R SIG Debian - Sep 2010 - Howto compile chemometrics package from source

Dear friends,

I'm confused about how to install packages from source.

I just updated R in Lenny from http://cran.fiocruz.br/bin/linux/debian/

I included in sources.list:

deb http://cran.fiocruz.br/bin/linux/debian lenny-cran/
deb-src  http://cran.fiocruz.br/bin/linux/debian lenny-cran/

Then:
apt-get update
apt-get install r-base r-base-dev

Then I downloaded the package chemometrics_0.8.tar.gz  from
http://cran.r-project.org/src/contrib/chemometrics_0.8.tar.gz

After untar I copied the dir chemometrics to /usr/lib/R/library and 
tried install.package(chemometrics) from R prompt (as root):

install.packages(chemometrics)
Erro em install.packages(chemometrics) : 
  objeto 'chemometrics' n?o encontrado

Could anyone give any help?

Thanks in advance,
Jose

On Mon, Sep 27, 2010 at 2:30 PM, Jose Brasil <c2o.pro.br at gmail.com>
wrote:
> Dear friends,
>
> I'm confused about how to install packages from source.
>
> I just updated R in Lenny from http://cran.fiocruz.br/bin/linux/debian/
>
> I included in sources.list:
>
> deb http://cran.fiocruz.br/bin/linux/debian lenny-cran/
> deb-src ?http://cran.fiocruz.br/bin/linux/debian lenny-cran/
>
> Then:
> apt-get update
> apt-get install r-base r-base-dev
>
> Then I downloaded the package chemometrics_0.8.tar.gz ?from
> http://cran.r-project.org/src/contrib/chemometrics_0.8.tar.gz
>
> After untar I copied the dir chemometrics to /usr/lib/R/library and
> tried install.package(chemometrics) from R prompt (as root):
Don't copy the package to /usr/lib/R/library.  In fact, you don't even
need to untar it.  Copy it to a convenient location, say /tmp then cd
to that directory and run

R CMD INSTALL chemometrics_0.8.tar.gz
> install.packages(chemometrics)
> Erro em install.packages(chemometrics) :
> ?objeto 'chemometrics' n?o encontrado
>
> Could anyone give any help?
>
> Thanks in advance,
> Jose
>
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>

Dear Jose Brasil
D. Bates already gave you a response on how to install from sources; however, as
chemometrics depends (at least on som, mvtnorm, mclust, pls, robustbase, e1071,
pcaPP, pls, lars) on other packages, you should have them already installed,
either
 binary or 
from sources before trying to install chemometrics (else, "R CMD
INSTALL" will complain and give the list of what is missing):
R CMD INSTALL e1071_1.5-24.tar.gz
R CMD INSTALL lars_0.9-7.tar.gz (
then, pcaPP_1.8-2.tar.gz, som_0.3.5.tar.gz, etc..)

The main drawback of this way of installing from sources is that you must manage
by yourself dependencies, and upgrade by yourself, even for complicated
packages....

BTW : you might have little isues if you install packages in /usr/lib/R, as you
might mess the packages you had compiled with the packages your package manager
automatically manages...
 Adding "export R_LIBS=/usr/local/lib/R/library" (or any name of a
directory you can write on)
before installing from source and before invoking the libraries might be useful.

Have nice days
D.Brion


--- En date de?: Lun 27.9.10, Jose Brasil <c2o.pro.br at gmail.com> a
?crit?:
> De: Jose Brasil <c2o.pro.br at gmail.com>
> Objet: [R-sig-Debian] Howto compile chemometrics package from source
> ?: r-sig-debian at r-project.org
> Date: Lundi 27 septembre 2010, 21h30
> Dear friends,
> 
> I'm confused about how to install packages from source.
> 
> I just updated R in Lenny from http://cran.fiocruz.br/bin/linux/debian/
> 
> I included in sources.list:
> 
> deb http://cran.fiocruz.br/bin/linux/debian
> lenny-cran/
> deb-src? http://cran.fiocruz.br/bin/linux/debian lenny-cran/
> 
> Then:
> apt-get update
> apt-get install r-base r-base-dev
> 
> Then I downloaded the package chemometrics_0.8.tar.gz?
> from
> http://cran.r-project.org/src/contrib/chemometrics_0.8.tar.gz
> 
> After untar I copied the dir chemometrics to
> /usr/lib/R/library and 
> tried install.package(chemometrics) from R prompt (as
> root):
> 
> install.packages(chemometrics)
> Erro em install.packages(chemometrics) : 
> ? objeto 'chemometrics' n?o encontrado
> 
> Could anyone give any help?
> 
> Thanks in advance,
> Jose
> 
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>

Dear Jose,

First of all let me explain why your first approach did not work:
> install.packages(chemometrics)
> Erro em install.packages(chemometrics) :
>   objeto 'chemometrics' n?o encontrado
R does not know an object named "chemometrics" and therefore
complains. You
should have typed
> install.packages("chemometrics")
Note the quotes around the name of the package.

I just tried this in my Ubuntu machine and it worked as expected without the 
need of manually downloading anything. Of course the r-base-dev package needs 
to be installed as you already know.

Kind regards,

Johannes