[BioC] Can't get RCurl...

James W. MacDonald jmacdon at med.umich.edu
Thu Apr 5 22:42:31 CEST 2007


Hi Jenny,

Seems odd that biocLite() didn't install all dependencies, but what do 
you get with biocLite("RCurl")?

You might also add RMySQL, which is much faster if you need to annotate 
lots of genes.

Best,

Jim

Jenny Drnevich wrote:
> 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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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