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

2013-11-09 Thread Ben Bolker
iles in UTF-8 encoding on Windows? i.e., instead of "convert R to output UTF-8 universally on Windows", "figure out how to make write.table output UTF-8 on Windows, or suggest a workaround" ? Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

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

2014-03-01 Thread Ben Bolker
>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

[Rd] reference classes, LAZY_DUPLICATE_OK, and external pointers

2014-03-02 Thread Ben Bolker
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 co

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

2014-03-02 Thread Ben Bolker
On 14-03-02 08:05 PM, Simon Urbanek wrote: > Ben, > > On Mar 2, 2014, at 7:38 PM, Ben Bolker 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_DUPLIC

Re: [Rd] [GSoC student proposal] Implementation of Modified Weibull-G Family Distribution in R

2014-03-06 Thread Ben Bolker
a potential mentor on the R lists seems reasonable, although I don't know whether R-devel or R-help would be a better venue. good luck, Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

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

2014-05-31 Thread Ben Bolker
> 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 tw

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

2014-06-02 Thread Ben Bolker
Ben Bolker 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.nab

Re: [Rd] cummax / cummin for complex numbers

2014-07-14 Thread Ben Bolker
Michael Haupt 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 - (0+3i),

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

2014-07-23 Thread Ben Bolker
ask it. >From http://cran.r-project.org/web/packages/policies.html : "Packages with licenses not listed 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 Bolk

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

2014-09-01 Thread Ben Bolker
ept for a "ggplot2 built under 3.2.0 warning"). Does 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?

2014-09-01 Thread Ben Bolker
thanks -- although I think `dplyr` is a red herring; my issue is with `plyr` (which is imported by `ggplot2` so should get installed automatically anyway ...) On Mon, Sep 1, 2014 at 4:08 PM, Carl Boettiger wrote: > Hi Ben, > > Just tested this on a fresh ubuntu 14:04 sandbox by usi

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

2014-09-01 Thread Ben Bolker
ot;011001" w2A <- .encode_numeric_version(e2, width = 2, maxlen = maxlen) ## "010701" w1A>w2A ## TRUE If I had the patience I would revert to before this SVN change and see what happened: = r66259 | hornik | 2014-07-27 15:45:29 -0400 (Sun, 27 Jul 2014) | 2 lines

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

2014-09-01 Thread Ben Bolker
a package version with an 8 in it ...) On Mon, Sep 1, 2014 at 9:27 PM, Ben Bolker 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 di

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

2014-09-01 Thread Ben Bolker
p-adic rationals. On Mon, Sep 1, 2014 at 9:38 PM, Ben Bolker 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

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

2014-09-02 Thread Ben Bolker
ything other than 1 if x == base > > Amazingly indeed, it does: From the few platforms I can try > here, I only see the problem > on 32 bit Linux, both an (old) ubuntu 12.04.5 and Fedora 19. > >> i <- 2:99; i[log(i, base=i) != 1] > [1] 5 8 14 18 19 25 58 60 64 6

[Rd] r wiki

2014-09-05 Thread Ben Bolker
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&q

[Rd] trivial typo in R-exts.texi

2014-09-17 Thread Ben Bolker
iod 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

2014-09-17 Thread Ben Bolker
-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, sorr

Re: [Rd] issue with compiling r6

2014-09-17 Thread Ben Bolker
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 14-0

Re: [Rd] organisation of packages & CRAN

2014-11-09 Thread Ben Bolker
Gábor Csárdi 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. > > Btw

Re: [Rd] organisation of packages & CRAN

2014-11-09 Thread Ben Bolker
On Sun, Nov 9, 2014 at 4:37 PM, Duncan Murdoch wrote: > Hi Ben. I agree with most of your points and questions, but just wanted > to nitpick one little point, inline below: > You're right -- I was being sloppy, that's worth clarifying. I think I originally meant to wri

Re: [Rd] organisation of packages & CRAN

2014-11-09 Thread Ben Bolker
ccess they could at any time. On Sun, Nov 9, 2014 at 4:40 PM, Gábor Csárdi wrote: > On Sun, Nov 9, 2014 at 3:26 PM, Ben Bolker wrote: > [...] > > * download information _is_ available, unofficially, from some > > mirrors other than the RStudio mirror: see > > http://www.r

Re: [Rd] organisation of packages & CRAN

2014-11-09 Thread Ben Bolker
about it many of them are puzzled that it's not part of the core R framework. I understand 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 fi

[Rd] robust updating methods

2015-03-22 Thread Ben Bolker
-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 pos

Re: [Rd] robust updating methods

2015-03-24 Thread Ben Bolker
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 15-03-23 12:55 PM, Thierry Onkelinx wrote: > Dear Ben, > > Last week I was struggling with incorporating lme4 into a package. > I traced the problem and made a reproducible example ( > https://github.com/ThierryO/testlme4). It loo

Re: [Rd] robust updating methods

2015-03-27 Thread Ben Bolker
eks at the very 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:

[Rd] misspellings

2015-04-12 Thread Ben Bolker
-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

[Rd] alternate licensing for package data?

2015-04-21 Thread Ben Bolker
contains only these 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

Re: [Rd] alternate licensing for package data?

2015-04-22 Thread Ben Bolker
Dirk Eddelbuettel debian.org> writes: > On 22 April 2015 at 11:34, Roger Bivand wrote: > | While I agree with Martyn with respect to code, documentation, and > | vignettes, the point Ben raises is relevant and not obvious. Data sets in > | say GLP-licensed packages are on occasio

Re: [Rd] model frames and update()

2015-04-23 Thread Ben Bolker
with a *reference* to a model frame; consider the situation where one is fitting 10 or 20 different models to a large data set, ending up with many copies (I'm not 100% sure, but I think that using model.frame() will end up creating an internal copy 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

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

2015-04-24 Thread Ben Bolker
n't think anyone else can guess very accurately ... Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

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

2015-04-24 Thread Ben Bolker
Uwe Ligges statistik.tu-dortmund.de> writes: > > > On 24.04.2015 22:44, Ben Bolker wrote: > > Prof J C Nash (U30A uottawa.ca> writes: > > > >> > >> I was preparing a fix for a minor glitch in my optimx package and R CMD > >> ch

[Rd] model.matrix and na.action

2015-04-29 Thread Ben Bolker
-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' argum

[Rd] minor typos

2011-10-29 Thread Ben Bolker
R-devel doc/NEWS.Rd (SVN 57472) contains: \item There are two new options for typesetting PDF manuals from Rd files. These are \samp{beramono} and \samp{inconsolata}, and used the named font for mononspaced output. They are intended to be used in combination with \samp{times

[Rd] strange behavior from cex="*"

2011-11-16 Thread Ben Bolker
erministic behaviour (and hanging) are a little disturbing. I haven't had a chance yet to try to dig in and see what's happening but thought I would report to see if anyone else could reproduce/figure it out. Ben Bolker ## n <- 100 ## hangs R n <- 3

Re: [Rd] strange behavior from cex="*"

2011-11-16 Thread Ben Bolker
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 11-11-16 05:18 PM, peter dalgaard wrote: > > On Nov 16, 2011, at 22:38 , Ben Bolker wrote: > >> Someone inquired on StackOverflow about apparently non-deterministic >> graphics behaviour in R. I noticed that they w

Re: [Rd] Case: package removed from CRAN, but not orphaned

2011-11-26 Thread Ben Bolker
ow many of the packages on CRAN have *no* reverse dependencies: library(packdep) d1 <- map.depends() c <- dependencies(d1) sum(c$reverse==0)/nrow(c) 66%. Furthermore, I would guess that orphaned packages would be more likely to be in this 66%. What about exempting

Re: [Rd] Undocumented functions

2011-12-15 Thread Ben Bolker
y function that is not exported from a package need not be documented. Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] pointers on including SVN revision number in package info?

2012-01-06 Thread Ben Bolker
ng track of which development (micro-)version a random user might be working with? thanks, Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Rnw file generated strange symbols in pdf file

2012-01-24 Thread Ben Bolker
Zhu Wang ccmckids.org> writes: > I found my Rnw file generated strange symbols in pdf file. > For instance, on page 4 of the following file, > > http://cran.r-project.org/web/packages/cts/vignettes/kf.pdf > you can see Belcher et~al on line 2, and Figure~1 on line 5. The > symbol ~ should not

[Rd] misfeature: forced file.copy() of a file over itself truncates the file ...

