r-devel@r-project.org discussions

0	[Rd] mcparallel (parallel:::mcexit) does not call finalizers

Hello, In the context of trying to cover a package code that use parallelized tests using the covr package, I realized that code executed using mcparallel() was not covered, cf ...

Karl Forner
Jun 16, 2016 at 4:09 pm
Jun 16, 2016 at 4:09 pm

6	[Rd] new function to tools/utils package: dependencies based on DESCRIPTION file

Hi all, Packages tools and utils have a lot of useful stuff for R developers. I find one task still not as straightforward as it could. Simply to extract dependencies of a package from DESCRIPTION ...

Jan Górecki
Jun 14, 2016 at 2:54 pm
Jun 16, 2016 at 1:00 pm

0	[Rd] as.array() on a data.frame

Wouldn't it make sense to have as.array() work on a data.frame and be equivalent to as.matrix()? df <- data.frame(stuff=1:3) # as.matrix(df) # stuff # [1,] 1 # [2,] 2 # [3,] 3 as.array(df) # Error in ...

Hervé Pagès
Jun 10, 2016 at 9:22 pm
Jun 10, 2016 at 9:22 pm

0	[Rd] typosquatting and trojan horses in packages

A friend passed along this interesting link: http://incolumitas.com/2016/06/08/typosquatting-package-managers/ about the strategy of using "typosquatting" (packages with very similar names to ...

Ben Bolker
Jun 10, 2016 at 9:20 pm
Jun 10, 2016 at 9:20 pm

0	[Rd] collapsing list of NULLs dimnames into a NULL

Hi, Here are two different ways to create a 0 x 0 logical matrix: m1 <- matrix(nrow=0, ncol=0) m1 # <0 x 0 matrix m2 <- as.matrix(data.frame()) m2 # <0 x 0 matrix Surprisingly: identical(m1, m2) # ...

Hervé Pagès
Jun 10, 2016 at 8:26 pm
Jun 10, 2016 at 8:26 pm

1	[Rd] cumsum method in Math group

When running a = runif(10) class(a) = "foo" Math.foo = function(x, ...) { NextMethod(.Generic) } signif(a, 3) cumsum(a) I don't understand why cumsum strips the class, but signif does not. Both claim ...

Edzer Pebesma
Jun 9, 2016 at 8:13 am
Jun 9, 2016 at 12:34 pm

1	[Rd] Trivial patch for merge.Rd

Hi all, After replying to r-help earlier today on the merge() related thread, I noted a trivial grammatical error in the description for the 'suffixes' argument in it's help file. A patch against the ...

Marc Schwartz
Jun 8, 2016 at 7:13 pm
Jun 9, 2016 at 7:35 am

1	[Rd] Small mistake in ?raw

In ?raw (src/library/base/man/raw.Rd), the final line of Examples seems to be off: The character "\x9c" is a control character in Latin-1. Maybe the example should use "\xa3" instead: [1] "?25.63" -- ...

Mikko Korpela
Jun 7, 2016 at 9:41 am
Jun 8, 2016 at 11:01 am

4	[Rd] getGraphicsEvent on X11 and event queuing

Hi R-Devel, I've been working on an oscilloscope project using an Arduino microcontroller board. I found that it's quite easy to get realtime updates, e.g. 30+ frames per second, if I read data from ...

Frederik
Jun 7, 2016 at 1:38 am
Jun 14, 2016 at 3:34 pm

2	[Rd] readlines() truncates text file with Codepage 437 encoding

Hello r-devel, The attached Code page 437-encoded file contains 245 characters (including the final newline), but readLines only reads 242 of them: Warning message: In ...

Adam Obeng
Jun 6, 2016 at 10:11 am
Jun 9, 2016 at 2:40 pm

0	[Rd] factors with non-unique ("duplicated") levels have been deprecated since 2009 -- are more deprecated now -- and why you should be hesitant misusing suppressWarnings()

https://bugs.r-project.org/bugzilla/show_bug.cgi?id895#c6 the fact that you can construct factors with non-unique aka "duplicated" levels in R has been re-raised. As mentioned there, we had a small ...

Martin Maechler
Jun 4, 2016 at 5:32 pm
Jun 4, 2016 at 5:32 pm

0	[Rd] complex NA's match(), etc: not back-compatible change proposal

With 'z' of length 8 below, or of length 12 previously, one may try sapply(rev(z), match, table = rev(z)) match(rev(z), rev(z)) I found that the two results were different in R devel r70604. A ...

