[BioC] Can't get RCurl...

[Jenny Drnevich]

HI,

I'm helping someone install the affycoretools package, but there 
seems to be a problem getting RCurl that's needed for biomaRt and 
hence affycoretools. Here's what was done and the sessionInfo():

I just uninstalled everything and re-installed R and Bioconductor 
packages using

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

After that I installed afyycoretools by:
 > biocLite("affycoretools")

It gave the following message:

 > biocLite("affycoretools")

Running biocinstall version 1.9.9 with R version 2.4.1
Your version of R requires version 1.9 of Bioconductor.
trying URL 
'http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/affycoretools_1.6.1.zip'
Content type 'application/zip' length 6867656 bytes
opened URL
downloaded 6706Kb

package 'affycoretools' successfully unpacked and MD5 sums checked

The downloaded packages are in
         C:\Documents and Settings\Hoyer Lab\Local 
Settings\Temp\RtmpDLCJrb\downloaded_packages
updating HTML package descriptions

It seems the installation is successful.

However, when I tried to load affycoretools by:
 >library(affycoretools)

It gave the fowllowings:
 > library(affycoretools)

Loading required package: affy
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

     Vignettes contain introductory material. To view, type
     'openVignette()' or start with 'help(Biobase)'. For details
     on reading vignettes, see the openVignette help page.

Loading required package: affyio
Loading required package: limma
Loading required package: GOstats
Loading required package: graph
Loading required package: GO
Loading required package: annotate
Loading required package: RBGL
Loading required package: Category
Loading required package: KEGG
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Loading required package: biomaRt
Loading required package: XML

Attaching package: 'XML'


         The following object(s) are masked from package:graph :

          addNode

Loading required package: RCurl
Error: package 'RCurl' could not be loaded
In addition: Warning message:
there is no package called 'RCurl' in: library(pkg, character.only = 
TRUE, logical = TRUE, lib.loc = lib.loc)

 > sessionInfo()

R version 2.4.1 (2006-12-18)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "methods"   "base"

other attached packages:
        XML    GOstats   Category genefilter   survival       KEGG       RBGL
    "1.6-0"    "2.0.4"    "2.0.3"   "1.12.0"     "2.30"   "1.14.1"   "1.10.0"
   annotate         GO      graph      limma       affy     affyio    Biobase
   "1.12.1"   "1.14.1"   "1.12.1"   "2.9.17"   "1.12.2"    "1.2.0"   "1.12.2"

 >



Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu