Re: [Rd] C code in packages with complex arguments/returned value

> Robin Hankin writes: > Professor Ripley > On Jul 1, 2005, at 02:58 pm, Prof Brian Ripley wrote: >> Search for uses of Rcomplex in package source code. The only >> packages on CRAN which use it are ifs and rimage. >>> > Thank you for this: either is perfect for my purposes. How did yo

Re: [Rd] Question about package's DESCRIPTION/Depends field

> Tuszynski, Jaroslaw W writes: > Hi, > My package "caMassClass" depends on several other packages, one of them > "PROcess" residing on "Bioconductor" website. Bioconductor repository is > not, listed in default set of repositories in current version of R (Windows > R 2.1.1). As a result peopl

Re: [Rd] R CMD check warning message "print.check_code_usage_in_package"

> Seth Falcon writes: > We're seeing many warnings like this: > Warning: S3 method 'print.check_code_usage_in_package' was declared in > NAMESPACE but not found > But the package's NAMESPACE does not contain such a declaration. > Seeing this in many Bioconductor packages when running R CMD ch

Re: [Rd] Tracebacks with tryCatch() and withCallingHandlers()?

> Henrik Bengtsson writes: > When batch processing analysis, I use tryCatch() for failure handling > and to prevent unwanted interrupts. I write detailed progress to log > file and conditions (warnings and errors) are written to the same log > file immediately by using withCallingHandlers(

Re: [Rd] CRAN, Bioconductor and ctv package dependency questions

> Gabor Grothendieck writes: > 1. Can CRAN packages depend on Bioconductor packages and still pass > R CMD check? That is can Suggests: and Depends: in the DESCRIPTION > file contain Bioconductor packages or only other CRAN packages? > Is there an example? Yes, yes, yes. (E.g., LMGene, limm

Re: [Rd] CRAN, Bioconductor and ctv package dependency questions

>>>>> Achim Zeileis writes: > On Thu, 8 Sep 2005 10:41:15 +0200 Kurt Hornik wrote: >> >>>>> Gabor Grothendieck writes: >> >> > 1. Can CRAN packages depend on Bioconductor packages and still pass >> > R CMD check? That is

Re: [Rd] C macros and Makevars/package building

> Kasper Daniel Hansen writes: > Hi > We are currently embedding a rather large C++ library in R (BioC), > and we want some comments on the portability of how we have approach > this. > First of, we are not really able to do much about the portability of > the basic library, which of co

Re: [Rd] \dontshow

> Gabor Grothendieck writes: > On 9/9/05, Gabor Grothendieck <[EMAIL PROTECTED]> wrote: >> In R 2.2.0 I find that even if I use \dontshow in the examples section >> of an .Rd file that the code still shows. >> >> Has anyone else seen this? >> >> Are there any packages that use this facility

Re: [Rd] Issue tracking in packages [was: Re: [R] change in read.spss, package foreign?]

> Thomas Lumley writes: > On Fri, 9 Sep 2005, Gabor Grothendieck wrote: >> How about if there were just a standard location and name such as inst/NEWS, >> inst/WISHLIST, inst/THANKS (which has the advantage that they are >> automatically >> made available in the built package under the curren

Re: [Rd] Contacting RDCOMClient Maintainer

> Gabor Grothendieck writes: > I tried to contact the maintainer of RDCOMClient as per the > DESCRIPTION file to report a bug but my mail bounced. Is there more > recent contact information? Yes. In case you want to have it . Duncan Temple Lang <[EMAIL PROTECTED]> -k > The original

Re: [Rd] Shy Suggestion?

> Roger D Peng writes: > I think the reason is that the standard for 'R CMD check' is that > examples in help pages are guaranteed to be executable by the user (as > long as the requirements are met). There is no way to guarantee this > without having the packages installed. So strictly spea

Re: [Rd] 'R CMD check' gets apparently confused by '%' (PR#8198)

> lgautier writes: > Full_Name: Laurent > 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

Re: [Rd] checking S3 generic/method consistency

> Paul Gilbert writes: > In R-2.2.0, how does "checking S3 generic/method consistency" > determine which generic to check against when there are two? I have a > generic "simulate" in dse1 and there is a new generic "simulate" in > stats, and I don't seem to be able to get my simulate

Re: [Rd] problem with \eqn (PR#8322)

> Duncan Murdoch writes: > On 11/18/2005 12:40 PM, Hin-Tak Leung wrote: >> Martin Maechler wrote: >> "Hin-Tak" == Hin-Tak Leung <[EMAIL PROTECTED]> on Fri, 18 Nov 2005 16:38:28 + writes: >>> >>> Hin-Tak> Your own fault. See below. It is basic LaTeX and any LaTeX person

Re: [Rd] [PATCH] Add fpicflags for Intel(R) Fortran Compiler (PR#8344)

> Prof Brian Ripley writes: > I've some playing with the Intel compilers, currently only on ia32. As > far as I can see Intel provides compilers for only two OSes and on 50% of > those -fPIC is wrong so I do think this is really Linux-specific. > I have put in a Linux-specific change to set

Re: [Rd] problem with \eqn (PR#8322)

>>>>> Hin-Tak Leung writes: > Ross Boylan wrote: >> On Mon, 2005-11-21 at 10:27 +, Hin-Tak Leung wrote: >> >>> Kurt Hornik wrote: >>> >>> >>>> Definitely a problem in Rdconv. >>>> >>>> E.g., >

Re: [Rd] Makefiles and other customization

> Ross Boylan writes: > Writing R Extensions mentions that a package developer can provide a > Makefile, but gives very little information about what should be in it. > It says there must be a clean target, and later on there's mention of > $(SHLIB): $(OBJECTS) > $(SHLIB_LIN

Re: [Rd] chron library: format.times, parse.format and h:m (PR#8507)

> spector writes: > Due to the following lines in parse.format: > else if (nf == 3) { > sep <- "" > fmt <- substring(format, first = 1:3, last = 1:3) > } > If a format code has 3 characters, it will not use a separator: >> library(chron) >> mytime = times('7:15:00') >> f

Re: [Rd] Numerical stability in chisq.test

> Jan Motl writes: > The chisq.test on line 57 contains following code: > STATISTIC <- sum(sort((x - E)^2/E, decreasing = TRUE)) The preceding 2 lines seem relevant: ## Sorting before summing may look strange, but seems to be ## a sensible way to deal with round

Re: [Rd] access an element with empty name

> Serguei Sokol writes: > Hi, > I came across a case where I cannot access a list element by its empty name. > Minimal example can be constructed as >     x=list("A", 1) >     names(x)=c("a", "") >     x[["a"]] >     #[1]  "A" >     x[[""]] >     #NULL >     x$`a` >     #[1]  "A" >  

Re: [Rd] agrep bug

> Kolter, Andreas writes: > Sorry, I don't understand how to file a bug properly. Nontheless I > want to report this one because it is still in the code after so many > years. Thanks. This is now fixed in the trunk with c74916. Best -k > This bug still exists: > https://stackoverflow.com/

Re: [Rd] Bug 16719: kruskal.test documentation for formula

> Thomas Levine writes: Thanks: this is now fixed in the trunk with c74945. Best -k > I submit a couple options for addressing bug 16719: kruskal.test > documentation for formula. > https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16719 > disallow-character.diff changes the documentatio

Re: [Rd] MARGIN in base::unique.matrix() and base::unique.array()

> Hervé Pagès writes: Thanks for spotting this. With c74978 I just committed, we now get R> unique(matrix(1:10, ncol=2), MARGIN=1:3) Error in unique.matrix(matrix(1:10, ncol = 2), MARGIN = 1:3) : MARGIN = 1,2,3 is invalid for dim = 5,2 Calls: unique -> unique.matrix R> unique(matr

Re: [Rd] premature use of startsWith in r75110

> Hugh Parsonage writes: Thanks, will fix. Best -k > In r75110 at line 1846 in src/library/tools/R/check.R the following > line was changed > - if(length(grep("^Found the defunct/removed function", out8))) > + if(any(startsWith(out8, "Found the defunct/removed function"))) > However, if `o

Re: [Rd] Argument 'dim' misspelled in error message

> Hervé Pagès writes: Thanks: fixed in the trunk with c75223. Best -k > Hi, > The following error message misspells the name of > the 'dim' argument: >> array(integer(0), dim=integer(0)) >Error in array(integer(0), dim = integer(0)) : > 'dims' cannot be of length 0 > The name of t

Re: [Rd] Segfault when performing match on POSIXlt object

> Marco Giuliano writes: Thanks. Should be fixed in the trunk with c75224: will close the PR after more testing. Best -k > Bug report submitted : > https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17459 > Thanks! > On Fri, Aug 31, 2018 at 6:48 PM Martin Maechler > wrote: >> > Marc

Re: [Rd] 2 minor typos

> Marie-Helene Burle writes: Thanks, will fix! Best -k > Hello, > I would like to report 2 very minor typos: > 1. help file for package:base function:function > The last sentence of the "Technical details" section reads: > "This is not normally user-visible, but it indicated when functio

Re: [Rd] Suggestion: Make CRAN source URLs immutable

> Kurt Wheeler writes: Try e.g. https://cran.r-project.org/package=httr&version=1.3.1 https://cran.r-project.org/package=httr&version=1.3.0 -k > Hello, I hope the is the right list to send this suggestion to. > I was wondering if it might be possible to have CRAN store the most current > ve

Re: [Rd] trivial typo in src/library/stats/man/ts.Rd

> Ben Bolker writes: Thanks, fixed in the trunk now. Best -k > "vector[s]" should be plural in line 54 ... > cheers >Ben Bolker > > Index: ts.Rd > === > --- ts.Rd (revision 75540) > +++ ts.Rd (working copy)

Re: [Rd] Patch idea: an environment variable for setting the user ID

> Will L writes: > To R-devel, > In `R CMD build`, the ID of the user is automatically inserted into the > DESCRIPTION file, e.g. > Packaged: 2018-11-06 14:01:50 UTC; > This is problematic for those of us who work in corporate settings. We must > not divulge our user IDs in the packages we

Re: [Rd] Spurious warning from checkReplaceFuns about a non-replacement function

> Hugh Parsonage writes: > If a function contains the pattern `<-` it is (with a few exceptions) > deemed to be a replacement function and in particular must have second > argument `value` to pass R CMD check. > Consider the function %<->% or any other function containing <- within > grapes.

Re: [Rd] Wrong IEEE reference in documentation for the Round function

> Kyle Hamilton writes: Thanks: I'll fix that. Best -k > Hello, > Since I can't open an account on Bugzilla and the website told me to > submit my bug report to the mailing list here's a patch addressing a > minor typo in the documentation for the Round function. The reference > section stat

Re: [Rd] [R] Open a file which name contains a tilde

> Duncan Murdoch writes: With c76695 in the trunk, we now only tilde expand file names starting with a tilde also when using readline. Best -k > On 11/06/2019 4:34 p.m., William Dunlap via R-devel wrote: >> Note that R treats tildes in file names differently on Windows and Linux. >> On Windo

Re: [Rd] eliminate a partial argument match warning in R CMD check

> Jennifer Bryan writes: Thanks: fixed with c76763 in the trunk. Best -k > Hello, > I'm seeing a nuisance warning when I run `R CMD check --as-cran > whatever_x.y.z.tar.gz`. > I generally work with these options set: > options( > warnPartialMatchArgs = TRUE, > warnPartialMatchAttr = TR

Re: [Rd] trivial typos in man/switch.Rd

> Ben Bolker writes: Thanks: fixed now in the trunk. Best -k > My colleague points out that these typos are probably still present > because almost no-one has the stamina to read that far down in ?switch ... > cheers > Ben Bolker > x[DELETED ATTACHMENT switch_patch.txt, plain text]

Re: [Rd] Addition of a meta viewport tag to HTML manuals

> Bob Rudis writes: > Thanks for both the support & sage advice, Martin! > And, aye, tis straightforward to convert the perl one-liner to a > shell/sed idiom. > A kind soul from the list has also offered to walk me through the > "provide a patch" process and I'll do my best to get it right on

Re: [Rd] Addition of a meta viewport tag to HTML manuals

>>>>> Kurt Hornik writes: >>>>> Bob Rudis writes: >> Thanks for both the support & sage advice, Martin! >> And, aye, tis straightforward to convert the perl one-liner to a >> shell/sed idiom. >> A kind soul from the list has also offer

Re: [Rd] R-intro: Appendix A: attach position

> Suharto Anggono Suharto Anggono via R-devel writes: Thanks: fixed now in the trunk. Best -k > In "An Introduction to R", in "Appendix A  A sample session", in the part on > Michelson data, information for > attach(mm) > is > Make the data frame visible at position 3 (the default). > In f

Re: [Rd] Error: package or namespace load failed for‘utils

> Laurent Gautier writes: > In case a search engine leads someone with the same issue here, I am > documenting the point I reached: > I can reproduce the issue with a small example when forcing R to not load > any package at startup time (using an Renviron file): > ``` > package <- "utils" >

Re: [Rd] Minor typo in recent commit

> Hugh Parsonage writes: Thanks: fixed now. Best -k > I believe should be February 2020 not 2010 > --- a/doc/manual/R-exts.texi > +++ b/doc/manual/R-exts.texi > @@ -2631,9 +2631,9 @@ not necessarily installed) on all known @R{} > platforms. As from @R{} > 4.0.0 a C++ compiler will be selec

Re: [Rd] quantile() type 1 for some ordered factors in R-devel

> Tobias Rockel writes: Thanks for spotting this, and also to Hadley for reporting to me directly. Fixed now with c78501. Best -k > Hi, > In R-devel (2020-05-17 r78478) quantile() type 1 seems to behave a little > bit strange for some ordered factors: > quantile(factor(1:3, ordered = TRUE),

Re: [Rd] quantile() type 1 for some ordered factors in R-devel

nteger(), but tracing down these breaks can be time-consuming. What > about a warning whenever code that would trigger c.factor() is called? This > way users are given a chance to update packages and code. > Thanks, > Trang > On Wed, May 20, 2020 at 1:53 AM Kurt Hornik wrote: >

Re: [Rd] NEWS and readNEWS

> Hadley Wickham writes: > readNEWS() states: > Read R's ‘NEWS’ file or a similarly formatted one. This is an > experimental feature, new in R 2.4.0 and may change in several > ways > and news() also indicates that this tool is supposed to work with > non-R news files. Howeve

Re: [Rd] Suggestion: Add DESCRIPTION 'Date' to R CMD check log header

> Martin Maechler writes: > Hi Henrik > "HB" == Henrik Bengtsson > on Tue, 14 Sep 2010 18:26:31 -0700 writes: HB> Hi, HB> in R CMD check, the version of the package being checked is reported, e.g. HB> Thu Sep 9 05:02:30 2010: Checking package R.utils (SVN revision 399) ... HB>

Re: [Rd] R package BibTex entries: looking for a more general solution

> Michael Friendly writes: Thanks for the suggestions. In fact, we are currently working on this issue. A lot of improvements have already been done, see ?person and ?bibentry for R 2.12.0 or later, especially the details and examples sections. Some more work still needs to be done, though. We

Re: [Rd] Minimum of an ordered factor

> Martin Maechler writes: I have 3 comments: > Thaler, Thorn, LAUSANNE, Applied Mathematics > > on Wed, 5 Jan 2011 11:20:47 +0100 writes: >> Hi everybody, Is there a particular reason, why this code >> does not work as intended: >> z <- factor(LETTERS[1:3], ordered = TRUE)

Re: [Rd] Minimum of an ordered factor

>>>>> Martin Maechler writes: >>>>> "TTLAM" == Thaler, Thorn, LAUSANNE, Applied Mathematics >>>>> >>>>> on Thu, 6 Jan 2011 15:37:01 +0100 writes: TTLAM> Kurt Hornik writes >>> >> if (!all(sapply(args,

Re: [Rd] print.citation, small bug?

> Nicholas Lewin-Koh writes: Thanks. Changed in r-devel now. Best -k > Hi, > I use Sweave extensively in my consulting work. When submitting reports to > the scientists I work > with I like to use the citation function to reference any packages I use, to > give proper acknowledgement. > I n

Re: [Rd] Accessing Package NEWS (NEWS.Rd)

> Paul Roebuck writes: > Okay. So, after having spent quite some time never really tracking down > why my package NEWS files were unacceptable to readNEWS(), I > noticed that there was recent (to me anyway) development that allowed > the NEWS to be done as an Rd file. Sweet! A more standard fo

Re: [Rd] all.equal doesn't work for POSIXlt objects

> Joris Meys writes: This is already fixed in r-devel. -k > Hi all, > following sample code illustrates the problem : > Date1 <- Date2 <- > as.POSIXlt(seq.Date(as.Date("2010-04-01"),as.Date("2011-04-01"),by='day')) > identical(Date1,Date2) > all.equal(Date1,Date2) > identical() gives

Re: [Rd] Referencing non-CRAN extension from CRAN package

> Tim Jurka writes: > Hi r-devel, > I would like to submit a package to CRAN that makes use of an Omegahat > extension, RStem ( http://www.omegahat.org/Rstem/ ). What is the best > way to reference it in my package, and ensure compliance with CRAN > submission guidelines? CRAN can deal with

