[Rd] Best style to organize code, namespaces

2010-02-22 Thread Ben
ike a module system or explicit object-orientation. How should we get around this limitation? I've looked at sample R code in the distribution and elsewhere, but so far it's been pretty disappointing---most people seem to write very long, hard to understand functions. Thanks for

Re: [Rd] Best style to organize code, namespaces

2010-02-23 Thread Ben
t it's taken a while to figure out what I needed. It could be in 6 months I'll discover something else and realize that I've been wasting my time all along. Anyway, thanks again for all the responses! -- Ben __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] proto and baseenv()

2010-02-24 Thread Ben
Wow, thanks for the heads-up. That is horrible behavior. But using baseenv() doesn't seem like the solution either. I'm new to proto, but it seems like this is also a big drawback: > z <- 1 > proto(baseenv(), expr={a=z})$a Error in eval(expr, envir, enclos) : object &quo

Re: [Rd] proto and baseenv()

2010-02-25 Thread Ben
'm not saying that p$b being 1 is an outright 2+2=5 bug, but it does seem to be surprising behavior that leads to bugs. But I'm sure you're right that there are historical/structural reasons for this to be the case, so perhaps there's no solution. -- Ben Escoto -

Re: [Rd] proto and baseenv()

2010-02-25 Thread Ben
can see why.) But as I mentioned I'm new to prototype programming. If it worked like in my snippet, would this lead to less effective prototype programming? Thanks, -- Ben __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] proto and baseenv()

2010-02-26 Thread Ben
t at http://r-proto.googlecode.com/#Applications). Its > not as fast as S3 (though sometimes you can get it that fast by > optimizing your code). The development version of proto is even > faster than the current version of proto due to the addition of la

Re: [Rd] proto and baseenv()

2010-02-26 Thread Ben
ecifically declared with a separate argument, even unused functions may need to be declared. That means any change in the implementation of an external function could break this code. Again, I may be missing something since I'm new to proto, but I don't see why you'

[Rd] Associative array?

2010-03-11 Thread Ben
are still characters. Also, I haven't heard anyone talking about it. Trees and hashtables are common data structures, so this problem must come up a lot. Thanks, -- Ben __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Associative array?

2010-03-11 Thread Ben
up > ;). But maybe I'm just missing your point ... Nope, this has come up before---I think R and I are just on different wavelengths. Various things that I think are a problem with R are apparently not, and it's fine the way it is. Anyway, sorry for getting off topic ;-) You p

[Rd] dgamma error condition?

2005-11-04 Thread Ben Bolker
more consistent (and would be more convenient for me -- the error-instead-of-warning is making me have to jump through additional hoops) if dgamma just returned NaN and a warning. Any thoughts? cheers Ben Bolker __ R-devel@r-project.org mailin

Re: [Rd] Brainstorm: Alpha and Beta testing of R versions

2005-11-07 Thread Ben Bolker
eta checking is that I like to keep using the same version of R as my classes are currently using, and I haven't yet gone to the trouble of maintaining different versions on my system. [did anyone have any thoughts on my 4 Nov query about errors vs warnings in dgamma?] cheers

Re: [Rd] dgamma error condition?

2005-11-08 Thread Ben Bolker
thanks. would you like a patch? (seems easy enough but I thought I'd offer) looks like library/stats/R/distn.R and nmath/rgamma.c need fixing; looks like qgamma may not check for scale<0 in C code either ... Ben Bolker Prof Brian Ripley wrote: > On Fri, 4 Nov 2005, Ben B

[Rd] minor suggestion for optim documentation

2005-11-18 Thread Ben Bolker
semicolon is.) Temperatures are decreased according to the logarithmic cooling schedule as given in Belisle (1992, p. 890); specifically, the temperature is set to \code{temp/(log((t-1) %/%tmax)*tmax+exp(1))}, where \code{t} is the current iteration step. sincerely Ben Bolker

[Rd] confint/nls

2006-01-07 Thread Ben Bolker
than my slogging through one case at a time ... apologies for the long message, but I am temporarily cut off from any way to post these files to the web. cheers Ben Bolker code that tests various combinations of numbers of parameters and algorithms: --- resmat = array(dim=c(3,2,3

