[BioC] GEOquery loading error

[Zhang, Jian]

Guess I missed the end:

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

Jian

-----Original Message-----
From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] 
Sent: Friday, May 25, 2012 4:01 PM
To: Jian Zhang [guest]
Cc: bioconductor at r-project.org; Zhang, Jian
Subject: Re: [BioC] GEOquery loading error

Hello Jian,

On Fri, May 25, 2012 at 3:39 PM, Jian Zhang [guest]
<guest at bioconductor.org> wrote:
>
> 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.
>
> Thanks.
>
>  -- output of sessionInfo():
>
>>library(GEOquery)
> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
>  there is no package called ‘RCurl’
> Error: package/namespace load failed for ‘GEOquery’
>
>>traceback()
> 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
>

It doesn't look like you are showing the full output of this command.
Did it complete successfully or was there an error? GEOquery is
failing because RCurl is not installed, so it's important to know the
full output of
biocLite("RCurl")

Dan


>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [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)
>
>
>
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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