On Dec 19, 2007 5:06 PM, James Anderson <janderson_net@yahoo.com> wrote:

> Sean,
>
> Thanks for your advice. I followed your suggestion and typed
>
> source("http://bioconductor.org/biocLite.R")
> biocLite()
> biocLite("affycoretools")
>
> and there is nothing abnormal. However, when I type
> library(affycoretools), it pops up the following lines:
>
> Loading required package: affy
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: affyio
> Loading required package: preprocessCore
> Loading required package: limma
> Loading required package: GOstats
> Loading required package: graph
> Loading required package: GO.db
> Loading required package: AnnotationDbi
> Loading required package: DBI
> Loading required package: RSQLite
> Loading required package: annotate
> Loading required package: xtable
> Loading required package: RBGL
> Loading required package: Category
> Loading required package: genefilter
> Loading required package: survival
> Loading required package: splines
> Loading required package: biomaRt
> Loading required package: RCurl
> Error: package 'RCurl' could not be loaded
> In addition: Warning message:
> In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
> lib.loc) :
>   there is no package called 'RCurl'
>
> Below is what I got from using sessionInfo() for diagnose
>
> R version 2.6.1 (2007-11-26)
> 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     datasets
> [8] methods   base
>
> other attached packages:
>  [1] GOstats_2.4.0        Category_2.4.0       genefilter_1.16.0
>  [4] survival_2.34        RBGL_1.14.0          annotate_1.16.1
>  [7] xtable_1.5-2         GO.db_2.0.2          AnnotationDbi_1.0.6
> [10] RSQLite_0.6-4        DBI_0.2-4            graph_1.16.1
> [13] limma_2.12.0         affy_1.16.0          preprocessCore_1.0.0
> [16] affyio_1.6.1         Biobase_1.16.2
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.9
>
> Seems that it still can not find the package Rcurl.
>

Unfortunately, biocLite() does not find dependencies of dependencies (and I
believe RCurl is a dependency of biomaRt).  My guess is that you have
installed other packages without using biocLite() in the past and have
missed installing the RCurl dependency for one of them.  Therefore, I would
suggest using biocLite() to install ALL PACKAGES ALL THE TIME so that this
doesn't occur in the future.  However, in the short term, you might try:

biocLite('RCurl')
library(affycoretools)

Hope that helps.

Sean

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