similar to: More strange R CMD build/check errors on Windows

Hi, I found the following problem with recent R-devel (2010-08-26 r52817) on Windows (32-bit and 64-bit): 'R CMD build <pkg>' gets stalled during vignette creation for packages that have a Makefile in <pkg>/inst/doc. It seems that the problem is that the commands used in the Makefile for converting .tex to .pdf are not able to locate the Sweave.sty file anymore (if I drop

Hi, Why isn't 'R CMD check --force-multiarch' installing the package for all the architectures that are going to be checked? For some packages, it only installs for the default arch ('i386'). Then testing the package for 'x64' fails. For example, Output of R CMD check --force-multiarch fabia_1.5.0.tar.gz: ----------------------------------------------------------- *

Hello, I have come across two separate packages that have a Makefile in inst/doc which use the R_HOME variable. In both cases, the path to R_HOME gets munged in such a way that commands that include R_HOME fail on Windows: For example, one Makefile, for the xmapcore package ( https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xmapcore/username/password: readonly) has this:

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

Hi, 'R CMD build' (with R 2.12.0 RC) fails to clean the src/ folder on Windows: D:\biocbld\bbs-2.7-bioc>ls meat/BUS/src BUS.cpp BUS.h D:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\BUS * checking for file 'meat\BUS/DESCRIPTION' ... OK * preparing 'BUS': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package

Hi, Every day a few Bioconductor packages (different ones each day) fail to build, on Windows only, with an error like this: D:\biocbld\bbs-2.13-bioc\meat>D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data OrganismDbi [...] Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : Failed to locate the 'texi2pdf' output file (by

We are trying to setup a Windows server that will allow any of our users to build a binary R package given a source package. The idea is to have a central R installation and allow users to install packages to their own package library for the purposes of binary package building. It seems, however, that write access to $R_HOME is required as part of the install step even when -l is used to

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) :

I am having a problem using two DLLs with the same name, but obviously located in different directories, in an R session. The troublesome package is the (Bioconductor) Rgraphviz package. It relies on (3rd party software) graphviz and imports functions from (Bioconductor) package graph. Unfortunately, the current stable release of graphviz for Windows

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

Just thought I would mention that the issue below (and in https://stat.ethz.ch/pipermail/r-devel/2013-April/066318.html) is still not resolved. It hasn't been a big problem, but it potentially could be, if a critical package were to have this error on release day, then all its dependencies would fail to build, which would probably require us to postpone our release. See the complete thread

Hi, Installing from binaries on Windows: > install.packages("multtest") Warning: dependency 'Biobase' is not available trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.12/multtest_2.6.0.zip' Content type 'application/zip' length 1645590 bytes (1.6 Mb) opened URL downloaded 1.6 Mb package 'multtest' successfully unpacked

Hi, On both Unix and Windows there is a mechanism to add variables to the environment when R is started. I noticed that, on Unix, this mechanism is not used when R is started normally at the command line but only when it's started using the 'R CMD' syntax. One problem with this is some lack of consistent cross-platform behaviour. For example: On Linux: $ echo $TEXINPUTS $

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:

Dear all, I am a PhD student working with Affymetrix HGU133atag array for analyzing the Latin square experiment. I was trying to generate gene expression index for hgu133atag array for PDNN model. While extracting the chiptype specific data structure, I got the following error- > library(affypdnn) Loading required package: affy Loading required package: Biobase Welcome to Bioconductor

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When

Hi, So in an interactive R session, R.home() returns the following: > R.home() [1] "D:/biocbld/bbs-3.2-bioc/R" However, if I call it from system2(), I get different results: > system2("R", "-q -e R.home()") > R.home() [1] "D:/biocbld/BBS-3~1.2-B/R" Similarly: > system2("R", "-q -e Sys.getenv('R_HOME')") >

Greetings! The Bioconductor core group would like to announce the 5th release of Bioconductor, version 1.4. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to upgrade existing tools and check out the new packages. Release 1.4 is intended to be operated with R version 1.9.x, which can be obtained at CRAN

On Wed, Aug 13, 2008 at 6:56 AM, Laurent Gautier <lgautier@gmail.com> wrote: > There is a chance that further changes in the handling of plotting > devices event appear; > I think that there is an ongoing effort to bring new features for R-2.8. > > What about bumping that to r-devel ? (Sorry if you already did and I missed > it). > The solution you came up with could be