Re: [Rd] system()/system2() using short paths of commands on Windows?

wrote: > > > On 10/31/23 10:05, Duncan Murdoch wrote: > > On 31/10/2023 4:32 a.m., Tomas Kalibera wrote: > >> > >> On 10/30/23 19:07, Yihui Xie wrote: > >>> Sure. I'm not sure if it's possible to make it easier to reproduce, > >>> but

Re: [Rd] system()/system2() using short paths of commands on Windows?

() has to use short paths, I will resort to workarounds. Many thanks again! Regards, Yihui On Tue, Oct 31, 2023 at 4:22 AM Tomas Kalibera wrote: > > On 10/30/23 21:36, Yihui Xie wrote: > > I have read about "system() not using a shell on Windows" on the help > page ma

Re: [Rd] system()/system2() using short paths of commands on Windows?

would work in system() today. If it still would not work because today's Windows is still like Windows 95 in this aspect, please ignore my question and I will ask Microsoft for a refund. Regards, Yihui On Mon, Oct 30, 2023 at 3:03 PM Prof Brian Ripley wrote: > > On 30/10/2023 16:18, Yihui X

Re: [Rd] system()/system2() using short paths of commands on Windows?

ine. Regards, Yihui -- https://yihui.org On Mon, Oct 30, 2023 at 12:34 PM Tomas Kalibera wrote: > > On 10/30/23 17:18, Yihui Xie wrote: > > Hi, > > > > It may have been so for 20+ years but I just discovered today that > system() > > would always try to

[Rd] system()/system2() using short paths of commands on Windows?

Hi, It may have been so for 20+ years but I just discovered today that system() would always try to use the short path of a command on Windows: https://github.com/wch/r-source/blob/635a67/src/gnuwin32/run.c#L141 If that's true, I wonder if it could provide an option to disable this behavior,

Re: [Rd] R-4.3 version list.files function could not work correctly in chinese

k that list.files() ends up skipping some > Chinese filenames in R-4.3.1 (but not R-4.2.2) on Windows, but would you > (or perhaps Yihui Xie who I see is also participating in the discussion) > mind translating the rest of your findings into English? Have you been > able to narrow down t

Re: [Rd] Undocumented change of dirname("C:/") on R-devel on Windows

Thanks a lot! I can confirm that it has been fixed indeed. Regards, Yihui On Mon, Feb 27, 2023 at 1:14 PM Tomas Kalibera wrote: > > On 2/27/23 17:02, Yihui Xie wrote: > > Hi Tomas, > > There has been an R CMD check error with xfun and r-devel on Windows for a > w

Re: [Rd] Undocumented change of dirname("C:/") on R-devel on Windows

Hi Tomas, There has been an R CMD check error with xfun and r-devel on Windows for a while: https://www.r-project.org/nosvn/R.check/r-devel-windows-x86_64/xfun-00check.html Basically it means that the following would return TRUE before: normalizePath('a/b', mustWork = FALSE) ==

Re: [Rd] New URL redirect checks

anymore. > > Kevin > > > On Thu, Sep 17, 2020 at 8:32 AM Yihui Xie wrote: >> >> I don't have an opinion on the URL shorteners, but how about the >> original question? Redirection can be extremely useful in general. >> Shortening URLs is only one of its

Re: [Rd] New URL redirect checks

I don't have an opinion on the URL shorteners, but how about the original question? Redirection can be extremely useful in general. Shortening URLs is only one of its possible applications. FWIW, CRAN uses (303) redirect itself, e.g., https://cran.r-project.org/package=MASS is redirected to

Re: [Rd] Possible Bug: file.exists() Function. Due to UTF-8 Encoding differences on Windows between R 4.0.1 and R 3.6.3?

and libraries to be rebuilt from source. > More details on my blog, also there is experimental build of R > (installer) and experimental toolchain available: > https://developer.r-project.org/Blog/public/2020/05/02/utf-8-support-on-windows/index.html > > Best > Tomas > > >

Re: [Rd] Possible Bug: file.exists() Function. Due to UTF-8 Encoding differences on Windows between R 4.0.1 and R 3.6.3?

