[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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