[Rd] aic() component in GLM-family objects

lihood and converts it back to an AIC (!) * family()$dev.resid() computes the squared deviance residuals * stats:::residuals.glm retrieves these values and takes the signed square root cheers Ben Bolker __ R-devel@r-project.org mailing list

Re: [R-pkg-devel] Courtesy methods and explosive dependencies

f worms (I know what would be on my list, but I wonder how much it would overlap everyone else's) FWIW I don't know of a better solution than #1 from the original post. cheers Ben Bolker On Fri, May 25, 2018 at 3:13 AM, Martin Maechler <maech...@stat.math.ethz.ch> wrote: >>

Re: [R-pkg-devel] separate Functions: and Datasets: indices?

to put customized information about the package into an overview help page (see Documenting packages) and/or a vignette (see Writing package vignettes). --- On 2018-05-18 03:44 PM, Ben Bolker wrote: > > I notice that when I say help(package="MASS") I get separate indices

[R-pkg-devel] separate Functions: and Datasets: indices?

being used in the relevant .Rd files; I don't see any other obvious magic in the .Rd files for MASS (in fact, they don't use the \docType{} tag at all ... Before I go spelunking, does anyone have any guesses/ideas/information about why MASS is special (or if it is)? cheers

[R-pkg-devel] questions about promptPackage(); -package.Rd; help(package="")

ry small, so there's not very much one could say in -package.Rd that's not already said by the Title: and Description: fields in DESCRIPTION ... I ended up making a minimal emdbook-package.Rd file, but I wonder if that's what's intended/what other developers would suggest here. cheers Ben Bolker

Re: [R-pkg-devel] mvrnorm, eigen, tests, and R CMD check

There have been various comments in this thread (by me, and I think Duncan Murdoch) about how you can identify the platform you're running on (some combination of .Platform and/or R.Version()) and use it to write conditional statements so that your tests will only be compared with reference values

Re: [R-pkg-devel] CRAN pretest archived because of 2 NOTEs

Your points are well taken, but it's also necessary (IMO) for the CRAN maintainers to have some flexibility, while still being able to hold package maintainers to account. Long-time package maintainers (like you) have some issues that new submitters don't; the large-component check was

Re: [R-pkg-devel] vignette via devtools: sometimes found, sometimes not (same package)

I don't have a good solution but wonder if you could narrow down the problem by getting them to send you sessionInfo() (or devtools::session_info()) from a clean R session with just devtools loaded. system.file() might be an alternative to paste0 + find.package() (won't help much with the

[Rd] Fwd: suggested patch for messages

Any follow-up/comments on this? If I don't hear back I'll submit to r-bugs so it doesn't get lost ... (Don't see any changes in QC.R in the last few days ... https://github.com/wch/r-source/commits/trunk/src/library/tools/R/QC.R ) -- Forwarded message -- From: Ben Bolker <b

Re: [R-pkg-devel] Saving output of check()

I have at various times tried the built-in (tools package) solution; fairly complex hand-rolled stuff I did myself; and revdepcheck. I found that revdepcheck handled installation of needed dependencies, including caching packages where necessary, more easily. It felt like the 'tools'

[Rd] suggested patch for messages

Does anyone have comments on the new wording here? Suggested: The Title field should be in title case. Current version is: (xxx) In title case this would be: (Xxx) Hoping R core will see this here and magically adopt it, otherwise I'll try posting it to the r bugs site ...

Re: [R-pkg-devel] Cannot submit package due to misspell note

running examples for arch 'x64' ... [16s] OK > * checking for unstated dependencies in 'tests' ... OK > * checking tests ... > ** running tests for arch 'i386' ... [4s] OK > Running 'testthat.R' [4s] > ** running tests for arch 'x64' ... [5s] OK > Running 'testthat.R' [5s] >

Re: [R-pkg-devel] Cannot submit package due to misspell note

I think it was reasonable to post this to the list for discussion -- it's good not to bother the CRAN maintainers unnecessarily. At this point it might be more productive to e-mail them (CRAN maintainers) for clarification: e.g., explain your interpretation of what they're asking you to do and

[Rd] trivial typo in man/pretty.Rd

patch against recent SVN ... as far as I can tell this trivial typo has been there for 20 years: https://github.com/wch/r-source/blame/ba7920a99fb2fb62b89e404e65f8b132ed4c150a/src/library/base/man/pretty.Rd === --- pretty.Rd