2012-01-27 Thread Ben Bolker
know if there's a good system-independent way to test file identity ... $ ls -i tmp.dat 114080 tmp.dat $ ls -i /home/bolker/R/pkgs/r2jags/pkg/tests/tmp.dat 114080 /home/bolker/R/pkgs/r2jags/pkg/tests/tmp.dat Would normalizePath() work for this ... ? > normalizePath("tmp

Re: [Rd] misfeature: forced file.copy() of a file over itself truncates the file ...

2012-01-31 Thread Ben Bolker
Ben Bolker gmail.com> writes: > Bump. Will I be scolded if I submit this as a bug report/wishlist item? Test case: > fn <- "tmp.dat" > x <- 1:3 > dump("x",file=fn) > file.info(fn) ## 9 bytes > file.copy(paste("./",fn

[Rd] ignorant question about Roxy- mode in ESS

2012-01-31 Thread Ben Bolker
gure out how to put these two pieces together. Perhaps I have an old ess version (5.14)? thanks Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] ignorant question about Roxy- mode in ESS

2012-01-31 Thread Ben Bolker
Ben Bolker gmail.com> writes: > I am slowly getting up to speed/being dragged into using Roxygen in a > project. I'm wondering if there's a way to emulate the behaviour of C-c > C-p (Rd-preview-help) in Rd-mode (create a preview in a new Emacs buffer > in "R He

[Rd] na.omit option in prcomp: formula interface only

2012-02-09 Thread Ben Bolker
it to handle na.action as well? (I can appreciate from looking at stats:::prcomp.formula that the NA-processing is not completely trivial ...) Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] building r-devel

2012-02-17 Thread Ben Bolker
include/Rinternals.h': No such file or directory make[2]: *** [Rinternals.ts] Error 1". Any thoughts about what's going on here or what I can do to further diagnose the problem? thanks Ben Bolker == bolker@ubuntu-10:~/R/r-devel$ svn update At revision 58

Re: [Rd] Jazzing up the Task Views index page

2012-02-21 Thread Ben Bolker
Barry Rowlingson lancaster.ac.uk> writes: > Anyway, I did say that Task Views were rather brilliant, but were let > down by their hidden position on the R web sites (tucked away as the > third element of a sub-menu of a CRAN mirror site linked to by the > CRAN link from the Download menu on the m

[Rd] prior.weights and weights()

2012-02-21 Thread Ben Bolker
late values from the model for a novel set of predictor variables ... (coincidentally, this would also allow our package to use the existing framework more easily). Are there any circumstances under which predict(object,type="response") is/could be *different* from fitted(object) for a 'glm

Re: [Rd] prior.weights and weights()

2012-02-27 Thread Ben Bolker
Ben Bolker gmail.com> writes: Bump? (Quoting with "> " removed to make Gmane happy) I've since realized that it will be harder to use the built-in $simulate methods in my application than I thought, but I'm still curious about this issue (and might still be able

[Rd] "note: symbols.rds is not available"

2012-03-13 Thread Ben Bolker
How would I fix the issue/suppress the note? thanks Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] serialization regression in 2.15.0 beta

2012-03-25 Thread Ben Goodrich
oreign_0.8-49 [5] abind_1.4-0 R2WinBUGS_2.1-18 coda_0.14-5 lme4_0.999375-42 [9] Matrix_1.0-4 lattice_0.20-0 MASS_7.3-17 loaded via a namespace (and not attached): [1] grid_2.15.0 nlme_3.1-103 Thanks, Ben __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] serialization regression in 2.15.0 beta

2012-03-27 Thread Ben Goodrich
-branch/doc/NEWS.Rd M /branches/R-2-15-branch/src/library/parallel/R/unix/forkCluster.R M /branches/R-2-15-branch/src/library/parallel/R/unix/mcfork.R revert to XDR serialization for 2.15.0 Thanks, Ben > I

