Re: [Rd] Vignette questions

2012-04-12 Thread Henrik Bengtsson
To have a prebuilt/static PDF appear as package vignette in the help, browseVignettes(), and on CRAN, you can do: 1. Copy the PDF to inst/doc/, e.g. inst/doc/manual.pdf 2. Create a dummy inst/doc/manual.Rnw that contains four lines or LaTeX code: %\VignetteIndexEntry{User manual} \documentclass{a

Re: [Rd] Vignette questions

2012-04-12 Thread Yihui Xie
If R-forge gives the warning, it is likely to be their configuration problem (they may be running R CMD check on the original source directory instead of the tarball), so it is better to report to R-forge admins directly. I believe Terry is correct and it is a better practice *not* to put PDF vign

Re: [Rd] [patch] giving library() a 'version' argument

2012-04-12 Thread Roebuck,Paul L
On 4/12/12 1:56 PM, "Ken Williams" wrote: > On April 12, 2012 1:48 PM, Paul Roebuck wrote: > >> Not sure I follow you here. The packageVersion() method is essentially a >> shortcut to packageDescription("MyPackage")$Version. I generally avoid >> doing package upgrades in my scripts so the loaded

[Rd] R-2.15.0 and Exporting Methods Converted To S4 Generic

2012-04-12 Thread Roebuck,Paul L
Late to the show on this release, unfortunately. One of our production packages no longer builds under R-2.15.0 with the following message. ** testing if installed package can be loaded Error: Function found when exporting methods from the namespace 'SuperCurve' which is not S4 generic: 'image'

Re: [Rd] [patch] giving library() a 'version' argument

2012-04-12 Thread Ken Williams
> -Original Message- > From: Roebuck,Paul L [mailto:proeb...@mdanderson.org] > Sent: Thursday, April 12, 2012 1:03 PM > To: R-devel > Cc: Ken Williams > Subject: Re: [Rd] [patch] giving library() a 'version' argument > > On 4/12/12 10:11 AM, Ken Williams wrote: > > >> On 4/12/12 7:22 AM,

[Rd] LazyData and CSV files in data/

2012-04-12 Thread Sebastian P. Luque
Hi, I'm trying to use 'LazyData: yes' in a package. A vignette and the Examples section of help pages contain this: ------ zz <- system.file(file.path("data", "fileA.csv"), package="myPackage") dfA <- read.csv

Re: [Rd] [patch] giving library() a 'version' argument

2012-04-12 Thread Duncan Murdoch
On 12/04/2012 1:46 PM, Ken Williams wrote: > -Original Message- > From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] > Sent: Thursday, April 12, 2012 12:27 PM > To: Ken Williams > Cc: r-devel@r-project.org > Subject: Re: [Rd] [patch] giving library() a 'version' argument > > I

Re: [Rd] [patch] giving library() a 'version' argument

2012-04-12 Thread Roebuck,Paul L
On 4/12/12 10:11 AM, Ken Williams wrote: >> On 4/12/12 7:22 AM, Duncan Murdoch wrote: > [SNIP] > ... > The main hats targeted here are really people (like me, of course) who are > trying to "productionize" results, not so much people who are doing offline > analysis. In a production system > >>

Re: [Rd] [patch] giving library() a 'version' argument

2012-04-12 Thread Ken Williams
> -Original Message- > From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] > Sent: Thursday, April 12, 2012 12:27 PM > To: Ken Williams > Cc: r-devel@r-project.org > Subject: Re: [Rd] [patch] giving library() a 'version' argument > > I haven't tested it, but according to the documentat

Re: [Rd] [patch] giving library() a 'version' argument

2012-04-12 Thread Duncan Murdoch
On 12/04/2012 11:11 AM, Ken Williams wrote: > -Original Message- > From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] > Sent: Thursday, April 12, 2012 7:22 AM > To: Ken Williams > Cc: r-devel@r-project.org > Subject: Re: [Rd] [patch] giving library() a 'version' argument > > O

Re: [Rd] [patch] giving library() a 'version' argument

2012-04-12 Thread Ken Williams
> -Original Message- > From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com] > Sent: Thursday, April 12, 2012 7:22 AM > To: Ken Williams > Cc: r-devel@r-project.org > Subject: Re: [Rd] [patch] giving library() a 'version' argument > > On 12-04-11 11:28 AM, Ken Williams wrote: > > > > Rea

Re: [Rd] Vignette questions

2012-04-12 Thread Uwe Ligges
On 12.04.2012 16:42, Paul Gilbert wrote: On 12-04-12 03:15 AM, Uwe Ligges wrote: On 12.04.2012 01:16, Paul Gilbert wrote: On 12-04-11 04:41 PM, Terry Therneau wrote: Context: R2.15-0 on Ubuntu. 1. I get a WARNING from CMD check for "Package vignette(s) without corresponding PDF: In th

Re: [Rd] Vignette questions

2012-04-12 Thread Paul Gilbert
On 12-04-12 03:15 AM, Uwe Ligges wrote: On 12.04.2012 01:16, Paul Gilbert wrote: On 12-04-11 04:41 PM, Terry Therneau wrote: Context: R2.15-0 on Ubuntu. 1. I get a WARNING from CMD check for "Package vignette(s) without corresponding PDF: In this case the vignettes directory had both the

Re: [Rd] [patch] giving library() a 'version' argument

2012-04-12 Thread Ken Williams
> -Original Message- > From: Prof Brian Ripley [mailto:rip...@stats.ox.ac.uk] > Sent: Thursday, April 12, 2012 7:54 AM > To: Duncan Murdoch > Cc: Ken Williams; r-devel@r-project.org > Subject: Re: [Rd] [patch] giving library() a 'version' argument > > A very important point is that library

Re: [Rd] unexpectedly high memory use in R 2.14.0

2012-04-12 Thread andre zege
Henrik, thanks for your reply. I might have misrepresented a bit my actual code . It seems that you are suggesting doing rm() on objects i don't use. In the real code which behavior i reported it is exactly what is being done, i.e i use rm(). I also use a small wrapper around load that lets me as

Re: [Rd] Vignette questions

2012-04-12 Thread Terry Therneau
On 04/12/2012 02:15 AM, Uwe Ligges wrote: On 12.04.2012 01:16, Paul Gilbert wrote: On 12-04-11 04:41 PM, Terry Therneau wrote: Context: R2.15-0 on Ubuntu. 1. I get a WARNING from CMD check for "Package vignette(s) without corresponding PDF: In this case the vignettes directory had both the

Re: [Rd] [patch] giving library() a 'version' argument

2012-04-12 Thread Prof Brian Ripley
A very important point is that library() *had* a 'version' argument for several years, and this is not what it did. So Mr Williams needs to do his homework From such a version of R: version: A character string denoting a version number of the package to be loaded, for use wit

Re: [Rd] [patch] giving library() a 'version' argument

2012-04-12 Thread Duncan Murdoch
On 12-04-11 11:28 AM, Ken Williams wrote: I've made a small enhancement to R that would help developers better control what versions of code we're using where. Basically, to load a package in R, one currently does: library(whateverPackage) and with the enhancement, you can e

Re: [Rd] Vignette questions

2012-04-12 Thread Uwe Ligges
On 12.04.2012 00:23, beleites,claudia wrote: Very quick& short answer: I made the transition to ./vignettes for hyperSpec (you can look at the source at r-forge) - it was a mess. It is almost working now (compression is missing, I'll have to figure out how to invoke ghostscript in an OS id

Re: [Rd] Vignette questions

2012-04-12 Thread Uwe Ligges
On 11.04.2012 23:28, Yihui Xie wrote: For 1, you should run R CMD check on the tar ball (pkg_x.x.tar.gz) from R CMD build instead of the source directory. R CMD build will build the PDF vignette into the tar ball. Just move vignette sources to :/vignettes in your package? Uwe For 2, I hav

Re: [Rd] Vignette questions

2012-04-12 Thread Uwe Ligges
On 12.04.2012 01:16, Paul Gilbert wrote: On 12-04-11 04:41 PM, Terry Therneau wrote: Context: R2.15-0 on Ubuntu. 1. I get a WARNING from CMD check for "Package vignette(s) without corresponding PDF: In this case the vignettes directory had both the pdf and Rnw; do I need to move the pdf to