similar to: Bug/problem reporting: Possible to modify posting guide FAQ?

Hi, in 'Writing R Extensions" of R v2.10.0, under Section 'Cross-references' (2009-09-07) it says: 1. "The markup \link{foo} (usually in the combination \code{\link{foo}}) produces a hyperlink to the help for foo. Here foo is a topic, that is the argument of \alias markup in another Rd file (possibly in another package)." 2. "You can specify a link to a different

Hi, Today we've seen the following problem with the R-2.12 that we use for our Windows builds: > installed.packages() Error: subscript out of bounds After some investigation we discovered that the cause of this failure was that 1 of the 890 packages currently installed on the machine (Windows Server 2003 R2) had its DESCRIPTION file empty:

Hi All, I posted this on the bioconductor list and didn't get a response there, so I'm hoping someone here can help. I don't know a heck of a lot about R, so I apologize if this seems like a trivial issue. This error comes up when trying to install the bioconductor globaltest package. Any clues? Thanks! Rusty -----Original Message----- From: bioconductor-bounces at r-project.org

Hi, On Windows, with last R-devel tarball (r40647) from ftp://ftp.stat.math.ethz.ch/Software/R/R-devel_2007-02-04.tar.gz I get the following build error: E:\biocbld\bbs-2.0-bioc\R\src\gnuwin32> make ... ... ---------- Making package utils ------------ adding build stamp to DESCRIPTION installing NAMESPACE file and metadata installing R files Error in namespaceExport(ns, exports) :

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-Edwards at agrsci.dk> Date: 2011/10/4 Subject: Re:

Naras, Thanks. I'm a bit confused, because Rmosek does not declare Matrix as a dependency: > tools::package_dependencies("Rmosek", which = "all")[[1L]] [1] "pkgbuild" nor does it contain code needing compilation: > packageDescription("Rmosek", fields="NeedsCompilation") [1] "no" Can you explain the

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. Having to call setRepositories causes

If I f = function() {} package.skeleton("PkgA", "f", path="/tmp") and then edit man/PkgA-pacakge.Rd to read in part \description{ More about what it does (maybe more than one line) \Sexpr{1} } and then R CMD build PkgA I end up with Saving output to ?/tmp/PkgA/build/PkgA.pdf? ... Warning in file.create(to[okay]) : cannot create file

Dear all, When running R CMD check on Windows XP to test my package I get the following warning message: "* checking line endings in C/C++/Fortran sources/headers ... WARNING Found the following sources/headers with CR or CRLF line endings: src/xpsDict.h" The problem is that this file is created by the compiler AUTOMATICALLY during the compilation process, and since the file is

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("%s > %s

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 (Ubuntu 12.04.4 LTS) the

A post on the Bioconductor mailing list https://stat.ethz.ch/pipermail/bioconductor/2009-May/027700.html suggests that install.packages now references .Rprofile (?), whereas in R-2-8 it did not. Is this intentional? The example is, in .Rprofile library(utils) install.packages("Biobase", repos="http://bioconductor.org/packages/2.4/bioc") then

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")) +

Hi list, Here is an example: ??? hpages at XPS15:~$ R CMD INSTALL CoreGx ??? * installing to library ?/home/hpages/R/R-4.4.r85388/site-library? ??? * installing *source* package ?CoreGx? ... ??? ** using staged installation ??? ** R ??? ** data ??? *** moving datasets to lazyload DB ??? ** inst ??? ** byte-compile and prepare package for lazy loading ??? Error : in method for

Hi, After updating R-2.12 on the Bioconductor build system about 1 week ago (we update R every 4-6 weeks for our devel builds), we've started to see something never seen before on Windows: for some BioC packages, 'R CMD build' would produce no output at all (0 byte) and, of course, no source tarball. Even though, the code returned by the command is 0! See an example of this is here:

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

I have observed a difference in behavior of R CMD check in older R vs R-2.10.x on windows. * using R version 2.10.0 (2009-10-26) * using R version 2.10.1 RC (2009-12-14 r50718) 2.10 seems to be looking on the internet for crossreferenced packages. I am not sure why it is looking. The string <pkg> is not in any of the Rd files. I think it is not finding any CRAN sites because I am

>>>>> Herv? Pag?s >>>>> on Fri, 3 Nov 2023 15:10:40 -0700 writes: > Hi list, > Here is an example: > ??? hpages at XPS15:~$ R CMD INSTALL CoreGx ??? * installing > ??? hpages at XPS15:~$ R CMD INSTALL CoreGx > ??? * installing to library ?/home/hpages/R/R-4.4.r85388/site-library?

In the context of installing a Bioconductor package using our biocLite() function, install.packages() warns > install.packages("RUVSeq", repos="http://bioconductor.org/packages/2.14/bioc") Installing package into '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1-2.14' (as 'lib' is unspecified) Warning message: package 'RUVSeq' is not available

Hi, I am expieriencing strange behaviour of llvm's optimization passes and I don't understand what I am doing wrong. Basically all I've done is extracting code for optimization of a llvm-function in a llvm-module and put it into a separate function for better readability. The original code looks like follows (and works as expected): ----------------------------- std::string