Re: [Rd] Surprising behavior of Negate()
On 08/30/2010 02:01 AM, Olaf Mersmann wrote: This matches 'f' when Negate() is called and not the first time the return value is used. If the current behavior is desired, maybe a note in the documentation could be added to clarify this peculiarity. Looks like a classic lazy eval gotcha -- almost never intentional. Testing your patch now. -p -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] S4 Method Rd Warning
Hello,
I am using R 2.11.0. I have a curious problem where I get a warning in R CMD
check which is seemingly not relevant to my Rd file.
The warning says :
* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'enrichmentCalc':
unescaped bkslS4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs,
organism, seqLen=NULL, ...)
unescaped bkslS4method{enrichmentCalc}{GenomeData, BSgenome}(rs,
organism, seqLen=NULL, do.warn=FALSE)
unescaped bkslS4method{enrichmentCalc}{GRanges, BSgenome}(rs, organism,
seqLen=NULL)
Functions with \usage entries need to have the appropriate \alias entries,
and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
But, I have documented all the arguments, and I have all the aliases. What else
could it be warning me about ?
The Rd file contents are :
\name{enrichmentCalc}
\alias{enrichmentCalc}
\alias{enrichmentCalc,GenomeDataList,BSgenome-method}
\alias{enrichmentCalc,GenomeData,BSgenome-method}
\alias{enrichmentCalc,GRanges,BSgenome-method}
\title{Calculate sequencing enrichment}
\description{A description}
\usage{
\S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism,
seqLen=NULL, ...)
\S4method{enrichmentCalc}{GenomeData, BSgenome}(rs, organism, seqLen=NULL,
do.warn=FALSE)
\S4method{enrichmentCalc}{GRanges, BSgenome}(rs, organism, seqLen=NULL)
}
\arguments{
\item{rs}{jjj}
\item{organism}{ghi}
\item{seqLen}{def}
\item{do.warn}{abc}
\item{...}{xyz}
}
\details{
Details.
}
\value{
Text here.
}
\author{A Person}
\examples{
#See the manual
}
Thanks,
Dario.
--
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
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Re: [Rd] No [[-.factor()
Prof Brian Ripley rip...@stats.ox.ac.uk on Mon, 30 Aug 2010 08:28:24 +0100 (BST) writes: On Thu, 26 Aug 2010, Martin Maechler wrote: WD == William Dunlap wdun...@tibco.com on Wed, 25 Aug 2010 17:31:27 -0700 writes: WD Should there be a [[-.factor() that either throws WD an error or acts like [-.factor() to avoid making WD an illegal object of class factor? Yes, one or the other. Note that both `[-` and `[[-` are Primitive and do some informal dispatch in addition to the formal method dispatch, I don't think so. do_subassign2 does formal method dispatch, albeit internally, but nothing else (do_assign2_dflt selects only by typeof()). One consider that as an informal dispatch, notably distinguishing lists and atomics... so there's no need for an explicit '[[-.factor' method definition. For factors, it seems rational and expectable that double bracket behaves as single bracket when *one* element is assigned. z[[2:3]] - c(Two, Three) however should continue to give an error. I added a [[-.factor yesterday. Note that we do have a [-.factor which works on the integer codes, and I simply copied its logic. thank you! BTW, you probably meant z[[2:3]] - c(Two, Three) yes, indeed! Martin z - factor(c(Two,Two,Three), levels=c(One,Two,Three)) z WD [1] Two Two Three WD Levels: One Two Three str(z) WD Factor w/ 3 levels One,Two,Three: 2 2 3 z[[2]] - One str(z) # the .Data part is now character WD Factor w/ 3 levels One,Two,Three: 2 One 3 z WD [1] NA NA NA WD Levels: One Two Three z[2] - One WD Error in class(x) - cx : adding class factor to an invalid object WD Bill Dunlap WD Spotfire, TIBCO Software WD wdunlap tibco.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] NEWS and readNEWS
* s.post - SERIES NEWS * s.pre - ^[\t ]*CHANGES IN R VERSION Is this a bug or is the documentation incorrect? readNEWS() is really for such 3-level files, but then R itself will move to an 2-level Rd format in R 2.12.0. Use news() to read package news files. Ah, ok, this is rather unclear from the current documentation. So if I want to read a NEWS file off disk to check that I have the right format (without installing the package first), I should use tools:::.build_news_db ? Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?
On 19/08/2010 5:25 PM, Duncan Murdoch wrote:
On 19/08/2010 5:07 PM, Kevin Coombes wrote:
I use it, frequently. The idea for it goes back to some of Knuth's
original literate programming ideas for developing weave and tangle when
he was writing TeX (the program). I want to be able to document the
pieces of some complex algorithm without having to see all of the gory
details. For instance, I have code that looks like the following.
(Note that this is typed on the fly rather than copied from actual
source, so there may be typos.)
Okay, thanks. I'll keep it in. So now I have a question: suppose
you have an error (syntax error at this point, maybe some other kinds of
error in the future) in the getInfoAboutThisSample chunk, but that
chunk wasn't eval'd, mainloop was eval'd. So the error is going to be
reported as occurring in chunk mainloop, but with a line number from
somewhere else in the file. Is that a problem?
I was out of town for a week, but I'm back now, and have just committed
these changes. Hopefully the reports of syntax errors will be a little
more helpful now. I don't think I'll have time to make the reports of
execution time errors better before the 2.12.0 release.
Duncan Murdoch
Duncan Murdoch
mainloop,keep.source=TRUE,expand=FALSE=
for (i in 1:nSamples) {
getInfoAboutThisSample
for (j in 1:nChromosomes) {
getChromosomeDataForCurrentSample
normalizeChromosomeData
findSegments
computeSignificance
writeResults
}
}
@
Each of the chunks is itself a fairly long piece of code defined and
documented somewhere else. (Some of them may themselves be written in
the same form to reduce the final size of a chunk to something a human
has a chance of understanding. That's the difference between weave and
tangle in the original implementation.) By blocking expansion, I can
focus on the main steps without having them lost in pages and pages of code.
So I vote strongly for retaining expand=FALSE.
Best,
Kevin
Duncan Murdoch wrote:
On 19/08/2010 4:29 PM, Claudia Beleites wrote:
I never used it.
I got curious, though. What would be a situation that benefits of
this option?
When I put it in, I thought it would be for people who were writing
about Sweave.
Duncan Murdoch
Maybe a use case could be found by brute force (grep all .Rnw files
on CRAN for the option?
Claudia
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Re: [Rd] introspective capabilities
On 27/08/2010 7:52 AM, Christophe Rhodes wrote: Hi, Is there any way, from R code, to perform introspection as to where certain names acquired their values? The specific functionality I'm looking for in this case is to be able to request my editor to view the definition corresponding to a name in its original source location (presuming for the moment that that location exists). Other functionality that I'm looking for is to identify where in the current image a particular name is used -- what functions use the value bound to a particular name? The context for these questions, in case anyone is interested, is that I am usually a Common Lisp programmer, and my programming environment for that (SLIME) is what I'm used to. R is sufficiently close to CL (the discovery of withCallingHandlers/withRestarts was a pleasant surprise) that I decided to experiment with implementing a SLIME backend for R -- and enough of it seems to work that I'm motivated to make it more complete. (The current state of the project is summarised at http://common-lisp.net/~crhodes/swankr/). There's the keep.source option to source() and the optional srcfile argument to parse() that tell R to keep this information. If you haven't changed the default getOption(keep.source) from TRUE, then source will default to keeping it, and you can find the original location of a function definition for function f by looking in attr(body(f), srcref). See ?srcref for the format; there aren't a lot of user-level utility functions for working with this. For packages, the relevant option is keep.source.pkgs at the time the package is installed. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R with multiple processors
Hello, I was taking a look at R code, and there is some places that should be easily parallelized, as the dist() function, for example. Is there an interest on do such thing on R? I would like to start making patches to parallelize, but how comfortable with this are the main developers team on R? Best regards, Michel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