Suharto Anggono Suharto Anggono
Jun 3, 2016 at 7:13 pm
Jun 3, 2016 at 7:13 pm

0	[Rd] [RfC] Family dispersion

Hi, I'd like to hear your opinion about the following proposal to make the computation of dispersion in GLMs more flexible. Dispersion is used in summary.glm; the relevant code chunk with the ...

Luis Carvalho
Jun 2, 2016 at 2:25 am
Jun 2, 2016 at 2:25 am

2	[Rd] segfault / crash when asking for large memory via strrep()

We've had this more general topic on R-help, and also in R-devel recently. There's one case here where I get the feeling R never gets into swapping but more directly aborts possibly from a bug we can ...

Martin Maechler
Jun 1, 2016 at 1:07 pm
Jun 1, 2016 at 6:38 pm

1	[Rd] Suggestion: pdf.options(embed=TRUE)

I learned last week that I generated a lot of PDFs and forgot to go back and embed the fonts in them. It would be very pleasant for me if pdf.options included an argument to turn on font embedding ...

Paul Johnson
May 31, 2016 at 11:59 pm
Jun 1, 2016 at 1:19 am

1	[Rd] factor(x, exclude=NULL) for factor x; names in as.factor(<integer>)

In R 3.3.0 (also in R 2.7.2), the documentation on 'factor', in "Details" section, has this statement. 'factor(x, exclude = NULL)' applied to a factor is a no-operation unless there are unused ...

Suharto Anggono Suharto Anggono
May 30, 2016 at 5:20 pm
May 31, 2016 at 3:59 pm

4	[Rd] Update CRAN submission process

The CRAN submission process seems in need of a massive overhaul. Why has this process not been automated yet? ? Patrick Perry Assistant Professor NYU Stern School of Business

Patrick Perry
May 27, 2016 at 7:58 pm
May 31, 2016 at 2:01 pm

0	[Rd] Evolution of the R native interface

Hi! I hope you don?t mind me posting this call for participation - I do think the matter at hand is very important for the people on this list, and the people on this list are very important for the ...

Lukas Stadler
May 27, 2016 at 1:49 pm
May 27, 2016 at 1:49 pm

0	[Rd] odd warning unlinking symlink on Windows

While constructing some tests of symbolic link code in R, I got an odd warning when trying the remove a symbolic link: file.create(tfile <- tempfile()) #[1] TRUE file.symlink(tfile, tlink <- ...

William Dunlap
May 25, 2016 at 5:27 pm
May 25, 2016 at 5:27 pm

4	[Rd] R without graphics

Is it possible to configure and build an R without any graphics support. I..e no grDevices or graphics packages? I tried "--with-x=no --with-cairo=no --with-grDevices=no --with-graphics=no" but it is ...

Mick Jordan
May 23, 2016 at 11:44 pm
May 24, 2016 at 2:48 pm

2	[Rd] data frame method for as.table()

Hello, Currently it's possible to convert an object of class table to a data frame with as.data.frame.table(), but there's no ready-made function, AFAIK, to do the reverse operation, i.e. conversion ...

Ernest Adrogué
May 23, 2016 at 4:46 pm
May 23, 2016 at 6:56 pm

2	[Rd] Submitting an updated package version to CRAN (Warning: non-ASCII characters)

Dear all: I am updating the version of an R package I submitted last year on CRAN and came across two questions that I would be grateful to seek any input about: 1) In the updated version of the ...

Luck Buttered
May 21, 2016 at 8:25 pm
Jun 4, 2016 at 4:45 pm

4	[Rd] identical on closures

I'm confused by this: [1] FALSE Yet, after loading the Matrix package (which redefines det), the following is checked (in library.checkConflicts): ignore.environment=T) [1] TRUE I've looked at the ...

Mick Jordan
May 20, 2016 at 7:40 pm
May 23, 2016 at 7:24 am

20	[Rd] Latest R-devel build failing on OS X

Dear R-devel, The latest version of R-devel (05-17) is throwing an error for me when building on OS X (v 10.11.4): making Rembedded.d from Rembedded.c making dynload.d from dynload.c making system.d ...

Keith O'Hara
May 18, 2016 at 12:18 pm
May 26, 2016 at 12:29 am

5	[Rd] [patch] Error in reg-tests-1c.R (R-devel)

I get an error when running "make check" after building R-devel r70629 on Ubuntu 14.04. Here are the relevant lines in the file "reg-tests-1c.Rout.fail": Error: unexpected input in "dv <- ...

