[Rd] S4 plus
Dear all,
I set a generic s4 funciton, then add a method.
When I do this, I notice that when pressing tab, the arguments to this
method do not appear like they do for generic functions, instead I get an
elipsis.
i.e.
> setClass("batchFile")
[1] "batchFile"
>
> setGeneric("Gen1", function(batchFile, ...) standardGeneric("Gen1"))
[1] "Gen1"
>
> setMethod("Gen1", signature = "batchFile", definition =
+ function(batchFile, xxx, yyy, zzz) { return(batchFile) }
+ )
[1] "Gen1"
> Gen1(
...=batchFile=
Note that xx, yy and zzz are not displayed when pressing after Gen1(
contrast that to
> Gen1 <- function(batchFile, xxx, yyy, zzz) { return(batchFile) }
> Gen1(
batchFile= xxx=yyy=zzz=
Is there a way to allow to show the extra options? Or has this been
deliberately disabled in order to allow someone to set a number of different
methods with method specific arguments with a single generic?
Many thanks,
Jim
--
James Perkins, PhD student
Institute of Structural and Molecular Biology
Division of Biosciences
University College London
Gower Steet
London, WC1E 6BT
UK
email: jperk...@biochem.ucl.ac.uk
phone: 0207 679 2198
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[Rd] Postscript can be very slow in R 2.13-0
Viewing certain postscript files under R 2.13-0 is very slow, at least using GSview on my 64 bit Windows 7 system. To see this, compare how long it takes to display these two files (fast.ps was created by removing the /srgb stuff in .ps.prolog): www.milbo.org/postscript/slow.ps www.milbo.org/postscript/fast.ps The code to produce the above two files is here: www.milbo.org/postscript/slow-postscript.R This is not exactly a bug, but is it a known issue? The hack used to produce fast.ps above is fragile and not suitable for regular use. Is there a option to the postscript() function (or could one be added) that would sacrifice sRGB support for speed? Stephen Milborrow www.milbo.users.sonic.net Version info: I'm using GSview 4.9 and Ghostscript 8.64. R.version _ platform x86_64-pc-mingw32 arch x86_64 os mingw32 system x86_64, mingw32 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Possible bug in 'relist()' and/or 'as.relistable()'
Dear list, I think I just stumbled across a bug in either 'relist()' and/or 'as.relistable()'. It seems that 'pairlists' can only be un- and relisted as long as they're not nested: Good: a <- as.relistable(as.pairlist(list(a=1, b=2))) a <- unlist(a) relist(a)# Works Bad: a <- as.relistable(as.pairlist(list(a=1, b=2, c=list(c.1=1, c.2=2 a <- unlist(a) relist(a) The help page didn't say anything about pairlists and I don't know if they're at all relevant, but I'm using them whenever I want my functions to recognize a clear 'name-value' structure (e.g. for batch assigning variables) as opposed to standard list structures. Cheers, Janko > sessionInfo() R version 2.12.1 (2010-12-16) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] codetools_0.2-8 tools_2.12.1 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Possible bug in 'relist()' and/or 'as.relistable()'
On Apr 14, 2011, at 5:13 PM, Janko Thyson wrote: > Dear list, > > I think I just stumbled across a bug in either 'relist()' and/or > 'as.relistable()'. It seems that 'pairlists' can only be un- and relisted as > long as they're not nested: > > Good: > a <- as.relistable(as.pairlist(list(a=1, b=2))) > a <- unlist(a) > relist(a)# Works > > Bad: > a <- as.relistable(as.pairlist(list(a=1, b=2, c=list(c.1=1, c.2=2 Technically, you're not nesting pairlists - you' are putting a generic vector in a parilist ... (not that it matters here). > a <- unlist(a) > relist(a) > relist() has no method for pairlists - but you can actually use the "list" method as-is: > relist.pairlist <- utils:::relist.list > str(src <- as.pairlist(list(a=1, b=2, c=list(c.1=1, c.2=2 Dotted pair list of 3 $ a: num 1 $ b: num 2 $ c:List of 2 ..$ c.1: num 1 ..$ c.2: num 2 > str(relist(unlist(as.relistable(src Dotted pair list of 3 $ a: num 1 $ b: num 2 $ c:List of 2 ..$ c.1: num 1 ..$ c.2: num 2 - attr(*, "class")= chr [1:2] "relistable" "pairlist" and that will also support actual nested pairlists: > str(src <- pairlist(a=1, b=2, c=pairlist(c.1=1, c.2=2))) Dotted pair list of 3 $ a: num 1 $ b: num 2 $ c:Dotted pair list of 2 ..$ c.1: num 1 ..$ c.2: num 2 > str(relist(unlist(as.relistable(src Dotted pair list of 3 $ a: num 1 $ b: num 2 $ c:Dotted pair list of 2 ..$ c.1: num 1 ..$ c.2: num 2 - attr(*, "class")= chr [1:2] "relistable" "pairlist" so I guess it should be easy to add relist.pairlist to utils ... I'm not sure about the implications, but it does sound appealing. Cheers, Simon > The help page didn't say anything about pairlists and I don't know if > they're at all relevant, but I'm using them whenever I want my functions to > recognize a clear 'name-value' structure (e.g. for batch assigning > variables) as opposed to standard list structures. > > Cheers, > Janko > >>sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > [5] LC_TIME=German_Germany.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] codetools_0.2-8 tools_2.12.1 > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] DESCRIPTION file and Rd examples
I have a confusing error from R CMD check that I don't get when running the
example manually by hand.
In the \examples section of an Rd file, I create a GRanges object, then I call
a function with the GRanges object, whose first 2 lines are
require(GenomicRanges)
annoDF <- as.data.frame(anno) # anno is the GRanges object.
and that second line gives:
Error in as.data.frame.default(anno) :
cannot coerce class 'structure("GRanges", package = "GenomicRanges")' into a
data.frame
Calls: annoGR2DF ... annoGR2DF -> .local -> as.data.frame ->
as.data.frame.default
I have GenomicRanges listed in my Imports: field, and IRanges in the Suggests:
of the DESCRIPTION file (it's require()d elsewhere). I'm trying to avoid
putting packages in Depends: , so my package loads fast. Any tips of what I'm
not understanding properly ?
Thanks.
--
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
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