[BioC] Can't get RCurl...

[Jenny Drnevich]

Hi Jim,

biocLite("RCurl") did work. I'm not sure what went wrong 
before...  The person I was helping had tried to download packages on 
his own before, and I don't think he was using biocLite. What may 
have happened is that he installed biomaRt via a local zip file, but 
then didn't remove it before doing biocLite("affycoretools"). Perhaps 
biocLite stopped because it saw he had biomaRt, which is a dependency 
of affycoretools, whereas RCurl is not a direct dependency of affycoretools.

Thanks,
Jenny


At 03:42 PM 4/5/2007, James W. MacDonald wrote:
>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
>
>
>**********************************************************
>Electronic Mail is not secure, may not be read every day, and should 
>not be used for urgent or sensitive issues.

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