R SIG Debian - May 2009 - build dependencies was Re: [R] problem with rgl package

Dear R-SIG-Debian,
>
> a) You still haven't explained why you need to rebuild it when
> ? ? ? sudo apt-get install r-cran-rgl
> ? gets you a binary
I  do not want to answer for the OP, but for myself, two things:

1)  I maintain a personal library in my HOME folder - for a few
reasons - and one of the benefits is that I can  install/update R
packages without needing to run R as root.

2) the list of supported packages in Synaptic is long enough to be
*too long* to remember, but short enough that it doesn't have many of
the packages I regularly use.  Rather than try to keep track of CRAN
vs Synaptic, it is easier to just use CRAN and forget about it.

I have been interested in learning about building Debian packages
myself, but haven't had the time to investigate yet. In addition, my
understanding from earlier messages on the mailing list is that work
is already underway to significantly lengthen the Synaptic list...


 >
> b) Yes, as
> ? ? ? sudo apt-get build-dep r-cran-rgl
> ? would have found out for you.


Is there any way to include some form of this information on the
README page of the Ubuntu section on CRAN? Here's how it reads right
now, under "ADMINISTRATION AND MAINTENANCE OF R PACKAGES":

"Installing R packages not provided with Ubuntu first requires tools
to compile the packages from source. These tools are installed via the
R development package with

   sudo apt-get install r-base-dev"



The above is, of course, true, but not the whole story.  In
particular, for a supported R package like rgl there are additional
tools needed to build it, which are not in r-base-dev, but which can
be obtained with "sudo apt-get build-dep r-cran-rgl".  Perhaps there
are other (supported) packages that require tools which aren't in
r-base-dev.


Under  "ADMINISTRATION AND MAINTENANCE OF R PACKAGES", how about
something like:

"Installing R packages not provided with Ubuntu first requires tools
to compile the packages from source. *For the majority of R packages
these* tools may be installed via the R development package with

   sudo apt-get install r-base-dev

Please note, however, that some packages may require tools not
contained in r-base-dev, and the user must find and install these on
an individual basis.  But in the case that R package 'foo' is
supported (with an Ubuntu package r-cran-foo), then the following will
identify and install such dependencies:

  sudo apt-get build-dep r-cran-foo"


I am sure that there are other people who could say what I am trying
to say in a much better and more accurate way.  I would invite and
welcome improvements.  I could imagine a similar statement or
reference in SUPPORTED PACKAGES.


Some may rightly argue that those experienced with Ubuntu will already
know about "sudo apt-get build-dep" and it does not need to be posted
on CRAN Ubuntu README.  But I was introduced to Ubuntu by way of R,
and not the other way around.  For people like me, this would be
great.


>
> We do _a lot of work_ for R on Debian/Ubuntu. Use it, you even have a
> money-back guarantee. And ...

Yes... I myself appreciate very much all of the hard work by Dirk,
Doug, Vincent, and Michael, all.  Both off-list administration and
on-list troubleshooting.  Thank you.


Best,
Jay







***************************************************
G. Jay Kerns, Ph.D.
Associate Professor
Department of Mathematics & Statistics
Youngstown State University
Youngstown, OH 44555-0002 USA
Office: 1035 Cushwa Hall
Phone: (330) 941-3310 Office (voice mail)
-3302 Department
-3170 FAX
E-mail: gkerns at ysu.edu
http://www.cc.ysu.edu/~gjkerns/

Howdy,

On 7 May 2009 at 11:28, G. Jay Kerns wrote:
| Dear R-SIG-Debian,
| 
| >
| > a) You still haven't explained why you need to rebuild it when
| >       sudo apt-get install r-cran-rgl
| >   gets you a binary
| 
| I  do not want to answer for the OP, but for myself, two things:
| 
| 1)  I maintain a personal library in my HOME folder - for a few
| reasons - and one of the benefits is that I can  install/update R
| packages without needing to run R as root.

I do that by setting the group mode of /usr/local/lib/R/site-library to, say,
'staff' and 'group-write mode' (numeric 0775).  I also share
that
/usr/local/lib/R tree over NFS at work across a few machines.