Re: [Rd] [EXTERNAL] Re: Fwd: Re: Re: backquotes and term.labels

ttributes > of the terms() structure, and all of those have the backticks.  I know > the second two will currently break the coxme and survival packages, I > haven't chased down the effect on the first. > > > On 03/08/2018 08:42 AM, Ben Bolker wrote: >> Meant to respond to this

Re: [Rd] Fwd: Re: [EXTERNAL] Re: backquotes and term.labels

On 18-03-08 10:07 AM, Martin Maechler wrote: >>>>>> Ben Bolker <bbol...@gmail.com> >>>>>> on Thu, 8 Mar 2018 09:42:40 -0500 writes: > > > Meant to respond to this but forgot. > > I didn't write a new terms() function

Re: [Rd] Fwd: Re: [EXTERNAL] Re: backquotes and term.labels

ery routine. > > Extrapolating: every R package that tries to examine formulas and partition > them into bits > needs its own terms function? This does not look like a good solution to > me. > > On 03/07/2018 07:39 AM, Ben Bolker wrote: >> >> I knew I had seen thi

Re: [Rd] backquotes and term.labels

I knew I had seen this before but couldn't previously remember where. https://github.com/lme4/lme4/issues/441 ... I initially fixed with gsub(), but (pushed by Martin Maechler to do better) I eventually fixed it by storing the original names of the model frame (without backticks) as an attribute

Re: [R-pkg-devel] How to (conditionally) use an archived package (without Suggests)?

Others may comment more knowledgeably, but I think what you want is impossible due to the combination of requirements. If you want to put it under additional repositories, I suggest Dirk Eddelbuettel's drat package as a simple way of generating the required repository structure. On Sun, Feb

Re: [Rd] sparse.model.matrix Generates Non-Existent Factor Levels if Ord.factor Columns Present

color and clarity are ordered factors, so sparse.model.matrix is generating orthogonal-polynomial contrasts (see ?contr.poly). This is by design ... what are you trying to do? Are you interested in fac2sparse? On 18-02-07 11:00 PM, Dario Strbenac wrote: > Good day, > > Sometimes,

[Rd] bugzilla issues

tl;dr is the R bug tracker down or am I being an idiot? Help please ... I decided I would follow up on https://stat.ethz.ch/pipermail/r-devel/2018-January/075410.html (reporting/suggesting a patch for an issue in stats::mantelhaen.test() with large data sets) Reading the instructions

[Rd] fix potential integer overflow in mantelhaen.test ?

ger and floating-point computations give different answers??? these values are going to get sent to qr.solve() a few lines later in any case ...) If people think this is worthwhile I could submit a bug report. cheers Ben Bolker __ R-devel@r-project.org mail

Re: [Rd] silent recycling in logical indexing

PS I'm tempted to insert a warning at this point and see how often it actually gets triggered ... On Thu, Jan 4, 2018 at 4:44 PM, Ben Bolker <bbol...@gmail.com> wrote: > Hmm. > > Chuck: I don't see how this example represents > incomplete/incommensurate recycling. Doesn't T

Re: [Rd] silent recycling in logical indexing

Charles <ccbe...@ucsd.edu> wrote: > > >> On Jan 4, 2018, at 11:56 AM, Ben Bolker <bbol...@gmail.com> wrote: >> >> >> Sorry if this has been covered here somewhere in the past, but ... >> >> Does anyone know why logical vectors are *silently* recycle

[Rd] silent recycling in logical indexing

n doing subsetting, or is there a sensible use case for incomplete recycling? Ll. 546ff of main/src/subscript.c suggest that there is a place in the code where we already know if incomplete recycling has happened ... Thoughts? cheers Ben Bolker __ R-devel@r-projec

Re: [R-pkg-devel] Semantic versioning and maintenance releases

On 17-10-25 03:47 PM, Duncan Murdoch wrote: > On 25/10/2017 2:23 PM, Shivaram Venkataraman wrote: >> Hello >> >> We have an R package that uses semantic versioning -- i.e. version >> numbers >> are of the form major_version.minor_version.patch_version >> >> One of the ways we use the

Re: [R-pkg-devel] R Package Submission Problem

Also from the CRAN submission guidelines: > If there are warnings or notes you cannot eliminate (for example because you believe them to be spurious) send an explanatory note as part of your covering email, or as a comment on the submission form. This would apply to your spelling issues. On

Re: [R-pkg-devel] Solaris SPARC, Fortran, and logical errors?

.tu-dortmund.de> wrote: > > > On 15.03.2017 18:30, Ben Bolker wrote: >> >> >> >> On 17-03-15 11:09 AM, J C Nash wrote: >>> >>> Possibly tangential, but has there been any effort to set up a Sparc >>> testbed? It >>> seems w

Re: [R-pkg-devel] Solaris SPARC, Fortran, and logical errors?

On 17-03-15 11:09 AM, J C Nash wrote: > Possibly tangential, but has there been any effort to set up a Sparc > testbed? It > seems we could use a network-available (virtual?) machine, since this > platform is > often the unfortunate one. Unless, of course, there's a sunset date. > > For

Re: [Rd] [Lme4-authors] Crash in the latest release

Thanks, posted to https://github.com/lme4/lme4/issues/412 for further discussion ... On Wed, Feb 22, 2017 at 10:03 AM, Therneau, Terry M., Ph.D. wrote: > I found this by accident yesterday. The program that crashes is the first > two lines of the example from the help page

[Rd] possible improvement to ?with examples

uld we have something more sensible like with(mtcars,mpg[cyl==8 & disp>350]) ? (It could be contrasted directly with mtcars$mpg[mtcars$cyl==8 & mtcars$disp>350] ) I'm happy to submit a bug report/patch if that seems appropriate. c

Re: [R-pkg-devel] UseR! Session: Navigating the jungle of R packages.

t is noteworthy and high quality, > and managing any conflicts -- and no one person has to be responsible > for any specific thing. > > > Spencer Graves > > > On 2017-02-10 10:51 AM, Ben Bolker wrote: >>I definitely read the task views and advise others t

Re: [R-pkg-devel] warning from win_build

Sorry, correction/clarification to my last post: it's *not* a bug in ggplot2, rather apparently (?) it's something in base R that has broken tests in both data.table and ggplot2. (Since your code calls ggplot, though, it's presumably in there somewhere, and (?) not your problem.) cheers

Re: [R-pkg-devel] warning from win_build

I think this is a ggplot2-related issue. Matt Dowle posted about it: http://blog.h2o.ai/2016/12/behind-the-scenes-of-cran/ On 16-12-29 01:16 PM, Roy Mendelssohn - NOAA Federal wrote: > Hi All: > > I am working on a new submission of my xtractomatic package (the > main change being the use

Re: [R-pkg-devel] Including Rcpp in an existing package

A mistake that I have made repeatedly is forgetting to add an appropriate UseDynLib() call to the NAMESPACE file. On 16-12-22 02:15 PM, Duncan Murdoch wrote: > On 22/12/2016 1:55 PM, Glenn Schultz wrote: >> All, >> My package was not initially built with the rcpp use in mind. I have >> to

[Rd] confusing error from model.frame when var name=function name

n flames here. cheers Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] ACM license link broken

? For what it's worth, the original page did exist as recently as 5 April 2016: https://web.archive.org/web/20160405100845/http://www.acm.org/publications/policies/softwarecrnotice/ Suggestions for where/to whom to report this? R-bugzilla? c...@r-project.org? Here? cheers Ben Bolker

Re: [R-pkg-devel] Source code of an existing package

Easiest way: library(boot) boot.ci Alternatively, go to https://cran.r-project.org/package=boot , download the tarball, unpack it, and look around in the R/ directory. On 16-08-10 09:42 PM, Marcelo Carvalho Fernandes wrote: > Hi all! > > I am interested in seeing the source code of the

[Rd] save/load + all.equal on reference class objects

After I save an object that contains reference class objects in some of its slots to a file and then re-load it, all.equal() seems to break for me. Is this a bug in all.equal, or is it likely caused by bad implementation of methods on my side? (I see that "'all.equal()' gains methods for

Re: [R-pkg-devel] Possible mis-spelled words ...

Previous conversation on r-devel: https://stat.ethz.ch/pipermail/r-devel/2014-December/070237.html Martin Mächler suggests that a patch to R-devel would be welcome: > I agree that some customization possibility would be great here. > Maybe it'll be sufficient to allow a short list of about a

Re: [R-pkg-devel] Warning that are Unintentionally OS-Specific (Maybe Bug in warning?)

a bug report ... Ben Bolker On 16-07-20 03:13 PM, Bill Denney wrote: > Hi François, > > I thought that was the issue, too, but I confirmed it wasn't that by > adding a print statement right above the warning in my code. The print > statement displays the message even when

Re: [Rd] summary() dispatch puzzle

I'm not doing a good job at explaining. See inline below ... On 16-07-18 11:02 AM, Martin Maechler wrote: >>>>>> Ben Bolker <bbol...@gmail.com> >>>>>> on Fri, 15 Jul 2016 16:45:50 -0400 writes:akram > > > I'm sorry I hav

[Rd] summary() dispatch puzzle

the additional columns I want. Ideas/directions for further diagnoses? Is this an S3/S4 confusion, or something funny about the way the broom and merModLmerTest package are talking to each other, or ... ? cheers Ben Bolker library(lme4) fm1 <- lmer(Reaction~Days+(Days|Subject),sleepst

[Rd] cat() in proc.time?

capture.output() to store this information ...) cheers Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] typosquatting and trojan horses in packages

low. The whole page is definitely worth reading. Thoughts? Ben Bolker = Defenses against typo squatting In short, read the thesis. If you are too lazy, do the following: Prevent Direct Code Execution on Installations This one is easy. Make sure that the software that unpacks an

Re: [Rd] Update CRAN submission process

Spencer Graves prodsyse.com> writes: > > Hi, Gavin et al.: > >Thanks for mentioning these new initiatives. > >What's the current status of R-Hub and the current advice > regarding trying to migrate from R-Forge to R-Hub? > >I ask, because I've complained to R-Forge

[Rd] r-bugzilla maintainer?

ainer info on the r-bugs page. cheers Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] trivial typo in ?colorRampPalette

an update. cheers Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] *tiny* inaccuracy in ?dbinom

under "Value", ?dbinom says If ‘size’ is not an integer, ‘NaN’ is returned. That should be something like If ‘size’ is not an integer, ‘NaN’ is returned (or 'NA' for rbinom). ... at least that's what happens for me under svn rev 70138, Ubuntu 14 > rbinom(1,size=0.5,prob=0.5)

Re: [R-pkg-devel] R CMD check yielding different results for me than CRAN reviewer

The most common scenario is that you're using R-release and the warnings are coming from the R-devel version, which often has a bunch of new, additional tests. The other frequent answer to this question (is there a FAQ list for this mailing list yet?) is that using CRAN's win-builder service is a

[Rd] trivial typo in R for windows FAQ

In https://cran.r-project.org/bin/windows/base/rw-FAQ.html#Package-TclTk-does-not-work_002e : "This [is] part of the R installation, so it should be there." cheers Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.

[Rd] typo in src/library/stats/man/family.Rd: names of 'validmu' and 'valideta' ??

alidmu" and "valideta" (no dots); try names(poisson()) or names(binomial()) and see ... Can someone on R-core fix this and save me the trouble of filing a bug report ... ? Or have I misunderstood something? cheers Ben Bolker _

Re: [Rd] identical(..., ignore.environment=TRUE)

Duncan Murdoch gmail.com> writes: BB> > >> It seems odd/inconvenient to me that the "ignore.environment" argument > >> of identical() only applies to closures (which I read as 'functions' -- > >> someone can enlighten me about the technical differences between > >> functions and closures if they

[Rd] identical(..., ignore.environment=TRUE)

thought this would be TRUE: > f1 <- function() {} > f2 <- function() {} > environment(f1) <- new.env() > environment(f2) <- new.env() > identical(f1,f2,ignore.environment=TRUE) ## FALSE Maybe the problem *is* that I don't know the di

Re: [Rd] Conditional importFrom (roxygen?)

Duncan Murdoch gmail.com> writes: > > On 04/10/2015 10:10 AM, Jonathan Greenberg wrote: > > Folks: > > [snip snip snip] > > > > Is there a way to do a conditional importFrom based on the OS? Or can I > > safely ignore this (I'm trying to submit to CRAN). > > > > Yes, you can put

[Rd] summary(lmList) issues

me, but it could be argued that this is just an edge case, too bad. I don't really mind getting scolded for submitting what is considered, but I'm trying to do my due diligence. Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] is R syntax closed?

FALSE) { ... }) see also http://stackoverflow.com/questions/1231195/multiline-comment-workarounds Ben Bolker Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] match()/%in% with language objects?

. Does anyone have any clues/see what I'm missing? cheers Ben Bolker -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) iQEcBAEBAgAGBQJV3JQLAAoJEOCV5YRblxUHTEkIAJluX0F2bLGW1jt1FP2UEZs1 hucBzPGxpHdGE0CAE2Q2rPtKPmJsZdOpkpBPcxorLj4F6C70yY9QmdNlZ1i/spQB

Re: [R-pkg-devel] .tar vs. binary builds

, but it is not designed for being locked down; if you really need security, the general advice is to provide a front-end to the users via a server you control. Glenn Sent from my iPhone On Aug 3, 2015, at 3:43 PM, Ben Bolker bbol...@gmail.com wrote: On 15-08-03 04:31 PM, Glenn Schultz

Re: [R-pkg-devel] .tar vs. binary builds

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 15-08-03 04:31 PM, Glenn Schultz wrote: Hello All, I have a package which I would like to distribute. However, there are some classes that are not exported if I provide a tar file can the user decompress the tar to the source and then export

Re: [R-pkg-devel] recreating CRAN Testing environment

). Can you adjust your DigitalOcean settings accordingly? Ben Bolker -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) iQEcBAEBAgAGBQJVrTcSAAoJEOCV5YRblxUHNqUIAKMpuDZ5viQSBlyXpIqjtjEW Na6LhC5O/XcjmmrZHDftXAat2gTrRM0OJAn0cfzSZttdcJKowbMYfJzDWe/5oBCE

Re: [Rd] Estimating overdispersion when using glm for count and binomial data

it is much more likely to find a home in an add-on package such as aods3 or glm2 than in base R ... cheers Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [R-pkg-devel] R CMD check package subdirectory warning on filenames

don't know when this was added ... Ben Bolker On 15-06-18 08:45 AM, Kevin Coombes wrote: Hello, In putting together my latest package, I'm getting the following warning from R CMD check --as-cran * checking package subdirectories ... WARNING Subdirectory 'inst/doc' contains invalid file

[Rd] building with tcltk on Ubuntu 14.04

() for 'tcltk', details: call: fun(libname, pkgname) error: Tcl/Tk support is not available on this system Any more suggestions on troubleshooting/diagnosing? I'm not sure what I should be telling R to look for ... thanks Ben Bolker PS (I chose /usr/lib/x86_64-linux_gnu for TCLTK_LIBS

Re: [Rd] building with tcltk on Ubuntu 14.04

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 False alarm. Completely wiping out my build directory followed by ../R-devel/configure --with-tcl-config=/usr/lib/tclConfig.sh - --with-tk-config=/usr/lib/tkConfig.sh; make seems to work. (My fault for assuming repeated cycles of ./configure;

[Rd] model.matrix and na.action

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I've finally been able to piece this together, but I wonder if I've got it right/whether there is anywhere the behaviour of `model.matrix` with respect to `na.action` is more *explicitly* documented. * model.matrix() respects the 'na.action'

Re: [Rd] Title case in DESCRIPTION for package where a word is a function name

Uwe Ligges ligges at statistik.tu-dortmund.de writes: On 24.04.2015 22:44, Ben Bolker wrote: Prof J C Nash (U30A nashjc at uottawa.ca writes: I was preparing a fix for a minor glitch in my optimx package and R CMD check gave an error that the title was not in title case

Re: [Rd] Title case in DESCRIPTION for package where a word is a function name

not get the complaint, but I'm not sure the underscore is allowed. Given that I've obeyed the RTFM rule, I'm wondering what to do now. Presumably you should ask the CRAN maintainers? That seems to be the only possible answer -- I don't think anyone else can guess very accurately ... Ben

Re: [Rd] model frames and update()

of the data even if it's not technically modified) of the same gigantic data ... Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] alternate licensing for package data?

, but it would seem to be more convenient for end users, and more future-proof, to put everything in one place. I know I will eventually need to take this up with CRAN, but I'm looking for reasonably informed opinions/suggestions ... cheers Ben Bolker -BEGIN PGP SIGNATURE- Version

[Rd] misspellings

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Against my better judgment I'm going to point out that misspelled is misspelled in the package-checking messages (at least according to the OED, the American Heritage Dictionary, and Google,which have it with no hyphen; further, mis-spelled gets

Re: [Rd] robust updating methods

least], so this might be problematic if your package needs to depend on it). I'm still curious whether there are any ideas/opinions from other readers. Has anyone else struggled with this? Is there a canonical solution? Ben Bolker On 15-03-24 07:55 PM, Ben Bolker wrote: On 15-03-23 12:55 PM

Re: [Rd] robust updating methods

Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey 2015-03-22 17:45 GMT+01:00 Ben Bolker bbol...@gmail.com: WARNING

[Rd] robust updating methods

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 WARNING: this is long. Sorry I couldn't find a way to compress it. Is there a reasonable way to design an update method so that it's robust to a variety of reasonable use cases of generating calls or data inside or outside a function? Is it even

Re: [Rd] organisation of packages CRAN

Gábor Csárdi csardi.gabor at gmail.com writes: Hi, I think much of this is simply impossible to do. CRAN packages are written and maintained by thousands of people, how are you planning to convince them to reorganize their packages? Or even just rename them? This obviously won't happen.

Re: [Rd] organisation of packages CRAN

to write R core/the CRAN team (i.e. referring to R core and the CRAN team as separate entities), but my fingers slipped ... Ben On 09/11/2014, 3:26 PM, Ben Bolker wrote: Gábor Csárdi csardi.gabor at gmail.com writes: Hi, I think much of this is simply impossible to do. CRAN packages

Re: [Rd] organisation of packages CRAN

they could at any time. On Sun, Nov 9, 2014 at 4:40 PM, Gábor Csárdi csardi.ga...@gmail.com wrote: On Sun, Nov 9, 2014 at 3:26 PM, Ben Bolker bbol...@gmail.com wrote: [...] * download information _is_ available, unofficially, from some mirrors other than the RStudio mirror: see http

Re: [Rd] organisation of packages CRAN

the arguments against migrating new functionality into core R, but this functionality is super-useful especially for beginners, and it seems worth it to lower the bar for finding help, at the cost of not a huge amount of extra code to maintain. Ben Bolker

[Rd] trivial typo in R-exts.texi

or comma. This field is what is reported by followed a should be followed by a, I think ... Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] issue with compiling r6

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I am painfully aware that this is most likely a problem with my system, but I am nevertheless going to ask if anyone has any ideas/suggestions for diagnosis and trouble-shooting. - From a clean checkout of release 66624 on Ubuntu 12.04 (32-bit,

Re: [Rd] issue with compiling r6

Thanks for the information. It's the old story -- it's only once you finally convince yourself that the problems are always on your end and never bugs in the other guy's (development) code that you actually encounter bugs in the other guy's code. Ben Bolker On 14-09-17 11:32 AM, peter

[Rd] r wiki

Does anyone happen to know the fate of the R wiki, which was formerly maintained (I think) at www.sciviews.org (now has information about a kids' play centre) by Philippe Grosjean (I think)? wiki.r-project.org redirects to http://rwiki.sciviews.org/ which gives a 404 not found ... Ben

Re: [Rd] log(i, base=i) not giving 1

way that makes the function less sensitive) or both? Ben Bolker On 02 Sep 2014, at 03:27 , Ben Bolker bbol...@gmail.com wrote: log(8, base=8L)-1 log(8, base=8)-1 logvals - setNames(log(2:25,base=2:25)-1,2:25) logvals[logvals!=0] ## 5,8,14,18,19,25 all

[Rd] ggplot2/plyr interaction with latest R-devel?

anyone else see this or is it just something weird about my setup? Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] ggplot2/plyr interaction with latest R-devel?

something to your local environment, but not sure what. On Mon, Sep 1, 2014 at 11:42 AM, Ben Bolker bbol...@gmail.com wrote: I apologize in advance for not having done more homework in advance, but thought I would send this along to see if anyone else was seeing this. I am having some

Re: [Rd] ggplot2/plyr interaction with latest R-devel?

and see what happened: = r66259 | hornik | 2014-07-27 15:45:29 -0400 (Sun, 27 Jul 2014) | 2 lines Have .encode_numeric_version() pad to common length with trailing zeros. Add [-.numeric_version(). On Mon, Sep 1, 2014 at 4:16 PM, Ben Bolker bbol...@gmail.com wrote: thanks

Re: [Rd] ggplot2/plyr interaction with latest R-devel?

version with an 8 in it ...) On Mon, Sep 1, 2014 at 9:27 PM, Ben Bolker bbol...@gmail.com wrote: Further losing my marbles. I *think* this is a subtle bug in the comparison operator for package_version objects that will be dependent on small (platform-dependent) numerical computation

Re: [Rd] ggplot2/plyr interaction with latest R-devel?

p-adic rationals. On Mon, Sep 1, 2014 at 9:38 PM, Ben Bolker bbol...@gmail.com wrote: PS this is on i686-pc-linux-gnu (32-bit). On x86_64-apple-darwin10.8.0, log(8,base=8)==1 is TRUE, so I'm guessing the problem wouldn't come up. (At this point I believe the problem occurs if (and only

Re: [Rd] Is the ISC license acceptable for CRAN?

at https://svn.r-project.org/R/trunk/share/licenses/license.db will generally not be accepted. You'd better write to c...@r-project.org to ask permission. Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] cummax / cummin for complex numbers

Michael Haupt michael.haupt at oracle.com writes: Dear all, in R 3.1.0, this is happening: cummin(c(1+1i,2-3i,4+5i)) Error in cummin(c(1 + (0+1i), 2 - (0+3i), 4 + (0+5i))) : 'cummax' not defined for complex numbers cummax(c(1+1i,2-3i,4+5i)) Error in cummax(c(1 + (0+1i), 2 -

Re: [Rd] A bug in princomp(), perhaps?

Ben Bolker bbolker at gmail.com writes: FWIW this seems to be a FAQ: https://stat.ethz.ch/pipermail/r-devel/2003-July/027018.html http://thr3ads.net/r-devel/2013/01/ 2171832-Re-na.omit-option-in-prcomp-formula-interface-only http://r.789695.n4.nabble.com/ na-omit-option

Re: [Rd] A bug in princomp(), perhaps?

FWIW this seems to be a FAQ: https://stat.ethz.ch/pipermail/r-devel/2003-July/027018.html http://thr3ads.net/r-devel/2013/01/ 2171832-Re-na.omit-option-in-prcomp-formula-interface-only http://r.789695.n4.nabble.com/ na-omit-option-in-prcomp-formula-interface-only-td4373533.html And

[Rd] reference classes, LAZY_DUPLICATE_OK, and external pointers

We (the lme4 authors) are having a problem with doing a proper deep copy of a reference class object in recent versions of R-devel with the LAZY_DUPLICATE_OK flag in src/main/bind.c enabled. Apologies in advance for any improper terminology. TL;DR Is there an elegant way to force non-lazy/deep

Re: [Rd] reference classes, LAZY_DUPLICATE_OK, and external pointers

On 14-03-02 08:05 PM, Simon Urbanek wrote: Ben, On Mar 2, 2014, at 7:38 PM, Ben Bolker bbol...@gmail.com wrote: We (the lme4 authors) are having a problem with doing a proper deep copy of a reference class object in recent versions of R-devel with the LAZY_DUPLICATE_OK flag in src/main

[Rd] trivial typo in src/library/base/man/timezone.Rd

From SVN r65092: line 111: Note that that the abbreviations have changed over the years (duplicated that) Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Support writing UTF-8 output in Windows

, or suggest a workaround ? Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Q-Q plot scaling in plot.lm(); bug or thinko?

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I've been looking fairly carefully at the Q-Q plots produced by plot.lm() and am having difficulty understanding why plot.lm() is doing what it's doing, specifically scaling the standardized residuals by the prior weights. Can anyone explain this to

[Rd] version comparison puzzle

Can anyone explain what I'm missing here? max(pp1 - package_version(c(0.9911.3,1.0.4,1.0.5))) ## [1] ‘1.0.4’ max(pp2 - package_version(c(1.0.3,1.0.4,1.0.5))) ## [1] ‘1.0.5’ I've looked at ?package_version , to no avail. Since max() goes to .Primitive(max) I'm having trouble figuring

[Rd] type=message possibility for capture.output() ?

As far as I can tell, there's no built-in way to get capture.output() to capture messages (stderr) instead of stdout ... suggested, fairly trivial, patch below. f - function() { message(abc) cat(def\n) } x - capture.output(f()) ## prints 'abc' x ## value: def

Re: [Rd] (no subject)

without making fairly major architectural changes. Ben Bolker For the record, you're referring to R-devel thread 'Correct NAMESPACE approach when writing an S3 method for a generic in another package' started on Aug 24, 2013 [https://stat.ethz.ch/pipermail/r-devel/2013-August/067221.html

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