[R] packages install dependencies

[Uwe Ligges]

On 18.04.2012 10:48, mail.bioinfo at fr.netgrs.com wrote:
> 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/")

install.packages("marginalmodelplots", dependencies=TRUE, 
contriburl="/home/bioadm/install/R_packages/test")

seems to be the documented way you want to try.

Uwe Ligges




> 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]]
>>>>
>>>>
>>>>
>>>>
>>>> ______________________________________________
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>>>> 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.