Hi Tomas, I received a report about R 4.0.0 in the knitr package (https://github.com/yihui/knitr/issues/1840), and I think it is related to the issue here. I created a minimal reproducible example below: owd = setwd(tempdir()) z = 'K\u00e4sch.txt' file.create(z) list.files()

Re: [Rd] [External] Re: quiet namespace load is noisy

I mentioned the same thing a couple of months ago but didn't get a response: https://stat.ethz.ch/pipermail/r-devel/2019-May/04.html In your case of package vignettes, it is easy enough to suppress the messages via the knitr chunk option message = FALSE. However, I still wonder if it will be

[Rd] Should requireNamespace(quietly = TRUE) suppress messages about overwritten S3 methods?

Hi, In the NEWS of R 3.6.0: > When loading namespaces, S3 method registrations which overwrite previous > registrations are now noted by default (using packageStartupMessage()). As a result, requireNamespace() with R 3.6.0 is no longer quiet as before, e.g., > requireNamespace('ggplot2',

Re: [Rd] R 3.5.3 and 3.6.0 alpha Windows bug: UTF-8 characters in code are simplified to wrong ones

Since it is "technically easy" to disable the best fit conversion and the best fit is rarely good, how about providing an option for code/package authors to disable it? I'm asking because this is one of the most painful issues in packages that may need to source() code containing UTF-8 characters

[Rd] Inconsistent returned values of normalizePath(NA_character_) on Windows and *nix

Hi, I just noticed normalizePath(NA_character_) returns NA_character_ on *nix but "%HOME%\\NA" on Windows (with a warning by default), where %HOME% denotes the HOME folder like "C:\\Users\\John". I'm not sure if this is a bug or by design. Regards, Yihui -- https://yihui.name

Re: [Rd] Parametrized Vignettest in R packages

I wonder if get(data(foo, package="myPackage")) could be rewritten as myPackage::foo. The latter will be a little more rigorous, because data(foo) simply returns a character string "foo", so you are essentially calling get ("foo"), and the default get(, inherits = FALSE) may cause you trouble

Re: [Rd] Parametrized Vignettest in R packages

So far you haven't provided a reproducible example yet. I wonder what exactly the object `sample_analysis` is. Sounds like it is an environment. If that is the case, devtools::build_vignettes() will tangle (for the meaning of "tangle", see ?tools::buildVignette) your vignette into an invalid R

Re: [Rd] Bug in RScript.exe for 3.5.0

It seems the fix has not been ported to the patched version of R on Windows yet. I just tested R version 3.5.0 Patched (2018-04-27 r74667). IMHO this bug is so bad that it is worth a new release R 3.5.1 before it starts biting more users like this one https://stackoverflow.com/q/50077412/559676.

Re: [Rd] Best practices in developing package: From a single file

Similarly, I created this example a couple of years ago: https://github.com/yihui/rlp which shows that you can create a package from R Markdown documents (or any documents that knitr supports). Basically you can start with an R Markdown document, and after clicking a button in RStudio, you will

Re: [Rd] R history: Why 'L; in suffix character ‘L’ for integer constants?

Yeah, that was what I heard from our instructor when I was a graduate student: L stands for Long (integer). Regards, Yihui -- https://yihui.name On Fri, Jun 16, 2017 at 11:00 AM, Serguei Sokol wrote: > Le 16/06/2017 à 17:54, Henrik Bengtsson a écrit : >> >> I'm just

Re: [Rd] [FORGED] Re: Replaying a recorded plot (mixed base and grid) from pdf() in cairo_pdf() crashes R

e cairo_pdf() for not initialising a Cairo >> surface at device startup. >> >> If anyone who knows more about Cairo (or cairo_pdf()) wants to point out >> a good reason for the way cairo_pdf() currently works, please don't hold >> back. >> >> P

[Rd] Suppress LaTeX log during R CMD build

xmf-dist/tex/latex/base/book.cls Document Class: book 2014/09/29 v1.4h Standard LaTeX document class (/usr/local/texlive/2016basic/texmf-dist/tex/latex/base/bk10.clo)) (/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty Regards, Yihui -- Yihui Xie <xieyi...@gmail

Re: [Rd] Warn on partial matches in R CMD check

+1 "What you write is **probably** what you get" sounds like a very bad idea to me. The real solution to laziness should be auto-completion instead of partial matching. Regards, Yihui On Wed, Jan 20, 2016 at 4:13 PM, Hadley Wickham wrote: > Hi all (but especially Kurt), >

Re: [Rd] MetaCran website v1.0.0-alpha

of creating a new one from the CRAN package. I'm not sure how technically difficult it would be for you. Thanks for the wonderful work! Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Tue, May 26, 2015 at 2:45 AM, Gábor Csárdi csardi.ga...@gmail.com wrote: On Mon, May 25, 2015

Re: [Rd] NEWS.md support on CRAN

That is more or less what I had been doing for a long time (having both NEWS.md and NEWS), but decided not to do it any more last year. In fact, you can easily convert NEWS.md to a NEWS file that R's news() can understand, e.g. https://github.com/yihui/knitr/blob/947ad5fc94/Makefile#L8-L10 (if

Re: [Rd] NEWS.md support on CRAN

removed from the tarball to make R CMD check happy. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Sat, May 23, 2015 at 8:25 AM, Gábor Csárdi csardi.ga...@gmail.com wrote: On Sat, May 23, 2015 at 8:14 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: [...] I think

Re: [Rd] NEWS.md support on CRAN

What I do is to use inst/NEWS.Rd as a placeholder that points to the NEWS.md on Github, e.g. http://cran.rstudio.com/web/packages/knitr/index.html Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Fri, May 22, 2015 at 8:08 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote

Re: [Rd] How best to get around shadowing of executables by system()'s prepending of directories to Windows' PATH?

+1 I have exactly the same problem. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Mon, May 18, 2015 at 12:29 PM, Josh O'Brien joshmobr...@gmail.com wrote: My question: On Windows, R's system() command prepends several directories to those in the Windows Path

Re: [Rd] UTF8 markdown vignette

the original problem, but apparently the former one is the ideal fix. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Wed, Dec 10, 2014 at 6:19 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 09/12/2014, 10:36 PM, Yihui Xie wrote: I took a look at the R source and I

Re: [Rd] UTF8 markdown vignette

these information, I can only guess blindly. BTW, you may also try HTML vignettes instead, which is much much easier to get right than LaTeX in terms of character encodings. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Tue, Dec 9, 2014 at 7:05 AM, Duncan Murdoch murdoch.dun

Re: [Rd] UTF8 markdown vignette

Thanks for the kind words. Actually we have more ambitious plans than just reverse search :) Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Tue, Dec 9, 2014 at 11:18 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 09/12/2014 11:13 AM, Yihui Xie wrote: Lastly

Re: [Rd] UTF8 markdown vignette

-- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Tue, Dec 9, 2014 at 3:42 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 09/12/2014, 4:38 PM, ONKELINX, Thierry wrote: Dear Yihui, I have created a reproducible example at https://github.com/ThierryO/utf8vignette

Re: [Rd] Use of tools:::httpdPort in a package for CRAN.

Perhaps I missed something, but isn't this just a one-liner function? help.index = function (pkg) help(package = (pkg), help_type = html) Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Fri, Dec 5, 2014 at 10:24 AM, Sven E. Templer sven.temp...@gmail.com wrote: Hello

Re: [Rd] Changing style for the Sweave vignettes

in this respect (pre/pre is more faithful), and this is one of the reasons that I'm in favor of HTML vignettes instead of PDF when I do not care that much about precise typesetting (which is not always the most important thing). Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name

Re: [Rd] Pkg creation: Sweave: multiple files vignette: Error in R CMD check

directory vignettes/ (it should be fine if it is under a sub directory). Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Thu, Nov 6, 2014 at 8:44 AM, rola...@uni-muenster.de wrote: Hello R-developers! First I want to thank Duncan, Sean and Ben (off-list-communication

Re: [Rd] formatR 1.0 caused error

of packages, which makes it even more difficult for others to tell what the problem could possibly be. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Thu, Sep 18, 2014 at 1:07 PM, Zhang,Jun jhzh...@mdanderson.org wrote: Recently in our R 3.1.0 installation the package

Re: [Rd] r wiki

on maintaining the content. Let the professionals do the hosting and compilation service, and my life has become so much better (no more worries about security holes and attacks). Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Mon, Sep 8, 2014 at 12:10 PM, Philippe GROSJEAN

Re: [Rd] timings for examples in R CMD check

I did not really try it, but perhaps setting _R_CHECK_TIMINGS_=false in your ~/.Renviron works? http://cran.rstudio.com/doc/manuals/r-release/R-ints.html#Tools Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Wed, Sep 3, 2014 at 2:58 PM, Brian G. Peterson br

Re: [Rd] Why R-project source code is not on Github

. I cannot think of anything else that is more efficient than being able to discuss the patch right in the lines of diff's. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Thu, Aug 21, 2014 at 10:58 AM, Simon Urbanek simon.urba...@r-project.org wrote: On Aug 21, 2014

Re: [Rd] Parsing and deparsing of escaped unicode characters

.1252 x [1] I like 寿司 deparse(x) [1] \I like U+5BFFU+53F8\ Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Mon, Jul 28, 2014 at 4:47 AM, Jeroen Ooms jeroeno...@gmail.com wrote: In both R and JSON (and many other languages), unicode characters can be escaped using

[Rd] Byte Order Mark in ?connections

('\UFEFF') [1] ef bb bf Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] user defined macros in Rd files

Hi Duncan, Thanks a lot for eventually implementing this and making the Rd world greener! https://github.com/wch/r-source/commit/ff3ea81ae87 Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Wed, Oct 9, 2013 at 3:55 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote

Re: [Rd] R CMD check warning with S3 method

is attached because A will also be at least attached. Then it will be perfect if `R CMD check` can stop warning against the missing documentation, which is not really missing. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Fri, Jun 20, 2014 at 1:34 AM, Yihui Xie x

Re: [Rd] R CMD check warning with S3 method

? Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Fri, Jun 20, 2014 at 12:19 AM, Winston Chang winstoncha...@gmail.com wrote: On Thu, Jun 19, 2014 at 3:15 PM, Martyn Plummer plumm...@iarc.fr wrote: Export filter in the NAMESPACE file *without copying it* in the R source

Re: [Rd] Package keyval Error: noupquote undefined

a homemade version of upquote in Rd.sty... Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Wed, Jun 4, 2014 at 1:18 PM, Yihui Xie x...@yihui.name wrote: Hi, Due to a change in Rd.sty a few days ago (https://github.com/wch/r-source/commit/620eb9a#diff

[Rd] Package keyval Error: noupquote undefined

12.04. I went through the R-admin manual, and I did not seem to find a requirement of the TeXLive version there. Here is a minimal foo.Rd that shows the problem when running `Rd CMD Rd2pdf foo.Rd`: \name{foo} \alias{foo} \title{Foo} \description{ Bar. } Regards, Yihui -- Yihui Xie xieyi...@gmail.com

Re: [Rd] R CMD check for the R code from vignettes

). Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Mon, Jun 2, 2014 at 10:19 AM, Paul Gilbert pgilbert...@gmail.com wrote: On 06/02/2014 12:16 AM, Gabriel Becker wrote: Carl, I don't really have a horse in this race other than a strong feeling that whatever check does

Re: [Rd] R CMD check for the R code from vignettes -- thread fraying?

I asked the same question privately yesterday since I did not receive it or find it in the archive, and it turned out he sent an off-line reply. I'm replying publicly just to avoid further confusion, and sorry to spam all in the list. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http

Re: [Rd] R CMD check for the R code from vignettes

code. My conclusion: Is tangle useful? Yes. Must we tangle package vignettes? Perhaps no. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Mon, Jun 2, 2014 at 12:44 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 03/06/2014, 12:58 AM, Yihui Xie wrote: Yes, I

Re: [Rd] R CMD check for the R code from vignettes

perspectives! Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Mon, Jun 2, 2014 at 9:18 PM, Kevin Coombes kevin.r.coom...@gmail.com wrote: Doc, it hurts when I do this. So, don't do that. If no one in R Core does anything about this issue (in terms of changing Sweave

Re: [Rd] R CMD check for the R code from vignettes

Note the test has been done once in weave, since R CMD check will try to rebuild vignettes. The problem is whether the related tools in R should change their tangle utilities so we can **repeat** the test, and it seems the answer is no in my eyes. Regards, Yihui -- Yihui Xie xieyi...@gmail.com

Re: [Rd] R CMD check for the R code from vignettes

script as a derivative from the source document, but we do not lose the code evaluation. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Sat, May 31, 2014 at 6:20 PM, Martin Morgan mtmor...@fhcrc.org wrote: On 05/31/2014 03:52 PM, Yihui Xie wrote: Note the test has been

Re: [Rd] R CMD check for the R code from vignettes

package vignettes? Sorry if I did not make it clear enough, my priority of this discussion is the necessity of tangle for package vignettes. After we finish this issue, I'll be happy to extend the discussion towards tangle in general. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http

Re: [Rd] R CMD check for the R code from vignettes

vignette engines that just ignore tangle. At the moment, it seems R CMD check is comfortable with vignettes that do not have corresponding R scripts, and I hope these R scripts will not become mandatory in the future. Thanks everyone for your comments! Regards, Yihui -- Yihui Xie xieyi...@gmail.com

[Rd] R CMD check for the R code from vignettes

, and I'd like to hear what other people think about it. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Latex errors (build on windows)

. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Sat, May 24, 2014 at 7:19 AM, Hualei Kong khl0...@163.com wrote: Dear Prof Brian Ripley: I am very sorry for that I use the unappropriate words It's my great pleasure when I read this mail again! I give my apology

Re: [Rd] Bug in read.dcf(all = TRUE)?

) Sys.setlocale(LC_CTYPE, C) although I do not really understand why LC_CTYPE has to be changed to C. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Wed, May 14, 2014 at 4:34 PM, Yihui Xie x...@yihui.name wrote: Hi, read.dcf() can modify the locale variable LC_CTYPE

[Rd] Bug in read.dcf(all = TRUE)?

] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.1.0 Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name __ R-devel@r-project.org mailing list https://stat.ethz.ch

[Rd] The regular expressions in compareVersion()

was immediately reverted for some reason: https://github.com/wch/r-source/commit/52b0a46e15136a7f9e4777e9960fdda6d84880c0 Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman

Re: [Rd] The regular expressions in compareVersion()

.789695.n4.nabble.com/Sweave-printing-an-underscore-in-the-output-from-an-R-command-td4675177.html As I said, it is a similar problem: someone tried to escape a character that did not need to be escaped in []. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Thu, Apr 24

Re: [Rd] Can the output of Sys.getenv() be improved?

For your first question, try str(as.list(Sys.getenv())). I do not know the answer for the JAGS question, and I'll leave it to someone else to tell you which mailing list to use for such questions... Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Fri, Apr 18, 2014 at 11

Re: [Rd] Package vignettes share the same environment?

shared in the same session such as options(). I guess the cleanest way is still to start new R sessions. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Sat, Apr 5, 2014 at 3:04 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 05/04/2014, 2:24 PM, Martin Morgan wrote

Re: [Rd] Where to put package vignettes

://yihui.name/knitr/demo/vignette/ If you still cannot work it out, please point us to the source of your package. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name On Thu, Feb 20, 2014 at 8:43 AM, guillermo.vi...@uv.es wrote: Dear Søren, Thank you very much for your

[Rd] Format an empty data frame

datasets methods base Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] cat with backspace and newline characters

Yes, that indeed sounds like a problem, but example(txtProgressBar), which is based on \r, works well in the RStudio console. Anyway, thanks for all the experiments, and (to Renaud) support.rstudio.org is the place to report such problems. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http

Re: [Rd] R CMD check problem with R 3.0.2

machines any more. For now, I think either `R CMD check --build` (must build before checking) or `R CMD check --force` (definitely check without building) sounds like a reasonable solution. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State