Re: [Rd] libtool FIXME

> Marco atzeri writes: > Hi, > looking on the build scripts, I noticed on configure.ac > ## > ## Completely disable using libtool for building shlibs until libtool > ## fully supports Fortran and C++. > ## AC_ARG_WITH([libtool], > ## [AS_HELP_STRING([--with-libtool],[use libtool for building

Re: [Rd] NEWS.md support on CRAN

. -k > -pd >> https://github.com/wch/r-source/commit/9ffe87264a1cd59a31a829f72d57af0f1bfa327a >> >> Sent from my iPad >> >> On 23 May 2015, at 6:05 pm, Kurt Hornik wrote: >> >>>>>>>> Duncan Murdoch writes: >>> >>

Re: [Rd] NEWS.md support on CRAN

>>>>> Duncan Murdoch writes: > On 02/06/2015 11:05 AM, Dirk Eddelbuettel wrote: >> Hi Kurt, >> >> On 1 June 2015 at 14:02, Kurt Hornik wrote: >> | >>>>> peter dalgaard writes: >> | >> | >> On 30 May 2015, at 01:20 , Ima

Re: [Rd] RFC: Declaring "foo.bar" as nonS3method() ?!

> Duncan Murdoch writes: > On 12/06/2015 4:12 AM, Martin Maechler wrote: >> This is a topic ' "apparent S3 methods" note in R CMD check ' >> from R-package-devel >> https://stat.ethz.ch/pipermail/r-package-devel/2015q2/000126.html >> >> which is relevant to here because some of us have been

Re: [Rd] RFC: Declaring "foo.bar" as nonS3method() ?!

>>>>> Duncan Murdoch writes: > On 12/06/2015 7:16 AM, Kurt Hornik wrote: >>>>>>> Duncan Murdoch writes: >> >>> On 12/06/2015 4:12 AM, Martin Maechler wrote: >>>> This is a topic ' "apparent S3 methods" note i

Re: [Rd] unlicense

> Charles Geyer writes: > In that case, perhaps the question could be changed to could CC0 be > added to the list of R licences. Right now the only CC licence that > is in the R licenses is CC-BY-SA-4.0. Hmm, I see Name: CC0 FSF: free_and_GPLv3_compatible (https://www.gnu.org/licenses/lice

Re: [Rd] R CMD Rd2pdf and macros

> Kasper Daniel Hansen writes: Interesting. When I take e.g. zTree as the last CRAN package using the \packageTitle macro, R CMD Rd2pdf zTree seems to work fine, but R CMD Rd2pdf zTree/man gives Converting Rd files to LaTeX Warning in parse_Rd("zTree/man/zTree-package.Rd", encodin

Re: [Rd] Dialect for shell scripts

> Iñaki Úcar writes: Same from here: in addition to what the standards say, it always pays to be defensive and check "Portable Shell Programming" in the Autoconf manual. Among other things, this says '$((EXPRESSION))' Arithmetic expansion is not portable as some shells (most notably

Re: [Rd] Region subtag in package 'Language' field

> Jeroen Ooms writes: All standard (not private use or grandfathered) IETF language tags should be fine. What WRE says about ISO-639 codes is meant to explain the language subtags. Hth -k > I am looking for the appropriate field to let package authors to > declare the pkg documentation lang

Re: [Rd] Possible bug in heatmap()?

> Viechtbauer, Wolfgang (SP) writes: Should be fixed now. Best -k > Dear All, > There might be a bug in heatmap(): > x <- matrix(rnorm(10*5), 10, 5) > heatmap(x, labCol=1:5) > Error in axis(1, 1L:nc, labels = labCol, las = 2, line = -0.5, tick = 0, : > 'at' and 'labels' lengths differ,

Re: [Rd] R-devel internal errors during check produce?

> Jan Gorecki writes: > So the unique.default is from the R tools package during checks. > I don't see those issues on CRAN checks. I cannot reproduce this locally (and have no clues about docker). Perhaps you can try to debug this on your end? And see what env_list is when the error occurs?

Re: [Rd] "R CMD Sweave --driver=..." woes

> Vincent Goulet via R-devel writes: Thanks: fixed now in the trunk with c78751. Best -k > In trying to change the driver used by Sweave on the command line using >R CMD Sweave --driver=foo > I consistently get the "directory 'foo' does not exist' error. (For any value > of 'foo', eve

Re: [Rd] R-devel internal errors during check produce?

