Yeah I just tried it and no dice.  At one point I looked into patching
R-devel so that this wouldn't be such an issue but the scope of the
extern/extern0 declarations foiled me.  Plus Prof Ripley probably would not
have accepted the patch anyways, as it's more of an Rstudio issue really

thanks!

--t



On Thu, Feb 28, 2013 at 1:56 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

> On Thu, Feb 28, 2013 at 1:54 PM, Tim Triche, Jr. <tim.triche@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@fhcrc.org>
> wrote:
> >>
> >> Hi Sean,
> >>
> >>
> >> On Thu, Feb 28, 2013 at 1:28 PM, Sean [guest] <guest@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@r-project.org
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > Search the archives:
> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> >
> >
> >
> > --
> > A model is a lie that helps you see the truth.
> >
> > Howard Skipper
>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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