Re: [Rd] serialization regression in 2.15.0 beta

2012-03-28 Thread Ben Goodrich
Quoting Prof Brian Ripley : On 27/03/2012 22:01, Ben Goodrich wrote: In case anyone is concerned that this regression will affect them, the code was reverted to the 2.14.x behavior by r58842 | ripley | 2012-03-26 08:12

[Rd] r-forge build failure bafflement

2012-03-29 Thread Ben Bolker
ons and seeing whether I can get back to a working version, but I'd like to see if I can get it fixed by moving forward rather than backward ... For anyone who is intrigued and wants to investigate farther: http://r-forge.r-project.org/R/?group_id=847 http://r-forge.r-project.org/scm/?group_id=847

Re: [Rd] r-forge build failure bafflement

2012-03-30 Thread Ben Bolker
ile("extdata", [model_obj], package="glmmADMB"). I would be curious if anyone has any other suggestions for ways to work around this issue, or if they feel that I am subverting the intended use of the data/ directory (and so it's my own fault). happy friday, and thanks to al

Re: [Rd] r-forge build failure bafflement

2012-03-30 Thread Ben Bolker
s and would trigger the search for the package -- I don't think this is avoidable. [cc'd back to r-devel for discussion/archival purposes] > -- Sent from my Android phone with K-9 Mail. Please excuse my > brevity. > > Ben Bolker wrote: > > Figured it out (I thin

[Rd] R CMD check with non-standard .libPaths

2012-04-14 Thread Ben Bolker
but I wonder if there's a way I can get the examples run to see the non-standard package location. I could (I guess) modify my .Rprofile temporarily ... ? But I'm curious if there's a right way to do this ... thanks Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Patch to add Beta binomial distribution. Mentor needed!

2012-05-22 Thread Ben Bolker
ture-requests-to-the-r-core-team/8066062#8066062 [url broken] for some context on why you should build a package instead of trying to get a patch accepted in base R ... Ben Bolker > > On Tue, May 22, 2012 at 8:27 AM, Joan Maspons > > wrote: > > > Hello, > > >

Re: [Rd] Patch to add Beta binomial distribution. Mentor needed!

2012-06-05 Thread Ben Bolker
ependencies, you have at least the *legal* right to take any piece of code you want from any open-source (BSD, GPL, ...) package and package it your own little package (provided it follows the rules of the original license) that includes only the stuff you need, without any other dependencies. It&#x

[Rd] semi-trivial documentation suggestion

2012-06-28 Thread Ben Bolker
in this I could submit a doc patch. (Thought sparked by http://www.r-bloggers.com/how-do-i-create-the-identity-matrix-in-r/ ) Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] confusion over S3/S4 importing

2012-07-30 Thread Ben Bolker
that, but I thought it was supposed to be a last resort and that I was *supposed* to be able to fix my problems by proper use of imports. Any insights? thanks Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Numerics behind splineDesign

2012-07-31 Thread Ben Bolker
pler references > anyone might recommend? [snip] Some of this stuff *might* be in the "White Book" (Statistical Models in S, ed Chambers & Hastie (esp. chapter 7?) Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Numerics behind splineDesign

2012-07-31 Thread Ben Bolker
, which may not > exist) is the ultimate reference. > > -- Bert > > On Tue, Jul 31, 2012 at 6:25 AM, Ben Bolker wrote: >> Nathaniel Smith pobox.com> writes: >> >>> I find myself needing to be able to reproduce the spline bases that R >>> compute

Re: [Rd] What's your opinion about the Transparency Layer feature of Oracle R Enterprise?

2012-10-17 Thread Ben Bolker
Xiaobo Gu gmail.com> writes: > > Hi, > > The Transparency Layer feature of Oracle R Enterprise overcomes the > RAM limitation of R, and can take advantage of multiple core > processing of the database server by translating R expression into > SQL, what about building a open source version of th

[Rd] suppress *specific* warnings?

2012-10-21 Thread Ben Bolker
I get back from here to the calling point ## *without* muffling warnings ... ? } }) } suppressWarnings2(sqrt(-1)) suppressWarnings2(sqrt(-1),"abc") It seems to me I'd like to have a restart option that just returns to the point where the warning was caught

Re: [Rd] suppress *specific* warnings?

