[BioC] GEOquery loading error

[Zhang, Jian]

Dan,

You are right on! I am behind a firewall of the company.
Starting with R --internet2 worked for downloading RCurl, and the subsequent library(GEOquery) worked.

Thanks a lot! 
Jian

-----Original Message-----
From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] 
Sent: Friday, May 25, 2012 5:31 PM
To: Zhang, Jian
Cc: Jian Zhang [guest]; bioconductor at r-project.org
Subject: Re: [BioC] GEOquery loading error

OK, see below:

On Fri, May 25, 2012 at 5:01 PM, Zhang, Jian <jianz at amgen.com> wrote:
> 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


I think this is the problem right here. RCurl is in this repository
(as you can see if you put that link into a browser) but biocLite()
can't see it. Are you behind a proxy or something? Try starting R like
this:
R --internet2
and see if that works better.

If that fails you can always download
http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.15/RCurl_1.91-1.1.zip

but biocLite() is very much the preferred approach.
Dan

>>
>
> 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.
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor