Re: [Rd] regenerate Rscript after moving R installation

2013-09-24 Thread Simon Urbanek
Murray, On Sep 24, 2013, at 2:18 AM, Murray Stokely mur...@stokely.org wrote: Simon, do you have some examples of packages with this attribute? As Brian pointed out, some of them concern linking (I'm typically worried about OS X and Dirk has fixed Rcpp there), but there are also others that

Re: [Rd] inconsistency/bug in recordPlot/replayPlot

2013-09-24 Thread Michael Weylandt
https://stat.ethz.ch/pipermail/r-devel/2013-September/067563.html Same instructions still apply -- this is a self-subscription list. M On Sep 24, 2013, at 0:42, Eric Malitz eric.mal...@gmail.com wrote: take me off here On Mon, Sep 23, 2013 at 10:31 PM, Gabriel Becker

Re: [Rd] Capture output of install.packages (pipe system2)

2013-09-24 Thread Jeroen Ooms
On Mon, Sep 23, 2013 at 6:50 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: x - system2(Rscript, -e \install.packages('MASS', repos='http://probability.ca/cran')\, stdout=TRUE, stderr=TRUE) Thank you, this suggestion seems to work (although I agree that starting 3 procs to install a single

Re: [Rd] Capture output of install.packages (pipe system2)

2013-09-24 Thread Hadley Wickham
You shouldn't assume - use file.path(R.home(bin), R) Hadley On Tue, Sep 24, 2013 at 9:37 AM, Jeroen Ooms jeroen.o...@stat.ucla.edu wrote: On Mon, Sep 23, 2013 at 6:50 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: x - system2(Rscript, -e \install.packages('MASS',

Re: [Rd] Capture output of install.packages (pipe system2)

2013-09-24 Thread Jeroen Ooms
On Mon, Sep 23, 2013 at 6:34 PM, Simon Urbanek simon.urba...@r-project.org wrote: On top of my head for full capture I can only think of custom C code that will re-direct stderr/out FDs as desired (it's really trivial to re-direct to files, for dynamic capture it's a little more involved but

[Rd] recordPlot() on non-interactive graphics device?

2013-09-24 Thread Henrik Bengtsson
Hi. Q. Is there a way to record a plot using grDevices::recordPlot() without opening an interactive (=visible GUI window) graphics device (not even for a flash of a second)? Related: help(recordPlot, package=grDevices) says: These functions record and replay the displaylist of the current

Re: [Rd] recordPlot() on non-interactive graphics device?

2013-09-24 Thread Gabriel Becker
Henrik, This works for me: png(test.png) dev.control(displaylist=enable) plot(1:10) rp = recordPlot() dev.off() X11cairo 2 rp HTH, ~G sessionInfo(): R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3]

Re: [Rd] recordPlot() on non-interactive graphics device?

2013-09-24 Thread Gabriel Becker
To be a little less terse: I agree that notes/discussion about what recordPlot/replayPlot do when there is no display list and that non-interactive devices don't create a displaylist by default but can be instructed to do so via dev.control (at least some, I don't claim to have checked them all)

Re: [Rd] Capture output of install.packages (pipe system2)

2013-09-24 Thread Duncan Murdoch
On 13-09-24 10:37 AM, Jeroen Ooms wrote: On Mon, Sep 23, 2013 at 6:50 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: x - system2(Rscript, -e \install.packages('MASS', repos='http://probability.ca/cran')\, stdout=TRUE, stderr=TRUE) Thank you, this suggestion seems to work (although I agree

Re: [Rd] recordPlot() on non-interactive graphics device?

2013-09-24 Thread Henrik Bengtsson
Thanks Gabriel. It works - I did not know about dev.control() and its help page clearly says that Initially recording is on for screen devices, and off for print devices. I've submitted a patch (PR#15472) for adding a see also linking to dev.control(): Bug 15472 - PATCH: Adding see also link

Re: [Rd] inconsistency/bug in recordPlot/replayPlot

2013-09-24 Thread Paul Murrell
Hi Unfortunately, my main advice would be not to rely on recordPlot() because it (or at least the underlying display list format) was never intended for this sort of thing. I doubt that helps though :) I might be able to help more, or look at developing a transportable object class for R

Re: [Bioc-devel] expand,VCF and the AD geno field

2013-09-24 Thread Valerie Obenchain
Michael, This is implemented in 1.7.48. AD is expanded as a list matrix where each list element holds a REF,ALT pair. Val On 09/05/2013 07:36 AM, Valerie Obenchain wrote: Hi, On 09/04/2013 04:23 PM, Michael Lawrence wrote: Hi, Val, I just fixed expand,VCF to support multiple 'A' columns

Re: [Bioc-devel] expand,VCF and the AD geno field

2013-09-24 Thread Michael Lawrence
That's great, thanks. On Tue, Sep 24, 2013 at 12:16 PM, Valerie Obenchain voben...@fhcrc.orgwrote: Michael, This is implemented in 1.7.48. AD is expanded as a list matrix where each list element holds a REF,ALT pair. Val On 09/05/2013 07:36 AM, Valerie Obenchain wrote: Hi, On