Grokbase Groups R r-devel April 2011

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94 discussions - 393 posts

  • Dear all, While R CMD check and R CMD INSTALL have always created the vignettes on R-2.12.1 or any earlier versions of R, I am no longer able to build the vignettes on R-2.13.0. Instead R CMD check ...
    Apr 23, 2011 at 7:50 pm
    May 9, 2011 at 6:40 pm
  • Years ago, I did lots of Perl programming. Perl will let you be lazy and write functions that refer to undefined variables (like R does), but there is also a strict mode so the interpreter will block ...
    Paul JohnsonPaul Johnson
    Apr 9, 2011 at 7:51 pm
    Apr 11, 2011 at 8:16 pm
  • Hi, apparently I sent my question about using R and C++ to the wrong list, ironically seeing as that list was called Rcpp. Anyway, I was directed to post my question here. To summarize my current ...
    Sean Robert McGuffeeSean Robert McGuffee
    Apr 20, 2011 at 3:33 pm
    Apr 23, 2011 at 9:56 am
  • Hello: 1. How can I tell when the development version of Rtools has changed? For the past few years, I've installed the development version of R tools with each new release of R. I encountered ...
    Spencer GravesSpencer Graves
    Apr 5, 2011 at 9:20 pm
    Apr 10, 2011 at 1:26 pm
  • Hello, I am writing an R interface for one of my C++ programs. The computations in C++ are very time consuming (several hours), so the user needs to be able to interrupt them. Currently, the only way ...
    Apr 25, 2011 at 9:22 am
    Apr 28, 2011 at 1:25 pm
  • Hello, In my description file, I have an example data package in Suggests: that I've deleted from my library to test what the user who doesn't have it will experience. However, R CMD check won't even ...
    Dario StrbenacDario Strbenac
    Apr 29, 2011 at 2:00 am
    May 4, 2011 at 7:00 pm
  • I need a function which is similar to duplicated(), but instead of returning TRUE/FALSE, returns indices of which element was duplicated. That is, [1] NA NA 1 NA 2 (so that I know that element 3 is a ...
    Duncan MurdochDuncan Murdoch
    Apr 8, 2011 at 2:59 pm
    Apr 12, 2011 at 1:26 pm
  • Here are some data frames: df3.2 <- data.frame(1:3, 7:9) df4.2 <- data.frame(1:4, 7:10) df3.3 <- data.frame(1:3, 7:9, 10:12) df4.3 <- data.frame(1:4, 7:10, 10:13) df3.4 <- data.frame(1:3, 7:9, 10:12, ...
    Patrick BurnsPatrick Burns
    Apr 27, 2011 at 5:44 pm
    Oct 8, 2011 at 6:15 pm
  • Is this a bug? Chad Goymer
    Chad GoymerChad Goymer
    Apr 30, 2011 at 4:35 pm
    May 4, 2011 at 4:50 pm
  • Dear R devel list, Good morning; I'm with the Sage ( project. (Some of you might have seen my talk on this at last summer's useR conference). We have some rudimentary support ...
    Karl-Dieter CrismanKarl-Dieter Crisman
    Apr 18, 2011 at 3:48 pm
    Apr 21, 2011 at 3:47 pm
  • Hi, More about the new --resave-data option As mentioned previously here 'R CMD build' and 'R CMD INSTALL' handle this new option ...
    Hervé PagèsHervé Pagès
    Apr 11, 2011 at 12:47 am
    Apr 13, 2011 at 5:54 pm
  • I have just committed some code to the rgl package on to allow rgl images to be inserted into Sweave documents. (This is not in the CRAN version yet.) It ...
    Duncan MurdochDuncan Murdoch
    Apr 19, 2011 at 6:18 pm
    Apr 21, 2011 at 4:48 pm
  • I have a confusing error from R CMD check that I don't get when running the example manually by hand. In the \examples section of an Rd file, I create a GRanges object, then I call a function with ...
    Dario StrbenacDario Strbenac
    Apr 15, 2011 at 3:00 am
    Apr 18, 2011 at 6:24 pm
  • I have a test directory for the survival suite, and dyn.load has ceased to work in it. Below shows the log: tmt1075% R --vanilla R version 2.12.2 (2011-02-25) Copyright (C) 2011 The R Foundation for ...
    Terry TherneauTerry Therneau
    Apr 13, 2011 at 6:00 pm
    Apr 14, 2011 at 12:53 am
  • Is anybody working on a way to standardize the creation of "newdata" objects for predict methods? When using predict, I find it difficult/tedious to create newdata data frames when there are many ...
    Paul JohnsonPaul Johnson
    Apr 26, 2011 at 3:13 pm
    Apr 28, 2011 at 8:31 pm
  • 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 ...
    Apr 18, 2011 at 4:12 pm
    Apr 19, 2011 at 9:02 am
  • Hi, I have seen several packages that with the most recent version of R are giving a warning like this: Assignments in \usage in documentation object 'marginalData-methods': marginalData(object) = ...
    Marc CarlsonMarc Carlson
    Apr 5, 2011 at 5:51 pm
    Apr 10, 2011 at 11:40 pm
  • How do you debug methods of a reference class? I've been using mtrace, which is excellent, but i cannot figure out how to mtrace a reference class method. Maybe there is some other way to debug ...
    A ZegeA Zege
    Apr 7, 2011 at 7:00 pm
    Apr 8, 2011 at 3:38 pm
  • Dear list subscriber, I am quite puzzled by the behaviour of processing Sweave files within an R session, i.e. Sweave("foo.Rnw") versus R CMD Sweave foo.Rnw In the former the environmental variable ...
    Pfaff, Bernhard Dr.Pfaff, Bernhard Dr.
    Apr 21, 2011 at 10:44 am
    Apr 21, 2011 at 1:30 pm
  • Hi, Has something changed regarding the useDynLib in the NAMESPACE file in packages? I've written a package that works in e.g. 2.12/2.13 but simply cannot find the dynamic library under windows. The ...
    Tobias AbeniusTobias Abenius
    Apr 20, 2011 at 11:30 am
    Apr 21, 2011 at 9:54 am
  • as.factor / as.ordered is not written as a generic. This differs from as.numeric, as.matrix, and other as.*. The following seems to address this and does not break make check-all. FWIW, the patch is ...
    Martin MorganMartin Morgan
    Apr 20, 2011 at 4:56 pm
    Apr 20, 2011 at 6:40 pm
  • Hello, I've got a DESCRIPTION file with a the first line: Package: Repitools But, when I run R CMD INSTALL Repitools I get: * installing *source* package Repitools ... ** R ** data ** inst ** ...
    Dario StrbenacDario Strbenac
    Apr 20, 2011 at 12:00 am
    Apr 20, 2011 at 4:15 am
  • I've narrowed my scope problems with predict.coxph further. Here is a condensed example: fcall3 <- as.formula("time ~ age") dfun3 <- function(dcall) { fit <- lm(dcall, data=lung, modelúLSE) ...
    Terry TherneauTerry Therneau
    Apr 18, 2011 at 9:51 pm
    Apr 19, 2011 at 7:37 am
  • Dear R-programmers, I am trying to program a Newton-Raphson in R (yes, i will try GSL, not right now), and it would be a real boon if R had tail call elimination, so that a recursive program has a ...
    Mohit DayalMohit Dayal
    Apr 17, 2011 at 5:34 am
    Apr 18, 2011 at 8:42 pm
  • I have a function in one of my packages that I would like to print using the original source rather than the deparse of the function. The package uses lazy loading and the help page for library ...
    Greg SnowGreg Snow
    Apr 4, 2011 at 7:19 pm
    Apr 18, 2011 at 8:01 pm
  • Hi ... I came across an old post on R-devel that describes a situation very similar to one I find myself in: As you can see in ...
    Geoff JentryGeoff Jentry
    Apr 11, 2011 at 6:34 pm
    Apr 12, 2011 at 1:52 pm
  • For some reason I want to let one data set in a package be known under two different names. Is that possible, and if so, how? I do not want to have two copies of the data set in the package. Thanks, ...
