I am having trouble updating GenomicFeatures package. Can you please look at it and let me know what I doing wrong. this is the error I get Error : object ???findSpliceOverlaps??? is not exported by 'namespace:GenomicRanges' ERROR: lazy loading failed for package ???GenomicFeatures??? thanks kavita > biocLite("GenomicFeatures") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.9. Installing package(s) 'GenomicFeatures' trying URL 'http://bioconductor.org/packages/2.10/bioc/src/contrib/Gen omicFeatures_1.8.3.tar.gz' Content type 'application/x-gzip' length 1749597 bytes (1.7 Mb) opened URL ================================================== downloaded 1.7 Mb * installing *source* package ???GenomicFeatures??? ... ** R ** inst ** preparing package for lazy loading Error : object ???findSpliceOverlaps??? is not exported by 'namespace:GenomicRanges' ERROR: lazy loading failed for package ???GenomicFeatures??? -- output of sessionInfo(): R version 2.15.3 (2013-03-01) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.4.9 lattice_0.20-13 Biostrings_2.26.3 [4] AnnotationDbi_1.20.6 Biobase_2.18.0 GenomicRanges_1.8.13 [7] IRanges_1.16.6 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] biomaRt_2.14.0 bitops_1.0-5 BSgenome_1.26.1 DBI_0.2-5 [5] grid_2.15.3 parallel_2.15.3 RCurl_1.95-4.1 RSQLite_0.11.2 [9] stats4_2.15.3 tools_2.15.3 XML_3.95-0.2 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.

Hi, On Mon, Apr 29, 2013 at 9:23 AM, Kavita Garg [guest] <guest at="" bioconductor.org=""> wrote: > > I am having trouble updating GenomicFeatures package. Can you please look at it and let me know what I doing wrong. > > this is the error I get > > Error : object ???findSpliceOverlaps??? is not exported by 'namespace:GenomicRanges' > ERROR: lazy loading failed for package ???GenomicFeatures??? > > thanks > kavita > >> biocLite("GenomicFeatures") > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.9. > Installing package(s) 'GenomicFeatures' > trying URL 'http://bioconductor.org/packages/2.10/bioc/src/contrib/G enomicFeatures_1.8.3.tar.gz' This seems very strange to me -- it looks like you are running R 2.15 but your installation seems out of date (and biocLite isn't helping here, even it is an loder version) -- seems like your setup is wonky. R 2.15 should be using version 2.11 of the bioc "release train". You need to update lots of things, and you can start with BiocInstaller (http://bioconductor.org/packages/2.11/bioc/html/GenomicRanges.html), but perhaps it's a good time to upgrade to R-3.0 and get the latest and greatest everything (by reinstalling all of your packages with biocLite) since you need to do a lot of housekeeping work now anyway. HTH, -steve -- Steve Lianoglou Computational Biologist Department of Bioinformatics and Computational Biology Genentech