[Rd] R check mis-identifying Illumina data file format as executable and other thoughts.

2011-08-03 Thread Hin-Tak Leung
This is somewhat a summary/continuation of an R bug report: (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14645) Illumina's cluster definition files (*.egt) are one of the proprietary and undocumented file formats used by their GenomeStudio line of products for genomic studies. snpMatrix

Re: [Rd] one way to solve bad looking density plots in postscript

2011-08-03 Thread Michael Lachmann
Sorry, I must have made a mistake before. In my R, the attached replacement for image.default DOES put the axes last, and does look better. I also tested my code for the change in the eps header on some linux machines (I'm using a mac), and there the grid effects were less pronounced, and my co

Re: [Rd] one way to solve bad looking density plots in postscript

2011-08-03 Thread baptiste auguie
Hi, I was going to suggest panel.last to redraw a box around the image, but for some reason it does not seem to come after the image neither (this is perhaps to be expected from the note in ?plot.default). plot(1,1, panel.last={box(lwd=50, col="#FF")}) image(volcano, panel.last={box(lwd=50,

Re: [Rd] Front ends handling help.search() results?

2011-08-03 Thread Duncan Murdoch
On 03/08/2011 1:23 PM, Thomas Friedrichsmeier wrote: On Wednesday 03 August 2011, Duncan Murdoch wrote: > I can't reproduce this. Can you get any more detail, e.g. by setting > options(error=recover) or similar? Interestingly, that does not start a browser, and options(error=dump.frames) appe

Re: [Rd] example package for devel newcomers

2011-08-03 Thread Simon Urbanek
Alexandre, On Aug 3, 2011, at 1:19 PM, Alexandre Aguiar wrote: > Simon, > > Em Quarta 03 Agosto 2011, vocĂȘ escreveu: >> In that light you may want to explain why you need 2-5 since the >> easiest way is to simply link to libphp. > > Resources accessible to libphp through apache are limited by s

Re: [Rd] Front ends handling help.search() results?

2011-08-03 Thread Duncan Murdoch
On 03/08/2011 1:23 PM, Thomas Friedrichsmeier wrote: On Wednesday 03 August 2011, Duncan Murdoch wrote: > I can't reproduce this. Can you get any more detail, e.g. by setting > options(error=recover) or similar? Interestingly, that does not start a browser, and options(error=dump.frames) appe

Re: [Rd] Front ends handling help.search() results?

2011-08-03 Thread Thomas Friedrichsmeier
On Wednesday 03 August 2011, Duncan Murdoch wrote: > I can't reproduce this. Can you get any more detail, e.g. by setting > options(error=recover) or similar? Interestingly, that does not start a browser, and options(error=dump.frames) appears to have no effect, either. geterrmessage() does list

Re: [Rd] example package for devel newcomers

2011-08-03 Thread Alexandre Aguiar
Simon, Em Quarta 03 Agosto 2011, vocĂȘ escreveu: > In that light you may want to explain why you need 2-5 since the > easiest way is to simply link to libphp. Resources accessible to libphp through apache are limited by ssytem configurations. With libphp fully available to every user there are p

Re: [Rd] 'data.frame' method for base::rep()

2011-08-03 Thread David Winsemius
On Aug 3, 2011, at 2:45 AM, Liviu Andronic wrote: Hello David On Tue, Aug 2, 2011 at 4:14 PM, David Winsemius > wrote: x <- data.frame(a = as.Date('2000-01-01'), b=as.Date('2001-01-01')) x$d <- x$a -x$b require(mefa) rep(x, 2) a bd 1 2000-01-01 2001-01-01 -366 2 2000-

Re: [Rd] example package for devel newcomers

2011-08-03 Thread Simon Urbanek
Alexandre, thanks, I see your point. Somehow I parsed your e-mail as the inverse (and Dan's suggestion which I feel did the same didn't help ;)). Embedding PHP into R sound like fun and in fact FastRWeb would benefit from your package :). In that light you may want to explain why you need 2-5 s

Re: [Rd] Front ends handling help.search() results?

2011-08-03 Thread Duncan Murdoch
On 03/08/2011 5:32 AM, Thomas Friedrichsmeier wrote: On Monday 01 August 2011, Duncan Murdoch wrote: > I've just committed the changes to R-devel. Let me know if there is > anything worse than what I described. Well, you did not give detail on that, but I was surprised about the "topic" field

Re: [Rd] Front ends handling help.search() results?

2011-08-03 Thread Duncan Murdoch
On 03/08/2011 5:32 AM, Thomas Friedrichsmeier wrote: On Monday 01 August 2011, Duncan Murdoch wrote: > I've just committed the changes to R-devel. Let me know if there is > anything worse than what I described. Well, you did not give detail on that, but I was surprised about the "topic" field

Re: [Rd] 'data.frame' method for base::rep()

2011-08-03 Thread Martin Maechler
> David Winsemius > on Tue, 2 Aug 2011 10:14:59 -0400 writes: > On Aug 2, 2011, at 7:55 AM, Liviu Andronic wrote: >> Dear R developers Would you consider adding a >> 'data.frame' method for the base::rep function? The need >> to replicate a df row-wise can easily aris

Re: [Rd] one way to solve bad looking density plots in postscript

2011-08-03 Thread Michael Lachmann
Some more digging. 1. The following code will fix density plots for me: --- .ps.prolog=grDevices:::.ps.prolog i=grep("/p2",.ps.prolog) .ps.prolog[i] = "/p2 { bg gsave fill grestore 0.001 setlinewidth stroke newpath } def" --- 2. It seems that it doesn't matter where in image.default() the box i

Re: [Rd] Front ends handling help.search() results?

2011-08-03 Thread Thomas Friedrichsmeier
On Monday 01 August 2011, Duncan Murdoch wrote: > I've just committed the changes to R-devel. Let me know if there is > anything worse than what I described. Well, you did not give detail on that, but I was surprised about the "topic" field for vignettes. Here (on a Debian/Linux system), for som

[Rd] one way to solve bad looking density plots in postscript

2011-08-03 Thread Michael Lachmann
Hi, When R generates density plots and these are exported to postscript( a=matrix(1:100,10,10);image(a,col=rainbow(100);dev.copy2eps(file="image.eps") ) The result often looks bad when rendered on screen. The help page states that this is because programs use anti-aliasing. That seems to be true