similar to: 7 arguments passed to .Internal(identical) which requires 6

Hello, I've just installed R-2.15.0 (I've had R 2.13.2 before it and I've deleted everything before I started to install new version). When I've tried to run my script by command "source()" I received this message: Error in source("script.R") : 7 arguments passed to .Internal(identical) which requires 6 I know I should delete my $R_HOME but it contain only

Hello, I see the following issue in R-devel since 'both' has become the default pkgType for binary platforms. update.packages() fails when you set options(repos). Looks like it is trying to download a tgz file from the src/contrib section of a repository (on a mac). To reproduce this you need to have an older version of AnnotationDbi installed, which I accomplished by faking it,

[Env: Win Xp / StatET 2.0 / R 2.15.0] In my heplots package I extended the HE-examples.Rnw vignette under inst/doc. The package passes R CMD check on my machine: * using log directory 'C:/eclipse-3.7/heplots.Rcheck' * using R version 2.15.0 (2012-03-30) * using platform: i386-pc-mingw32 (32-bit) ... * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files

Dear list, as I started installing R-2.15.0 on a Red Hat 4.5.1-4 as well a Ubuntu 10.04.3 systems. While the basic installation went fine (like the previous R-2.14.2), now I'm having trouble installing almost one third of the additional libraries I want (which installed flawlessly with R-2.14.2), among them RODBC for which I show the message below (obtained on Ubuntu) :

Hi All, I tried to install AnnotationDBI like so: source("http://bioconductor.org/biocLite.R") biocLite("AnnotationDbi") and got this error: .... Loading required package: RSQLite Error in dyn.load(file, ...) : unable to load shared library '/RHEL3/local/lib64/R/library/ RSQLite/libs/RSQLite.so': /RHEL3/local/lib64/R/library/RSQLite/libs/RSQLite.so: undefined

Hi All, I tried to install AnnotationDBI like so: source("http://bioconductor.org/biocLite.R") biocLite("AnnotationDbi") and got this error: .... Loading required package: RSQLite Error in dyn.load(file, ...) : unable to load shared library '/RHEL3/local/lib64/R/library/ RSQLite/libs/RSQLite.so': /RHEL3/local/lib64/R/library/RSQLite/libs/RSQLite.so: undefined

I've started to use the parallel package and it works very well speeding things up. Thank you for making this easy to do. Should I have expected that parCapply would return a vector when parApply returns a matrix? library(parallel) x <- matrix(rnorm(8), nc = 2) apply(x, 2, function(y) y) [,1] [,2] [1,] -0.9649685 0.91339851 [2,] -1.4313140 0.13457671 [3,] 1.0499248

I am the maintainer of a Bioconductor package (affylmGUI) which uses tcltk. It freezes inconsistently on MS Windows, but not Mac or Unix. see details below. After considerable testing I have reduced the problem from a few thousand lines of code to 30 lines! If you paste the following lines of code into an R window: testGUI <- function(){ require(tcltk) MainWindow <-

Being rather inept at all things Linux, I paid a consultant to fix some things on my computer,? Unforntately, good help is hard to find.? Here's where I am: ? ... Loading required package: Matrix Loading required package: lattice Error in dyn.load(file, DLLpath = DLLpath, ...) : ? function 'cholmod_l_start' not provided by package 'Matrix' Error: package/namespace load failed

Hello everyone, I have a problem when loading the library: IlluminaHumanMethylation27k.db I installed the package from zip (from the Bioconductor website), and also installed all the packages it asked for. It went all succesfull: "package 'IlluminaHumanMethylation27k.db' successfully unpacked and MD5 sums checked" But when I am trying to load this library I get an error:

Greetings I am trying to make a multiple panel plot from a tool (genoPlotR) that is layered on grid. My code and session info are below. When I execute the code, I get a single plot in the center of the graphics page. I have tried various pop/push/down/seekViewport commands at the end of the plotpush method. There must be something I'm missing in the documentation, I believe what I

> sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid datasets splines utils stats [6] graphics grDevices methods base other attached packages: [1] effects_2.1-0 colorspace_1.1-1 [3] nnet_7.3-1

Hi all, I was installing a package *RBGL* of bioconductor. However, I had some issues while installing it. I asked the devel group of bioconductor and they told me to consult this group. Here is my conversation with the bioconductor group related to the problem *Me->* I was trying to install the RBGL package using the following command biocLite("RBGL") However, I got the

Hello, I am working with a database system from which I can retrieve these kinds of user defined fields formed as XML ... <udf:field unit="uM" type="Numeric" name="facs.Stain final concentration">5</udf:field> You can see in the above example that "field" is defined in the namespace "udf", but that the "udf" namespace is

Hi all, I was installing a package *RBGL* of bioconductor. However, I had some issues while installing it. I asked the devel group of bioconductor and they told me to consult this group. Here is my conversation with the bioconductor group related to the problem *Me->* I was trying to install the RBGL package using the following command biocLite("RBGL") However, I got the

Hi, Many S4 objects in Bioconductor support "combining" via a "c" method. A common use case is to combine a collection of S4 objects stored in a list with the following idiom: do.call("c", list_of_objects) For many users this doesn't return what they expect though, because their 'list_of_objects' is a named list and this seems to "break"

Hi, Here is a problem we see with the Mac and Windows binaries of rJava (0.9-3) currently available on CRAN for R-devel (i.e. under bin/macosx/leopard/contrib/2.16/ and bin/windows/contrib/2.16/): > library(rJava) > .jinit("gaggle/inst/jars/gaggleRShell.jar") Error in .Call("R_do_new_object", ClassDef, PACKAGE = "base") :

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

mogene10stprobeset.db is generated with AnnotationDbi for mouse gene array. I don't find a package that seems generated by AnnotationDbi for exon arrays on the webpage you mentioned. Is it correct? On Tue, Oct 27, 2009 at 7:00 PM, Marc Carlson <mcarlson at fhcrc.org> wrote: > Hi Peng, > > I am not completely clear from your post what you want. ?But most of our > annotation

Dear R-devel, While tracking down some hard-to-reproduce bugs in a package I maintain, I stumbled on a behavior change between R 2.15.0 and the current R-devel (or SVN trunk). In 2.15.0 and earlier, if you passed an 0-length vector of the right mode (e.g., double(0) or integer(0)) as one of the arguments in a .C() call with DUP=TRUE (the default), the C routine would be passed NULL (the C