUPPORTED PACKAGES
    DEBIAN WHEEZY (STABLE)
    DEBIAN JESSIE (TESTING)
    DEBIAN SQUEEZE (OLD STABLE)
    DEBIAN SID (UNSTABLE)
    SECURE APT
    SUPPORTED PLATFORMS
REPORTING PROBLEMS
BACKPORTING FOR DEBIAN
ACKNOWLEDGEMENT

I added at the bottom of this message a few modifications of some of these 
(sub-)sections. The vast majority of the information is already there, so 
these are really minor changes, except for the Jessie sub-section.

Hope this helps,
Mathieu.


=========================================================================
INSTALLATION

With an appropriate entry in /etc/apt/sources.list *(see below according to 
the branch of Debian used)*, the newest R release *including recommended 
packages* can be installed using a command sequence like


SUPPORTED PACKAGES

[Remove:]   r-cran-rmatrix


DEBIAN JESSIE (TESTING)

As of end of January 2015, there is a new repository containing binaries 
for Jessie (current testing). This repository hosts all supported packages 
presented above, and is updated upon new R releases.

To use R supported packages on Debian Jessie, simply add something like

    deb http://<favorite-cran-mirror>/bin/linux/debian jessie-cran3/

to the file /etc/apt/sources.list on your computer. You need to substitute 
<favorite-cran-mirror> by one of the mirror URLs listed in

    http://cran.r-project.org/mirrors.html

Alternatively, it is possible to use APT-pining to install only R-related 
packages from SID using Debian official repositories (/!\ Warning: should 
be reserved to advanced users already familiar with pining their Debian 
system). Simply add the supported packages (and other r-cran-* of interest) 
in /etc/apt/preferences with a priority greater or equal than the priority 
of regular testing packages:

    Package: r-base r-base-core r-base-dev r-recommended r-cran-boot 
r-cran-cluster r-cran-class r-cran-codetools r-cran-foreign 
r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv 
r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival littler 
r-cran-rodbc python-rpy python-rpy2 rkward r-cran-jags r-cran-coda
    Pin: release o=Debian,a=unstable,l=Debian
    Pin-Priority: 900


DEBIAN SID (UNSTABLE)

The latest stable versions of R and R packages are readily available in 
official Debian SID repositories.



-- 

~$ whoami
Mathieu Basille
http://ase-research.org/basille

~$ locate --details
University of Florida \\
Fort Lauderdale Research and Education Center
(+1) 954-577-6314

~$ fortune
? Le tout est de tout dire, et je manque de mots
Et je manque de temps, et je manque d'audace. ?
  -- Paul ?luard

Hi Mathieu,

thanks for your input. It reminds me how I got involved in the Debian 
backports, as I thought the Debian README on CRAN needed an update...

At the moment I do not have the time to reorganize the README, so if you would 
like to go ahead and implement your changes into a README.html, I wouldn't 
mind. Otherwise I am willing to pick up your suggestions, but it will take me 
some time to get around to do it.
>From my work on R package vignettes I know that pandoc is able to generate 
single html documents with linked TOC from markdown, which is more flexible 
than the text2html stuff I am using at the moment (as well as Michael does). 
But maybe you or someone else on this list knows another convenient way? Or it 
could be written in HTML using div tags and a hand-crafted css...

