similar to: To run or not to run examples, CTFS package

The package I am writing is for the Center for Tropical Forest Science, CTFS. This "center" is a collaboration of 15+ institutions world wide that are investigating properties of tropical forest dynamics, species diversity, species distributions. The investigation is composed of the same sampling design of the forest: a large 50 hectare plot (usually) in which every tree >= 10 mm in

Is there a good strategy for testing examples which should not be run by default? For instance, I have examples which get data from the Internet. If I wrap them in try() then they can be skipped if the Internet is not available, but may not be tested in cases when I would like to know about the failure. (Not to mention that the example syntax is ugly.) If I mark them \dontrun or \donttest

Dear list, I have just started to use roxygen and cannot find out how to specify NOT RUN examples. I know that to include R code examples works via the @examples tag followed by the code. Without roxygen, if I want R code not to be run when processing the .Rd files I would include the \dontrun tag \examples{\dontrun{ ... some example R code} } How can I achieve this using roxygen? Thanks Mark

On 14-11-26 05:49 PM, Duncan Murdoch wrote: > On 26/11/2014, 1:45 PM, Paul Gilbert wrote: >> Is there a good strategy for testing examples which should not be run by >> default? For instance, I have examples which get data from the Internet. >> If I wrap them in try() then they can be skipped if the Internet is not >> available, but may not be tested in cases when I

Hi, source(file,echo=T) will not echo the last comment in "file" if it is the last line in the file. For instance, when sourcing a file containing the following lines #comment 1 a<-1 #comment 2 R will echo > #comment 1 > a<-1 What is the solution to have R echo all of the comment lines? Specific context: This problem arises e.g. in the context of help files (.Rd) whose

Hello, The package I'm finishing up contains a series of functions intended to be run one after the other, as in: do data-prep using A() run complicated, slow, analysis B() do complicated, slow additional analysis C() plot the results with D() and E() Now, in the documentation for each of those functions, I put the entire sequence to illustrate the proper sequence. But this means that the

Dear R-helpers, making a package (windowsXP), that includes a bunch of functions, but none have examples (all example code is within \dontrun{} blocks). I do R CMD check Maeswrap, all bits get OK-ed, except: "Running examples in 'Maeswrap-Ex.R' failed." When I run the 'Maeswrap-Ex.R' file myself, there are no problems. Any pointers? thanks Remko

You've answered my question 2 about why the manual was in odd order > R CMD check was more of a check of the latex version of the files, not > the final manual. I was looking at the result of R CMD check, and it was in random order (perhaps file date?), not just a different collation choice. Very odd. I will cease worrying about what I might have "done wrong". I omitted the

1. I often like to put bits of the output into the manual pages. (We can have a discussion of the value of this elsewhere -- I think it is sometimes a good thing.) In R I need to surround these with \dontrun{} for the sake of the tester, which is fine. But the printed output contains ## Not run and ## End (not run) comments, which defeats the purpose of the lines by breaking them

Hi, Paul: "if(!fda::CRAN())" runs code except with "R CMD check ?as-cran". I use it so CRAN checks skip examples that (a) need the Internet or (b) take too long for CRAN. Hope this helps. Spencer On 11/26/2014 10:45 AM, Paul Gilbert wrote: > Is there a good strategy for testing examples which should not be run > by default? For instance,

I am stumped in determining the proper syntax for including displayed S code within an R .Rd documentation file, in places other than \examples{}. I have tried \code{ line 1 line 2 } but the lines get run together. When I terminate the lines by \cr, the "\cr" actually appears in the resulting html file. This is all inside a customized \section{}. On a related note, what is

Dear list, When I run an R CMD check --as-cran on my package (pROC) I get the following note: > Uses the superseded package: ?doSNOW? The fact that it uses the doSNOW package is correct as I have the following example in an .Rd file: > #ifdef windows > if (require(doSNOW)) { > registerDoSNOW(cl <- makeCluster(2, type = "SOCK")) > ci(roc2,

Dear all, I (and a colleague) have been working on our first package (for fitting a certain type of cognitive models: http://www.psychologie.uni-freiburg.de/Members/singmann/R/mptinr) for quite a while now and have the feeling, that it is "good to go". That is, we want to submit it to CRAN. However, I still have two questions before doing so and would appreciate any comments. 1. How

Hello, All: The CRAN checks for the "fda" package includes one error: The error most likely occurred in ... file.copy2 ... Error: unprotect_ptr: pointer not found Execution halted (http://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian/fda-00check.html) The help page for "file.copy2" includes "\examples" with everything wrapped in

Hello, Is there an way to easy comment of sections of code? I was thinking something along the lines of \dontrun{ codeline 1 .... codeline k } but that could be used in regular script files. When I am still working on a script, I often want to being using what is done, but I would like the parts I am still working on not to be run when I use source() on the file. I can set everything off

I have tried and tried unsuccessfully to place a legend outside the plot frame of a graph. This would allow me to draw a legend for an image() plot. But any legend I add is cut off outside the axes. Is there a way of doing this? Thanks for any advice on how to make this work (I'm using R1.5.1 with Windows 2000). Richard Condit Smithsonian Tropical Research Institute Unit 0948 APO AA

Oh, I completely missed that one. It's very neat as it seems to work both on Windows and Unix. Thanks! Xavier On 10/02/15 10:52, Martyn Plummer wrote: > The CRAN package snow is superseded by the parallel package which is > distributed with R since version 2.14.0. Here are the release notes > > \item There is a new package \pkg{parallel}. > > It incorporates (slightly

Hello all, My name is Ashish Kumar Gahlot and I am a final year undergraduate student of Engineering College Ajmer(Rajasthan, India) majoring in Computer Science. I am interested in working on project *Integrate with Z3 SMT solver to reduce false positives *for GSOC 2018. I am having experience with SMT solvers as I play CTFs and have used z3 to solve reverse engineering problems. How can I

Dear All, I'am looking for examples showing that correlation does not imply causality, the targeted audience consists of undergraduate students (their first year at the university but in the BioMathStat track). All practicals are under R. I was able to extract this from R datasets: ### begin data(sunspots) data(lynx) spots <- window(sunspots, freq = 1, start = 1880, end = 1900) lnx <-

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