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Howto compile chemometrics package from source

7 messages · Jose Brasil, Douglas Bates, denis brion +2 more

Original
Jose Brasil
# 
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
Douglas Bates
#
On Mon, Sep 27, 2010 at 2:30 PM, Jose Brasil <c2o.pro.br at gmail.com> wrote:
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
denis brion
# 
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?:
Dirk Eddelbuettel
# 
Denis,

I still fail to understand why keep posting on this as you obviously do not
use Debian or Ubuntu.
On 28 September 2010 at 14:27, denis brion wrote:
| 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)

Yes, that idea is *so good* that it has been the *implemented default* since
2003.  From the file /etc/R/Renviron:

# edd Apr 2003  Allow local install in /usr/local, also add a directory for
#               Debian packaged CRAN packages, and finally the default dir 
# edd Jul 2007  Now use R_LIBS_SITE, not R_LIBS
R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}


Dirk


| 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
| > 
| 
| 
| 
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian
denis brion
# 
Because:
I still fail to understand why keep posting on this as you
1) I obviously could help him (reminding /usr/local/xxx or any directory  should be writable  does not hurt, does it? Even if it has been done 7 years ago - docs change and are forgotten- )

2 )Some friends of mine use Debian derived or Windows  : I I find _a_ good reason to keep/use Debian, I am not of the sectary kind (any objections?)
...
3 ) I sincerely thought R was sect/distribution agnostic

4 ) I have a mind open enough to look for other distributions/ package managers (binary P.M.  should be easier - available recent doc, etc... -
 than compiling from source, should not they???)

5) talking about doc: GNU linux magazine dedicated a full _and interesting_  release to Debian package managing: that the bright side, not the "looking for  political correctness" ? la McCarthy, , of Debian...


--- En date de?: Mar 28.9.10, Dirk Eddelbuettel <edd at debian.org> a ?crit?:
Dirk Eddelbuettel
#
On 28 September 2010 at 15:45, denis brion wrote:
| I still fail to understand why keep posting on this as you
| > obviously do not
| > use Debian or Ubuntu.
| > 
| 1) I obviously could help him (reminding /usr/local/xxx or any directory  should be writable  does not hurt, does it? Even if it has been done 7 years ago - docs change and are forgotten- )
| 
| 2 )Some friends of mine use Debian derived or Windows  : I I find _a_ good reason to keep/use Debian, I am not of the sectary kind (any objections?)
| ...
| 3 ) I sincerely thought R was sect/distribution agnostic

It most certainly is, but check the name of this list every once in a
while. This is not r-help, or r-sig-linux, or r-sig-whateverdenislikes

The list is for Debian/Ubuntu users.  

Help is of course appreciated, but so is fact checking.

Dirk
 
| 4 ) I have a mind open enough to look for other distributions/ package managers (binary P.M.  should be easier - available recent doc, etc... -
|  than compiling from source, should not they???)
|
| 5) talking about doc: GNU linux magazine dedicated a full _and interesting_  release to Debian package managing: that the bright side, not the "looking for  political correctness" ? la McCarthy, , of Debian...
| 
| --- En date de?: Mar 28.9.10, Dirk Eddelbuettel <edd at debian.org> a ?crit?:
| 
| > De: Dirk Eddelbuettel <edd at debian.org>
| > Objet: Re: [R-sig-Debian] Re : Howto compile chemometrics package from source
| > ?: "denis brion" <dbrion1 at yahoo.fr>
| > Cc: 
| > Date: Mardi 28 septembre 2010, 17h11
| > 
| > Denis,
| > 
| > I still fail to understand why keep posting on this as you
| > obviously do not
| > use Debian or Ubuntu.
| >
| > On 28 September 2010 at 14:27, denis brion wrote:
| > | 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)
| > 
| > Yes, that idea is *so good* that it has been the
| > *implemented default* since
| > 2003.? From the file /etc/R/Renviron:
| > 
| > # edd Apr 2003? Allow local install in /usr/local,
| > also add a directory for
| > #? ? ? ? ? ?
| > ???Debian packaged CRAN packages, and finally
| > the default dir 
| > # edd Jul 2007? Now use R_LIBS_SITE, not R_LIBS
| > R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}
| > 
| > 
| > Dirk
| > 
| > 
| > | 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
| > | > 
| > | 
| > | 
| > | 
| > | 
| > | _______________________________________________
| > | R-SIG-Debian mailing list
| > | R-SIG-Debian at r-project.org
| > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| > 
| > -- 
| > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
| > 
| 
| 
|
Johannes Ranke
# 
Dear Jose,

First of all let me explain why your first approach did not work:
R does not know an object named "chemometrics" and therefore complains. You 
should have typed
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