2012-10-21 Thread Ben Bolker
On 12-10-21 09:08 PM, Martin Morgan wrote: > On 10/21/2012 12:28 PM, Ben Bolker wrote: >> >>Not desperately important, but nice to have and possibly of use to >> others, is the ability to suppress specific warnings rather than >> suppressing warnings indiscrim

Re: [Rd] 12-bit functionality in tiff package

2012-10-23 Thread Ben Bolker
Joseph Barry embl.de> writes: > We have recently been using the tiff package for reading tiff images > into the Bioconductor Package EBImage. This has been extremely > helpful in conjunction with other steps to eliminate dependencies on > ImageMagick. > However, it seems that 12-bit images are

[Rd] trivial typo in relist.Rd

2012-10-25 Thread Ben Bolker
in src/library/utils/man/relist.Rd, line 50: objects into a vector representation. \code{relist()}, it's methods and spurious apostrophe ... Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] R CMD check fails when run in a directory with parentheses in the pathname

2012-11-27 Thread Ben Bolker
within src/library/tools/R/check.R to protect parentheses in the shell argument string ... Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] read.csv reads more rows than indicated by wc -l

2012-12-19 Thread Ben Bolker
G See gmail.com> writes: > > When I have a csv file that is more than 6 lines long, not including > the header, and one of the fields is blank for the last few lines, and > there is an extra comma on of the lines with the blank field, > read.csv() makes creates an extra line. > > I attached an

[Rd] sQuote() on zero-length inputs

2013-01-01 Thread Ben Bolker
It's not desperately important, but it would seem more consistent to me if sQuote(character(0)) or sQuote(NULL) returned character(0) rather than "‘’" . This could easily be achieved by putting if (length(x)==0) return(character(0)) at the beginning ..

Re: [Rd] Bounty on Error Checking

2013-01-03 Thread Ben Bolker
ut (1) well-worked out proofs of concept would go a long way to convincing R-core; (2) a lot can be done outside of core R if (for example) you moved over to using data.table everywhere instead of data frames (only translating to data frames where absolutely necessary). (I would

Re: [Rd] Bounty on Error Checking

2013-01-04 Thread Ben Bolker
On 13-01-04 07:48 AM, Laurent Gautier wrote: > On 2013-01-04 12:00, r-devel-requ...@r-project.org wrote: >> Message: 16 Date: Thu, 3 Jan 2013 22:52:44 +0000 From: Ben Bolker >> To: Subject: Re: [Rd] >> Bounty on Error Checking Message-ID: >> Content-Type: text/plain

[Rd] .print.via.format not found when building r61617?

2013-01-11 Thread Ben Bolker
here anything else I can try? Ben Bolker > cd r-devel svn update At revision 61617. > cd ../r-devel-build ../r-devel/configure --enable-R-shlib R is now configured for i686-pc-linux-gnu Source directory: ../r-devel Installation directory:/usr/local C compiler:

Re: [Rd] .print.via.format not found when building r61617?

2013-01-11 Thread Ben Bolker
On 13-01-11 12:59 PM, Ben Bolker wrote: > I wouldn't be at all surprised if I turned out to be doing something > boneheaded, but I've *tried* to follow all the relevant rules ... > Based on a clean SVN checkout of R-devel r61617, building in a > separate directory, I end

Re: [Rd] Incorporating single functions from other packages: rules and regulations?

2013-01-13 Thread Ben Bolker
om > > the _original author_ of that code. > > > > Dirk I agree/sympathize but can also think of cases, if the function is short/simple enough, that it would actually make sense to copy it. It's a judgment call, I think. Most R packages are under sufficiently permissive licenses (plotrix is 'GPL >=2') that copying is allowed, although it would be courteous to inform/ask permission from the author(s). Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Who does develop the R core and libs, and how / where is it hosted?

2013-01-15 Thread Ben Bolker
Oliver Bandel first.in-berlin.de> writes: > Am 15.01.2013 um 01:11 schrieb Brian Lee Yung Rowe muxspace.com>: > > On Jan 14, 2013, at 6:32 PM, oliver first.in-berlin.de> wrote: > >> BTW: I looked up the string "wish list" > in some of the mentioned docs (mentioned in this thread) > >> but

Re: [Rd] (patch) Layers for pdf() grDevice

2013-01-26 Thread Ben Bolker
interested/willing to incorporate your patch or one like it. library("sos"); findFn("{graphics device} driver") finds packages incorporating alternative graphics devices. Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Regression stars

2013-02-12 Thread Ben Bolker
Duncan Murdoch gmail.com> writes: [snip] > > Regarding stringsAsFactors: I'm not going to defend keeping it as is, > I'll let the people who like it defend it. Would someone (anyone) like to come forward and give us a defense of stringsAsFactors=TRUE -- even someone who doesn't personal

Re: [Rd] Regression stars

2013-02-12 Thread Ben Bolker
On 13-02-12 09:20 AM, Uwe Ligges wrote: > > > On 12.02.2013 14:54, Ben Bolker wrote: >> Duncan Murdoch gmail.com> writes: >> >>[snip] >>> >>> Regarding stringsAsFactors: I'm not going to defend keeping it as is, >>> I'll l

Re: [Rd] Depreciating partial matching

2013-03-21 Thread Ben Bolker
Terry Therneau mayo.edu> writes: > To summarize: my own interactive mix of emacs/R may be unusual. > For pure interactive folks completion does most of the work. I > hadn't tried the newest ESS interactive-within-emacs till today, > it's slick as well. The number of people howling will be less

[Rd] locking down R

2013-05-19 Thread Ben Bolker
ilers, etc.. * I suspect the answer given here will be "if you really want to secure R, run it within a standard restricted-access shell (e.g. chroot on a Linux system)". If anyone has experience of 'locking down' R on Windows (XP) in a sensitive environment, I'd be curiou

Re: [Rd] locking down R

2013-05-20 Thread Ben Bolker
On 13-05-20 04:42 AM, Barry Rowlingson wrote: > On Sun, May 19, 2013 at 7:16 PM, Ben Bolker wrote: >> >> The workstations have no access to external networks, >> nor to external media (thumb drives etc.) [information transfer to the >> outside world is via shared dri

Re: [Rd] locking down R

2013-05-20 Thread Ben Bolker
On 13-05-19 06:08 PM, R. Michael Weylandt wrote: > On Sun, May 19, 2013 at 7:16 PM, Ben Bolker wrote: >> >> Is anyone on this list aware of discussions about locking down/securing R? >> >> My colleagues and I are working with health statistics in an office >>

[Rd] quick question about glm() example

2013-05-29 Thread Ben Bolker
,1,9), treatment=gl(3,3)) print(d.AD) glm.D93 <- glm(counts ~ outcome + treatment, family = poisson(), data=d.AD) Thoughts? Ben Bolker __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] quick question about glm() example

2013-05-29 Thread Ben Bolker
On 13-05-29 03:05 PM, peter dalgaard wrote: > > On May 29, 2013, at 19:58 , Ben Bolker wrote: > >> >> I don't have a copy of Dobson (1990) from which the glm.D93 example >> is taken in example("glm"), but I'm strongly suspecting that these >>

[Rd] View() crashy on Ubuntu 9.04

2009-05-12 Thread Ben Bolker
ut my installed version (2.9.0) doesn't have debugging symbols, and I'm having trouble building the latest SVN version (./configure gives "checking for recommended packages... ls: cannot access ./src/library/Recommended/boot_*.tar.gz: No such file or directory") Can anyone confirm?

Re: [Rd] View() crashy on Ubuntu 9.04

2009-05-12 Thread Ben Bolker
Cannot find new threads: generic error > Cannot find new threads: generic error ?? cheers Ben Bolker Kjetil Halvorsen wrote: > I can reproduce this too. > Run from within emacs: > >> v <- data.frame(1:3,2:4) >> sessionInfo() > R version 2.9.0 (2009-04-17

Re: [Rd] View() crashy on Ubuntu 9.04

2009-05-13 Thread Ben Bolker
This patch fixes the problem for me with latest R-devel. Thanks! (This kind of X-hacking would take me hours if not days to figure out ...) cheers Ben Bolker Ei-ji Nakama wrote: > Hi > > 2009/5/13 Dirk Eddelbuettel : > >> #0 0xb70e685e in XmbLookupString () from /u

Re: [Rd] simple add error (PR#13699)

2009-05-13 Thread Ben Bolker
#x27;s just my ignorance/unwilling to think about numerical computation more carefully at the moment. Check out various threads on the mailing lists about bc and yacas (although I'm not sure if yacas runs on Windows or not). Ben Bolker -- View this message in context: http://www.nabble.c

Re: [Rd] View() crashy on Ubuntu 9.04

2009-05-15 Thread Ben Bolker
Prof Brian Ripley wrote: > > Thank you, included in R-patched and R-devel now. > [snip] thanks! > I do wonder sometimes if people who only work with data in ASCII or in > a Western European language covered by Latin-1 realize the extent of > the overhead that using a UTF-8 locale impli

Re: [Rd] install.packages hangs RGui with frozen rpwd process at bottom of process tree (PR#13734)

2009-06-02 Thread Ben Bolker
astokes wrote: > > Full_Name: Allan Stokes > Version: 2.8.1 > OS: XP > Submission from: (NULL) (24.108.0.245) > > > I've just spent a hellish six hours trying to create my own R package with > a > bare bones "hello world" R function inside. I was able to create a > package.tar.gz file eventu

Re: [Rd] The default position of plot title

2009-06-02 Thread Ben Bolker
mpatibility/surprise issues for all the other users who expect the title to be at the top ... Ben Bolker -- View this message in context: http://www.nabble.com/The-default-position-of-plot-title-tp23828342p23831792.html Sent from the R devel mailing list archive at Nabble.com. ___

[Rd] Reduce: extra args wishlist?

2009-06-06 Thread Ben Bolker
ersion of Reduce() Reduce(merge,z,by="state",all=TRUE) The change is simple -- just add "..." to every call to the function in Reduce() -- patch is included below my signature ... It's not a big deal -- I could also do Reduce(function(x,y) { merge(x,y,by="st

Re: [Rd] Reduce: extra args wishlist?

2009-06-10 Thread Ben Bolker
curious what the protocol is when R-core members differ? (I would have guessed that conservatism would rule, or the opinion of the original author of the functions (I don't know who contributed Reduce et al.), but perhaps Kurt doesn't have strong feelings about this ... cheers Ben -

Re: [Rd] box and whisker (PR#13821)

2009-07-12 Thread Ben Bolker
x27;s really necessary since as you've shown the point is pretty general. Ben Bolker -- View this message in context: http://www.nabble.com/box-and-whisker-%28PR-13821%29-tp24446795p24453549.html Sent from the R devel mailing list archive at Nabble.com. ___

[Rd] model.matrix evaluation challenges

2009-08-09 Thread Ben Bolker
z)) fails -- because model.matrix() is explicitly evaluating the variables in the formula in the environment of z (i.e., ignoring the first argument of "with" ...) Any advice on how to solve this without making a bigger mess? sincerely Ben Bolker ## set up a data frame for predic

Re: [Rd] Bug in nlm, found using sem; failure in several flavors (PR#13883)

2009-08-10 Thread Ben Bolker
gs, but perhaps someone else can comment ...) Ben Bolker Adam D. I. Kramer-2 wrote: > > This message is in MIME format. The first part should be readable text, > while the remaining parts are likely unreadable without MIME-aware > tools. > > --1660387551-150661043-1249

Re: [Rd] model.matrix evaluation challenges

2009-08-11 Thread Ben Bolker
that seems to work, thank you. would anyone care to explain *why* it works ... ? or where I could go to read more about why it works ... ? cheers Ben Bolker Felix Andrews wrote: > how about... > > nrow(with(cc, model.matrix(params, data=environment( > > cheers >

[Rd] unnecessary braces?

2009-08-18 Thread Ben Bolker
trial probability distribution. } -- Ben Bolker Associate professor, Biology Dep't, Univ. of Florida bol...@ufl.edu / www.zoology.ufl.edu/bolker GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc signature.asc Description: OpenPGP digital signature __

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