Re: [Bioc-devel] depends on packages providing classes

2014-10-29 Thread Henrik Bengtsson
On Wed, Oct 29, 2014 at 1:07 PM, Vincent Carey st...@channing.harvard.edu wrote: On Wed, Oct 29, 2014 at 2:15 PM, Hervé Pagès hpa...@fredhutch.org wrote: Hi, On 10/28/2014 08:51 PM, Vincent Carey wrote: On Tue, Oct 28, 2014 at 5:48 PM, Hervé Pagès hpa...@fredhutch.org

Re: [Bioc-devel] depends on packages providing classes

2014-10-29 Thread Michael Lawrence
On Wed, Oct 29, 2014 at 11:15 AM, Hervé Pagès hpa...@fredhutch.org wrote: Hi, On 10/28/2014 08:51 PM, Vincent Carey wrote: On Tue, Oct 28, 2014 at 5:48 PM, Hervé Pagès hpa...@fredhutch.org mailto:hpa...@fredhutch.org wrote: On 10/28/2014 12:42 PM, Vincent Carey wrote:

[Rd] terms function bug?

2014-10-29 Thread Patrick O'Reilly
Hi, I've noticed something strange when using the terms {stats} function. R documentation describes the factors attribute of the terms.object as follows: A matrix of variables by terms showing which variables appear in which terms. The entries are 0 if the variable does not occur in the term, 1

[Rd] Unexpected behavior of identical() with language objects

2014-10-29 Thread Winston Chang
I ran into this and found the result very surprising: identical( quote({ a }), quote({ a }) ) # FALSE It seems related to curly braces. For example, parens work fine: identical( quote(( a )), quote(( a )) ) # TRUE Is this expected behavior? I can't seem to find anything in the help for

Re: [Rd] Unexpected behavior of identical() with language objects

2014-10-29 Thread Joshua Ulrich
On Wed, Oct 29, 2014 at 3:26 PM, Winston Chang winstoncha...@gmail.com wrote: I ran into this and found the result very surprising: identical( quote({ a }), quote({ a }) ) # FALSE It seems related to curly braces. For example, parens work fine: identical( quote(( a )), quote(( a )) ) #

Re: [Rd] Unexpected behavior of identical() with language objects

2014-10-29 Thread Lorenz, David
Fascinating! I tried the comparisons with all.equal(), expecting a description of the difference, but TRUE was returned in both cases. Dave On Wed, Oct 29, 2014 at 3:26 PM, Winston Chang winstoncha...@gmail.com wrote: I ran into this and found the result very surprising: identical( quote({ a

Re: [Rd] Unexpected behavior of identical() with language objects

2014-10-29 Thread Hadley Wickham
Is this expected behavior? I can't seem to find anything in the help for identical that relates to this. It's not in ?identical, but ?Paren gives you some pointers. str(quote((a))) and str(quote({a})) are also informative. Yes, looks like srcrefs are to blame: x - quote({ a }) y - quote({ a

Re: [Rd] Unexpected behavior of identical() with language objects

2014-10-29 Thread Winston Chang
Ah, I was using identical() to compare two function bodies. It returns FALSE even when you remove srcrefs from the body: f1 - function(x) { if (TRUE) { x } } f2 - function(x) { if (TRUE) { x } } f1b - body(f1) f2b - body(f2) attributes(f1b) - NULL attributes(f2b) - NULL # The bodies look the

[Rd] Milestone: 6000 packages on CRAN

2014-10-29 Thread Henrik Bengtsson
Another 1000 packages were added to CRAN and this time in less than 12 months. Today (2014-10-29) on The Comprehensive R Archive Network (CRAN) [1]: Currently, the CRAN package repository features 6000 available packages. Going from 5000 to 6000 packages took 355 days - which means that it's on

Re: [Rd] Unexpected behavior of identical() with language objects

2014-10-29 Thread Mark.Bravington
[See below for full email trail-- Outlook has beaten me into submission] I ran into this and found the result very surprising: identical( quote({ a }), quote({ a }) ) # FALSE ... -Winston Yes, looks like srcrefs are to blame: x - quote({ a }) y - quote({ a }) identical(x, y) #

Re: [Rd] Unexpected behavior of identical() with language objects

2014-10-29 Thread Duncan Murdoch
On 29/10/2014, 6:22 PM, mark.braving...@csiro.au wrote: [See below for full email trail-- Outlook has beaten me into submission] I ran into this and found the result very surprising: identical( quote({ a }), quote({ a }) ) # FALSE ... -Winston Yes, looks like srcrefs are to blame: x -

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

2014-10-29 Thread Mike Beddo
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 to build the packages I need. Rcpp is crucial. I