[Rd] prod(numeric(0)) surprise

2006-01-08 Thread Ben Bolker
)) produce? I couldn't find the answer documented anywhere. (And how about sum(numeric(0))==0, which for some reason makes more intuitive sense to me, but is really exactly the same thing -- consider exp(sum(log(numeric(0 ... ?) cheers Ben Bolker -- 620B Bartram

Re: [Rd] prod(numeric(0)) surprise

2006-01-08 Thread Ben Bolker
Duncan Murdoch wrote: > On 1/8/2006 9:24 PM, Ben Bolker wrote: > >>It surprised me that prod(numeric(0)) is 1. >> I guess if you say (operation(nothing) == identity >> element) this makes sense, but ?? > > > What value were you expecting, or were you expe

[Rd] Wikis (was about prod(numeric(0)))

2006-01-09 Thread Ben Bolker
Tony Plate acm.org> writes: > > Since the virtue and reliability of Wikis was brought up, I created a R > Wiki page for this at > http://www.sciviews.org/_rgui/wiki/doku.php?id=beginners:surprises:emptysetfuncs > > > Anyone: please correct errors and improve it! > > Tony Plate > O

[Rd] nls profile with port/constraints

2006-01-17 Thread Ben Bolker
being an idiot ... cheers Ben Bolker --- rm(list=ls()) npts=10 set.seed(1001) a =2 b =0.5 x= runif(npts) y = a*x/(1+a*b*x)+rnorm(npts,sd=0.2) gfun <- function(a,b,x) { if (a<0 || b<0) stop("bounds violated") a*x/(1+a*b*x) } m1 = nls(y~gfun(a,b,x

Re: [Rd] Display an Image on a Plane

2006-01-19 Thread Ben Bolker
) function (i.e., manually recreating an image() by drawing colored squares, but transforming each of the to the 3D perspective). If the former, you might be able to do something with the pixmap package ... Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] nls profiling with algorithm="port" may viol ate bounds (PR#8508)

2006-01-21 Thread Ben Bolker
Spencer Graves pdf.com> writes: > > Hi, Ben, et al.: > > The issue Ben identified with confint(nls(... )) generates a hard > failure for me. "We" (being Brian Ripley and I) know about this already. I'm sorry I failed to specify enough info in

[Rd] too-large notches in boxplot (PR #7690)

2006-01-23 Thread Ben Bolker
PR #7690 points out that if the confidence intervals (+/-1.58 IQR/sqrt(n)) in a boxplot with notch=TRUE are larger than the hinges -- which is most likely to happen for small n and asymmetric distributions -- the resulting plot is ugly, e.g.: set.seed(1001) npts <- 5 X <- rnorm(2*npts,rep(3:4

[Rd] R on the brain

2006-01-30 Thread Ben Bolker
I was sitting in the coffee room at work listening to people complain about a recent seminar about nanotechnology using the terms nanofluidics, nanofactory, nano-this, and nano-that ... I found myself thinking "well the speaker should just have said with(nano, ...) Un(?)fortunate

[Rd] silent recycling in logical indexing

2018-01-04 Thread Ben Bolker
ing, 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: [Rd] silent recycling in logical indexing

2018-01-04 Thread Ben Bolker
, Berry, Charles wrote: > > >> On Jan 4, 2018, at 11:56 AM, Ben Bolker wrote: >> >> >> Sorry if this has been covered here somewhere in the past, but ... >> >> Does anyone know why logical vectors are *silently* recycled, even >> when they are incommens

Re: [Rd] silent recycling in logical indexing

2018-01-04 Thread Ben Bolker
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 wrote: > Hmm. > > Chuck: I don't see how this example represents > incomplete/incommensurate recycling. Doesn't TRUE replicate

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

2018-01-24 Thread Ben Bolker
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

[Rd] bugzilla issues

2018-01-25 Thread Ben Bolker
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

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

2018-02-08 Thread Ben Bolker
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, sparse.mo

Re: [Rd] backquotes and term.labels

2018-03-07 Thread Ben Bolker
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 fo

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

2018-03-08 Thread Ben Bolker
ve an upstream fix ... On Thu, Mar 8, 2018 at 9:39 AM, Therneau, Terry M., Ph.D. via R-devel wrote: > Ben, > > > Looking at your notes, it appears that your solution is to write your own > terms() function > for lme. It is easy to verify that the "varnames.fixed" a

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

2018-03-08 Thread Ben Bolker
On 18-03-08 10:07 AM, Martin Maechler wrote: >>>>>> Ben Bolker >>>>>> 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 -- I added an attribute to t

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

2018-03-08 Thread Ben Bolker
c names will be quoted by backticks: this makes it easier to re-construct the formula from the term labels. This suggests, alas, that this was an intentional design decision -- so harder to change. cheers Ben On 18-03-08 11:24 AM, Therneau, Terry M., Ph.D. wrote: > Ben, > I

[Rd] trivial typo in man/pretty.Rd

2018-03-19 Thread Ben Bolker
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 (r

[Rd] suggested patch for messages

2018-04-08 Thread Ben Bolker
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 ... ===

[Rd] Fwd: suggested patch for messages

2018-04-13 Thread Ben Bolker
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 -- Fr

[Rd] readLines() behaves differently for gzfile connection

2018-05-10 Thread Ben Heavner
ace (and not attached): [1] compiler_3.5.0 ---- (note: I'm running 3.5.0 via the docker rocker/tidyverse:3.5 container, and 3.4.3 on my mac desktop machine) Thanks! Ben Heavner [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] readLines() behaves differently for gzfile connection

2018-05-10 Thread Ben Heavner
You bet - it's available on github at https://github.com/UW-GAC/wgsaparsr/blob/master/tests/testthat/1k_annotation.gz -Ben On Thu, May 10, 2018 at 4:17 PM, Michael Lawrence wrote: > Would it be possible to get that file or a representative subset of it > somewhere so that I can rep

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

2018-06-03 Thread Ben Bolker
g-likelihood 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 ma

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

2018-06-17 Thread Ben Bolker
ds to set a starting value for the next fit +# need to set a starting value for the next fit glm(y ~ x, family = quasi(variance = "mu(1-mu)", link = "logit"), start = c(0,1)) } \keyword{models} On Mon, Jun 4, 2018 at 10:46 AM, Martin Maechler wrote: >>>>&g

[Rd] image() method for Matrix fails on empty matrices (?)

2018-08-18 Thread Ben Bolker
Reasonably easy to avoid, but maybe an edge case that should be handled? Haven't looked yet to see how easy it would be to fix ... Am I missing something? > library(Matrix) > m <- Matrix(0,nrow=3,ncol=3) > m 3 x 3 sparse Matrix of class "dsCMatrix" [1,] . . . [2,] . . . [3,] . . . > image(m)

[Rd] proposed patch to /src/library/datasets/man/mtcars.Rd

2018-08-26 Thread Ben Bolker
Ben Bolker === --- mtcars.Rd (revision 75186) +++ mtcars.Rd (working copy) @@ -35,6 +35,14 @@ Building multiple regression models interactively. \emph{Biometrics}, \bold{37}, 391--411. } +\details{ +Henderson and Velleman

Re: [Rd] Bias in R's random integers?

2018-09-19 Thread Ben Bolker
On 2018-09-19 09:40 AM, David Hugh-Jones wrote: > On Wed, 19 Sep 2018 at 13:43, Duncan Murdoch > wrote: > >> >> I think the analyses are correct, but I doubt if a change to the default >> is likely to be accepted as it would make it more difficult to reproduce >> older results. > > > I'm a b

Re: [Rd] Bias in R's random integers?