Mikko Korpela
May 18, 2016 at 10:05 am
May 19, 2016 at 6:53 am

0	[Rd] gcc optimization

Hi, I have noticed that the run times for MCMCglmm models (mainly written in C/C++) have suddenly jumped up on Linux machines (Ubuntu/Linaro 4.6.4 and Scientific Linux 6.6) yet they have remained ...

Jarrod Hadfield
May 18, 2016 at 5:28 am
May 18, 2016 at 5:28 am

1	[Rd] discussion of change in R 3.3.0 to [<-

In the NEWS for R 3.3.0 is this change: * [<- with an S4 value into a list currently embeds the S4 object into its own list such that the end result is roughly equivalent to using [[<-. That behavior ...

Richard Morey
May 17, 2016 at 1:43 pm
May 17, 2016 at 2:09 pm

2	[Rd] R-3.3.0 Base: Windows compilation fails while building 'base' package

Hi, I'm trying to builda R-3.3.0 base package on Windows 8.1, and it fails while building 'base' package with an error about unable to create a directory under /tmp. I am running the make from my D:\ ...

Venkat Ramakrishnan
May 17, 2016 at 3:32 am
May 20, 2016 at 10:15 am

0	[Rd] meaning of 'Depends: R (> 3.0.2)'

In knitr-1.13 the DESCRIPTION file's Depends line uses a " " instead of the usual " =". Depends: R ( 3.0.2) I don't see the strict greater than in Writing R Extensions. Does it really mean that 3.0.2 ...

William Dunlap
May 16, 2016 at 8:22 pm
May 16, 2016 at 8:22 pm

0	[Rd] R devel: install.packages(..., type="both") not supported on Windows

Is the following intentional or something that has been overlooked? [HB-X201]{hb}: R --vanilla R Under development (unstable) (2016-05-13 r70616) -- "Unsuffered Consequences" Copyright (C) 2016 The R ...

Henrik Bengtsson
May 15, 2016 at 1:33 am
May 15, 2016 at 1:33 am

2	[Rd] R external pointer and GPU memory leak problem

My question is based on a project I have partially done, but there is still something I'm not clear. My goal is to create a R package contains GPU functions (some are from Nividia cuda library, some ...

Yuan Li
May 14, 2016 at 3:43 pm
May 16, 2016 at 5:58 pm

1	[Rd] LaTeX errors new with R 3.3.0

Hello: I could use help understanding an error reported by "R CMD build sos" that's new with R 3.3.0: Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on ...

Spencer Graves
May 13, 2016 at 2:41 pm
May 13, 2016 at 4:34 pm

1	[Rd] objects intermittently shared between vignettes

Hello: Is it widely known that objects not explicitly deleted from one vignette in a package can be available to a second in "R CMD build" and "R CMD check" but not when the second vignette is built ...

Spencer Graves
May 13, 2016 at 1:21 am
May 13, 2016 at 8:13 am

9	[Rd] Single-threaded aspect

R Developers, Could someone help explain what it means that R is single threaded? I am trying to understand what is actually going on inside R when users want to parallelize code. For example, using ...

Charles Determan
May 12, 2016 at 12:45 pm
May 12, 2016 at 2:52 pm

12	[Rd] Suggestion: mkString(NULL) should be NA

I would like to propose that Rf_mkString(NULL) and Rf_mkChar(NULL) return NA rather than segfault. Case: the mkString() and mkChar() functions are convenient to wrap strings returned by e.g. external ...

Jeroen Ooms
May 12, 2016 at 11:20 am
May 26, 2016 at 2:06 am

1	[Rd] unloadNamespace problem in 3.3

The following used to work in R 3.2.5 but not in 3.3.0: library(MASS) ns <-.getNamespace("MASS") unloadNamespace(ns) Calling unloadNamespace("MASS") directly still works.

Jeroen Ooms
May 10, 2016 at 2:39 pm
May 10, 2016 at 3:07 pm

5	[Rd] complex NA's match(), etc: not back-compatible change proposal

This is an RFC / announcement related to the 2nd part of PR#16885 https://bugs.r-project.org/bugzilla/show_bug.cgi?id885 about complex NA's. The (somewhat rare) incompatibility in R's 3.3.0 match() ...

Martin Maechler
May 10, 2016 at 2:08 pm
May 30, 2016 at 10:48 am

1	[Rd] recursion problem using do.call(rbind, list(..,<S4>,..))

