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6 messages · Ed Siefker, Jim Robison-Cox, Paul Gilbert +1 more

Original
Ed Siefker
# 
Hi, I am running Debian Sid. I am having
trouble with the R packages.

Executing 'help()' or 'demo()' launches 'most' with no text.
'help.start()' works properly.

When I try to install a package, I get the following problem:

*********************************************************************
Installing package(s) into ?/usr/local/lib/R/site-library?
(as ?lib? is unspecified)
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
Warning: unable to access index for repository
http://cran.cnr.Berkeley.edu/src/contrib
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
  package ?ctv? is not available (for R version 2.14.2)
*********************************************************************

The system in question has a direct connection to the internet.
I can browse to the repository and find the ctv package.
The user has read and write permissions on '/usr/local/lib/R/site-library'

I don't know what to do here.  Can someone advise?
Ed Siefker
# 
Also, I have the following R packages installed:

ebs15242 at biox:~$ dpkg --get-selections | grep ^r-
r-base						install
r-base-core					install
r-base-dev					install
r-cran-boot					install
r-cran-class					install
r-cran-cluster					install
r-cran-codetools				install
r-cran-foreign					install
r-cran-kernsmooth				install
r-cran-lattice					install
r-cran-mass					install
r-cran-matrix					install
r-cran-mgcv					install
r-cran-nlme					install
r-cran-nnet					install
r-cran-rpart					install
r-cran-spatial					install
r-cran-survival					install
r-doc-html					install
r-doc-info					install
r-doc-pdf					install
r-recommended					install
On 2/29/12, Ed Siefker <ebs15242 at gmail.com> wrote:
Jim Robison-Cox
# 
Hi Ed,

   R 2.14.2 just came out, So I'm guessing that most packages are not 
yet rebuilt for it.

You should still be able to load them as in (from terminal prompt)

wget http://cran.fhcrc.org/src/contrib/ctv_0.7-4.tar.gz
R CMD INSTALL ctv_0.7-4.tar.gz

Jim Robison-Cox
On 02/29/2012 11:33 AM, Ed Siefker wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
      #
    

  


  

      
On 29 February 2012 at 12:36, Ed Siefker wrote:

        
| Also, I have the following R packages installed:
| 
| ebs15242 at biox:~$ dpkg --get-selections | grep ^r-
| r-base						install
| r-base-core					install
| r-base-dev					install
| r-cran-boot					install
| r-cran-class					install
| r-cran-cluster					install
| r-cran-codetools				install
| r-cran-foreign					install
| r-cran-kernsmooth				install
| r-cran-lattice					install
| r-cran-mass					install
| r-cran-matrix					install
| r-cran-mgcv					install
| r-cran-nlme					install
| r-cran-nnet					install
| r-cran-rpart					install
| r-cran-spatial					install
| r-cran-survival					install
| r-doc-html					install
| r-doc-info					install
| r-doc-pdf					install
| r-recommended					install
| 
| 
|

        
| On 2/29/12, Ed Siefker <ebs15242 at gmail.com> wrote:

        
| > Hi, I am running Debian Sid. I am having
| > trouble with the R packages.
| >
| > Executing 'help()' or 'demo()' launches 'most' with no text.

You need to set / change the default browser -- from /etc/R/Renviron:

   ## Default browser
   R_BROWSER=${R_BROWSER-'xdg-open'}

so the xdg-open command picks most, and most does not know what to do with
the arguments. Works with less.

| > 'help.start()' works properly.
| >
| > When I try to install a package, I get the following problem:
| >
| > *********************************************************************
| >> install.packages("ctv")
| > Installing package(s) into ?/usr/local/lib/R/site-library?
| > (as ?lib? is unspecified)
| > --- Please select a CRAN mirror for use in this session ---

No error. You provided no default.

| > Loading Tcl/Tk interface ... done
| > Warning: unable to access index for repository
| > http://cran.cnr.Berkeley.edu/src/contrib

No idea. Network?  Try a different site.

| > Warning message:
| > In getDependencies(pkgs, dependencies, available, lib) :
| >   package ?ctv? is not available (for R version 2.14.2)

So install ctv.

Dirk

| > *********************************************************************
| >
| > The system in question has a direct connection to the internet.
| > I can browse to the repository and find the ctv package.
| > The user has read and write permissions on '/usr/local/lib/R/site-library'
| >
| > I don't know what to do here.  Can someone advise?
| >
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Paul Gilbert
    

    

      
      #
    

  


  

      
Could be packages for new R have not yet migrated to the mirrors. You 
might try Austria rather than Berkley.

Paul

        
On 12-02-29 01:33 PM, Ed Siefker wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Dirk Eddelbuettel
    

    

      
      #
    

  


  

      
On 29 February 2012 at 11:45, Jim Robison-Cox wrote:

        
| Hi Ed,
| 
|    R 2.14.2 just came out, So I'm guessing that most packages are not 
| yet rebuilt for it.

This is not Windows, so binary packages are not being rebuilt anyway --
install.packages() only looks at src/contrib/.

As R 2.14.2 itself, that actually was uploaded to Debian 'unstable' this
morning as I usually find the time to do so on release day.  

Dirk
 
| You should still be able to load them as in (from terminal prompt)
| 
| wget http://cran.fhcrc.org/src/contrib/ctv_0.7-4.tar.gz
| R CMD INSTALL ctv_0.7-4.tar.gz
| 
| Jim Robison-Cox
|

        
| On 02/29/2012 11:33 AM, Ed Siefker wrote:

        
| > Hi, I am running Debian Sid. I am having
| > trouble with the R packages.
| >
| > Executing 'help()' or 'demo()' launches 'most' with no text.
| > 'help.start()' works properly.
| >
| > When I try to install a package, I get the following problem:
| >
| > *********************************************************************
| >> install.packages("ctv")
| > Installing package(s) into ?/usr/local/lib/R/site-library?
| > (as ?lib? is unspecified)
| > --- Please select a CRAN mirror for use in this session ---
| > Loading Tcl/Tk interface ... done
| > Warning: unable to access index for repository
| > http://cran.cnr.Berkeley.edu/src/contrib
| > Warning message:
| > In getDependencies(pkgs, dependencies, available, lib) :
| >    package ?ctv? is not available (for R version 2.14.2)
| > *********************************************************************
| >
| > The system in question has a direct connection to the internet.
| > I can browse to the repository and find the ctv package.
| > The user has read and write permissions on '/usr/local/lib/R/site-library'
| >
| > I don't know what to do here.  Can someone advise?
| >
| > _______________________________________________
| > R-SIG-Debian mailing list
| > R-SIG-Debian at r-project.org
| > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
| >
| 
| 
| -- 
| ---
| Jim Robison-Cox
| Department of Math Sciences
| 2-214 Wilson Hall
| Montana State University
| Bozeman, MT 59717-2400
|   e-mail: jimrc at math.montana.edu
|   phone: (406)994-5340
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian