Question: BSgenome.Dmelanogaster.UCSC.dm3 in R 3.0
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gravatar for Dan Tenenbaum
6.8 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
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/d66e07d977913bb6ce3e69df2e10 f94ed48a0216 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/BSg enome.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 >>> >>> _______________________________________________ >>> 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 >> >> >> >> >> -- >> A model is a lie that helps you see the truth. >> >> Howard Skipper
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