similar to: install.packages() removes package on Windows

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, 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 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, 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

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

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, 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 *

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, 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, 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

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

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

Dear Forum my machine runs Ubuntu 9.04. I am trying to install Biomart, what I realize is that something is missing and it can't install XML, RCurl but I don't know what more to do, I looked in previous posts but I did not find infoprmation that helped. Thanks Andreia biocLite("biomaRt") Running biocinstall version 2.3.14 with R version 2.8.1 Your version of R requires version

I know I cannot be the only one who is not able to install the XML package from CRAN (zip or tar file) Many packages depend on this XML package. Can someone help me either access the source for a good binary? I have received no assistance from the author/developer of the package. Steven Steven D. Randolph Associate Consultant Enterprise Capabilities - Business Intelligence & Analytics Eli

The following two patches fixes / reimplements the oVirt appliance project, installing the entire oVirt stack including all server and node components on one machine. These patches are intended to be checked out and used to build the appliance rpm, after which it is installed provides the /usr/sbin/ovirt-appliance-ctrl script to install/uninstall the appliance. The first patch merely removes

I always followed http://cran.r-project.org/bin/linux/ubuntu/ to install R on Ubuntu 8.1. I had no errors before! > install.packages("XML") Warning in install.packages("XML") : argument 'lib' is missing: using '/usr/local/lib/R/site-library' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL

Hi, I am new to bioconductor, trying to install KEGGSOAP package, but got warnings() when installing and error message when trying to load the package, can anyone suggest what went wrong? many thanks John > source("http://bioconductor.org/biocLite.R") Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > biocLite("KEGGSOAP") BioC_mirror:

Hi, Using latest R 2.5.0 Patched, I'm unable to install the Matrix package from cran.fhcrc.org. I get: Creating a new generic function for "isSymmetric" in "Matrix" Creating a new generic function for "unname" in "Matrix" Error in conformMethod(signature, mnames, fnames, f) : In method for function "!": formal arguments omitted in

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,

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' >