Re: [Rd] checking dependencies in R code ... WARNING

2014-05-08 Thread Knut Krueger
Am 08.05.2014 08:35, schrieb Tobias Verbeke: Hi Knut, The code will contain library or require statements, which do not belong there, but need to replaced by specifying the dependencies on these packages in the DESCRIPTION file (Depends / Imports field). For imports you also need to make sure th

Re: [Rd] checking dependencies in R code ... WARNING

2014-05-08 Thread Tobias Verbeke
Hi Knut, I was primarily referring to the issues reported on the line 'library' or 'require' calls not declared from: 'Hmisc' 'R2HTML' 'tcltk' but what you say for .win32consoleCompletion does not seem wrong, esp. that it is not recommended to make use of ::: operators inside a package. Best,

Re: [Rd] precedence (was 'historical NA question')

2014-05-08 Thread Barry Rowlingson
On Wed, May 7, 2014 at 11:00 PM, Duncan Murdoch wrote: > > > Is there a language where "- 2^2" gives a different answer than "-2^2"? > (Substitute ** or any other exponentiation operator for ^ if you > like.) This is important, because I'd like to avoid ever attempting any > important calculati

Re: [Rd] historical significance of Pr(>Chisq) < 2.2e-16

2014-05-08 Thread peter dalgaard
On 08 May 2014, at 08:38 , Prof Brian Ripley wrote: > Only in very unusual circumstances does it matter how small a p-value less > than, say, 1e-6 is. Slight disagreement: It does matter when there are multiple comparisons in the order of several thousands, which is not so unusual in bioinfor

Re: [Rd] checking dependencies in R code ... WARNING

2014-05-08 Thread Knut Krueger
Am 08.05.2014 09:34, schrieb Tobias Verbeke: Hi Knut, I was primarily referring to the issues reported on the line Hi Tobias, ok the warning is a little bit misleading, it was an additional use of require(foo) of the import packages in NAMESPACE and DESCRIPTION do you have a hint for this to

Re: [Rd] precedence (was 'historical NA question')

2014-05-08 Thread Gábor Csárdi
On Thu, May 8, 2014 at 3:35 AM, Barry Rowlingson < b.rowling...@lancaster.ac.uk> wrote: [...] This is an example to show to everyone who says "Can we use + to > concatenate strings in R please!?". > This is one of my main complaints against the R syntax. In general, R code is often somewhat unrea

[Rd] trivial patch solve.Rd (typo)

2014-05-08 Thread Tobias Verbeke
L.S. Please find below a trivial patch which corrects a typo in solve.Rd from base. Best, Tobias Index: solve.Rd === --- .architect/workspace/R_svn/src/library/base/man/solve.Rd(revision 65545) +++ .architect/workspace/R_svn/src

Re: [Rd] access environment in which an error occurred

2014-05-08 Thread Winston Chang
I think this should do the trick: test <- function() { b <- 3 stop('error here') } df3 <- function() { saveRDS(sys.frame(1), file = "dump.rds") } options(error = df3) test() # Error in test() : error here # Read in the file and examine the environment frame <- readRDS("dump.rds") ls(fr