As an aside, this point is orthogonal to the OP having problems compiling
something by hand that exists pre-compiled.

| 2) the list of supported packages in Synaptic is long enough to be
| *too long* to remember, but short enough that it doesn't have many of
| the packages I regularly use.  Rather than try to keep track of CRAN
| vs Synaptic, it is easier to just use CRAN and forget about it.

Synaptic is just one of many interfaces to the packaging system. At the end
of the day, both 20,000 Debian packages and 1,700 CRAN packages are hard to
search nomatter what you do.  

Debian has several front-end, a system called 'tags' and intelligent
searching.  I personally still mostly do 'apt-cache search foo' and some
grepping.  Also, my personal favourite is 'wajig' which calles out to
dpkg,
apt-get, aptitude, ... as needed and provides a single interface.

| I have been interested in learning about building Debian packages
| myself, but haven't had the time to investigate yet. In addition, my
| understanding from earlier messages on the mailing list is that work
| is already underway to significantly lengthen the Synaptic list...

Yes. But presumably via another external repository, most likely on CRAN, and
probably first for Debian before we get to Ubuntu.

|  >
| > b) Yes, as
| >       sudo apt-get build-dep r-cran-rgl
| >   would have found out for you.
| 
| 
| 
| Is there any way to include some form of this information on the
| README page of the Ubuntu section on CRAN? Here's how it reads right
| now, under "ADMINISTRATION AND MAINTENANCE OF R PACKAGES":
| 
| "Installing R packages not provided with Ubuntu first requires tools
| to compile the packages from source. These tools are installed via the
| R development package with
| 
|    sudo apt-get install r-base-dev"
| 
| 
| 
| The above is, of course, true, but not the whole story.  In
| particular, for a supported R package like rgl there are additional
| tools needed to build it, which are not in r-base-dev, but which can
| be obtained with "sudo apt-get build-dep r-cran-rgl".  Perhaps there
| are other (supported) packages that require tools which aren't in
| r-base-dev.

Good point!  Patches welcome. Vincent and Michael read this list too so maybe
that is something we can take off-list for some constructive work?

| Under  "ADMINISTRATION AND MAINTENANCE OF R PACKAGES", how about
something like:
| 
| "Installing R packages not provided with Ubuntu first requires tools
| to compile the packages from source. *For the majority of R packages
| these* tools may be installed via the R development package with
| 
|    sudo apt-get install r-base-dev
| 
| Please note, however, that some packages may require tools not
| contained in r-base-dev, and the user must find and install these on
| an individual basis.  But in the case that R package 'foo' is
| supported (with an Ubuntu package r-cran-foo), then the following will
| identify and install such dependencies:
| 
|   sudo apt-get build-dep r-cran-foo"

Not bad, but if 'apt-get install r-cran-foo' works, why do we need to
explain
how to re-compile it ?
 
| I am sure that there are other people who could say what I am trying
| to say in a much better and more accurate way.  I would invite and
| welcome improvements.  I could imagine a similar statement or
| reference in SUPPORTED PACKAGES.
| 
| 
| Some may rightly argue that those experienced with Ubuntu will already
| know about "sudo apt-get build-dep" and it does not need to be
posted
| on CRAN Ubuntu README.  But I was introduced to Ubuntu by way of R,
| and not the other way around.  For people like me, this would be
| great.

Generally speaking, there are too many little tips and tricks so there is
always scope to do better, learn more, teach more, ...
 
| >
| > We do _a lot of work_ for R on Debian/Ubuntu. Use it, you even have a
| > money-back guarantee. And ...
| 
| 
| Yes... I myself appreciate very much all of the hard work by Dirk,
| Doug, Vincent, and Michael, all.  Both off-list administration and
| on-list troubleshooting.  Thank you.

Always a pleasure, especially when we see that it actually helps other
people.

Dirk

| 
| 
| Best,
| Jay
| 
| 
| 
| 
| 
| 
| 
| ***************************************************
| G. Jay Kerns, Ph.D.
| Associate Professor
| Department of Mathematics & Statistics
| Youngstown State University
| Youngstown, OH 44555-0002 USA
| Office: 1035 Cushwa Hall
| Phone: (330) 941-3310 Office (voice mail)
| -3302 Department
| -3170 FAX
| E-mail: gkerns at ysu.edu
| http://www.cc.ysu.edu/~gjkerns/

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