Re: [Bioc-devel] plotPCA for BiocGenerics

2014-10-31 Thread Thomas Lin Pedersen
With regards to abstraction - I would personally much rather read and write code that contained plotScores() and plotScree() etc. where the intend of the code is clearly communicated, instead of relying on a plot() function whose result is only known from experience. Trying to squeeze every

Re: [Bioc-devel] plotPCA for BiocGenerics

2014-10-31 Thread Steve Lianoglou
Hi, On Fri, Oct 31, 2014 at 2:35 PM, Thomas Lin Pedersen thomas...@gmail.com wrote: With regards to abstraction - I would personally much rather read and write code that contained plotScores() and plotScree() etc. where the intend of the code is clearly communicated, instead of relying on a

Re: [Rd] 'library' or 'require' call not declared from: 'rgl'

2014-10-31 Thread Martyn Plummer
On Thu, 2014-10-30 at 17:18 -0400, Michael Friendly wrote: On 10/30/2014 4:19 PM, Simon Urbanek wrote: Did you intend rgl to be optional? If so, then you should use Suggests: instead. When you use Imports: it will load rgl automatically so require() does't make sense (since it will be always

[Rd] proposed: minor change to error message

2014-10-31 Thread Dan Tenenbaum
When checking a package (call it A) that has Enhances: B in DESCRIPTION, I get the message: Package which this enhances but not available for checking: ‘B’ Can this be changed to: Package which enhances this but not available for checking: ‘B’ ? Because really, B is not enhanced by A, B does

[Rd] ScalarLogical and setAttrib

2014-10-31 Thread Jeroen Ooms
Is it expected that attributes set on a LGLSXP created by ScalarLogical will apply to all future objects created by ScalarLogical as well? For example: the 'test1' function below returns FALSE and 'test2' returns FALSE with an attribute: library(inline) test1 - cfunction(body = 'return

Re: [Rd] proposed: minor change to error message

2014-10-31 Thread Duncan Murdoch
On 31/10/2014, 2:22 PM, Dan Tenenbaum wrote: When checking a package (call it A) that has Enhances: B in DESCRIPTION, I get the message: Package which this enhances but not available for checking: ‘B’ Can this be changed to: Package which enhances this but not available for checking:

[Rd] Options that are local to the package that sets them

2014-10-31 Thread Gábor Csárdi
Dear All, I am trying to do the following, and could use some hints. Suppose I have a package called pkgA. pkgA exposes an API that includes setting some options, e.g. pkgA works with color palettes, and the user of the package can define new palettes. pkgA provides an API to manipulate these

Re: [Rd] Options that are local to the package that sets them

2014-10-31 Thread Gabor Grothendieck
On Fri, Oct 31, 2014 at 7:34 PM, Gábor Csárdi csardi.ga...@gmail.com wrote: Dear All, I am trying to do the following, and could use some hints. Suppose I have a package called pkgA. pkgA exposes an API that includes setting some options, e.g. pkgA works with color palettes, and the user of

Re: [Rd] Options that are local to the package that sets them

2014-10-31 Thread William Dunlap
You can put the following 3 objects, an environment and 2 functions that access it, in any package that need some package-specific storage (say your pkgB1 and pkgB2). .pkgLocalStorage - new.env(parent = emptyenv()) assignInPkgLocalStorage - function(name, object) {

Re: [Rd] Options that are local to the package that sets them

2014-10-31 Thread Gábor Csárdi
On Fri, Oct 31, 2014 at 8:16 PM, William Dunlap wdun...@tibco.com wrote: You can put the following 3 objects, an environment and 2 functions that access it, in any package that need some package-specific storage (say your pkgB1 and pkgB2). .pkgLocalStorage - new.env(parent = emptyenv())

[Rd] Appropriately Crediting Use of R Source Code in Package

2014-10-31 Thread brodie gaslam
I'm developing packages that in some places use code that started off as a direct copy-paste from the R sources (this is C code). The finished code is fairly different from what I started with, but clearly uses similar algorithms / tricks as the original code, and some lines here and there are

Re: [Rd] Trouble installing Rcpp on AIX - missing execinfo.h

2014-10-31 Thread Edward Davignon
Mike, Perhaps this will help: http://cygwin.com/ml/cygwin/2012-04/msg00346.html Regards, Ed Davignon On Thu, Oct 30, 2014 at 12:13 AM, Mike Beddo mike.be...@dataventures.com wrote: Greetings, When I try install.packages('Rcpp') it fails when compiling api.cpp (line 39). This is Rcpp

Re: [Rd] Options that are local to the package that sets them

2014-10-31 Thread Gabor Grothendieck
On Fri, Oct 31, 2014 at 8:43 PM, Gábor Csárdi csardi.ga...@gmail.com wrote: On Fri, Oct 31, 2014 at 8:10 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: [...] Is there a better way? I have a feeling that this is already supported somehow, I just can't find out how. Try the settings

Re: [Rd] Options that are local to the package that sets them

2014-10-31 Thread Martin Morgan
On 10/31/2014 05:55 PM, Gábor Csárdi wrote: On Fri, Oct 31, 2014 at 8:16 PM, William Dunlap wdun...@tibco.com wrote: You can put the following 3 objects, an environment and 2 functions that access it, in any package that need some package-specific storage (say your pkgB1 and pkgB2).

Re: [Rd] Options that are local to the package that sets them

2014-10-31 Thread Gábor Csárdi
On Fri, Oct 31, 2014 at 9:20 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: [...] Isn't your problem really just that you want multiple sets of settings? That's what settings provides. Almost. Multiple sets of settings, set up by the same package. So essentially I want pkgA to use

Re: [Rd] Options that are local to the package that sets them

2014-10-31 Thread Gábor Csárdi
On Fri, Oct 31, 2014 at 9:26 PM, Martin Morgan mtmor...@fredhutch.org wrote: [...] You'll need pkgA to be able to know that pkgB1's invokation is to use pkgB1's parameters, so coupling state (parameters) with function, i.e., a class with methods. So a solution is to use an S4 or reference class

Re: [Rd] Trouble installing Rcpp on AIX - missing execinfo.h

2014-10-31 Thread Dirk Eddelbuettel
On 30 October 2014 at 04:13, Mike Beddo wrote: | Greetings, | | When I try install.packages('Rcpp') it fails when compiling api.cpp (line 39). This is Rcpp 0.11.3. I searched my filesystem, and indeed I do not have execinfo.h anywhere. After some effort, I got R build on AIX. Now I am trying

Re: [Rd] Trouble installing Rcpp on AIX - missing execinfo.h

2014-10-31 Thread Mike Beddo
Dirk and Edward, Thanks for the help. I found for AIX that execinfo.h basically did nothing that I could tell. What I ended up doing was replacing the line in api.cpp #include execinfo.h with the following from gnulib: int backtrace (void **buffer, int size) { (void) buffer; (void)