Question: BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
6.8 years ago by
Guest User • 12k
Guest User • 12k wrote:
I am trying to get myself more familiar with Bioconductor, so I have been walking through the vignette of the 2013 Intermediate R/Bioconductor for Sequence Analysis course offered earlier this month (February 2013). (Link to course page and vignette: http://www.bioconductor.org/help/course- materials/2013/SeattleFeb2013/). I have installed R 3.0 and Bioconductor 2.12 as per the instructions in the vignette. I now have two problems: The first seems relatively minor: I cannot seem to get RStudio to open R 3.0. I simply get a message that says that "The R session had a fatal error." I can open R using its own GUI, but it would be nice to work within RStudio. The second is a bit more problematic. I have been able to follow the vignette without too many problems up until Chapter 5 "Strings and Reads". The exercise has you load the BSgenome.Dmelanogaster.UCSC.dm3 data package. I am able to download the package using the provided link to the development version of the Drosophila genome (http://bioconductor.org/packages/devel/data/annotat ion/html/BSgenome.Dmelanogaster.UCSC.dm3.html) and by entering the following code: >source("http://bioconductor.org/biocLite.R") >biocLite("BSgenome.Dmelanogaster.UCSC.dm3") However, when I try to load the library, I get the following: > library(BSgenome.Dmelanogaster.UCSC.dm3) Error: package ???BSgenome.Dmelanogaster.UCSC.dm3??? was built before R 3.0.0: please re-install it The library installs on earlier releases of R, but I cannot convince it to run on R 3.0 where I can make use of the current vignette. Any advice on either of these two issues, but particularly the second, would be greatly appreciated. Sean -- output of sessionInfo(): > sessionInfo() R Under development (unstable) (2013-02-21 r62017) Platform: x86_64-w64-mingw32/x64 (64-bit) locale:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  parallel stats graphics grDevices utils datasets methods  base other attached packages:  Biostrings_2.27.11  IntermediateSequenceAnalysis2013_0.1.1  SequenceAnalysisData_0.1.4  edgeR_3.1.4  limma_3.15.14  GenomicFeatures_1.11.11  AnnotationDbi_1.21.10  Biobase_2.19.2  GenomicRanges_1.11.30  IRanges_1.17.35  BiocGenerics_0.5.6 loaded via a namespace (and not attached):  biomaRt_2.15.0 bitops_1.0-5 BSgenome_1.27.1 DBI_0.2-5  RCurl_1.95-3 Rsamtools_1.11.17 RSQLite_0.11.2 rtracklayer_1.19.9  stats4_3.0.0 tools_3.0.0 XML_3.95-0.1 zlibbioc_1.5.0 > -- Sent via the guest posting facility at bioconductor.org.
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