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

[Dan Tenenbaum]

On Thu, Feb 28, 2013 at 1:54 PM, Tim Triche, Jr. <tim.triche at gmail.com> wrote:
> Hi Dan,
>
> Was the bug you reported regarding recent Rstudio-server and R-devel (3.0)
> builds resolved?
>

Not yet as far as I know, I hope to see an update here soon:

http://support.rstudio.org/help/discussions/problems/4946-rstudio-server-broken-with-recent-r-devel

Dan


> thanks,
>
> --t
>
>
>
> On Thu, Feb 28, 2013 at 1:45 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> 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.
>> >
>> > _______________________________________________
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>> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
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>
>
>
>
> --
> A model is a lie that helps you see the truth.
>
> Howard Skipper