Re: [Rd] R CMD check problem with R 3.0.2

, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Fri, Oct 25, 2013 at 10:37 AM, Sanford Weisberg sa...@umn.edu wrote: Using SUSE Linux, Windows 32 bit and Windows 64 bit R 3.0.2 , I am unable to use R CMD

Re: [Rd] appropriate work-around for problems with a specific plot device (Rstudio)?

is not always reliable. I'm not sure if grDevices::quartz, grDevices::x11, and grDevices::windows can fix the NOTE. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Fri, Oct 25, 2013 at 9:24 AM

Re: [Rd] png(type='cairo'): point symbols without boarders are not anti-aliased?

Thanks for the hints! I was originally wondering the difference between grDevices::png(type='cairo') and Cairo::CairoPNG() for the case pch=16, a solid point without border. Cairo does a nice job for such point symbols, but png() renders them very poorly. Regards, Yihui -- Yihui Xie xieyi

[Rd] png(type='cairo'): point symbols without boarders are not anti-aliased?

TRUE TRUEFALSE TRUE TRUE libxml fifo clediticonv NLS profmemcairo TRUE TRUE TRUE TRUE TRUE TRUE TRUE Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State University 2215

Re: [Rd] png(type='cairo'): point symbols without boarders are not anti-aliased?

Sorry, typo in the subject: I mean borders. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Mon, Oct 21, 2013 at 4:43 PM, Yihui Xie x...@yihui.name wrote: Hi, It seems that anti-aliasing

Re: [Rd] png(type='cairo'): point symbols without boarders are not anti-aliased?

(Cairo::CairoPNG, 'png-Cairo.png') Thanks! Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Mon, Oct 21, 2013 at 5:28 PM, Paul Murrell p...@stat.auckland.ac.nz wrote: Hi Is this the same as Bug

Re: [Bioc-devel] Linking to HTML documents in a package on the BioC web site

I remember that is not allowed in R if both are package vignettes, so perhaps you should avoid naming HTML and PDF files with the same base name. Of course, when it comes to linking on BioC website, that is totally up to the webmaster. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http

Re: [Rd] user defined macros in Rd files

+1. As an example, there are 91 instances of \newcommand{\CRANpkg} in R source, and this number is still growing as I see: $ grep newcommand{CRANpkg} -r . | wc 91 91 10317 Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa

Re: [Rd] user defined macros in Rd files

if the package author can define these macros in one place, and use them in his/her package. When we have to copy and paste a macro 91 times, it seems to have defeated the purpose of a macro. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State

Re: [Rd] Error in Writing R Extensions

, encoding = , quiet = FALSE, ...) I admit the engine name knitr is also confusing. There are other engine names in knitr, though. For example, knitr::docco_classic http://cran.r-project.org/web/packages/knitr/vignettes/docco-classic.html Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http

[Rd] getParseData() for imaginary numbers

-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base Regards, Yihui -- Yihui Xie xieyi

Re: [Rd] declaring package dependencies

final point: requests from package authors do not necessarily mean more work for CRAN. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Sun, Sep 15, 2013 at 6:11 PM, Ben Bolker bbol...@gmail.com

Re: [Bioc-devel] org-mode vignettes

R functions, you can do whatever you want; see the R-exts manual. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA From: Wolfgang Huber whu...@embl.de Date: Aug 28, 2013 2:51 AM Subject: [Bioc

Re: [Rd] ‘:::’ call

else should bring tests. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Wed, Aug 28, 2013 at 1:50 PM, Paul Gilbert pgilbert...@gmail.com wrote: On 13-08-28 12:29 PM, Marc Schwartz wrote: On Aug

Re: [Rd] legitimate use of :::

-- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State University 102 Snedecor Hall, Ames, IA On Fri, Aug 23, 2013 at 11:05 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-08-22 11:54 PM, Yihui Xie wrote: Maybe it is not a good idea for R CMD check

Re: [Rd] packages with Sweave and knitr vignettes?

