r-devel@r-project.org discussions for May 2015

49	[Rd] NEWS.md support on CRAN

Are there any plans for CRAN to support NEWS files in markdown? Bit of a hassle to go the the package?s Github (or other like) site to read NEWS.

Imanuel Costigan
May 23, 2015 at 12:49 am
Jun 5, 2015 at 4:39 pm

25	[Rd] MetaCran website v1.0.0-alpha

Dear All, [ I was wondering if this should have gone to the new mailing list. Maybe. ] As some of you maybe know from my earlier posts, I am building a simple search engine for R packages. Now the ...

Gábor Csárdi
May 23, 2015 at 2:02 pm
May 27, 2015 at 10:11 am

10	[Rd] Alternative for wildcard gnu extension in Makevars

I have some cpp-files from another library (boost) in a subdirectory in my src directory (src/boost_src). I include these using the following two lines in my Makevars: SOURCES = $(wildcard *.cpp ...

Jan van der Laan
May 13, 2015 at 3:27 pm
May 20, 2015 at 6:13 am

10	[Rd] Why is the diag function so slow (for extraction)?

(I asked this question on StackOverflow <http://stackoverflow.com/q/30035939/1191259 a short time ago; sorry if you're seeing it again. Feel free to answer there as well if you like. The code ...

Franknarf
May 4, 2015 at 5:59 pm
May 16, 2015 at 3:05 pm

9	[Rd] Wrong MD5 checksums in R 3.2.0

Dear R-devel members, Several R user recently reported <https://github.com/talgalili/installr/issues/30 (while using the installr <http://cran.r-project.org/web/packages/installr package) that when ...

Tal Galili
May 10, 2015 at 8:13 pm
May 11, 2015 at 3:19 pm

8	[Rd] example fails during R CMD CHECK but works interactively?

Greetings, I am collaborating with developing the bigmemory package and have run in to a strange problem when we run R CMD CHECK. For some reason that isn't clear to us one of the examples crashes ...

Charles Determan
May 13, 2015 at 6:31 pm
May 15, 2015 at 2:44 pm

7	[Rd] Unicode display problem with data frames under Windows

Here's a data frame with some Unicode symbols (set intersection and union). d <- data.frame(x = "A \u222a B \u2229 C") Printing this data frame under R 3.2.0 patched (r68378) and Windows 7, I see d ...

Richard Cotton
May 25, 2015 at 1:38 pm
May 26, 2015 at 7:29 am

6	[Rd] C-API: check whether R has been initialized ?

Hi, There appear to be no way to check whether R has already been initialized. Could a function like "Rf_isinitialized" be added to the API ? Best, Laurent [[alternative HTML version deleted]]

Laurent Gautier
May 3, 2015 at 8:34 pm
May 4, 2015 at 4:46 pm

5	[Rd] building with tcltk on Ubuntu 14.04

I'm having some issues trying to compile R-devel on Ubuntu 14.04. library("tcltk") works fine on the version of R as installed from Debian packages; I've done "apt-get build-dep r-base" so I think I ...

Ben Bolker
May 26, 2015 at 2:00 pm
May 28, 2015 at 11:34 am

5	[Rd] That 'make check-all' problem with the survival package

'make check-all' for current R has been showing this error in the middle for a few months now - any thought on fixing this? I think cmprsk should be either included in the recommended bundle, or the ...

Hin-Tak Leung
May 16, 2015 at 5:22 am
May 17, 2015 at 10:19 pm

5	[Rd] Reading exit code of pipe()

Is there a way to get the status code of a pipe() command? The documentation suggests that it might be returned by close, however this does not seem to be the case. con <- pipe("cat /etc/passwd", ...

Jeroen Ooms
May 14, 2015 at 12:24 am
May 14, 2015 at 5:07 pm

5	[Rd] Shouldn't vector indexing with negative out-of-range index give an error?

In Section 'Indexing by vectors' of 'R Language Definition' (http://cran.r-project.org/doc/manuals/r-release/R-lang.html#Indexing-by-vectors) it says: "Integer. All elements of i must have the same ...

