Re: [Rd] Rcmd_environ and R_LIBS_{USER,SITE}

2012-10-18 Thread Keith Jewell
No reply in a number of hours, so here is a suggestion from ignorance :-} ?Startup refers to a number of other site and user files to process for setting environment variables but not to Rcmd_environ. The contents of $R_HOME/etc/Rcmd_environ seem to reflect (some of) the contents of (some)

[Rd] S4 fails to initialize linear hierarchies with intermediate VIRTUAL classes

2012-10-18 Thread Martin Morgan
Initialization of this simple hierarchy A = setClass(A, representation(x=numeric)) setClass(B, contains=c(VIRTUAL, A)) C = setClass(C, contains=B) fails (neat that setClass returns generators; I hadn't realized that before!) C(A()) Error: evaluation nested too deeply: infinite recursion

Re: [Rd] Rcmd_environ and R_LIBS_{USER,SITE}

2012-10-18 Thread Dirk Eddelbuettel
Keith, On 18 October 2012 at 09:14, Keith Jewell wrote: | No reply in a number of hours, so here is a suggestion from ignorance :-} | | ?Startup refers to a number of other site and user files to process for Thanks, and I know, and use those on Linux (and on 'doze when I use it). My question

Re: [Rd] Rcmd_environ and R_LIBS_{USER,SITE}

2012-10-18 Thread Kasper Daniel Hansen
Dirk, I set my user libraries in .Rprofile for this very reason. I agree it is weird that .Renviron is not always read etc. Kasper On Thu, Oct 18, 2012 at 10:12 AM, Dirk Eddelbuettel e...@debian.org wrote: Keith, On 18 October 2012 at 09:14, Keith Jewell wrote: | No reply in a number of

Re: [Rd] Rcmd_environ and R_LIBS_{USER,SITE}

2012-10-18 Thread Dirk Eddelbuettel
Kasper, On 18 October 2012 at 10:41, Kasper Daniel Hansen wrote: | I set my user libraries in .Rprofile for this very reason. I agree it | is weird that .Renviron is not always read etc. Sorry, no cigar either -- this equivalent to using files in $R_HOME/etc/ and is also ignored by R CMD

Re: [Rd] S4 fails to initialize linear hierarchies with intermediate VIRTUAL classes

2012-10-18 Thread John Chambers
On 10/18/12 6:31 AM, Martin Morgan wrote: Initialization of this simple hierarchy A = setClass(A, representation(x=numeric)) setClass(B, contains=c(VIRTUAL, A)) C = setClass(C, contains=B) fails (neat that setClass returns generators; I hadn't realized that before!) Yes, from

[Rd] Mac and Windows binaries of rJava broken for R-devel?

2012-10-18 Thread Hervé Pagès
Hi, Here is a problem we see with the Mac and Windows binaries of rJava (0.9-3) currently available on CRAN for R-devel (i.e. under bin/macosx/leopard/contrib/2.16/ and bin/windows/contrib/2.16/): library(rJava) .jinit(gaggle/inst/jars/gaggleRShell.jar) Error in .Call(R_do_new_object,