[BioC] Can't get RCurl...
Christos Hatzis
christos at nuverabio.com
Thu Apr 5 23:32:27 CEST 2007
RCurl is available from the Omegahat site:
http://www.omegahat.org/RCurl/RCurl_0.8-0.tar.gz
-Christos
Christos Hatzis, Ph.D.
Nuvera Biosciences, Inc.
400 West Cummings Park
Suite 5350
Woburn, MA 01801
Tel: 781-938-3830
www.nuverabio.com
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of
> Jenny Drnevich
> Sent: Thursday, April 05, 2007 5:21 PM
> To: James W. MacDonald
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Can't get RCurl...
>
> 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/contr
> ib/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
>
> _______________________________________________
> 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
>
>
More information about the Bioconductor
mailing list