Re: [Rd] should `data` respect default.stringsAsFactors()?

2016-02-18 Thread Michael Nelson
As Peter pointed out. data loads data from packages. Various formats are supported. The package author(s) will decide how best to ship (and load) any such data. When you call `data(iris)`, it loads iris as it is defined in the datasets package The definition can be seen here:

Re: [Rd] should `data` respect default.stringsAsFactors()?

2016-02-18 Thread Joshua Ulrich
On Thu, Feb 18, 2016 at 6:03 PM, Cook, Malcolm wrote: > Hi Peter, > > Sorry if I was not clear. Perhaps an example will make my point: > >> data(iris) >> class(iris$Species) > [1] "factor" >> write.table(iris,'data/myiris.tab') >> data(myiris) >> class(myiris$Species) > [1]

Re: [Rd] should `data` respect default.stringsAsFactors()?

2016-02-18 Thread Cook, Malcolm
Hi Peter, Sorry if I was not clear. Perhaps an example will make my point: > data(iris) > class(iris$Species) [1] "factor" > write.table(iris,'data/myiris.tab') > data(myiris) > class(myiris$Species) [1] "factor" > rm(myiris) > options(stringsAsFactors = FALSE) > data(myiris) >

Re: [Rd] inconsistency in treatment of USE.NAMES argument

2016-02-18 Thread Hervé Pagès
On 02/11/2016 07:02 AM, Michael Lawrence wrote: Changing the vapply() behavior makes sense in principle. Sorry to disagree, Changing the behavior of sapply() so we end up with consistent treatment of USE.NAMES across sapply(), vapply(), and mapply() sounds much better *in principle*. I

Re: [Rd] should `data` respect default.stringsAsFactors()?

2016-02-18 Thread peter dalgaard
What the are you on about? data() does many things, only some of which call read.table() et al., and the ones that do have no special treatment of stringsAsFactors. -pd > On 18 Feb 2016, at 21:25 , Cook, Malcolm wrote: > > Hiya, > > Probably been debated elsewhere >

Re: [Rd] configure statement for R-devel with updated zlib in user account

2016-02-18 Thread Paul Johnson
On Mon, Feb 15, 2016 at 3:28 AM, Jesper Gådin wrote: > Hi Paul, > > This might be what you are looking for. > https://stat.ethz.ch/pipermail/r-devel/2015-April/070951.html > > Jesper > Thanks to help form Wes Mason at KU and Jesper Gadin in r-devel, I compiled R-devel on

[Rd] should `data` respect default.stringsAsFactors()?

2016-02-18 Thread Cook, Malcolm
Hiya, Probably been debated elsewhere I note that R's `data` function does not respect default.stringsAsFactors By my lights, it should, especially as it is documented to call read.table, which DOES respect. Oh, but:

Re: [Bioc-devel] specify the color in plotMutationSpectrum() of SomaticSignatures library

2016-02-18 Thread Wolfgang Huber
Dear Rebecca can you please post this in the Bioconductor user forum - this is not really a developer question. > On Feb 17, 2016, at 20:33 GMT+1, sun wrote: > > Hi All, > > How can I specify the color that I would like to use in > plotMutationSpectrum()? > > eg. > >

Re: [Bioc-devel] Strand-Awareness for Restrict Function

2016-02-18 Thread Hervé Pagès
On 02/18/2016 01:00 AM, Maintainer wrote: Hello, Hi, I'm putting this back to bioc-devel and setting the Subject to "Strand-Awareness for Restrict Function" since this seems to be a continuation of this thread (that you started here). I hope you don't mind. Setdiff automatically reduces

Re: [Bioc-devel] Efficient Random Sampling of Positions in GRanges

2016-02-18 Thread Hervé Pagès
Hi, On 02/18/2016 03:00 AM, Dario Strbenac wrote: Good day, Thank you for these two suggestions. I have questions about both options. GPos seems to have a limit on the number of bases it can represent. I get an error: Error in GPos(samplingAreas) : too many genomic positions in 'pos_runs'.

Re: [Bioc-devel] Efficient Random Sampling of Positions in GRanges

2016-02-18 Thread Dario Strbenac
Good day, Thank you for these two suggestions. I have questions about both options. GPos seems to have a limit on the number of bases it can represent. I get an error: Error in GPos(samplingAreas) : too many genomic positions in 'pos_runs'. What exactly is this limit ? Could it be added to the

[Rd] default destfile in download.file()

2016-02-18 Thread Jeroen Ooms
A nice default value for the `destfile` argument in download.file() would be `basename(url)` i.e. the name of the downloaded file. This would correspond to default behavior in many other web/ftp clients and makes code slightly more concise:

Re: [Rd] R Package Installation Ignores libPaths Setting

2016-02-18 Thread Prof Brian Ripley
You misunderstand what .libPaths does: it changes the path in the current session only. Installation uses a different R process. Set R_LIBS to change the library path for new sessions: see ?.libPath . On 18/02/2016 07:00, Dario Strbenac wrote: Good day, If the library path is changed with