This was originally a bug report about Matrix, https://r-forge.r-project.org/tracker/?funcÞtail&atid)4&aidc25&group_ida but the bug is rather a "design" bug in R, or a limitation. This e-mail is a ...

Martin Maechler
May 10, 2016 at 10:43 am
May 13, 2016 at 8:11 pm

2	[Rd] Regression in match() in R 3.3.0 when matching strings with different character encodings

Hi I think the following behavior is a regression from R 3.2.5: "\u00f8") [1] 1 NA incomparables = NA) [1] 1 I'm seeing this in R 3.3.0 on both Windows and Ubuntu 15.10. The specific behavior makes ...

Kirill Müller
May 9, 2016 at 2:07 pm
May 10, 2016 at 6:40 am

0	[Rd] Suggestion on default 'levels' in 'factor'

At first read, the logic of the following fragment in code of function 'factor' was not clear to me. if (missing(levels)) { y <- unique(x, nmax = nmax) ind <- sort.list(y) # or possibly order(x) ...

Suharto Anggono Suharto Anggono
May 6, 2016 at 8:05 am
May 6, 2016 at 8:05 am

0	[Rd] ctrl-R in Rgui

When in the Rgui editor sometimes ctrl-R does not cause anything to be sent to the R console. It can be reproduced like this: - when in the Rgui console press ctrl-F N to get a new editor window - ...

Gabor Grothendieck
May 5, 2016 at 10:47 pm
May 5, 2016 at 10:47 pm

0	[Rd] In R for Windows RGui, plain text help files open up at bottom of help file

Hello, When using the R for Windows installer, I typically choose a customized startup and specify "Plain text" (rather than "HTML help") as my preferred help style. In R-3.3.0, R-3.2.5, and (IIRC) ...

Josh O'Brien
May 5, 2016 at 7:50 pm
May 5, 2016 at 7:50 pm

1	[Rd] Max OSX 3.3.0 and lzma

I have lzma installed (in /usr/local) but R-3.3.0 configure doesn't like something about it: checking for lzma_version_number in -llzma... yes checking lzma.h usability... no checking lzma.h ...

Mick Jordan
May 5, 2016 at 6:40 pm
May 5, 2016 at 7:02 pm

1	[Rd] Too many spaces in deparsed complex numbers with digits17 control option

If you set the "digits17" control option in deparse, you get a lot of unnecessary space in the representation of complex numbers. [1] "0 + 0i" As far as I can tell, the logic for this comes from this ...

Richard Cotton
May 5, 2016 at 6:37 am
May 12, 2016 at 9:18 am

4	[Rd] Is it possible to retrieve the last error? (not error message)

Hi, at the R prompt, is it possible to retrieve the last error (as in condition object of class "error")? I'm not asking for geterrmessage(), which only returns the error message (as a character ...

Henrik Bengtsson
May 4, 2016 at 7:41 pm
May 6, 2016 at 1:17 am

11	[Rd] unix readline signal handling patches

Hello R Developers, I posted some patches yesterday to your bug tracking system but I'm not sure if I should have notified the mailing list as well. I haven't gotten any responses yet ...

Frederik
May 4, 2016 at 7:09 pm
May 17, 2016 at 8:10 pm

0	[Rd] nlme: lme gives incorrect answers without warning with redundant data

I think this issue will be of interest to the list. It seems like a problem with nlme, and I was drawn into it because of a collaborator who encountered this issue in a simple experiment and wound up ...

Jonathan Dushoff
May 4, 2016 at 3:12 am
May 4, 2016 at 3:12 am

16	[Rd] R process killed when allocating too large matrix (Mac OS X)

Dear expeRts, The following code leads to R being killed (under Mac OS X 10.11.4; R installed from source; also happened under a previous unstable version): m <- matrix(0, 100000, 100000) I expected ...

Marius Hofert
May 4, 2016 at 1:51 am
May 13, 2016 at 9:03 am

4	[Rd] vignette/knitr help

I need some help understanding a problem running the tests on the 'digest' package. Initially, I got the message that the 'knitr' package was needed to run vignettes: Running vignettes for package ...

Mick Jordan
May 3, 2016 at 6:10 pm
May 3, 2016 at 9:50 pm

4	[Rd] R-3.2.5 Mac OS X package

When is the R-3.2.5 binary for Mac OS X likely to show up? Mick Jordan

Mick Jordan
May 2, 2016 at 10:45 pm
May 3, 2016 at 5:58 pm

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