, and knitr itself also uses knitr to build LaTeX, HTML, and Markdown vignettes. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State University 102 Snedecor Hall, Ames, IA On Fri, Aug 23, 2013 at 4:49 PM, Henrik Bengtsson h...@biostat.ucsf.edu

Re: [Rd] legitimate use of :::

r63654 has fixed this particular issue, and R-devel will no longer warn against the use of ::: on packages of the same maintainer. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http://yihui.name Department of Statistics, Iowa State University 102 Snedecor Hall, Ames, IA On Thu, Aug 22

Re: [Rd] legitimate use of :::

reasons for :::, which might make it difficult for R to cover all these cases, and also bring additional communications between package authors and CRAN. In conclusion, R CMD check cannot really stop :::, and ::: can be there for good reasons, so how about just let it go? Regards, Yihui -- Yihui Xie

[Rd] legitimate use of :::

authors about these internal functions since I'm the only author and I know clearly what I'm doing, and I want to avoid copying and pasting the code across packages just to avoid the NOTE in R CMD check. What should I do in this case? Regards, Yihui -- Yihui Xie xieyi...@gmail.com Web: http

Re: [Rd] SweaveParseOptions, quoted commas, and knitr vignettes

will emit an error that knitr was not installed, which can be more helpful for the users to realize the real problem. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 206-667-4385 Web: http://yihui.name Fred Hutchinson Cancer Research Center, Seattle On Tue, Jul 16, 2013 at 7:34 PM, Ben Bolker

[Rd] should the text for RIGHT_ASSIGN be - in getParseData()?

] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 206-667-4385 Web: http://yihui.name Fred Hutchinson Cancer Research Center, Seattle

Re: [Rd] Patch proposal for R style consistency (concerning deparse.c)

I second the change of } else {. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Thu, Apr 18, 2013 at 11:16 AM, Paul Johnson pauljoh...@gmail.com wrote: OK, I concede

[Rd] savePlot() under Windows

grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.0.0 Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA

Re: [Rd] missing exported methods when compiling vignettes in R 3.0.0 RC

builder. Now I have forced the evaluation to be in the global environment, and pushed the changes to the knitr development version on Github: https://github.com/yihui/knitr Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa

Re: [Rd] the case of building R snapshot without svn nor network connection.

the only place for it is /dev/null -- hi Achim, I bet this is a nice fortune candidate :) Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Sat, Mar 16, 2013 at 9:39 AM, Simon

[Rd] Why cannot `Rscript -e` accept an empty line?

-e 1 -e -e 2 [1] 1 Error: object 'e' not found Execution halted I can certainly save the code in a script and run Rscript foo.R, but I'm curious why Rscript stops when the -e argument is an empty string. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name

Re: [Rd] enabling reproducible research R package management install.package.version BiocLite

of computing) Probably not. Long live the reproducible research! Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Mon, Mar 4, 2013 at 3:13 PM, Cook, Malcolm m...@stowers.org

Re: [Rd] CRAN task views: markdown? better .CSS?

See this page by Barry Rowlingson: https://stat.ethz.ch/pipermail/r-devel/2012-February/063338.html Given that CRAN maintainers do not even use JavaScript, I bet CSS does not matter either; plain text is plain good. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http

Re: [Rd] Bug in R CMD check for \ in Rd?

/knitr/blob/bf793ca67ac6b78a5b09ab8eb08976ec7667e6e2/man/knit_expand.Rd https://github.com/yihui/knitr/blob/bf793ca67ac6b78a5b09ab8eb08976ec7667e6e2/R/template.R Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University

[Rd] Bug in R CMD check for \ in Rd?

. The text/html help page rendered from my Rd shows \\{\\{((.|\n)+?)\\}\\} correctly. So I'm wondering if this is a bug of R CMD check, or I misunderstood anything. Thanks! Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State

[Rd] customize building package vignettes

be considered and implemented in the future. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA __ R-devel@r-project.org mailing list https

Re: [Rd] Changes to parser in R-devel

Great. I just tested it and did not find any more problems. Thanks! Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Fri, Jul 20, 2012 at 12:22 PM, Duncan Murdoch murdoch.dun

Re: [Rd] Changes to parser in R-devel

] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web

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