[BioC] GEOquery loading error

Jian Zhang [guest] guest at bioconductor.org
Sat May 26 00:39:40 CEST 2012

I was able to download and install GEOquery,  but can't seem to load it into R. See the following error message included.  Also included some potentially useful info.

I use R version: 2.15.0, Bioconductor 2.10.


 -- output of sessionInfo(): 

Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : 
  there is no package called ‘RCurl’
Error: package/namespace load failed for ‘GEOquery’

2: stop(gettextf("package/namespace load failed for %s", sQuote(package)), 
       call. = FALSE, domain = NA)
1: library(GEOquery)

> biocLite("RCurl")
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.4.
Installing package(s) 'RCurl'
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.15
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.15

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: i386-pc-mingw32/i386 (32-bit)

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] hgu133plus2hsrefseq.db_15.1.0 hgu133plus2hsrefseqcdf_15.1.0
 [3] hgu133plus2cdf_2.10.0         hgu133plus2.db_2.7.1         
 [5] org.Hs.eg.db_2.7.1            RSQLite_0.11.1               
 [7] DBI_0.2-5                     altcdfenvs_2.18.0            
 [9] hypergraph_1.28.0             graph_1.34.0                 
[11] Biostrings_2.24.1             IRanges_1.14.3               
[13] makecdfenv_1.34.0             ecoliprobe_2.10.0            
[15] gcrma_2.28.0                  arrayQualityMetrics_3.12.0   
[17] ecoliLeucine_1.2.8            ecolicdf_2.10.0              
[19] AnnotationDbi_1.18.0          affy_1.34.0                  
[21] Biobase_2.16.0                BiocGenerics_0.2.0           
[23] BiocInstaller_1.4.4          

loaded via a namespace (and not attached):
 [1] affyio_1.24.0         affyPLM_1.32.0        annotate_1.34.0      
 [4] beadarray_2.6.0       BeadDataPackR_1.8.0   Cairo_1.5-1          
 [7] cluster_1.14.2        colorspace_1.1-1      genefilter_1.38.0    
[10] grid_2.15.0           Hmisc_3.9-3           hwriter_1.3          
[13] KernSmooth_2.23-7     lattice_0.20-6        latticeExtra_0.6-19  
[16] limma_3.12.0          plyr_1.7.1            preprocessCore_1.18.0
[19] RColorBrewer_1.0-5    reshape2_1.2.1        setRNG_2011.11-2     
[22] splines_2.15.0        stats4_2.15.0         stringr_0.6          
[25] survival_2.36-14      SVGAnnotation_0.9-0   tools_2.15.0         
[28] vsn_3.24.0            XML_3.9-4.1           xtable_1.7-0         
[31] zlibbioc_1.2.0       

Warning message:
package ‘RCurl’ is not available (for R version 2.15.0) 

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