[R] packages install dependencies

[Uwe Ligges]

On 18.04.2012 14:01, mail.bioinfo at fr.netgrs.com wrote:
> Hi Uwe
>
> I tried
> install.packages("marginalmodelplots", dependencies=TRUE, contriburl="/home/bioadm/install/R_packages/test")


Whoops, this was untested an it turns out you need:

contriburl="file:/home/bioadm/install/R_packages/test"

reaing the help file tell us it must be an URL rather than a file 
specification.

Uwe Ligges



> But I got always the same error
>
> install.packages("marginalmodelplots", dependencies=TRUE, contriburl="/home/bioadm/install/R_packages/test/")
> Warning: unable to access index for repository /home/bioadm/install/R_packages/test/
> Warning message:
> package âmarginalmodelplotsâ is not available (for R version 2.15.0)
>
>
> below, I paste the content of my PACKAGES file
>
> Package: locfit
> Version: 1.5-7
> Depends: R (>= 2.0.1)
> Imports: akima, lattice
> Suggests: gam
> License: GPL (>= 2)
> MD5sum: 6c90e03f93305789b74c7fc6a56ebdc1
>
> Package: marginalmodelplots
> Version: 0.4.2
> Depends: R (>= 2.0.1), locfit (>= 1.5-4), grid
> License: GPL (>= 2)
> MD5sum: 1c4c0325a5f9f0e29d669207a7ad6b68
>
> Regards,
>
> Joël
> -----Message d'origine-----
> De : Uwe Ligges [mailto:ligges at statistik.tu-dortmund.de]
> Envoyé : mercredi 18 avril 2012 10:51
> À :<FRsr BioInfo
> Cc : r-help at r-project.org
> Objet : Re: [R] packages install dependencies
>
>
>
> 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/marginalmodelpl
>> ots_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/marginalmodelp
>>> l 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.gz
>>> â 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/marginalmod
>>>> e 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.