Dear list, I am trying to install some of the Bioconductor packages using the following code lines and get the warnings: source("http://www.bioconductor.org/biocLite.R") biocLite() Running bioCLite version 0.1 with R version 2.2.1 Warning message: 'CRAN.packages' is deprecated. Use 'available.packages' instead. See help("Deprecated") Warning: unable to access index for repository http://www.bioconductor.org/packages/bioc/devel/bin/windows/contrib/2. 2 also installing the dependencies 'GO', 'KEGG', 'RColorBrewer' trying URL 'http://www.bioconductor.org/packages/data/annotation/1.7/bin/windows/ contrib/2.2/GO_1.10.0.zip' Content type 'application/zip' length 14507935 bytes opened URL downloaded 14167Kb ............ Running biocinstall version 1.1 with R version 2.2.1 package 'geneplotter' successfully unpacked and MD5 sums checked Warning: unable to move temporary installation 'C:\Program Files\R\R-2.2.1\library\file767d7a5a\geneplotter' to 'C: \PROGRA~1\R\R-22~1.1\library\geneplotter' package 'hgu95av2' successfully unpacked and MD5 sums checked package 'limma' successfully unpacked and MD5 sums checked Warning: unable to move temporary installation 'C:\Program Files\R\R-2.2.1\library\file1e1f3b25\limma' to 'C: \PROGRA~1\R\R-22~1.1\library\limma' package 'marray' successfully unpacked and MD5 sums checked Warning: unable to move temporary installation 'C:\Program Files\R\R-2.2.1\library\file1ad46e5d\marray' to 'C: \PROGRA~1\R\R-22~1.1\library\marray' package 'matchprobes' successfully unpacked and MD5 sums checked package 'multtest' successfully unpacked and MD5 sums checked Warning: unable to move temporary installation 'C:\Program Files\R\R-2.2.1\library\file7ff57f96\multtest' to 'C: \PROGRA~1\R\R-22~1.1\library\multtest' package 'reposTools' successfully unpacked and MD5 sums checked package 'ROC' successfully unpacked and MD5 sums checked package 'vsn' successfully unpacked and MD5 sums checked Warning: unable to move temporary installation 'C:\Program Files\R\R-2.2.1\library\file30a6b89\vsn' to 'C: \PROGRA~1\R\R-22~1.1\library\vsn' package 'xtable' successfully unpacked and MD5 sums checked I am running Windows XP and R 2. 2.1. How can I fix the problem? Thanks, Caimiao

Hi Caimiao, On 7 Feb 2006, caiwei at mdanderson.org wrote: > I am trying to install some of the Bioconductor packages using the > following code lines and get the warnings: > > > source("http://www.bioconductor.org/biocLite.R") > biocLite() > > Running bioCLite version 0.1 with R version 2.2.1 > > Warning message: 'CRAN.packages' is deprecated. Use > 'available.packages' instead. See help("Deprecated") This warning you can ignore. I thought it was fixed, but it seems not. It will be soon. > Warning: unable to access index for repository > http://www.bioconductor.org/packages/bioc/devel/bin/windows/contrib/ 2.2 This one has me a bit puzzled. The URL doesn't look right and I don't know where it would have come from. Do you have a custom setting for the repos global option (getOption("repos"))? > Running biocinstall version 1.1 with R version 2.2.1 > package 'geneplotter' successfully unpacked and MD5 sums checked > Warning: unable to move temporary installation 'C:\Program > Files\R\R-2.2.1\library\file767d7a5a\geneplotter' to 'C: > \PROGRA~1\R\R-22~1.1\library\geneplotter' > I am running Windows XP and R 2. 2.1. > > How can I fix the problem? Just to clarify, are you sure that the packages actually failed to install? Have you tried: library("geneplotter") I've seen the message about unable to move temp install, but can't recall how to resolve it. You might try searching the archives of this list. Does this look familiar to any Windows users out there? Best, + seth