Kind regards,

Johannes

Am Donnerstag, 26. Februar 2015, 15:49:58 schrieb Mathieu
Basille:
> After Johannes set up the CRAN repository for Jessie, I had quite some
> trouble figuring out what any user should do to have a running and
> up-to-date R in Debian (particularly Testing). Part of the problem is, I
> think, the overwhelming documentation on the page "DEBIAN PACKAGES OF
R
> SOFTWARE" which is provided on CRAN at /bin/linux/debian. Some
information
> is also lacking in places.
> 
> So here are a few suggestions to try to arrange this page. The main one is
> actually a reorganization of the whole page, which should make it easier
> from a user perspective. Note that I think all information I added is
> correct, but it might not be entirely accurate.
> 
> I think the page in itself would benefit largely from the inclusion of a
> table of contents (with links to sections). With the page reorganized, that
> would follow this:
> 
> INSTALLATION
>     ADMINISTRATION AND MAINTENANCE
>     PATHWAYS TO R PACKAGES
> BACKPORTS ON CRAN
>     SUPPORTED PACKAGES
>     DEBIAN WHEEZY (STABLE)
>     DEBIAN JESSIE (TESTING)
>     DEBIAN SQUEEZE (OLD STABLE)
>     DEBIAN SID (UNSTABLE)
>     SECURE APT
>     SUPPORTED PLATFORMS
> REPORTING PROBLEMS
> BACKPORTING FOR DEBIAN
> ACKNOWLEDGEMENT
> 
> I added at the bottom of this message a few modifications of some of these
> (sub-)sections. The vast majority of the information is already there, so
> these are really minor changes, except for the Jessie sub-section.
> 
> Hope this helps,
> Mathieu.
> 
> 
>
=========================================================================>
> INSTALLATION
> 
> With an appropriate entry in /etc/apt/sources.list *(see below according to
> the branch of Debian used)*, the newest R release *including recommended
> packages* can be installed using a command sequence like
> 
> 
> SUPPORTED PACKAGES
> 
> [Remove:]   r-cran-rmatrix
> 
> 
> DEBIAN JESSIE (TESTING)
> 
> As of end of January 2015, there is a new repository containing binaries
> for Jessie (current testing). This repository hosts all supported packages
> presented above, and is updated upon new R releases.
> 
> To use R supported packages on Debian Jessie, simply add something like
> 
>     deb http://<favorite-cran-mirror>/bin/linux/debian jessie-cran3/
> 
> to the file /etc/apt/sources.list on your computer. You need to substitute
> <favorite-cran-mirror> by one of the mirror URLs listed in
> 
>     http://cran.r-project.org/mirrors.html
> 
> Alternatively, it is possible to use APT-pining to install only R-related
> packages from SID using Debian official repositories (/!\ Warning: should
> be reserved to advanced users already familiar with pining their Debian
> system). Simply add the supported packages (and other r-cran-* of interest)
> in /etc/apt/preferences with a priority greater or equal than the priority
> of regular testing packages:
> 
>     Package: r-base r-base-core r-base-dev r-recommended r-cran-boot
> r-cran-cluster r-cran-class r-cran-codetools r-cran-foreign
> r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
> r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival littler
> r-cran-rodbc python-rpy python-rpy2 rkward r-cran-jags r-cran-coda
>     Pin: release o=Debian,a=unstable,l=Debian
>     Pin-Priority: 900
> 
> 
> DEBIAN SID (UNSTABLE)
> 
> The latest stable versions of R and R packages are readily available in
> official Debian SID repositories.
-- 
PD Dr. Johannes Ranke
Kronacher Str. 8
79639 Grenzach-Wyhlen

Hi Johannes,

I didn't know what would be the best approach to modify the page?how it was 
generated, is there a central place, etc.?which is why I posted on 
r-sig-debian in the first place. Anyway, although I'm more or less familiar 
with markdown and pandoc, it was easier for me to edit directly README.html 
as it was on CRAN. Please find attached a revision with the modifications I 
suggested earlier. Again, I tried to be correct to the best of my 
knowledge, but I may not be entirely accurate.

I simply edited (and formated the file) using Emacs, and manually added the 
TOC and other suggested modifications (notably reorganization). I think 
there is still room for improvement, but this should get things started. I 
cleaned the layout, but left most of the actual code and text unchanged.

I think the whole page would also benefit from a CSS, e.g. for titles 
(instead of caps), but left it without it.

Best,
Mathieu.


