[BioC] queries regarding bioconductor installation

Stephen Eglen stephen at inf.ed.ac.uk
Mon May 26 16:59:22 MEST 2003


Hello,

I have just tried to install bioconductor.  I noted some problems (at
least for me) when using getBioC() to install packages.

Here is my setup:  R 1.7.0 under redhat 7.1 linux.
I currently put my R libraries in ~/langs/R/library
since I do not have access to the /usr/lib/R/library.  So I have
export R_LIBS=$HOME/langs/R/library 
in my .bashrc

Then, within R I did:

> source("http://www.bioconductor.org/getBioC.R")

[fine]

> getBioC(libName="all")
Running getBioC version 1.2.29....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R

Please direct any concerns or questions to bioconductor at stat.math.ethz.ch.

Please select an installation directory: 
1:~/langs/R/library 
2:/usr/lib/R/library 
Selection: 1
[1] "Installing reposTools ..."
ERROR: cannot write to or create directory '/usr/lib/R/library'
Error in upDatePkgs(relLevel, PLATFORM, destdir, method = method) : 
	Failed to install package Biobase


So, despite me asking it to install in my home dir, it tried to update
/usr/lib/R/library. I checked my paths:

> .libPaths()
[1] "~/langs/R/library"  "/usr/lib/R/library"

so that presumably is fine.

I think I found the problem: the installPack() function does not
currently accept the "destdir" argument.  When I amended this
function, it seemed to work okay.

[One other problem I noted; during the install process, it asked me
several times if I wanted to install standard packages like "eda",
"methods", "tcltk", "stepfun".  Is this intended?]

Here is a possible patch against the current getBioC.R.

Stephen


*** /tmp/getBioC.R~	Sat May 17 16:48:02 2003
--- /tmp/getBioC.R	Sat May 17 16:48:02 2003
***************
*** 236,242 ****
              ## Download and install
              download.file(sourceUrl, fileName,
                            mode = getMode(platform), quiet = TRUE, method=method)
!             installPack(platform, fileName)
              if (!(i %in% installed.packages()[,"Package"]))
                  stop(paste("Failed to install package",i))
              unlink(fileName)
--- 236,242 ----
              ## Download and install
              download.file(sourceUrl, fileName,
                            mode = getMode(platform), quiet = TRUE, method=method)
!             installPack(platform, fileName, destdir)
              if (!(i %in% installed.packages()[,"Package"]))
                  stop(paste("Failed to install package",i))
              unlink(fileName)
***************
*** 288,297 ****
  }
  
  ## Installs a given package
! installPack <- function(platform, fileName){
      if(platform == "unix"){
          cmd <- paste(file.path(R.home(), "bin", "R"),
!                      "CMD INSTALL", fileName)
          system(cmd)
      }else{
          if(platform == "windows"){
--- 288,297 ----
  }
  
  ## Installs a given package
! installPack <- function(platform, fileName, destdir){
      if(platform == "unix"){
          cmd <- paste(file.path(R.home(), "bin", "R"),
!                      "CMD INSTALL -l", destdir, fileName)
          system(cmd)
      }else{
          if(platform == "windows"){



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