search for: codoc

I have a function: source_dir <- function(path, pattern = "\\.[rR]$", chdir = TRUE) ... documented with ... \usage{source_dir(path, pattern="\\.[rR]$", chdir=TRUE)} ... But I get Codoc mismatches from documentation object 'source_dir': source_dir Code: function(path, pattern = "\\.[rR]$", chdir = TRUE) Docs: function(path, pattern = "\.[rR]$", chdir = TRUE) Mismatches in argument default values: Name: 'pattern' Code: "\\.[rR]$&qu...

Hi, Doing 'R CMD check diveMove' is now throwing this message: Data codoc mismatches from documentation object 'sealLocs': Variables in data frame 'sealLocs' Code: id.time.class.lon.lat Docs: class id lat lon time with: R> sessionInfo() R version 2.10.1 (2009-12-14) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C...

...y is present in the code but missing in the documentation , although it is actually NOT in the code. In order to make this reproducible for everybody, I put together a little dummy package in which one of the methods leads to exactly this warning: http://www.bioinf.jku.at/people/bodenhofer/codocMismatchTest_0.0.1.tar.gz Just run 'R CMD check' on this archive and you'll see. You will also see from the code and the corresponding documentation that the warning seems unjustified. I tried the following R versions: 2.12.1, 2.13.0, 2.13.1, 2.14.0, 2.14.1, 2.15.0, 2.15.1, 2.15.2, 2...

...y is present in the code but missing in the documentation , although it is actually NOT in the code. In order to make this reproducible for everybody, I put together a little dummy package in which one of the methods leads to exactly this warning: http://www.bioinf.jku.at/people/bodenhofer/codocMismatchTest_0.0.1.tar.gz Just run 'R CMD check' on this archive and you'll see. You will also see from the code and the corresponding documentation that the warning seems unjustified. I tried the following R versions: 2.12.1, 2.13.0, 2.13.1, 2.14.0, 2.14.1, 2.15.0, 2.15.1, 2.15.2, 2...

...an odd and repeatedly irritating error I noticed when running the check Perl script on my R 1.3 project. In following it line by line, I traced my problem down to the code/documentation matching within check, the most recent version of which seems to verify proper .Rd formatting by means of R's codoc and undoc functions. Under R --vanilla, those two then unpack and repack my project, with each assembling a kind of test tempfile to ensure various structural requirements within my project. At first, I got bogged down in a mysterious "parse" problem, R's not-too-revealing result of a...

Hi, I would like to get a hint on how to debug in the case of #> R CMD check pllib signalling * checking for code/documentation mismatches ... WARNING Error in parse(file, n, text, prompt) : syntax error on line 22 I am able to sort out which of the files is the culprit is by swapping files in and out of the /R and /man directories. But I cannot find the syntax error, the .Rd file seems

...#39;: The following object(s) are masked from package:tools : .checkDemoIndex .checkVignetteIndex .installMD5sums .installPackageDescription .installPackageIndices buildVignettes checkAssignFuns checkDocArgs checkDocStyle checkFF checkMD5sums checkMethods checkTnF checkVignettes codoc md5sum pkgVignettes print.checkAssignFuns print.checkDemoIndex print.checkDocArgs print.checkDocStyle print.checkFF print.checkMethods print.checkTnF print.checkVignetteIndex print.checkVignettes print.codoc print.undoc Rdindex Rtangle RtangleSetup RtangleWritedoc RweaveLatex RweaveLatexOptions Rwe...

...ent Version: R-2.0.0-beta-from-a-week-ago OS: linux Submission from: (NULL) (202.156.6.77) When running 'R CMD check' for a package that contains the symbol '%' in the signature of a function (say the default parameter for a string argument is like "10% - 20%"), the 'codoc' part of the check throws a warning about mismatching doc and codoc. While the '%' has apparently to be escaped in the .Rnw (otherwise latex soon figures out that what is after on the same line is a comment), the warning remains whether or not '%' is escaped in the code. The p...

...s time: I have a data set in my R package "micEcon", which has many variables (82). Therefore, I would like to avoid to describe all variables in the "\format" section of the documentation (.Rd file). However, doing this lets "R CMD check" complain about "data codoc mismatches" (details see below). Is there a way to avoid the description of all variables without getting a complaint from "R CMD check"? Thanks, Arne ---------- Forwarded Message ---------- Subject: Documenting data sets with many variables Date: Friday 05 August 2005 14:03 Fr...

What is the Rd file alias and usage syntax for an S4 assignment method? I have been trying variations on \alias{TSdoc<-,default-method} \usage{ \S4method{TSdoc}{default}(x) <- value but so far I have not got it right according to various codoc, etc, checks. Paul Gilbert ==================================================================================== La version fran?aise suit le texte anglais. ------------------------------------------------------------------------------------ This email may contain privileged and/or confidential...

