similar to: What is the preferred method to view a pdf (not a vignette) in a package /doc ?

When constructing an R extension, how can a hyperlink from an .Rd file to a pdf (not generated by Sweave, so not a vignette) located in the inst/doc folder be constructed? Bill Morphet ATK, Space Launch Systems Postflight Evaluation Eng [[alternative HTML version deleted]]

Colleagues, I am interesting in opening a PDF document via the command line from both Windows, OS X, and Linux ( R version 2.8.0). I found a command openPDF in Biobase. However, I would rather execute the command myself. For example, in OS X: > system("open filename.pdf") is successful. Is there a comparable command line command for Windows or Linux? Dennis Dennis Fisher

The statement Globals <<- list() in the body of a function in a package was intended to write an empty list to the R workspace to collect results during the computations of the function. A package name space has not been specified. The package appears to function correctly, but during the R CMD check of the package while "checking R code for possible problems ... NOTE", no

Hello All R-Gurus: ISSUE: Cannot view R vignettes due in Ubuntu Linux (a debian variant). note: this issue has been posted to this list before with no responses given see https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html DETAILS: I am trying to view an R vignette. Here is the situation: I issue the openvignette(), then select the vignette I wish to view...and the system returns:

The package list was accessed October 28, 10:13 am MST using Windows XP and mirror USA (CA 1). Bill Morphet, Ph.D.

If I try to build a package with a vignette R CMD build Biobase I see * checking for file 'Biobase/DESCRIPTION' ... OK * preparing 'Biobase': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes * creating vignettes ... OK * cleaning src Error in setwd(pkgname) : cannot change working directory Execution halted This is

Hello I can''t manage to install VB on osx via puppet and pkgdmg provider. puppet client : 2.6.8 on osx snow leopard 10.6.7 puppetmaster : 2.6.8-1~bpo60+1 on debian squeeze The puppet logs say : [...] debug: Puppet::Type::Package::ProviderPkgdmg: Executing ''/usr/bin/curl -o /tmp/VirtualBox-4.0.8-71778-OSX.dmg -C - -k -s --url

To install from a local zip file, install.packages option repos=NULL. Then, how can dependencies of the local zip file, which are located in the repository of contributor packages, be automatically installed? Or, is there a better way than to tell the person installing from local zip what the dependent files are, and to install them from the repository first? Bill Morphet [[alternative HTML

Hello, The vignette concept, which started in Bioconductor, seems to be catching on. They are supported by R CMD build/check and documented in the Writing R Extensions manual. I think vignettes are a fantastic way to introduce new users to a package. However, getting new users to realize that a vignette is available can be challenging. For some time now, we have had a function in Biobase that

Hi, This is a follow-up to the problem reported here: https://stat.ethz.ch/pipermail/r-devel/2010-September/058460.html After I updated R-2.12 to 2010-09-13 r52905 on the Bioc build system, some of the packages that have a Makefile in <pkg>/inst/doc still don't build on Windows. For example, 'R\bin\R.exe CMD build adSplit' gives: * checking for file

Colleagues, Several days ago, I queried about using the "system" command to open a PDF file. A number of people responded, each providing useful ideas. I integrated these ideas into a function that others can tailor to their needs: OPENPDF <- function(PDFFILENAME) { OPENPDFCOMMAND <- "open" # applies to OS X if (!UNIX)

Dear all, In my package I have a computational expensive Rnw file which can't pass R CMD check. Therefore I set eval=FALSE in the Rnw file. But I would like to have the pdf vignette generated by the Rnw file with eval=TRUE. It seems to me a static pdf vignette is an option. Any suggestions on this? Thanks, Zhu Wang **Connecticut Children's Confidentiality Notice** This e-mail

Hello there, on a CentOS 6 box, in the need for `meson`, I've installed rh-python36 using yum, then meson and ninja using `pip3.6 install meson ninja`. Later at run-time, while building atk 2.29.1: $ meson --prefix /opt/atk _build $ ninja-build -C _build FAILED: atk/atkmarshal.c /opt/gimp-2.8/bin/glib-genmarshal --prefix atk_marshal --output atk/atkmarshal.c --body ../atk/atkmarshal.list

On page 11 of the Extensions manual it says that "R CMD build will automatically create PDF versions of the vignettes for distribution" however, I have not been successful on Windows 2.0.1 beta. I tried creating a simple package by entering the code in the ?package.skeleton example then adding the Rnw file from the utils package to AnExample\inst\doc but when I ran R CMD build it

Hi Everybody, I am having a problem with loading Biobase package. I typed 2 lines below at R prompt > source ("http://boconductor.org/biocLite.R") > biocLite (lib="/usr/local/lib/R/library") which attempted to install a bunch of packages with varying degree of success. Out of 29, 13 failed. Biobase is one of them. As a matter of fact, when I looked at logs, most

I get the following error message when trying to start a pdf file: > pdf("hi.pdf") Error in PDF(file, old$family, old$encoding, old$bg, old$fg, width, height, : unable to start device pdf In addition: Warning message: cannot open `pdf' file argument `hi.pdf' *** malloc[477]: Deallocation of a pointer not malloced: 0x143cf5c0; This could be a double free(), or free()

Hi, in Section 'Writing package vignettes' of 'Writing R Extensions' it says: "Whenever a Makefile is found, then R CMD build will try to run make after the Sweave runs, so PDF manuals can be created from arbitrary source formats (plain LaTeX files, ...). [...] Note that the make step is executed even if there are no files in Sweave format, [...]". In my package,

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

Dear all, While R CMD check and R CMD INSTALL have always created the vignettes on R-2.12.1 or any earlier versions of R, I am no longer able to build the vignettes on R-2.13.0. Instead R CMD check gives me the following output: * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... WARNING Package vignette(s) without corresponding PDF:

I've been having problems building vignettes in bioconductor packages with R-devel. Turns out that Rdevel/share/texmf/hyperref.cfg wants Blue and Red predefined, when only blue and red are defined (as of rsync Rdevel, Sept 10th). This is on a Debian unstable system (Sept 9th version). Might not apply to all other tetex systems. Seems to have bitten the bioconductor build system, though.