[R] packages install dependencies

Wed Apr 18 10:48:47 CEST 2012

Hi 

I created  a directory which contains just the two packages "marginalmodelplots_0.4.2.tar.gz " and " locfit_1.5-7.tar.gz " called test

I launched the command write_PACKAGES as follows
write_PACKAGES("/home/bioadm/install/R_packages/test/", type ="source")

As you can see I have now in my directory 4 files.

[bioadm at srsu148 test]$ ll
total 228
-rw-r--r-- 1 bioadm bio 200614 Apr 18 10:33 locfit_1.5-7.tar.gz
-rw-r--r-- 1 bioadm bio  18559 Apr 18 10:32 marginalmodelplots_0.4.2.tar.gz
-rw-r--r-- 1 bioadm bio    305 Apr 18 10:34 PACKAGES
-rw-r--r-- 1 bioadm bio    222 Apr 18 10:34 PACKAGES.gz
[bioadm at srsu148 test]$ pwd
/home/bioadm/install/R_packages/test

So the files PACKAGES are created but if I run the command install.packages as follows in the R editor, I get always the same error.

install.packages("/home/bioadm/install/R_packages/test/marginalmodelplots_0.4.2.tar.gz", repos=TRUE, 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 don't understand the error because my files PACKAGES are inside the directory that I specified using the option contriburl and this directory is full access for everyone.

Is the command not correct ?

Joël

-----Message d'origine-----
De : Uwe Ligges [mailto:ligges at statistik.tu-dortmund.de] 
Envoyé : mardi 17 avril 2012 15:30
À : <FRsr BioInfo
Cc : r-help at r-project.org
Objet : Re: [R] packages install dependencies

On 17.04.2012 15:21, mail.bioinfo at fr.netgrs.com wrote:
> 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" )

Errr, given your path specifications, I assume you are not under Windows and given the extensions of the files, I assume you have source packages, hence you need a PACKAGES file for a source repository.

Uwe Ligges

>
> I retried  the command but I got the same error.
>
> install.packages("/home/bioadm/install/R_packages/test/marginalmodelpl
> ots_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/marginalmode
>> l 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.