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

[Dan Tenenbaum]

Hi Sean,


On Thu, Feb 28, 2013 at 1:28 PM, Sean [guest] <guest at bioconductor.org> 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/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.
>

Try this:
biocLite("BSgenome.Dmelanogaster.UCSC.dm3", type="source")

As for RStudio, I'm not sure, what is your OS and output of
sessionInfo()? I successfully use RStudio with R-3.0.0. Make sure that
the first R in your path is R-devel.

Dan


> 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
>>
>
> --
> 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