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

[Dan Tenenbaum]

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

Looks like they are working on this:

https://github.com/rstudio/rstudio/commit/d66e07d977913bb6ce3e69df2e10f94ed48a0216

Dan



> 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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>>>
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>>
>>
>>
>>
>> --
>> A model is a lie that helps you see the truth.
>>
>> Howard Skipper