; l = list(a=new.env(), b=new.env()) R> unique(l) [[1]] [[2]] Best -k > Best regards, > Jan > On Mon, Jun 29, 2020 at 5:42 PM Martin Maechler > wrote: >> >> >>>>> Kurt Hornik >> >>>>> on Mon, 29 Jun 2020 16:13:03 +020

Re: [Rd] Compilation error for R 4.0.2

> Wim R Cardoen writes: > Hello, > I experienced a compiler error when I tried to compile the latest version > of R i.e. R4.0.2 > making iosupport.d from iosupport.c > making lapack.d from lapack.c > making list.d from list.c > making localecharset.d from localecharset.c > grep.c(74): catastro

Re: [Rd] Typo in ?base::Bessel

> EDUARDO GARCIA PORTUGUES writes: Thanks, will fix and add a DOI ... Best -k > "So*c*kne, David J. (1973)." -> "Sookne, David J. (1973)." > "Sookne" is referred previously in the documentation and is the correct > surname in the publication >

Re: [Rd] Typos in file.path documentation.

> Rui Barradas writes: Thanks: both fixed now in the trunk with c79004. Best -k > Hello, > R 4.0.2 on Ubuntu 20.04, sessionInfo() below. > I believe there are two typos in ?file.path, section Value, 2nd paragraph. > 1. There is a close parenthesis missing after Encoding, as it is > readi

Re: [Rd] Stale link from ?check to R Internals

> Duncan Murdoch writes: > On 19/08/2020 12:26 p.m., Toby Hocking wrote: >> Hi the reference to R Internals >> https://cran.r-project.org/doc/manuals/r-release/R-ints.html#Tools >> in ?check (PkgUtils.Rd in utils package) is stale. Here is my proposed >> patch (use named reference rather than

Re: [Rd] utils::isS3stdGeneric chokes on primitives and identity

> Gabriel Becker writes: > I added that so I can look at the proposed fix and put it or something > similar in bugzilla for review final review. > Apologies for the oversight. Fixed now with -while(as.character(bdexpr[[1L]]) == "{") +while(is.call(bdexpr) && (as.character(bdexpr[[1L

Re: [Rd] Error in ?lowess

> Duncan Murdoch writes: Thanks, fixed now. Best -k > The lowess() help page refers to documentation in "src/appl/lowess.doc". > This was moved to "src/library/stats/src/lowess.doc" in 2007. This > patch fixes it: > Index: src/library/stats/man/lowess.Rd > =

Re: [Rd] Named class vector

> Duncan Murdoch writes: > The source to the noquote() function looks like this: > noquote <- function(obj, right = FALSE) { > ## constructor for a useful "minor" class > if(!inherits(obj,"noquote")) > class(obj) <- c(attr(obj, "class"), > if(right)

Re: [Rd] order() and sort() on single row data.frames

> Benjamin Becker writes: > Hi, > not sure whether this belongs here or has been reported/asked before. > In the current R devel the behavior of order() and sort() on data.frames > with a single row has changed. > Before (release): >> sort(data.frame("b", "a")) >   X.a. X.b. > 1    a    b

Re: [Rd] Silent failure with NA results in fligner.test()

> Karolis K writes: Any preferences? Best -k > Hello, > In certain cases fligner.test() returns NaN statistic and NA p-value. > The issue happens when, after centering with the median, all absolute values > become constant, which ten leads to identical ranks. > Below are a few examples: >

Re: [Rd] WRE still hints at the "styles" field in R_FortranMethodDef

> Ivan Krylov writes: Thanks: fixed now in the trunk with c79735. Best -k > The field has been removed in R 3.4.0 after being deprecated in R > 3.3.3. Indeed, the paragraph describing it has been commented out > (lines 10144-10151 in R-exts.texi), but another paragraph above (lines > 10101-1

Re: [Rd] Silent failure with NA results in fligner.test()

> Karolis K writes: > To me it seems like returning chi-sq = 0 and p-value = 1 would make sense. > It would also be consistent with other scenarios of equal variance in all > groups. One example: > fligner.test(1:8, gl(2,4)) > #Fligner-Killeen test of homogeneity of variances > # > #

Re: [Rd] help(".libPaths"): Paragraph lacks mentioning of R_LIBS_SITE

> Henrik Bengtsson writes: Thanks: Tomas and I have now improved this. Best -k > In ?base::.libPaths, there's a paragraph saying: > The library search path is initialized at startup from the environment > variable R_LIBS (which should be a colon-separated list of directories > at which R lib

Re: [Rd] Possible bug in help file name generation

> Deepayan Sarkar writes: > On Thu, Jun 24, 2021 at 5:31 PM Iñaki Ucar wrote: >> >> Hi, >> >> I noticed that R 4.1 places html files into the packages' help >> directory, compared to previous versions, which used an RDS. I found a >> possible bug in the code that processes the aliases from

Re: [Rd] Should seq.Date() return double storage?

> Michael Chirico via R-devel writes: > today <- Sys.Date() > typeof(today) > # [1] "double" > typeof(seq(today, by=1, length.out=2)) > # [1] "integer" > Clearly minor as it doesn't seem to have come up before (e.g. coercion > to numeric will happen automatically whenever fractional dates are

Re: [Rd] Should Position() use match.fun()?

> Steve Martin writes: > Hello, > All of the funprog functions except Position() use match.fun() early > in the body of the function. (Filter() seems to rely on lapply() for > this, but the effect is the same.) Right. > In most cases this isn't a problem, but I can't see why Position() > s

Re: [Rd] Should Position() use match.fun()?

>>>>> Kurt Hornik writes: >>>>> Steve Martin writes: >> Hello, >> All of the funprog functions except Position() use match.fun() early >> in the body of the function. (Filter() seems to rely on lapply() for >> this, but the effect is the sam

Re: [Rd] LOGNAME env var in the check code

> Gábor Csárdi writes: > While trying to reproduce a NOTE for > * checking for new files in some other directories ... NOTE > I noticed that the check code uses > Sys.getenv("LOGNAME") > to query the name of the current user. However on many systems this is > not set, so this is the empty s

Re: [Rd] LOGNAME env var in the check code

> Gábor Csárdi writes: Thanks. c81206 changes to use user <- Sys.info()[["effective_user"]] which afawct should always give the same as the uname for files created by the current user. Pls check: if not, we can go for something like foo <- function() { writeLines("ABC", tf <- temp

Re: [Rd] documentation of asplit

> SOEIRO Thomas writes: > Dear list, > The documentation of `asplit` currently says (section Details): "apply > *always* simplifies common length results, so attempting to split via > apply(x, MARGIN, identity) does not work (as it simply gives x)." > This may be updated (e.g., by simply rem

Re: [Rd] Respecting custom repositories files in interactive/batch R sessions

> Gabriel Becker writes: Friends, I always keep forgetting how these things currently/precisely work, but I guess the principle is that utils:::.onLoad() does options(repos = c(CRAN = "@CRAN@")) unless the repos option was already set (in the user or site profiles). As the latter are not

Re: [Rd] [External] Time to drop globalenv() from searches in package code?

> luke-tierney writes: > On Thu, 15 Sep 2022, Duncan Murdoch wrote: >> The author of this Stackoverflow question >> https://stackoverflow.com/q/73722496/2554330 got confused because a typo in >> his code didn't trigger an error in normal circumstances, but it did when he >> ran his code in

Re: [Rd] Date method of as.POSIXct does not respect tz

> Martin Maechler writes: Currently in R-devel, R> as.POSIXlt.Date function (x, ...) { if (any((y <- unclass(x)) > .Machine$integer.max, na.rm = TRUE)) as.POSIXlt(.POSIXct(y * 86400), tz = "UTC") else .Internal(Date2POSIXlt(x)) } R> as.POSIXct.Date function (x, ...) .POSIX

Re: [Rd] Bug with `[<-.POSIXlt` on specific OSes

> Davis Vaughan writes: > I've got a bit more information about this one. It seems like it > (only? not sure) appears when `TZ = "UTC"`, which is why I didn't see > it before on my Mac, which defaults to `TZ = ""`. I think this is at > least explainable by the fact that those "optional" fields

Re: [Rd] Not documenting a function and not getting a check error?