    Göran BroströmGöran Broström
    Apr 5, 2011 at 2:52 pm
    Apr 5, 2011 at 10:23 pm
  • Hi, I have R version 2.8.1 and Rtools 28 installed (as you might guess, set up years ago). In Rtools the MinGW GCC 4.2 compiler toolset is included. For my regular C/C++ programs I have also ...
    Thomas MangThomas Mang
    Apr 3, 2011 at 7:36 pm
    Apr 4, 2011 at 1:46 pm
  • Hello all, I hope I'm writing to the correct place. I believe that the R homepage will benefit from including the "description" meta tag in it's homepage. The reason is that google uses that tag to ...
    Tal GaliliTal Galili
    Apr 1, 2011 at 6:49 am
    Apr 2, 2011 at 2:24 pm
  • I have somehow managed to made a source tar ball which "R CMD check" accepts but "R CMD INSTALL" rejects with: ------------------ Warning in untar2(tarfile, files, list, exdir) : checksum error for ...
    Hin-Tak LeungHin-Tak Leung
    Apr 1, 2011 at 2:19 pm
    Apr 1, 2011 at 8:01 pm
  • Hi! In R 2.14.0dev (R version 2.14.0 Under development (unstable) (2011-04-29 r55692), Windows release (, the line : options(widthU) in code ...
    Alexander FavorovAlexander Favorov
    Apr 30, 2011 at 11:25 pm
    May 3, 2011 at 1:09 am
  • Dear all, I'm puzzled by the behavior of stringHeight in the grid package. Consider the following test, library(grid) test <- function(lab="dog", ...){ g1 <- textGrob(lab) g2 <- ...
    Baptiste auguieBaptiste auguie
    Apr 26, 2011 at 11:06 pm
    May 2, 2011 at 6:08 am
  • Based on a discussion on SO I ran some tests and found that converting to a factor is best done early in the process. Hence, I propose to rewrite the gl() function as : gl2 <- function(n, k, length = ...
    Joris MeysJoris Meys
    Apr 11, 2011 at 9:53 pm
    Apr 12, 2011 at 4:12 pm
  • If x has an S3 class then returns a value without an S3 class but which has the is.object flag set, which, I think, causes identical() give a false/misleading report: [1] FALSE The files ...
    William DunlapWilliam Dunlap
    Apr 11, 2011 at 5:10 pm
    Apr 11, 2011 at 6:07 pm
  • Hi, I observed a slight problem in deparse(): it will add spaces around most operators except /. I wonder if this is easy to fix. I know this is quite trivial, but I will appreciate if / is not ...
    Yihui XieYihui Xie
    Apr 10, 2011 at 1:43 am
    Apr 10, 2011 at 6:26 pm
  • Dear all, I do not completely understand following behaviour : Classes 'file', 'connection' atomic [1:1] 3 ..- attr(*, "conn_id")=<externalptr Why do I get an error, indicating an invalid connection, ...
    Joris MeysJoris Meys
    Apr 8, 2011 at 2:56 pm
    Apr 8, 2011 at 4:19 pm
  • In a conversation with a programmer new to writing R packages, he mentioned that he was very confused by phrase "package writer" used in the document, and said that he "[was] literally imagining some ...
    Davor CubranicDavor Cubranic
    Apr 1, 2011 at 6:22 pm
    Apr 2, 2011 at 12:13 am
  • Several Bioconductor packages were expecting Windows Rzlib.dll to provide gzopen / gzread / gzseek / gzgets / gzrewind / gzclose. Are these gone for good, viz., r55624 ? Martin -- Computational ...
    Martin MorganMartin Morgan
    Apr 29, 2011 at 10:13 pm
    May 17, 2011 at 6:41 pm
  • I discovered that the Kendall's tau calculation in R uses all pairwise comparisons which is O(n^2) and takes a long time for large vectors. I implemented a O(n*log(n)) algorithm based on merge-sort ...
    Apr 30, 2011 at 3:20 pm
    Apr 30, 2011 at 10:11 pm
  • Hello, I'm sending this to R-devel under the guideline that the ensuing discussion would probably be unintelligible to people who aren't programmers. If that's not right, I apologize ...
