[Rd] stats::screeplot suggestion

= xlab, ylab = ylab, ...)     axis(2)     axis(1, at = xp, labels = names(pcs[xp]))     }     invisible() } -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. & Chair, ASA Statistical Graphics Section York University

[Rd] re-submission of package after CRAN-pretest notes

like to re-submit. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. & Chair, ASA Statistical Graphics Section York University Voice: 416 736-2100 x66249 4700 Keele StreetWeb: http://www.datavis.ca | @datavisFriendly Toronto, ONT M3J

[Rd] passing extra arguments to devtools::build

r_on_status =TRUE,:System command error| I've tried other alternatives with other |devtools| commands, like just passing a single argument, but still get the same error |args ='--compact-vignettes="gs+qpdf"'devtools::check_win_devel(args=args)| I'm using devtools 2.2.0, under R 3

[Rd] packages: Examples with CPU or elapsed time > 10s

again, and the NOTE appears for another file. Very annoying. It would be far more helpful to see these all together, rather than having to do this incrementally. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. & Chair, Quantitative Methods York Univer

Re: [Rd] Installing/updating packages on a lab network

, all that disappears, so I have to start over again to install or update a package. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb:http

Re: [Rd] update.packages(checkBuilt=TRUE, ask=FALSE): possible bug

On 7/19/2015 3:50 AM, peter dalgaard wrote: For some, but not allI repositories I get the error message below: Error in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : specifying 'contriburl' or 'available' requires a single type, not type = both Is it a bug?

[Rd] Installing/updating packages on a lab network

mapped to the X: drive What is the code to be added to Rprofile.site to make this work? thanks, -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele

[Rd] 'library' or 'require' call not declared from: 'rgl'

definition ... went away, but I'm stuck with * checking dependencies in R code ... WARNING 'library' or 'require' call not declared from: 'rgl' See the information on DESCRIPTION files in the chapter 'Creating R packages' of the 'Writing R Extensions' manual. How can I solve this? -- Michael

Re: [Rd] 'library' or 'require' call not declared from: 'rgl'

-devel now gave be all those no visible global function definition for ... messages. Achim suggested using explicitly rgl:: everywhere. That's quite ugly, but seems to work. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York

Re: [Rd] no visible binding for global variable for data sets in a package

On 8/27/2014 5:24 AM, Martin Maechler wrote: Michael Friendly frien...@yorku.ca on Tue, 26 Aug 2014 17:58:34 -0400 writes: I'm updating the Lahman package of baseball statistics to the 2013 release. In addition to the main data sets, the package also contains several

Re: [Rd] no visible binding for global variable for data sets in a package

On 8/27/2014 9:29 AM, Michael Friendly wrote: It works in the sense that Lahman::Label(yearID) will work even when Lahman is not in the search path, but R-devel CMD check will still give the same NOTE, though you can argue that that note is actally a false positive. So, this would

Re: [Rd] no visible binding for global variable for data sets in a package

, something like exportData() would be useful. (Or some other mechanism. You might want to be able to export data selectively.) - pd [*] Burdened with pressing obligations, if you like. On 27 Aug 2014, at 16:07 , Michael Friendly frien...@yorku.ca wrote: On 8/27/2014 9:29 AM, Michael Friendly wrote

[Rd] no visible binding for global variable for data sets in a package

'Teams' One such function: ## function for accessing variable labels Label - function(var, labels=rbind(battingLabels, pitchingLabels, fieldingLabels)) { wanted - which(labels[,1]==var) if (length(wanted)) labels[wanted[1],2] else var } -- Michael Friendly Email: friendly AT yorku

Re: [Rd] listof

An interesting topic, but I'll only respond with my own experience, and that is, while 'listof' could be usefully extended there was not enough meat on the bones to want to do so. I think this is a limitation of the S3 class/method structure, as I see it. In several packages (effects, heplots,

[Rd] historical significance of Pr(Chisq) 2.2e-16

*** B:Age 1130.4 8 2.2e-16 *** W:Age 332.9 8 2.2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814

Re: [Rd] Historical NA question

On 03/05/2014 12:39 PM, Hadley Wickham wrote: Can anyone tell me what the significance of 1954 is in R's NA? Just ask R: 2*(1-pnorm(1954)) [1] 0 2*(1-pnorm(1954)) %in% NA [1] 0 __ R-devel@r-project.org mailing list