> Duncan Murdoch writes: > On 06/01/2023 5:25 a.m., Kevin Coombes wrote: >> I am fairly certain that the check for documentation is really just a >> check for the presence of the function name in an "alias" line. > Yes, that's what the test does, and that's fine. The problem is with > the

Re: [Rd] Incorrect behavior of ks.test and psmirnov functions with exact=TRUE

> Alexey Sergushichev writes: Thanks. This is now fixed for the upcoming 4.3.0 release. Best -k > HI, > I've noticed what I think is an incorrect behavior of stats::psmirnov > function and consequently of ks.test when run in an exact mode. > For example: > psmirnov(1, sizes=c(50, 50), z=1:

Re: [Rd] Should '@" now be listed in tools:::.get_internal_S3_generics() ?

> Karolis Koncevičius writes: Can you pls try again with r84341 or later? Best -k > A more concrete example in order to correct my vague messages below. > Writing an R package that uses `@` and `@<-` as S3 generics. Line from manual > pages in .Rd files: > \method{@}{newclass}(object,

Re: [Rd] Should '@" now be listed in tools:::.get_internal_S3_generics() ?

>> On Apr 29, 2023, at 4:44 PM, Karolis Koncevičius >> wrote: >> >> Hello Kurt, >> >> With r84341 it now works on my side. >> >> Warm regards, >> Karolis K. >> >>> On Apr 29, 2023, at 1:24 PM, Kurt Hornik wrote: >>&

Re: [Rd] bug in utils:::format.person

> Achim Zeileis writes: Thanks---Ivan's fix committed now with c84497. Best -k > Apologies, I missed Ivan's fix to the problem (my day was too long...) > which is, of course, better than mine. > On Sat, 3 Jun 2023, Achim Zeileis wrote: >> Thierry, >> >> thanks for this, this is a bug in

Re: [Rd] [R-pkg-devel] Problem with "compacting" pdf files.

> Ivan Krylov writes: Thanks: committed now. Best -k > Dear Rolf, > (Moving this one to R-devel...) > On Sun, 1 Oct 2023 21:01:13 + > Rolf Turner wrote: >> I *really* think that the instructions from CRAN could have been >> clearer! Without your guidance I'd have been at a total los

Re: [Rd] Small typo in Sweave.Rnw

> Enrico Schumann writes: Great, thanks: changed now. Best -k > In the first paragraph of Sweave.Rnw > (./src/library/utils/vignettes/Sweave.Rnw), it reads > for literate programming \cite{fla:Knuth:1984}. > but probably should be > for literate programming \citep{fla:Knuth:1984}. >

Re: [Rd] as.roman upper limit

> Jonathan Carroll writes: Thanks. Fascinating ... I strongly suspect that when I wrote the code in 2006 the docs said the largest possible number was 3899. Of course, I should have added a comment on this with a pointer to the docs ... In any case, clearly

Re: [Rd] Question regarding .make_numeric_version with non-character input

> Andrea Gilardi via R-devel writes: Thanks: should be fixed now in the trunk. Best -k > Thank you very much Dirk for your kind words and for confirming the bug. > Next week I will open a new issue on Bugzilla adding the related patch. > Kind regards > Andrea > On 29/03/2024 20:14, Dirk

Re: [Rd] Petition to set warnPartialMatch* options to TRUE during R CMD check by default

> Michael Chirico writes: Michael, You may have seen that some time ago I added check.R:cprof <- Sys.getenv("_R_CHECK_EXAMPLES_PROFILE_", "") etc so one can use the _R_CHECK_EXAMPLES_PROFILE_ env var to specify a profile to use when running the examples, e.g. options(warnPartia

Re: [Rd] Question regarding .make_numeric_version with non-character input

_ON_INVALID_NUMERIC_VERSION_INPUTS_=false but I don't > seem to be able to find any of this mentioned in the NEWS file. That's what I added for smoothing the transition: it will be removed from the trunk shortly. Best -k > Thanks, > H. > On 4/1/24 05:28, Kurt Hornik wrote: &g

Re: [Rd] Question regarding .make_numeric_version with non-character input

>>>>> Dirk Eddelbuettel writes: > Hi Kurt, > On 25 April 2024 at 08:07, Kurt Hornik wrote: > | >>>>> Hervé Pagès writes: > | > | > Hi Kurt, > | > Is it intended that numeric_version() returns an error by default on > | > non-chara

Re: [Rd] Question regarding .make_numeric_version with non-character input

>>>>> Hervé Pagès writes: > On 4/24/24 23:07, Kurt Hornik wrote: >>>>>>> Hervé Pagès writes: >>> Hi Kurt, >>> Is it intended that numeric_version() returns an error by default on >>> non-character input in R 4.4.0? >> Dear

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