[BioC] BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0

[Sean [guest]]

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/annotation/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:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] Biostrings_2.27.11                    
 [2] IntermediateSequenceAnalysis2013_0.1.1
 [3] SequenceAnalysisData_0.1.4            
 [4] edgeR_3.1.4                           
 [5] limma_3.15.14                         
 [6] GenomicFeatures_1.11.11               
 [7] AnnotationDbi_1.21.10                 
 [8] Biobase_2.19.2                        
 [9] GenomicRanges_1.11.30                 
[10] IRanges_1.17.35                       
[11] BiocGenerics_0.5.6                    

loaded via a namespace (and not attached):
 [1] biomaRt_2.15.0     bitops_1.0-5       BSgenome_1.27.1    DBI_0.2-5         
 [5] RCurl_1.95-3       Rsamtools_1.11.17  RSQLite_0.11.2     rtracklayer_1.19.9
 [9] stats4_3.0.0       tools_3.0.0        XML_3.95-0.1       zlibbioc_1.5.0    
> 

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