[BioC] help with getBioC

Gordon Smyth smyth at wehi.edu.au
Wed Jun 18 20:14:45 MEST 2003


I have never managed to use "getBioC" to install bioconductor from a unix 
machine. I have appended my latest effort below:

1. Can you tell me what stupid thing I am doing wrong?
2. Why does getBioC ignore my attempt to specify the destination directory, 
notice it tries to write to /usr/local/lib which I don't have write 
priveleges to. I certainly do have write priveleges to the directory I've 
specified.
3. Any thoughts why it takes getBioC 3-4 minutes to give me this error 
message? I can download reposTools using cvs from this machine in just a 
few seconds, so internet speed doesn't seem to be the problem.

Thanks
Gordon

 > source("http://www.bioconductor.org/getBioC.R")
 > system("pwd")
/home/users/lab0605/smyth/gordon
 > 
getBioC(libName="all",relLevel="devel",destdir="/home/users/lab0605/smyth/gordon/Rlibs")
Running getBioC version 1.2.34....
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.

[1] "Installing reposTools ..."
ERROR: cannot write to or create directory '/usr/local/lib/R/library'
Loading required package: Biobase
Welcome to Bioconductor
          To view some introductory material -- look at our vignettes
          Simply type: openVignette()
          to see the available vignettes
          To read a vignette see the openVignette help page for details
Creating a new generic function for "summary" in package
Biobase

Synching your local package management information ...
Error in file(file, "wb") : unable to open connection
In addition: Warning message:
cannot open file `/usr/local/lib/R/library/liblisting.Rda'
 > version
          _
platform i686-pc-linux-gnu
arch     i686
os       linux-gnu
system   i686, linux-gnu
status
major    1
minor    7.0
year     2003
month    04
day      16
language R



More information about the Bioconductor mailing list