...; make[5]: Leaving directory `/data/prog/R-2.9.1/src/library/tools/src' make[4]: Leaving directory `/data/prog/R-2.9.1/src/library/tools' Error in namespaceExport(ns, exports) :   exportations non définies : checkDocFiles, checkDocStyle, checkFF, checkReplaceFuns, checkS3methods, checkTnF, codoc, codocClasses, codocData, undoc Calls: ::: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> In addition: Warning message: les méthodes S3 ‘print.checkDocFiles’, ‘print.checkDocStyle’, ‘print.checkFF’, ‘print.checkReplaceFuns’, ‘print.checkS3methods’, ‘print.checkTnF’, ‘prin...

Hi the list, I build a package. They was a mistake in it, but R CMD check did not find it. Is that normal ? Here is what Kurt gets (which is right, I did this mistake): --- 8< ---------------- * checking for code/documentation mismatches ... WARNING S4 class codoc mismatches from documentation object 'LongData-class': Slots for class 'LongData' Code: id other time traj varName Docs: id time traj varName --- 8< ---------------- But here is what I get : --- 8< ---------------- R CMD check longitudinalData * checking for working pdfl...

....4.0) and a "new" one with R (>= 3.4.0). Probably easiest would be to comment the \usage{.} / \arguments \item{...} parts for the time being {as long as you don't want R (>= 3.4.0) in your package DESCRIPTION "unconditionally"}. -- Tweaking R-devel's tools::codoc() for this special case may be a solution liked more by package maintainers for this case. OTOH, we can only change R-devel's version of codoc(), so it would be that platform which would show slightly inaccurate "Usage:" for these (by not showing "...") which also seems a...

An update of the VR bundle was released on Monday and should have propagated around CRAN now. It is a collection of bug fixes (many to documentation, thanks to Kurt Hornik's great tools undoc and codoc) and small enhancements for R. It does need R 1.2.2 to install (the help files make use of new markup for methods) but only 1.2.0 to run. Thus the precompiled Windows version will run on rw1021. -- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http...

An update of the VR bundle was released on Monday and should have propagated around CRAN now. It is a collection of bug fixes (many to documentation, thanks to Kurt Hornik's great tools undoc and codoc) and small enhancements for R. It does need R 1.2.2 to install (the help files make use of new markup for methods) but only 1.2.0 to run. Thus the precompiled Windows version will run on rw1021. -- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http...

...iable name is included as-is and when I run R CMD CHECK I get a latex error because latex considers '_' a special character (used for subscripts) which is only allowed in math mode. When I replace the variable name with 'Health\_Env' in the Rd file latex runs fine, but I get a codoc-mismatch warning because the backslash is not part of the variable name in the data frame. Is there a way to completely satisfy R CMD CHECK in this case and avoid both errors and warnings?? I'm using > version _ platform i386-pc-mingw32 arch i386 os mingw32 system...

Running R CMD check on a package can take quite a lot of time. Checks seem like they could be run in parallel (separate processes for, e.g., codoc, examples, tests, ...). Is there a way to do this? My current usage is typically R CMD build <pkg> R CMD check pkg_x.y.z.tar.gz Thanks for any hints, Martin -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Locat...

...at is, since everything is copied into the pkg.Rcheck directory, it is difficult to make any changes to source files without having to completely re-do "R CMD check pkg". For example, I would like to be able to make changes to src/pkg1/man/foo.Rd and have dependencies that indicate only codoc and examples need to be re-run, not tests and vignettes. (R CMD check can to do this, the problem is moving the appropriate new pieces, in the appropriate way, into the pkg1.Rcheck directory.) The difficulty is exacerbated for me because I have pkg3 depends on pkg2 depends on pkg1. If I make a cha...

...s source/Rd are below: https://github.com/yihui/knitr/blob/master/R/template.R#L43-L44 https://github.com/yihui/knitr/blob/master/man/knit_expand.Rd When I run R CMD check on the package I get this warning (with both R 2.15.2 and R-devel): * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'knit_expand': knit_expand Code: function(file, ..., text = readLines(file, warn = FALSE), delim = "\\{\\{((.|\n)+?)\\}\\}") Docs: function(file, ..., text = readLines(file, warn = FALSE), delim = "\{\...

Hi, sorry for this lengthy post. I am using R-2.0.0 on Unix, compiled. Overview: A) R CMD check: Unaccounted top-level text B) In which sections of *.Rd is LaTeX notation allowed, where *not*? C) Codoc mismatches and polyvalent parameters D) Successful R CMD INSTALL and R CMD build E) cp ../Rd.sty . is copy necessary? F) latex ./CWHstat-manual.tex runs into trouble When running >R CMD check CWHstat I get ===== ... * checking foreign function calls ... OK * checki...