similar to: Recent snapshot tarballs of R-devel don't compile

Hi, I'm running into a case where byte-compilation changes the semantic of a function. This is with R 3.4.0: foo <- function(x) { TRUE && x } foo(c(a=FALSE)) # [1] FALSE # OK foo(c(a=TRUE)) # [1] TRUE # OK foo(c(a=FALSE)) # a # ???? # FALSE The 3rd call returned a result that it different from the 1st call! After

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

Hi there, Is that change in R-devel intentional? library(Matrix) m <- as(matrix(c(0, 1)), "sparseMatrix") isS4(m) # [1] TRUE x <- I(m) # Warning message: # In `class<-`(x, unique.default(c("AsIs", oldClass(x)))) : # Setting class(x) to multiple strings ("AsIs", "dgCMatrix", ...); result will no longer be an S4 object

Hi, I created a package as follows: > a = 1 > package.skeleton() Then I got the following output when building the package: * checking for file ?anRpackage/DESCRIPTION? ... OK * preparing ?anRpackage?: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories * looking to see if a ?data/datalist?

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) :

The Bioconductor build for a package DirichletMultinomial on R Under development (unstable) (2013-02-26 r62077) -- "Unsuffered Consequences" at http://bioconductor.org/checkResults/devel/bioc-LATEST/DirichletMultinomial/george2-buildsrc.html shows * creating vignettes ... ERROR ... Error: processing vignette ?DirichletMultinomial.Rnw? failed with diagnostics: chunk 21 (label

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: ----------------------------------------------------------- *

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, 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

On 26/04/2017 4:36 PM, Herv? Pag?s wrote: > Hi, > > I'm running into a case where byte-compilation changes > the semantic of a function. This is with R 3.4.0: > > foo <- function(x) { TRUE && x } > > foo(c(a=FALSE)) > # [1] FALSE # OK > > foo(c(a=TRUE)) > # [1] TRUE # OK > > foo(c(a=FALSE)) > #

Thanks for the report. Fixed in R_devel with r72631; I'll port to R-patched later today or tomorrow. The default setting and how to get the current settings are documented in the Details section of the enableJIT help page at the end of the paragraph for enableJIT. Best, luke On Wed, 26 Apr 2017, Herv? Pag?s wrote: > Hi, > > I'm running into a case where byte-compilation

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 there, > Is that change in R-devel intentional? > > library(Matrix) > m <- as(matrix(c(0, 1)), "sparseMatrix") > > isS4(m) > # [1] TRUE > > x <- I(m) > # Warning message: > # In `class<-`(x, unique.default(c("AsIs", oldClass(x)))) : > # Setting class(x) to multiple strings ("AsIs",

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, 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

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

The release version of ChemmineR is failing on windows. It seems to be a build script issue though, possibly something on your side. The package was building fine a few weeks ago and I have not modified it. Can you please have a look? Thanks. "C:/Users/BIOCBU?1/BBS-3?1.6-B/R/bin/Rscript" -e "library(rmarkdown); library(BiocStyle); rmarkdown::render('ChemmineR.Rmd')"

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, The acrobatics that as.data.frame.factor() is going thru in order to recognize a direct call don't play nice if as.data.frame() is an S4 generic: ??? df <- as.data.frame(factor(11:12)) ??? suppressPackageStartupMessages(library(BiocGenerics)) ??? isGeneric("as.data.frame") ??? # [1] TRUE ??? df <- as.data.frame(factor(11:12)) ??? # Warning message: ??? # In

In the process of updating R to R 2.7 alpha or R 2.7 beta for the BioConductor 2.2 builds on Windows, I have hit a snag because the BioC build system has long path names (e.g. D:\biocbld\bbs-2.2-bioc\R) and these path names are not resolving properly by MiKTeX 2.7 during vignette construction. Take, for example, the attached vignette from Biobase, Bioconductor.Rnw. I have built R from source