similar to: Missing PROTECT in mkPRIMSXP ?

Hi, After updating to R-3.0 beta r62328, I get the following: > install.packages("Biobase", type="source", repos="http://george2/BBS/2.12/bioc") Error in do.call(op, list(v_c, v_t[[op]])) : could not find function "R (>=2.15.1)" The problem can be fixed by adding a space after >= in the offending package's DESCRIPTION file and re-generating

Hi, Starting with ordinary vectors, so we know what to expect: > mapply(function(x, y) {x * y}, 101:106, rep(1:3, 2)) [1] 101 204 309 104 210 318 > mapply(function(x, y) {x * y}, 101:106, 1:3) [1] 101 204 309 104 210 318 Now with an S4 object: setClass("A", representation(aa="integer")) a <- new("A", aa=101:106) > length(a)

Hi, The current implementation for utils::tar() seems to generate broken tarballs when some of the files to include in the tarball are >= 2GB. For example, when running 'R CMD build' on a big Bioconductor data package, we see this warning: * checking for file ?ChIPXpressData/DESCRIPTION? ... OK * preparing ?ChIPXpressData?: * checking DESCRIPTION meta-information ... OK *

Hi, Trying to compile one of the latest snapshot tarballs of R-devel gives me the following error (64-bit openSUSE 10.3): ... make[2]: Entering directory `/loc/home/biocbuild/bbs-2.4-bioc/R/src/library/Recommended' make[2]: *** No rule to make target `VR.ts', needed by `stamp-recommended'. Stop. make[2]: Leaving directory

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

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, Starting with the XML package installed: > "XML" %in% rownames(installed.packages()) [1] TRUE > I ran the following script: pkgs <- c("XML") for (i in 1:100) { install.packages(pkgs, repos="http://cran.fhcrc.org") if (!all(pkgs %in% rownames(installed.packages()))) { print("failed to install pkgs!")

Hi, I can't load XML_1.4-0.zip in last R devel (Windows): R version 2.5.0 Under development (unstable) (2007-01-05 r40386) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for

Hello, Man page for 'install.packages' says that if the 'lib' arg is missing, then it "defaults to '.libPaths()[1]' with a warning". But, given the 'install.packages' source code, it seems that this warning is issued only when 'length(.libPaths()) > 1'. So typically, this warning will appear on Mac OS X but not on a Linux or Windows systems

Full_Name: Brian K. Boonstra Version: 2.2.1 OS: WinXP, OSX Submission from: (NULL) (63.172.178.137) The maxdrawdown function in tseries defines the maximum drawdown in terms of absolute dollars (or whatever units the input is in). Industry convention is to do this in percentage terms. I have written the code below as maximumdrawdown(), which retains backward compatibility with the current

I downloaded: http://www.bioconductor.org/data/metaData/hgu95av2_1.7.0.tar.gz described as: Package: hgu95av2 Title: A data package containing annotation data for hgu95av2 Version: 1.7.0 Created: Wed Jan 12 16:57:23 2005 Author: Lin,Chenwei Description: Annotation data file for hgu95av2 assembled using data from public data repositories Maintainer:

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

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 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'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, After installing Rtools 3.1.0.1939 into c:\rtools31, when I call any (most?) of the commands in c:\rtools31\bin, I see strange messages printed to stderr. Example: C:\Rtools31>bin\tar 0 [main] tar 6084 shared_info::initialize: size of shared memory region changed from 27984 to 21136 bin/tar: You must specify one of the `-Acdtrux' options Try `bin/tar --help' or `bin/tar

Hi, we noticed that since some time after Aug 24th the daily snapshots provided on ftp://ftp.stat.math.ethz.ch/Software/R/ no longer have their default tarball file name but dropped the date stamp, i.e. R-devel_.tar.bz2 Same for R-patched snapshots. Could one of the maintainers please take a look. We rely on the default naming convention for automatic builds. Regards, Matthias --

Hi, I've successfully used it on a Linux setup, but when I try to load rJava on Windows 7 64-bit (session info below) I get: % R --vanilla > library("rJava") Error : .onLoad failed in loadNamespace() for 'rJava', details: call: dirname(this$RuntimeLib) error: a character vector argument expected Error: package/namespace load failed for 'rJava' >

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