Re: [Rd] Crash report: regexpr("a{2-}", "")

2010-09-22 Thread Brian Diggs
[Accidentally posted this to r-help instead of r-devel; reposting to put it into the correct list and thread. My apologies for the duplication.] On 9/21/2010 8:04 PM, Henrik Bengtsson wrote: Each of the following calls crash ("core dumps") R (R --vanilla) on various versions and OSes: regexpr(

[Rd] Sweave and absolute escaped backslashed Windows paths in R 2.12.0

2010-10-25 Thread Brian Diggs
I've noticed a change in behavior in R 2.12.0 from 2.11.1 regarding the treatment of absolute paths in the file argument of Sweave in a Windows environment. Consider the minimal Rnw file, attached and reproduced below my signature in case .Rnw files get stripped. This file is stored on my (W

[Rd] Link to R 2.12.0 patched build for windows

2010-10-26 Thread Brian Diggs
On the download page for windows builds of R 2.12.0: http://cran.r-project.org/bin/windows/base/ The link for "r-patched snapshot build" goes to: http://cran.r-project.org/bin/windows/base/rpatched.html which has a link for R-2.11.1 patched. I believe that link should go to: http://cran.r-pr

[Rd] Minor typo in "Writing R Extensions"

2011-03-04 Thread Brian Diggs
In "Writing R Extensions", section 1.1.1, the paragraph talking about the Depends field has an extra right parenthesis at the end of the second sentence (or is missing a left parenthesis somewhere). This is on line 392 of R-exts.texi (revision 54667). I have attached a diff, thought I don't kn

Re: [Rd] Dangerous Bug with IF function of R

2011-04-18 Thread Brian Diggs
On 4/18/2011 9:12 AM, salmajj wrote: hi! there is a bug with the IF operator that is really dangerous! please try the code below and if someone could explain to me why when (q is equal to 0.8, 0.9 or 1) R do not print it? q=0 for (j in 1:11){ if ((q==1)){ print(q) }

Re: [Rd] Strategies for keeping autogenerated .Rd files out of a Git tree

2013-12-13 Thread Brian Diggs
On 12/11/2013 4:39 PM, Kirill Müller wrote: Hi Quite a few R packages are now available on GitHub long before they appear on CRAN, installation is simple thanks to devtools::install_github(). However, it seems to be common practice to keep the .Rd files (and NAMESPACE and the Collate section in

Re: [Rd] proposed change of check message when VIgnetteBuilder package is not declared as a dependency

2014-07-14 Thread Brian Diggs
On 7/11/2014 4:49 PM, Dan Tenenbaum wrote:> Hi, > > I notice in R-3.1.1, if a package specifies a VignetteBuilder (such > as knitr) in its DESCRIPTION file, butdoes not also depend on the > specified package (in either Depends, Imports, or Suggests), that R > CMD check will say: > > * checking pac

[Rd] No R 2.15.2 or R 2.15.2 patched version option in bug tracker

2012-11-28 Thread Brian Diggs
When I went to report a (very minor) bug today, I noticed that under the choices for Version, there was no entry for "R 2.15.2" nor "R 2.15.2 patched". I could not find a contact email for the bug tracker itself, so I figured the next best place to send this was r-devel. Perhaps adding new vers

Re: [Rd] Baffled with as.matrix

2012-11-30 Thread Brian Diggs
On 11/30/2012 4:53 AM, Terry Therneau wrote: I'm puzzled by as.matrix. It appears to work differently for Surv objects. Here is a session from my computer: tmt% R --vanilla > library(survival) Loading required package: splines > ytest <- Surv(1:3, c(1,0,1)) > is.matrix(ytest) >[1] TRUE It

Re: [Rd] stringsAsFactors

2013-02-11 Thread Brian Diggs
On 2/11/2013 5:50 AM, Terry Therneau wrote: I think your idea to remove the warnings is excellent, and a good compromise. Characters already work fine in modeling functions except for the silly warning. It is interesting how often the defaults for a program reflect the data sets in use at the t

[Rd] Correction to documentation of print.ls_str in utils package

2009-04-15 Thread Brian Diggs
isplay all the nesting levels; NA does that (based on the documentation of str). A value of 0 does not display any nested levels. I recommend changing that sentence to "If NA, display all nesting levels. Default 1: Display only the first nested level." -- Brian Diggs, Ph.D. Senio

Re: [Rd] suggestion for R >= 3.0: computer-readable CHANGELOG

2009-04-17 Thread Brian Diggs
his would be at least a starting point. R code and output, including a complete list of which packages do and do not have a ChangeLog entry, is below. I have not used any of the Bioconductor packages, so I don't know if a similar idea would work for them. > Dirk -- Brian Diggs, Ph.D. Senior

[Rd] Error with cut.POSIXt and daylight savings time switchover dates

2010-02-01 Thread Brian Diggs
Angeles") tm$hour <- 0 as.POSIXct(tm) # [1] NA Is there a timezone/daylight savings time safe way to get to the beginning of the day in cut.POSIXt so that invalid dates are not sent to the other functions? Alternatively, can as.POSIXct.POSIXlt be made to handle these manually manipula

Re: [Rd] Error with cut.POSIXt and daylight savings time switchover dates

2010-02-03 Thread Brian Diggs
On 2/1/2010 3:57 PM, Brian Diggs wrote: > The following code: > > cut(as.POSIXct("2009-11-01 04:00:00", tz="America/Los_Angeles"), "1 day") > > gives the error: > > Error in seq.int(0, to - from, by) : 'to' must be finite > > T

Re: [Rd] Error with cut.POSIXt and daylight savings time switchover dates (patch included)

2010-02-04 Thread Brian Diggs
On 2/3/2010 7:48 AM, Brian Diggs wrote: > On 2/1/2010 3:57 PM, Brian Diggs wrote: >> The following code: >> >> cut(as.POSIXct("2009-11-01 04:00:00", tz="America/Los_Angeles"), "1 day") >> >> gives the error: >> >>

Re: [Rd] (PR#13180) Wrong behavior of lines.survfit for conf.int="only"

2008-10-20 Thread Brian Diggs
got encoded that way. Additionally, this was meant as a follow-up to PR#13171. Both PR#13171 and PR#13180 can be considered dealt with. Please accept my apologies for messing the process up so much. -- Brian Diggs, Ph.D. Senior Research Associate, Department of Surgery, Oregon Health