Skip to content

install.packages now intentionally references .Rprofile?

5 messages · Martin Morgan, Brian Ripley, Mark Kimpel +2 more

Original
Martin Morgan
# 
A post on the Bioconductor mailing list

  https://stat.ethz.ch/pipermail/bioconductor/2009-May/027700.html  

suggests that install.packages now references .Rprofile (?), whereas
in R-2-8 it did not. Is this intentional?

The example is, in .Rprofile

  library(utils)
  install.packages("Biobase",
                   repos="http://bioconductor.org/packages/2.4/bioc")

then starting R from the command line results in repeated downloads
of Biobase

mtmorgan at mm:~/tmp> R --quiet
trying URL
'http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.gz'
Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb)
opened URL
==================================================
downloaded 1.9 Mb

trying URL
'http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.gz'
Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb)
opened URL
==================================================
downloaded 1.9 Mb

^C
Execution halted
R version 2.9.0 Patched (2009-05-20 r48588)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
 
Martin
Brian Ripley
#
On Wed, 20 May 2009, Martin Morgan wrote:

            

      
      
      
    

        
Yes.  And in fact it did in earlier versions, to find the default 
library into which to install.

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        
      

    

    

      
      

        


  

        

      Heather Turner
    

    

      
      #
    

  


  

      
I had a similar problem when moving to R-2.9.0 as my .Rprofile called
update.packages(). The solution was to use

if(interactive()) {
	utils:::update.packages(ask = FALSE)
}

HTH,

Heather

        
Mark Kimpel wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    
7 days later

    

      
      

        


  

        

      McGehee, Robert
    

    

      
      #
    

  


  

      
I see that related to this thread, 'R CMD INSTALL' (like
'install.packages') also reads the .Rprofile before beginning. This
caused package installation headaches for me that developers should be
aware (as it was very difficult to debug).

I added a setwd() to my .Rprofile [for example: setwd("/tmp")] to keep
.Rhistory files from popping up in directories throughout my computer.
This causes package installation to fail completely with an unhelpful
error message. For example (any package will do here):

            

      
      
      
    

        
Warning: invalid package 'zoo_1.5-6.tar.gz'
Error: ERROR: no packages specified

Removing 'setwd(...)' from the .Rprofile restores normal package
installation behavior.

I'd like to request that either setwd() not break installation, or the
user can disable .Rprofile reading on R CMD INSTALL (for instance with
an option such as --no-init-file). I'll use Heather's solution below for
the short-term, but would rather not have to completely turn off my
.Rprofile for non-interactive scripts.

Thanks, Robert


-----Original Message-----
From: r-devel-bounces at r-project.org
[mailto:r-devel-bounces at r-project.org] On Behalf Of Heather Turner
Sent: Friday, May 22, 2009 6:13 AM
To: Mark Kimpel
Cc: Prof Brian Ripley; r-devel at stat.math.ethz.ch
Subject: Re: [Rd] install.packages now intentionally references
.Rprofile?

I had a similar problem when moving to R-2.9.0 as my .Rprofile called
update.packages(). The solution was to use

if(interactive()) {
	utils:::update.packages(ask = FALSE)
}

HTH,

Heather

        
Mark Kimpel wrote:

            

      
      
      
    

        
modified by

            

      
      
      
    

        
not

            

      
      
      
    

        
correctly,

            

      
      
      
    

        
reason

            

      
      
      
    

        
the

            

      
      
      
    

        
date of

            

      
      
      
    

        
quite

            

      
      
      
    

        
-- B.

            

      
      
      
    

        
<ripley at stats.ox.ac.uk>wrote:

            

      
      
      
    

        
library

            

      
      
      
    

        
http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.
gz

            

      
      
      
    

        
http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.
gz

            

      
      
      
    

        
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
TF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=
C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATI
ON=C

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
http://www.stats.ox.ac.uk/~ripley/<http://www.stats.ox.ac.uk/%7Eripley/>

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        
______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel