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@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