[BioC] installation of affycoretools

[Martin Morgan]

Try RCurl, with a capital C. Also once successful try the directions
for updating packages

http://www.bioconductor.org/docs/install-howto.html

(the link Sean mentioned earlier and the one above should, but do
not, point to the same text; expect this to change shortly).

Martin

James Anderson <janderson_net at yahoo.com> writes:

>   Sean,
>  
>  Thanks for your reply. I actually rebooted machine and restarted R. Then I typed biocLite() after sourcing it, after that I found there is no package named affycoretools, I type biocLite("affycoretools") and it seems to be working fine. The error I reported is because it can not find package Rcurl when I type library(affycoretools).
>  
>  I typed biocLite("Rcurl") and below is the response:
> Running biocinstall version 2.1.8 with R version 2.6.1 
> Your version of R requires version 2.1 of Bioconductor.
> Warning message:
> package ‘Rcurl’ is not available 
>
> It still does not work. 
>
> James
>
>
>   
>
> Sean Davis <sdavis2 at mail.nih.gov> wrote: 
>
> On Dec 19, 2007 5:06 PM, James Anderson <janderson_net at 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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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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