Le 02/03/2015 04:09, Johannes Ranke a ?crit :
> Hi Mathieu,
>
> thanks for your input. It reminds me how I got involved in the Debian
> backports, as I thought the Debian README on CRAN needed an update...
>
> At the moment I do not have the time to reorganize the README, so if you
would
> like to go ahead and implement your changes into a README.html, I
wouldn't
> mind. Otherwise I am willing to pick up your suggestions, but it will take
me
> some time to get around to do it.
>
>  From my work on R package vignettes I know that pandoc is able to generate
> single html documents with linked TOC from markdown, which is more flexible
> than the text2html stuff I am using at the moment (as well as Michael
does).
> But maybe you or someone else on this list knows another convenient way? Or
it
> could be written in HTML using div tags and a hand-crafted css...
>
> Kind regards,
>
> Johannes
>
> Am Donnerstag, 26. Februar 2015, 15:49:58 schrieb Mathieu Basille:
>> After Johannes set up the CRAN repository for Jessie, I had quite some
>> trouble figuring out what any user should do to have a running and
>> up-to-date R in Debian (particularly Testing). Part of the problem is,
I
>> think, the overwhelming documentation on the page "DEBIAN PACKAGES
OF R
>> SOFTWARE" which is provided on CRAN at /bin/linux/debian. Some
information
>> is also lacking in places.
>>
>> So here are a few suggestions to try to arrange this page. The main one
is
>> actually a reorganization of the whole page, which should make it
easier
>> from a user perspective. Note that I think all information I added is
>> correct, but it might not be entirely accurate.
>>
>> I think the page in itself would benefit largely from the inclusion of
a
>> table of contents (with links to sections). With the page reorganized,
that
>> would follow this:
>>
>> INSTALLATION
>>      ADMINISTRATION AND MAINTENANCE
>>      PATHWAYS TO R PACKAGES
>> BACKPORTS ON CRAN
>>      SUPPORTED PACKAGES
>>      DEBIAN WHEEZY (STABLE)
>>      DEBIAN JESSIE (TESTING)
>>      DEBIAN SQUEEZE (OLD STABLE)
>>      DEBIAN SID (UNSTABLE)
>>      SECURE APT
>>      SUPPORTED PLATFORMS
>> REPORTING PROBLEMS
>> BACKPORTING FOR DEBIAN
>> ACKNOWLEDGEMENT
>>
>> I added at the bottom of this message a few modifications of some of
these
>> (sub-)sections. The vast majority of the information is already there,
so
>> these are really minor changes, except for the Jessie sub-section.
>>
>> Hope this helps,
>> Mathieu.
>>
>>
>>
=========================================================================>>
>> INSTALLATION
>>
>> With an appropriate entry in /etc/apt/sources.list *(see below
according to
>> the branch of Debian used)*, the newest R release *including
recommended
>> packages* can be installed using a command sequence like
>>
>>
>> SUPPORTED PACKAGES
>>
>> [Remove:]   r-cran-rmatrix
>>
>>
>> DEBIAN JESSIE (TESTING)
>>
>> As of end of January 2015, there is a new repository containing
binaries
>> for Jessie (current testing). This repository hosts all supported
packages
>> presented above, and is updated upon new R releases.
>>
>> To use R supported packages on Debian Jessie, simply add something like
>>
>>      deb http://<favorite-cran-mirror>/bin/linux/debian
jessie-cran3/
>>
>> to the file /etc/apt/sources.list on your computer. You need to
substitute
>> <favorite-cran-mirror> by one of the mirror URLs listed in
>>
>>      http://cran.r-project.org/mirrors.html
>>
>> Alternatively, it is possible to use APT-pining to install only
R-related
>> packages from SID using Debian official repositories (/!\ Warning:
should
>> be reserved to advanced users already familiar with pining their Debian
>> system). Simply add the supported packages (and other r-cran-* of
interest)
>> in /etc/apt/preferences with a priority greater or equal than the
priority
>> of regular testing packages:
>>
>>      Package: r-base r-base-core r-base-dev r-recommended r-cran-boot
>> r-cran-cluster r-cran-class r-cran-codetools r-cran-foreign
>> r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv
>> r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival
littler
>> r-cran-rodbc python-rpy python-rpy2 rkward r-cran-jags r-cran-coda
>>      Pin: release o=Debian,a=unstable,l=Debian
>>      Pin-Priority: 900
>>
>>
>> DEBIAN SID (UNSTABLE)
>>
>> The latest stable versions of R and R packages are readily available in
>> official Debian SID repositories.
-- 

~$ whoami
Mathieu Basille
http://ase-research.org/basille

~$ locate --details
University of Florida \\
Fort Lauderdale Research and Education Center
(+1) 954-577-6314

~$ fortune
? Le tout est de tout dire, et je manque de mots
Et je manque de temps, et je manque d'audace. ?
  -- Paul ?luard