[R] packages install dependencies

[mail.bioinfo at fr.netgrs.com]

Hi

I checked inside the directory but I have the PACKAGE file as you can see 

ls /home/bioadm/install/R_packages/test/PACKAGES
PACKAGES     PACKAGES.gz

I created them using this command 
write_PACKAGES("../test/", type="win.binary" )


I retried  the command but I got the same error.

install.packages("/home/bioadm/install/R_packages/test/marginalmodelplots_0.4.2.tar.gz", repos=NULL, dependencies =TRUE, contriburl="/home/bioadm/install/R_packages/test/")
Installing package(s) into â/soft/R-2.8.1/lib64/R/libraryâ
(as âlibâ is unspecified)
Warning: unable to access index for repository /home/bioadm/install/R_packages/test/
Warning message:
package â/home/bioadm/install/R_packages/test/marginalmodelplots_0.4.2.tar.gzâ is not available (for R version 2.15.0)

i checked also the permissions for this directory but it's OK as I created it with full acess for everyone
drwxrwxrwx 2 bioadm test 155648 Apr 17 14:49 test

Do you have any suggestions ?

Joël

-----Message d'origine-----
De : Uwe Ligges [mailto:ligges at statistik.tu-dortmund.de] 
Envoyé : mardi 17 avril 2012 14:25
À : <FRsr BioInfo
Cc : r-help at r-project.org
Objet : Re: [R] packages install dependencies



On 17.04.2012 10:57, mail.bioinfo at fr.netgrs.com wrote:
> Hi Uwe
>
> Thanks for your answer.
>
> I tried to install the packages "marginalmodelplots_0.4.2.tar.gz" from 
> a local repository "/home/bioadm/install/R_packages/120416/" using 
> your suggestion (i.e. install.packages(...., 
> contriburl="/home/joel/RPacks"))
>
> I paste below the command
>
> install.packages("/home/bioadm/install/R_packages/120416/marginalmodel
> plots_0.4.2.tar.gz", repos=NULL, dependencies= TRUE, type="source", 
> contriburl="/home/bioadm/install/R_packages/120416/")
>
> Warning: unable to access index for repository 
> /home/bioadm/install/R_packages/120416/
> Warning message: In install.packages("/home/bioadm/install/R_packages/120416/marginalmodelplots_0.4.2.tar.gz",  :
>    package 
> â/home/bioadm/install/R_packages/120416/marginalmodelplots_0.4.2.tar.g
> zâ is not available


Then you do not have a repository. Its defintiion is that it contains a PACKAGES file which it obviously does not contain.

Nevertheless, you can create a PACKAGE file via function
write_PACKAGES() in package tools.

Uwe Ligges



>
> For info this package depends of the "locfit" package.
>
> What should I do ?
>
> Thanks in advance
>
> Joël Masciocchi
>
>
>
> -----Message d'origine-----
> De : Uwe Ligges [mailto:ligges at statistik.tu-dortmund.de]
> Envoyé : lundi 16 avril 2012 19:06
> À :<FRsr BioInfo
> Cc : r-help at r-project.org
> Objet : Re: [R] packages install dependencies
>
>
>
> On 16.04.2012 15:41, mail.bioinfo at fr.netgrs.com wrote:
>> Hello R-Members
>>
>>
>>
>> I have to install several R packages on a Unix server which doesn't have internet connection.
>>
>> I downloaded some packages manually and I installed it from source using the command R CMD INSTALL and it's work but in some cases I can't install the package because of the dependencies.
>>
>>
>>
>> So I download all the R packages into a directory for example /home/joel/RPacks.
>>
>>
>>
>> Is it possible to configure the R commands (i.e. CMD INSTALL command or install.packages() function) in order that R looks for dependencies in my repository.
>
>
> install.packages(...., contriburl="/home/joel/RPacks")
>
> Uwe Ligges
>
>
>>
>>
>>
>> Thanks in advance,
>>
>> Best Regards - Cordialement,
>>
>> Joël
>>
>> ---------------------------------------------------------------------
>> --
>>
>> Joel Masciocchi
>>
>> Bioinformatician
>>
>> Informatics Department
>>
>> Institut de Recherches SERVIER (I.d.R.S)
>>
>> 125, chemin de Ronde
>>
>> 78290 CROISSY-SUR-SEINE - FRANCE
>>
>>
>>
>>
>>
>>
>> 	[[alternative HTML version deleted]]
>>
>>
>>
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide 
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.