2018-09-19 Thread Ben Bolker
A quick point of order here: arguing with Duncan in this forum is helpful to expose ideas, but probably neither side will convince the other; eventually, if you want this adopted in core R, you'll need to convince an R-core member to pursue this fix. In the meantime, a good, well-tested impl

[Rd] NEWS typos, download.file.Rd tweaks

2018-10-09 Thread Ben Bolker
on. Currently the ‘"internal"’, ‘"wininet"’ and ‘"libcurl"’ methods will remove the file if there the URL is unavailable except when ‘mode’ specifies appending when the file should be unchanged. Obligatory xkcd: https://xkcd.com/293

[Rd] broken link to Titanic data

2018-10-16 Thread Ben Bolker
ubmit this as a bug report if that's recommended ... Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

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

2018-11-04 Thread Ben Bolker
"vector[s]" should be plural in line 54 ... cheers Ben Bolker Index: ts.Rd === --- ts.Rd (revision 75540) +++ ts.Rd (working copy) @@ -54,7 +54,7 @@ } \details{ The function \code{ts} is used

Re: [Rd] Suggestion for `glm.fit`

2018-11-26 Thread Ben Bolker
I don't know whether this helps or not, but using residuals(fit) rather than fit$residuals returns 0 for the last value. This is different from (predict(fit,type="response")[25] - Y[25]) (or the equivalent Pearson residual) because the *weighted* residuals are returned by definition (not that I

Re: [Rd] issue with testInstalledPackage

2018-11-26 Thread Ben Bolker
FWIW I've been reasonably happy with the revdepcheck package: it's not base-R, but it's pretty robust (lme4 'only' has 286 dependencies to check ...) I've had much better luck running it on a remote server (where the sysadmin is responsive so it's not too much trouble to get extra system depen

Re: [Rd] Bug report: Function ppois(0:20, lambda=0.9) does not generate a non-decreasing result.

2018-12-04 Thread Ben Bolker
I do think it's plausible to expect that we could get *non-decreasing* results. I get any(diff(exp(ppois(0:19, lambda=0.9, log.p=TRUE)))<0) as FALSE. But I do get diff(ppois(18:19, lambda=0.9)) < 0. Looking at the code of ppois, it's just (within C code) calling pgamma with pgamma(lambda,

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

2018-12-12 Thread Ben Bolker
Line 23: "In theory up they can to" should be "In theory they can be up to" or (slightly more formally) "In theory they can contain up to" cheers Ben Bolker __ R-devel@r-project.org mailing list https://s

Re: [Rd] Documentation examples for lm and glm

2018-12-13 Thread Ben Bolker
Agree. Or just create the data frame with those variables in it directly ... On 2018-12-13 3:26 p.m., Thomas Yee wrote: > Hello, > > something that has been on my mind for a decade or two has > been the examples for lm() and glm(). They encourage poor style > because of mismanagement of data

Re: [Rd] Unnecessary apostrophe in English base::summary() NA count output?

2018-12-17 Thread Ben Bolker
There seem to be a variety of opinions about style in this case; do you omit the apostrophe ("NAs") because it's not a possessive or a contraction, or do you include the apostrophe ("NA's") to clearly distinguish the acronym from the plural form? I personally prefer "NAs" to "NA's" but both are d

[Rd] history of objects() and ls()

2019-01-03 Thread Ben Bolker
ary/base/R/attach@2 | grep objects I had a quick look at the Becker & Chambers brown book (1984) and Becker and Wilks blue book (1988) on Google books and could find ls but not objects() ... ? Anyone happen to know? cheers Ben Bolker __

[Rd] long-standing documentation bug in ?anova.lme

2019-01-17 Thread Ben Bolker
at least once. Is there a publicly accessible SVN server for recommended packages (in general) and nlme (in particular) anywhere? cheers Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] long-standing documentation bug in ?anova.lme

2019-01-20 Thread Ben Bolker
Silence on this so far? Trying here one more time, otherwise I'll submit it as a bug report ... cheers Ben Bolker On 2019-01-17 12:32 p.m., Ben Bolker wrote: > tl;dr anova.lme() claims to provide sums of squares, but it doesn't. And > some names are misspelled in ?lme.

Re: [Rd] long-standing documentation bug in ?anova.lme

2019-01-21 Thread Ben Bolker
Here are relevant patches to address the various issues described below. Thanks for the SVN info! cheers Ben Bolker On 2019-01-21 4:54 a.m., Martin Maechler wrote: >>>>>> Ben Bolker >>>>>> on Thu, 17 Jan 2019 12:32:20 -0500 writes: > >

Re: [Rd] Runnable R packages

2019-02-02 Thread Ben Bolker
remotes has fewer dependencies. I believe that the current version of devtools just re-exports install_github etc. from the remotes package. On 2019-02-02 11:31 a.m., David Lindelof wrote: > I see some value in Duncan’s proposal to implement this as an extra package > instead of a change to b

Re: [Rd] code for sum function

2019-02-19 Thread Ben Bolker
This SO question may be of interest: https://stackoverflow.com/questions/38589705/difference-between-rs-sum-and-armadillos-accu/ which points out that sum() isn't doing anything fancy *except* using extended-precision registers when available. (Using Kahan's algorithm does come at a computat

Re: [Rd] mle (stat4) crashing due to singular Hessian in covariance matrix calculation

2019-02-19 Thread Ben Bolker
as a slightly more flexible and robust version of stats4::mle(); I don't remember/can't promise that it handles fits with singular Hessians, but I'm guessing it does ... cheers Ben Bolker On 2019-02-19 12:02 p.m., Francisco Matorras wrote: > Hi, R developers. > when running m

[Rd] model.matrix.default() silently ignores bad contrasts.arg

2019-02-20 Thread Ben Bolker
properly ... Thoughts? Should I submit this as a bug report/patch? cheers Ben Bolker Index: src/library/stats/R/models.R === --- src/library/stats/R/models.R (revision 76140) +++ src/library/stats/R/models.R (working copy) @

Re: [Rd] model.matrix.default() silently ignores bad contrasts.arg

2019-02-21 Thread Ben Bolker
On Thu, Feb 21, 2019 at 7:49 AM Fox, John wrote: > > Dear Ben, > > Perhaps I'm missing the point, but contrasts.arg is documented to be a list. > From ?model.matrix: "contrasts.arg: A list, whose entries are values (numeric > matrices or character strings nam

Re: [Rd] code for sum function

2019-02-21 Thread Ben Bolker
Specifically: https://svn.r-project.org/R/trunk/src/main/summary.c And if you don't want to deal with Subversion, you can look at the read-only github mirror: https://github.com/wch/r-source/blob/e5b21d0397c607883ff25cca379687b86933d730/src/main/summary.c#L115-L131 On Thu, Feb 21, 2019 at 11:57

Re: [Rd] model.matrix.default() silently ignores bad contrasts.arg

2019-02-23 Thread Ben Bolker
thanks! On 2019-02-23 5:42 a.m., Martin Maechler wrote: >>>>>> Fox, John >>>>>> on Fri, 22 Feb 2019 17:40:15 + writes: > > > Dear Martin and Ben, I agree that a warning is a good idea > > (and perhaps that wasn't clea

[Rd] r76237 broken?

2019-03-14 Thread Ben Bolker
uot;shQuotee"') The new line reads: res <- system2(qpdf, c(qpdf_flags, shQuote(p), shQuotee(tf)), FALSE, FALSE) see: svn diff -r76237:76236 src/library/tools/R/admin.R Seems like a straight-up typo? cheers Ben Bolker __ R

Re: [Rd] r76237 broken?

2019-03-14 Thread Ben Bolker
PS there's also a "shQoute(tf2)" on line 1063 that will presumably also cause trouble at some point ... On 2019-03-14 3:57 p.m., Ben Bolker wrote: > It looks like the most recent SVN commit changed line 1068 of > src/library/tools/R/admin.R to include a call to "s

Re: [Rd] [PATCH 1/2] readtable: add hook for type conversions per column

2019-03-26 Thread Ben Bolker
-requests-to-the-r-core-team cheers Ben Bolker On 2019-03-26 4:20 p.m., Kurt Van Dijck wrote: > On di, 26 mrt 2019 12:48:12 -0700, Michael Lawrence wrote: >>Please file a bug on bugzilla so we can discuss this further. > > All fine. > I didn't find a way to crea

Re: [Rd] [RFC] readtable enhancement

2019-03-27 Thread Ben Bolker
nce) thinks this is worth looking at is very encouraging (and somewhat unusual for feature/enhancement suggestions)! Ben Bolker On Wed, Mar 27, 2019 at 5:29 PM Michael Lawrence via R-devel wrote: > > This has some nice properties: > > 1) It self-documents the input expectations in

Re: [Rd] Bug in the "reformulate" function in stats package

2019-03-29 Thread Ben Bolker
I suspect that the issue is addressed (obliquely) in the examples, which shows that variables with spaces in them (or otherwise 'non-syntactic', i.e. not satisfying the constraints of legal R symbols) can be handled by protecting them with backticks (``) ## using non-syntactic names: refo

Re: [Rd] Bug in the "reformulate" function in stats package

2019-04-04 Thread Ben Bolker
Proposed patch (I think .txt files work OK as attachments to the list?) On 2019-04-04 2:21 a.m., Martin Maechler wrote: >>>>>> Ben Bolker >>>>>> on Fri, 29 Mar 2019 12:34:50 -0400 writes: > > > I suspect that the issue is addressed (ob

Re: [Rd] Bug in the "reformulate" function in stats package

2019-04-18 Thread Ben Bolker
cussed there, if you want to purseu this ... cheers Ben Bolker On 2019-04-18 7:30 a.m., Saren Tasciyan wrote: > Hi, > > Sorry for writing this late, I was very busy. I started this discussion > here. I wish I could write to bugs.r-project.org, but I don't have an > account

Re: [Rd] Staged installation fail on some file systems

2019-05-05 Thread Ben Bolker
This happens to me, too, on an Ubuntu virtual machine (with a "vboxsf" file system, over an underlying MacOS (HFS) file system), but only when installing as part of R CMD check ... I did find the workaround, so I don't think I reported it before. On 2019-05-04 10:35 p.m., Henrik Bengtsson wrot

Re: [Rd] R optim(method="L-BFGS-B"): unexpected behavior when working with parent environments

2019-05-06 Thread Ben Bolker
That's consistent/not surprising if the problem lies in the numerical gradient calculation step ... On 2019-05-06 10:06 a.m., Ravi Varadhan wrote: > Optim's Nelder-Mead works correctly for this example. > > >> optim(par=10, fn=fn, method="Nelder-Mead") > x=10, ret=100.02 (memory) > x=11, ret

Re: [Rd] Calculation of e^{z^2/2} for a normal deviate z

2019-06-23 Thread Ben Bolker
I agree with many the sentiments about the wisdom of computing very small p-values (although the example below may win some kind of a prize: I've seen people talking about p-values of the order of 10^(-2000), but never 10^(-(10^8)) !). That said, there are a several tricks for getting more rea

[Rd] trivial typos in man/switch.Rd

2019-07-02 Thread Ben Bolker
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 Index: switch.Rd === --- switch.Rd (revision 76766

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

2019-07-23 Thread Ben Bolker
Does setting message=FALSE in the chunk options of the vignette help? Or less preferably, using supressMessages() ? On 2019-07-23 9:36 a.m., Lenth, Russell V wrote: > Lionel, > > Thanks for your response. I understand that method overriding can be a > serious issue, but as you say, this i

Re: [Rd] Underscores in package names

2019-08-09 Thread Ben Bolker
Creeping code complexity ... I like to think that the cuteR names will have a Darwinian disadvantage in the long run. FWIW Hadley Wickham argues (rightly, I think) against mixed-case names: http://r-pkgs.had.co.nz/package.html#naming. I too am guilty of picking mixed-case package names in th

Re: [Rd] Underscores in package names

2019-08-09 Thread Ben Bolker
Ugh, but not *as* ambiguous as the proposed example (you can still split unambiguously on "_"; yes, you could split on "last _" in Gabriel's example, but ...) On 2019-08-09 4:17 p.m., Duncan Murdoch wrote: > On 09/08/2019 2:41 p.m., Gabriel Becker wrote: >> Note that this proposal would make my

[Rd] depending on orphaned packages?

2019-09-24 Thread Ben Bolker
ng call to statmod::rinvgauss ? Would a patch be considered? Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] depending on orphaned packages?

2019-09-29 Thread Ben Bolker
On 2019-09-25 3:26 a.m., Martin Maechler wrote: >>>>>> Ben Bolker >>>>>> on Tue, 24 Sep 2019 20:09:55 -0400 writes: > > > SuppDists is orphaned on CRAN (and has been since 2013). > > https://cran.r-project.org/web/checks/check_

Re: [Rd] Inconsistencies in wilcox.test

2019-12-07 Thread Ben Bolker
Your second issue seems like a more or less unavoidable floating-point computation issue. The paired test operates by computing differences between corresponding values of x and y. It's not impossible to try to detect "almost-ties" (by testing for differences less than, say, sqrt(.Machine$do

Re: [Rd] as-cran issue

2020-01-13 Thread Ben Bolker
From R NEWS (changes in 3.6.0) Experimentally, setting environment variable _R_CHECK_LENGTH_1_LOGIC2_ will lead to warnings (or errors if the variable is set to a ‘true’ value) when && or || encounter and use arguments of length more than one. On 2020-01-13 11:46 a.m., Therneau, Terry M., Ph.D.

Re: [Rd] [External] Re: rpois(9, 1e10)

2020-01-20 Thread Ben Bolker
Ugh, sounds like competing priorities. * maintain type consistency * minimize storage (= current version, since 3.0.0) * maximize utility for large lambda (= proposed change) * keep user interface, and code, simple (e.g., it would be easy enough to add a switch that provided user contro

Re: [Rd] R 3.6.3 scheduled for February 29

2020-02-06 Thread Ben Bolker
Because it's the fifth recurrence of the date (29 February). https://en.wikipedia.org/wiki/The_Pirates_of_Penzance On Thu, Feb 6, 2020 at 3:32 PM Abby Spurdle wrote: > > Congratulations! > > > celebrate (beeR=TRUE, loud.music=FALSE, > nbeeRs=2L, > proportion.of.tech.talk=0.4) > > Why

[Rd] trivial typo in man page Quote.Rd

2020-02-21 Thread Ben Bolker
Attn: someone on R-core: "ran" should be "can". Also, thanks for this feature! Index: Quotes.Rd === --- Quotes.Rd (revision 77845) +++ Quotes.Rd (working copy) @@ -74,7 +74,7 @@ Raw character constants are also availa

Re: [Rd] specials issue, a heads up

2020-02-24 Thread Ben Bolker
In the long run, coming up with a way to parse specials in formulas that is both clean and robust is a good idea - annoying users are a little bit like CRAN maintainers in this respect. I think I would probably do this by testing identical(eval(extracted_head), survival::Surv) - but this has lots o

Re: [Rd] dput()

2020-02-29 Thread Ben Bolker
I think Robin knows about FAQ 7.31/floating point (author of 'Brobdingnag', among other numerical packages). I agree that this is surprising (to me). To reframe this question: is there way to get an *exact* ASCII representation of a numeric value (i.e., guaranteeing the restored value is ide

Re: [Rd] survival bug?

2020-03-03 Thread Ben Bolker
. cheers Ben Bolker On 2020-03-03 4:02 p.m., Gabriel Becker wrote: > Hi Terry, > > http://win-builder.r-project.org/ and the rhub build service (which can be > invoked by the rhub package) allow on demand checks in windows > environments, though for active debugging the iterat

[Rd] help with rchk warnings on Rf_eval(Rf_lang2(...))

2020-03-23 Thread Ben Bolker
orrections, pointers to further documentation, etc. would be most welcome ... Web searching for this stuff hasn't gotten me very far, and it seems to be deeper than most of the introductory material I can find (including the Rcpp vignettes) ... cheers Ben Bolker

Re: [Rd] help with rchk warnings on Rf_eval(Rf_lang2(...))

2020-03-23 Thread Ben Bolker
re a way I can use Shield() since this an Rcpp-based project anyway? Sorry for all the very basic questions, but I'm flying nearly blind here ... cheers Ben Bolker On 2020-03-23 4:01 p.m., Tomas Kalibera wrote: > On 3/23/20 8:39 PM, Ben Bolker wrote: >> Dear r-devel folk

[Rd] unstable corner of parameter space for qbeta?

2020-03-25 Thread Ben Bolker
I've discovered an infelicity (I guess) in qbeta(): it's not a bug, since there's a clear warning about lack of convergence of the numerical algorithm ("full precision may not have been achieved"). I can work around this, but I'm curious why it happens and whether there's a better workaround -

Re: [Rd] unstable corner of parameter space for qbeta?

2020-03-26 Thread Ben Bolker
On 2020-03-26 4:02 a.m., Martin Maechler wrote: >>>>>> Ben Bolker >>>>>> on Wed, 25 Mar 2020 21:09:16 -0400 writes: > > > I've discovered an infelicity (I guess) in qbeta(): it's not a bug, > > since there

[Rd] closing R graphics windows?

2020-05-26 Thread Ben Bolker
   Does anyone have any idea how hard it would be/where to start if one wanted to hack/patch R to allow X11 graphics windows that had keyboard focus to be closed with standard keyboard shortcuts (e.g. Ctrl-W to close on Linux)?  Has this been suggested/tried before?    cheers     Ben

Re: [Rd] Disappearance of the file "NEWS"

2010-08-01 Thread Ben Bolker
Laurent gmail.com> writes: > > Dear R-developpers, > > The file NEWS disappeared in r5243, and the authoritative source of > information for what has changed in R is in ./doc/NEWS.Rd. > > A quick glance at NEWS was extremely helpful for knowing what has > changed, and whether building a (mor

[Rd] adding a built-in drop.levels option for subset() in 2.12 ?

2010-08-15 Thread Ben Bolker
ost of the time ... cheers Ben Bolker -- Ben Bolker bbol...@gmail.com , bol...@mcmaster.ca http://www.math.mcmaster.ca/~bolker GPG key: http://www.math.mcmaster.ca/~bolker/benbolker-publickey.asc __ R-devel@r-project.org mailing list https://st

Re: [Rd] No RTFM?

2010-08-21 Thread Ben Bolker
package, send your question to r-devel, rather than r-help. > > D. For operating-system or R interface questions, there are dedicated > lists. See R-sig-Mac, R-sig-Debian, R-sig-Fedora, etc. > > ====== > > It will be necessary to add, toward the e

[Rd] doc bug in ?residuals.gls

2010-09-14 Thread Ben Bolker
one who had been happily using the code without looking at the docs would see a sudden change in the results ... This is in nlme 3.1-96, from a fresh tools/rsync-recommended. Sending it to r-devel for comment because r-core is listed as the maintainer. sincerely Ben Bolker

Re: [Rd] How to set up an own package repository

2010-09-17 Thread Ben Bolker
Janko Thyson ku-eichstaett.de> writes: > > Dear List, > > I'd like to set up a package repository so I can use install.packages() on > it for home-grown packages. I set up an AMPP infrastructure on a windows box > already, but I'm pretty lost with respect to what to do next as I didn't do > any

[Rd] r-forge down?

2010-10-17 Thread Ben Bolker
anyone have a status report on r-forge ... ? From here (Hamilton, ON) I can't ping ... PING r-forge.wu-wien.ac.at (137.208.57.38) 56(84) bytes of data. cheers Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/ma

Re: [Rd] Bug in read.table?

2010-11-07 Thread Ben Bolker
ctor, it hurts when I do this"; "well then, don't do that!") sort of situation. Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Bug in read.table?

2010-11-07 Thread Ben Bolker
Ben Bolker gmail.com> writes: > > ija.csic.es> writes: > > > > > Thanks. Yes, quote="" solves the problem. > > > > I would never say, however, from the documentations, that this was causing > > the duplicate records. Rather, I wou

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