[Rd] version numbers for CRAN submissions that give warnings/notes

for a minor warning or note. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA

[Rd] forking a CRAN project

version to CRAN; just a public repo a reader could download from. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http

[Rd] proposal: stats::as.matrix.ftable method

351 24 317 -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA

[Rd] bug/infelicity in citation(base)

) entry = toBibtex(cite) entry[1] = sub(\\{,$, sprintf({R-%s,, pkg), entry[1]) gsub(, , entry) }, simplify = FALSE) Is there some reason why citation() can't simply ignore auto=TRUE (perhaps with a message) for the base package? -- Michael Friendly Email: friendly

Re: [Rd] declaring package dependencies

with this. The effort by R Core members that goes into R and CRAN is certainly herculean and I appreciate it very much. Like Dirk, I'm just looking for a little more predictability as CRAN evolves. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative

[Rd] declaring package dependencies

under R version 3.0.1 2: package ‘MASS’ was built under R version 3.0.1 Note: these CRAN errors do not occur on R-Forge, using R version 3.0.1 Patched (2013-08-21 r63645) and the latest devel version (0.5-11) of vcdExtra. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor

[Rd] packages with Sweave and knitr vignettes?

a package exist that does this? TIA -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3

[Rd] Confusion about Depends:, Imports:, Enhances:, import(), inportFrom()

’ field lists packages whose namespaces are imported from (as specified in the NAMESPACE file) but which do not need to be attached, but how can I tell if gnm needs to be attached? Also, what is the difference between Imports: in DESCRIPTION and imports() in NAMESPACE? -Michael -- Michael

Re: [Rd] legitimate use of :::

wasteful. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA

[Rd] probable bugs in stats::loglin calculation of pearson chisq

program start chisq(obs, fit); *-- Find Pearson and likelihood ratio chisquares; gf = sum ( (obs - fit)##2 / ( fit + (fit=0) ) ); lr = 2 # sum ( obs # log ( (obs+(obs=0)) / (fit + (fit=0)) ) ); return (gf // lr); finish; -Michael -- Michael Friendly Email: friendly AT yorku

Re: [Rd] vignettes: problems with PDF compaction

, as I understand things, vignettes are re-built by R CMD build and --compact-vignettes=gs+qpdf has no effect. So my Ubuntu-compacted file will be overwritten. It's somewhat maddening to have to spend so much time to save ~373Kb in order to avoid a CRAN warning. -- Michael Friendly Email: friendly

Re: [Rd] vignettes: problems with PDF compaction

On 4/21/2013 1:28 PM, Michael Friendly wrote: [Env: OS: Win Xp; R 2.15.2; IDE: eclipse/StatET] Each time I update my heplots package, I get warnings from R CMD check on R-Forge, * checking sizes of PDF files under ‘inst/doc’ ... WARNING ‘gs+qpdf’ made some significant size reductions

[Rd] vignettes: problems with PDF compaction

, but, this problem (and others with vignettes) discourages me from using vignettes in packages, a bad thing. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb

Re: [Rd] vignettes: problems with PDF compaction

this on my end. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA [[alternative HTML

Re: [Rd] assignInNamespace to create a setwd() replacement: how to use unlockBinding()?

Ligges -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA

[Rd] assignInNamespace to create a setwd() replacement: how to use unlockBinding()?

() .my.env - local({ # all my local definitions }) attach(.my.env) -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca

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

dense page. Are there any markdown-like tools for writing a CTV? Is it possible to apply a custom .css to a CTV? -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736

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

to the packagelist -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA

[Rd] Declaring/importing non-exported functions [car] in another package

to my package, also unexported? thx, -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3

Re: [Rd] Declaring/importing non-exported functions [car] in another package

in the manual to make this clearer: Using |foo:::f| directly in a function instead of |foo::f| allows access to unexported objects (rather than in importsFrom()). ... -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University

Re: [Rd] Declaring/importing non-exported functions [car] in another package

' applied to an object of class c('mlm', 'lm') Calls: coefplot - coefplot.mlm - Anonymous Execution halted So, the semantics of importFrom() do not allow non-exported functions (I still wonder why), and my only direct option is to copy these functions to my package. -Michael -- Michael

Re: [Rd] Declaring/importing non-exported functions [car] in another package

. Best, John On Wed, 16 Jan 2013 11:40:37 -0500 Duncan Murdoch murdoch.dun...@gmail.com wrote: On 13-01-16 11:25 AM, Michael Friendly wrote: A new function in my heplots package wants to use a non-exported utility function in the car package, df.terms, but this depends on other non-exported

Re: [Rd] R CMD check: better diagnosis for non-ASCII characters

a patch. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA

[Rd] stumped on re-building package vignette

::compactPDF(HE-examples.pdf) on the .pdf file under inst/doc in the package, but no change is made to the .pdf file. I can't see any way to correct this. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736

[Rd] setting global options for a package

,darkgray)) } My function could then use foo - function(x, getOption(heplot.colors), ...) {} -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto

Re: [Rd] uncompressed saves warning

-4 mgcv_1.7-13 car_2.0-12 nnet_7.3-1 rgl_0.92.798 vcd_1.2-13 colorspace_1.1-1 MASS_7.3-17 loaded via a namespace (and not attached): [1] lattice_0.20-6 Matrix_1.0-4 nlme_3.1-103 tools_2.14.1 -- Michael Friendly Email: friendly AT yorku DOT ca Professor

[Rd] uncompressed saves warning

-data old_size new_size compress gfrance.rda 300Kb179Kb xz gfrance85.rda295Kb176Kb xz What is the equivalent R command to compress these files in my project tree? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York

[Rd] R-devel now triggers nags on notes from vignettes

, particularly from vignettes? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb:http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R

Re: [Rd] nobs() and logLik()

of zero weights naturally allows a variety of simple robust methods via a weight function that descends to 0. A discontinuity at 0 in the handling of weights prevents this use. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115

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

of package names. best, -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA

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

(Converted, n.converted, of, n.installed, package citations to BibTeX, \nResults written to file, filename, \n) ## return Bibtex items invisibly invisible(bibs) } -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416

Re: [Rd] How to deal with package conflicts

. best, -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA

[Rd] How to deal with package conflicts

’ so will not be detached I don't see any solution to this, other than (a) renaming my ridge() to something else -- don't want to do this (b) use \dontrun{} for the examples that use car Or, is there some other way? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept

[Rd] NAMESPACES for data only packages

-- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA [[alternative HTML version deleted

Re: [Rd] CRAN: How to list a non-Sweave doc under Vignettes: on package page?

. Consequently, the .pdf vignette remains in the package, but it is not listed as a vignette on CRAN, nor found via vignette() best, -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele

Re: [Rd] NOTE: unstated dependencies in examples

this note. Is it possible that this note could be specious? -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Street Web: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA

[Rd] NOTE: unstated dependencies in examples

But I have no way to find the .Rd file(s) that triggered this note. What is the tool used in R CMD check to make this diagnosis? It would be better if this reported the .Rd file(s) that triggered this note. Is it possible that this note could be specious? -Michael -- Michael Friendly Email

[Rd] R license for a derived data-only package

a bunch of non-free ones, http://ctan.mirror.rafal.ca/help/Catalogue/licenses.html But I don't know if any of these are acceptable in R packages (e.g., will pass R CMD check). I'd rather not have to consult a lawyer, so any guidance is welcome. -- Michael Friendly Email: friendly AT yorku

Re: [Rd] CRAN packages maintained by you

to Authors@R, remove the DESCRIPTION Author and Maintainer fields in the package sources, and then run R CMD build from a current version of r-devel.) Best -k -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416

[Rd] Consistency of messages from R CMD {check,build,install}

directories * building 'heplots_0.9-8.tar.gz' Some checking/building processes take a while, so it would also be nice if more of the info lines ended with ... OK tia, -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115

[Rd] system.file() to read a text file from a vignette

this? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r-project.org

Re: [Rd] system.file() to read a text file from a vignette

(), *noting that the inst directory is moved up a level when it is installed and should not be mentioned in the path used in system.file().* -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele

Re: [Rd] aperm() should retain class of input object

-- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb:http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology

[Rd] aperm() should retain class of input object

* dotplot.array* [7] duplicated.arraylevelplot.array*unique.array -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb:http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA

Re: [Rd] warning creating an as.array method in a package

States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.11.1 On 12/9/2010 10:05 AM, Michael Friendly wrote: I posted on this topic

[Rd] warning creating an as.array method in a package

Is there some work-around so I can have an S3 as.array() method in my package and avoid this warning? -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http

[Rd] Request: kronecker to get a sep= argument

the logic inside kronecker() in my application function. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA

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

ideas. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb:http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-devel@r