similar to: R CMD check issue with R 3.0.2

Hi, I have a function knit_expand() and its 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

I cannot speak for other package authors, but for all my own packages, I have provided the BugReports field in DESCRIPTION that points to the Github issues page. You can probably use this field to check if a package is on Github or not. If it is, you may just fork the original repo instead of creating a new one from the CRAN package. I'm not sure how technically difficult it would be for you.

Hi, When a package's documentation contains \Sexpr{}, R CMD build will build the manual to PDF. I wonder if the full LaTeX log could be suppressed in this case. Currently it looks like this: $ R CMD build foo * checking for file ?foo/DESCRIPTION? ... OK * preparing ?foo?: * checking DESCRIPTION meta-information ... OK * installing the package to process help pages * building the PDF package

Isn't the whole concept of DOI basically link-shortening/redirecting? For example, this link https://doi.org/10.2134/agronj2016.07.0395 redirects to https://acsess.onlinelibrary.wiley.com/doi/abs/10.2134/agronj2016.07.0395 As a side note, I got so fed up with CRAN check complaints about (perfectly valid) re-directs that I refuse to use the \url{} tag anymore. Kevin On Thu, Sep 17, 2020 at

The current coxme code has functions that depend on bdsmatrix and others that depend on Matrix, both those pacakges define S4 methods for diag. When loaded, the message appears: replacing previous import ?diag? when loading ?Matrix? Questions: 1. Do I need to worry about this? If so, what can I do about it? I suppose I could add an importFrom directive, but it will be a pain unless there

Almost all of the coxme package and an increasing amount of the survival package are now written in noweb, i.e., .Rnw files. It would be nice to process these using the Sweave function + a special driver, which I can do using a modified version of Sweave. The primary change is to allow the following type of construction <<coxme>> coxme <- function(formula, data, subset, blah blah

R version 2.9.0 running on Centos (Red Hat linux). I have a pair of packages coxme and bdsmatrix. The latter is installed in my local library (I don't have permission for global install at work.) That is, it is in the location pointed to in R_LIBS_USER. In R, the command library(bdsmatrix) works fine. Coxme depends on bdsmatrix, in fact uses some cross-calls to it's C routines, which

Hi, Recently I saw a couple of cases in which the package vignettes were somewhat complicated so that Stangle() (or knitr::purl() or other tangling functions) can fail to produce the exact R code that is executed by the weaving function Sweave() (or knitr::knit(), ...). For example, this is a valid document that can pass the weaving process but cannot generate a valid R script to be source()d:

Hi, A new package Rd2roxygen has been released on CRAN: http://cran.r-project.org/package=Rd2roxygen (source package available; binaries to come) This package can be useful for developers who used to document their functions in the raw Rd files but want to switch to roxygen now using inline roxygen comments (e.g. me). The main functionality of this package is to parse the Rd files under the

Me too. I have changed some valid URLs in \url{} to \verb{} just to avoid these check NOTEs. I do appreciate the check for the validity of URLs in packages, especially those dead links (404), but discouraging URLs with status code other than 200 (such as 301) feels like overdoing the job. After I "hide" links from R CMD check with \verb{} , it will be hard to know if these links are

Dear R developers, I asked this question in r-help list but have not got a definite solution yet, and I think it might be more appropriate to ask developers or CRAN maintainers directly. Many software packages often have a menu item like "Check for updates" under the "Help" menu, e.g. Filezilla and Firefox, and I believe it is also necessary for R (at least for R GUI under

Hi I decided to blame cairo_pdf(). There is a fix in r-devel (r72242) that works for the reported case, plus some basic sanity checks. I could not complete 'make check-devel' because it was failing on reg-tests-1d.R ... > stopifnot(length(fd) == 10, identical(fd, format(dct <- as.POSIXct(dlt)))) Error: identical(fd, format(dct <- as.POSIXct(dlt))) is not TRUE ... anyone

I took a look at the R source and I realized that the encoding was actually never passed to the vignette engine: https://github.com/wch/r-source/blob/e721ef5f4/src/library/tools/R/Vignettes.R#L507 Apparently only the file and quiet arguments are passed to the vignette engine. Did I miss anything? To Thierry: I explicitly asked for library(rmarkdown);sessionInfo(), but you only told me the version

Using SUSE Linux, Windows 32 bit and Windows 64 bit R 3.0.2 , I am unable to use R CMD check successfully. Here is the Windows 64 bit report: Z:\R\source\effects>R CMD check pkg * using log directory 'Z:/R/source/effects/pkg.Rcheck' * using R version 3.0.2 (2013-09-25) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file

Hi, Here seems to be a corner case in which format() fails: > format(data.frame()) Error in .subset2(x, i, exact = exact) : subscript out of bounds > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8

Will there be anything wrong if you do not set these options? Regards, Yihui -- https://yihui.name On Mon, Jun 12, 2017 at 2:24 AM, <G.Maubach at weinwolf.de> wrote: > Hi Yihui, > Hi Duncan, > > I corrected my typo. Unfortunately knitr did not find my plots in the > directory where they reside which is different from the Rmd document. > > The documentation of knitr

On 09/12/2014, 10:36 PM, Yihui Xie wrote: > I took a look at the R source and I realized that the encoding was > actually never passed to the vignette engine: > https://github.com/wch/r-source/blob/e721ef5f4/src/library/tools/R/Vignettes.R#L507 > Apparently only the file and quiet arguments are passed to the > vignette engine. Did I miss anything? I think it's actually a little

I've been fighting a CMD check error for coxme this morning.?? I thought I had it fixed, but instead I had forgotton --as-cran on my last test run.? So the version just submitted to CRAN has warning messages in the log. I think it is an issue with CRAN.?? I've sent a message to R-devel asking for help.?? Since then, as a guess, I renamed my internal "ismat" function to

I'd say it is an expert-only option. If you do not understand what it means, I strongly recommend you not to set it. Similarly, you set the root_dir option and I don't know why you did it, but it is a typo anyway (should be root.dir). Regards, Yihui -- https://yihui.name On Fri, Jun 9, 2017 at 4:50 AM, <G.Maubach at gmx.de> wrote: > Hi Yi, > > many thanks for your reply.

Hi, A Windows user asked me a question and I believe this is a bug of R 3.0.0 under Windows: > plot(1:10) > savePlot('test.wmf') Error in .External(C_savePlot, device, filename, type, restoreConsole) : Incorrect number of arguments (4), expecting 3 for 'savePlot' > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1]