    Brett SmithBrett Smith
    Apr 27, 2011 at 4:55 pm
    Apr 28, 2011 at 3:07 pm
  • While checking packages against R 2.13.0-beta on Windows, I have run into a few strange error messages related to copying files. The errors all relate to file.copy() and have the form of: Error in ...
    Apr 7, 2011 at 8:59 pm
    Apr 24, 2011 at 4:00 pm
  • Hello dear R developers, I recently found out that it is not possible to limit update.packages() to update only a few packages at a time. The patch offered simply adds a 'subset' parameter and the ...
    Tal GaliliTal Galili
    Apr 18, 2011 at 6:51 am
    Apr 21, 2011 at 8:46 am
  • When I re-use a code chunk in Sweave, together with keep.source=TRUE, I would like to follow usual programming conventions in which the amount of white space on the left indicates logical structure ...
    Apr 19, 2011 at 8:59 pm
    Apr 20, 2011 at 2:17 pm
  • I was writing Rd documentation for a new package when I came across this issue. Here's the smallest example: Error in parse_Rd(file.path(tempdir(), "test.Rd")) : Unexpected end of input (in ' quoted ...
    Jeffrey HornerJeffrey Horner
    Apr 12, 2011 at 4:24 pm
    Apr 12, 2011 at 4:38 pm
  • Dear List, I'm not even sure this is an issue or not, but ?rowMeans has: Value: A numeric or complex array of suitable size, or a vector if the result is one-dimensional. The ?dimnames? (or ?names? ...
    Gavin SimpsonGavin Simpson
    Apr 5, 2011 at 11:33 am
    Apr 11, 2011 at 3:11 pm
  • The inst/doc directory of the DAAG package has 6 files, ... that are around 0.85 MB each. It would be useful to be able to zip then, but that as matters stand interferes with the use of ...
    John MaindonaldJohn Maindonald
    Apr 9, 2011 at 5:38 am
    Apr 9, 2011 at 8:17 am
  • Hi there, Suppose the cmd is "a<-3", I can parse the cmd sexp with R_ParseVector and eval it. My question is - is it possible to parse a cmd like "a <- ?", afterwards evaluation will give ...
    Zheng, Xin (NIH) [C]Zheng, Xin (NIH) [C]
    Apr 7, 2011 at 9:18 pm
    Apr 7, 2011 at 9:47 pm
  • Hi, I have a couple of new errors in our package when I check it on R 2.13-rc (r55310). The first one that's mystifying me is * checking R code for possible problems ... NOTE Error : object ...
    Dario StrbenacDario Strbenac
    Apr 6, 2011 at 12:00 am
    Apr 7, 2011 at 6:00 am
  • Apologies for asking something that is probably very obvious, i just started with S4 classes and i guess i am not finding documentation that lays out the grammar rules and gives enough examples. I ...
    A ZegeA Zege
    Apr 6, 2011 at 2:54 pm
    Apr 6, 2011 at 8:41 pm
  • I apologize in advance for probably missing something obvious, but if someone could point me in the right direction I'd be grateful. This NOTE is not unique to our package (I list a few others, ...
    Jay EmersonJay Emerson
    Apr 3, 2011 at 5:31 pm
    Apr 3, 2011 at 6:30 pm
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108 users for April 2011

Duncan Murdoch: 32 posts Simon Urbanek: 24 posts Prof Brian Ripley: 16 posts Peter dalgaard: 14 posts Uwe Ligges: 13 posts Gabor Grothendieck: 12 posts Martin Maechler: 12 posts Dario Strbenac: 10 posts Sean Robert McGuffee: 10 posts Cstrato: 9 posts Hadley Wickham: 9 posts Martin Morgan: 9 posts Hervé Pagès: 8 posts Terry Therneau: 8 posts Henrik Bengtsson: 7 posts William Dunlap: 7 posts A Zege: 6 posts Dirk Eddelbuettel: 6 posts Sharpie: 6 posts Spencer Graves: 6 posts
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