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Hello, This question popped up on the bioc-devel list, I'm forwarding it here. I know that sources for R-2.14 alpha can be found here: http://cran.r-project.org/src/base-prerelease/ But the OP (below) is asking about Windows binaries. Dan ---------- Forwarded message ---------- From: Stefan McKinnon H?j-Edwards <Stefan.Hoj-Edw...

...xing the DESCRIPTION file for EBImage. FYI, the Windows > >> version does not build: > >> > >> * creating vignettes ... ERROR > >> Error in inDL(x, as.logical(local), as.logical(now), ...) : > >> unable to load shared library > >> > 'D:/biocbld/bbs-2.3-bioc/tmpdir/Rinst415629052/EBImage/libs/EBImage.dll': > >> LoadLibrary failure: The specified procedure could not be found. > >> > >> Error: processing vignette 'AnalysisWithEBImage.Rnw' failed with > >> diagnostics: > >> chunk...

...ccomplished by faking it, installing pkgKitten and then doing: library(pkgKitten) kitten("AnnotationDbi") Then exiting R and doing R CMD INSTALL AnnotationDbi. Here's the problem: > packageVersion("AnnotationDbi") [1] ?1.0? > options(repos=structure(c("http://bioconductor.org/packages/3.1/bioc", "http://bioconductor.org/packages/3.1/data/annotation", + "http://bioconductor.org/packages/3.1/data/experiment", "http://bioconductor.org/packages/3.1/extra", + "http://cran.fhcrc.org"), .Names = c("BioCsoft",...

Dear all, My gRbase package imports functionality from the bioconductor packages graph, Rgraphviz and RBGL. To make installation of gRbase easy, I would like to have these bioconductor packages installed in connection with installation of gRbase, but to do so the user must use setRepositories() to make sure that R also installs packages from bioconductor. Hav...

I have just finished a graduate introductory R & BioC class, and found them very interesting. At this moment, I am not doing any R & BioC related-work, which might end up with "use it or lose it". My plan is to get into bioinformatics fields shortly after the completion of master's degree in bioinformatics that I am studying. Co...

(xposted to bioc-devel and r-devel as I feel it is relevant to both communities) As someone whose body of work is likely to consist mostly of infrastructural packages and research directly in computing I wholeheartedly agree with Kasper's suggestion that we as a community should work to provide and use package...

...t really necessary to issues this warning message? - If yes, could it be suppressed on Windows XP, since there it should obviously be no problem. One more issue: While I have always received this warning on my WinXP installation, for some lucky reason the warning did until now not appear on the Bioconductor Windows server, see BioC 2.6 with R-2.11.1: http://bioconductor.org/checkResults/2.6/bioc-LATEST/xps/liverpool-checksrc.html However, for some reason on BioC 2.7 running R-2.12.0 this warning does appear, see: http://bioconductor.org/checkResults/2.7/bioc-LATEST/xps/liverpool-checksrc.htm...

In pvec(list(1, 2), FUN, mc.cores=2) FUN sees integer() arguments whereas pvec(list(1, 2, 3), FUN, mc.cores=2) FUN sees list() arguments; the latter seems consistent with pvec's description. This came up in a complicated Bioconductor thread about generics and parallel evaluation https://stat.ethz.ch/pipermail/bioc-devel/2012-October/003745.html One relevant point is that a light-weight re-write of parallel/R/unix/pvec.R (below) appears to avoid the need for an object v to satisfy is.vector as.list [ an...

Hi, The R-based version of R CMD build doesn't work for me on Windows: E:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\Biobase * checking for file 'meat\Biobase/DESCRIPTION' ... OK * preparing 'Biobase': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes Warning in shell(sprintf(&quo...

[CC:ing package maintainer of 'impute' package and crossposting to r-devel and bioc-devel because this affects both audiences] Hi, the 'impute' package is published both on CRAN and Bioconductor; http://cran.r-project.org/web/packages/impute/ http://bioconductor.org/packages/2.3/bioc/html/impute.html The one on CRAN is v1.0-5, and the one on BioC is v1.14.0. The two...

...hat packages are attached. > > If showMethods or a wrapper for it could be convinced to output a link > to a help file, then it might actually be a good way to go... > > + seth > > -- > Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center > http://bioconductor.org > > _______________________________________________ > Bioc-devel at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org

Dear all, i was working under R 1.6.2 but i wanted to install bioconductor under WinXP, and because R 1.7.1 contains the TclTk package and automatic installation of bioconductor packages, so i install it. Everything is fine except this message which appear after the installation of packages. "> local({a<- CRAN.packages(CRAN=getOption("BIOC&quo...

Dear All, There is a question I met when using Affy package in Bioconductor. I asked it in BioC and didn't get any responses. Sorry to post again: Could anyone tell me how to draw a deep-blue Affymetrix image through Image() function in Affy package? The default settings of image() draw me a black-white image and if I modify it to 256 colors, I get a someho...

I'm trying to load an annotation file on a new R installation on a new machine (Win 7 x64, R 2.15.0) Loading this package fails; I've tried re-installing R and BioC from scratch, including all new packages etc, to no avail. Any ideas? > require("hugene10sttranscriptcluster.db") Loading required package: hugene10sttranscriptcluster.db Loading required package: AnnotationDbi Loading required package: BiocGenerics Attaching package: ?BiocGenerics?...

Hi, This is a follow up to: https://stat.ethz.ch/pipermail/r-devel/2010-July/057921.html The Bioconductor daily builds have been reporting a lot of strange things lately on Windows using R-2.12. This started 2 or 3 months ago and things are not getting better with recent R-2.12. Here is a sample from today's build results. We use Windows Server 2003 R2 for the 32-bit builds, Windows Server...

Hi, I started this post on bioc-devel but this seems to be more general: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html See reproducible example from Martin below. Thank you. Renaud ---------- Forwarded message ---------- From: Martin Morgan <mtmorgan at fhcrc.org> Date: 7 May 2013 19:55 Subject: Re: [B...

Dear all, Since many years the following C++ code does compile on ALL Bioconductor servers (Linux, Windows, Mac) without any warnings: Int_t numsels = 0; //number of selected entries ... for (Int_t i=0; i<size; i++) { numsels = (arrMask[i] == 1) ? ++numsels : numsels; }//for_i Even on the recently added release server 'zin2' Linux (Ub...

You asked the same question on the Bioconductor mailing list back in August. At that time, you suggested yourself a solution for how the adjusted p-values should be interpreted. I answered your query and told you that your interpretation was correct. So I'm not sure what more can be said, except that you should read the article Wr...

Hello, I'm seeing three different vignette-related errors with recent versions of R-3.0.0 alpha. First, with the package BitSeq (http://bioconductor.org/packages/2.12/bioc/html/BitSeq.html), I get the following when trying to build the package: Error: processing vignette ?BitSeq.Rnw' failed with diagnostics: Failed to locate the ?weave? output file (by engine ?utils::Sweave?) for vignette with name ?BitSeq?. The following files exi...

Dear lists: I am somewhat puzzled by the use of texi2dvi/pdflatex in R2.7.0. When building EBImage (bioconductor) with 2.7.0 I get the same error both in Windows and Linux, which reads the following: ** building package indices ... * DONE (EBImage) * creating vignettes ... ERROR /usr/bin/texi2dvi: pdflatex exited with bad status, quitting. Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, qui...