Henrik Bengtsson
May 4, 2015 at 7:20 pm
May 6, 2015 at 5:53 pm

4	[Rd] Compiling 64bit static library for Windows (Rtools33, MSYS2, cross-compile on linux)

My apologies for cross-posting. I found this site, after I had posted on stack-overflow. I need to compile several static libraries (C & Fortran) which will later be linked with an R package ...

Sue McDonald
May 29, 2015 at 8:16 pm
Jun 1, 2015 at 10:49 pm

4	[Rd] Why my messages are filtered from the list?

Hello, Over the last two months I have sent two messages (same topic) to the list. None of them showed on the list. For the first, I got a message that it is in some queue and waiting for an ...

Ivan Popivanov
May 29, 2015 at 4:11 am
May 29, 2015 at 12:17 pm

4	[Rd] S4 inheritance and old class

Hey everyone, I would like to develop a package using S4 classes. I have to define several S4 classes that inherits from each others as follow: # A <- B <- C <- D I also would like to define ...

Julien Idé
May 28, 2015 at 9:49 am
May 28, 2015 at 9:32 pm

4	[Rd] How best to get around shadowing of executables by system()'s prepending of directories to Windows' PATH?

My question: On Windows, R's system() command prepends several directories to those in the Windows Path variable. The search path for 'command' may be system-dependent: it will include the R 'bin' ...

Josh O'Brien
May 18, 2015 at 5:29 pm
May 19, 2015 at 6:12 pm

4	[Rd] CRAN check for package on Sparc Solaris

Dear All, The metafor package currently fails CRAN checks on Sparc Solaris: http://cran.r-project.org/web/checks/check_results_metafor.html The problem is probably due to an unintended (= stupid) use ...

Viechtbauer Wolfgang (STAT)
May 13, 2015 at 7:48 pm
May 15, 2015 at 9:57 am

4	[Rd] R Language Definition: Subsetting matrices with negative indices is not an error

Hi, I spotted what looks like another(*) mistake in 'R Language Definition' on how subsetting should work. In Section 'Indexing matrices and arrays' ...

Henrik Bengtsson
May 9, 2015 at 12:53 am
May 9, 2015 at 9:17 pm

3	[Rd] A "bug" in plot.dendrogram - can't plot lty with character color

The problem: =========== Once a dendrogram has a branch with both a line type AND a color (which is a character color), the plot.dendrogram function will not plot and return an error. I say this is a ...

Tal Galili
May 18, 2015 at 8:01 pm
May 25, 2015 at 8:57 am

3	[Rd] Creating a vignette which depends on a non-distributable file

Dear all, I am writing a vignette that requires a file which I am not allowed to distribute, but which the user can easily download manually. Moreover, it is not possible to download this file ...

January Weiner
May 14, 2015 at 10:04 pm
May 16, 2015 at 7:39 am

3	[Rd] S4 method dispatch sometimes leads to incorrect when object loaded from file?

Loading an S4 object from a file without first loading the library sometimes (?, the example below and actual example involves a virtual base class and the show generic) leads to incorrect dispatch ...

Martin Morgan
May 10, 2015 at 3:19 pm
May 12, 2015 at 3:11 pm

3	[Rd] IdntoAscii issue with KERNEL32.dll on 64-bit R on Windows Server 2003 x64 SP2

Dear list, With the new R 3.2.0 on the aforementioned platform, I get the following pop-up error when I enter "?update.packages" using R64: "The procedure entry point IdnToAscii could not be located ...

Vinh Nguyen
May 6, 2015 at 2:57 pm
May 6, 2015 at 6:54 pm

3	[Rd] Problem with adding slots to S4 object

Dear all, I'm trying to create a virtual S4 class with some subclasses. I noticed that adding slots to this class increases the memory use and slows the functions down. Note that I'm adding very ...

Thierry Onkelinx
May 4, 2015 at 3:10 pm
May 6, 2015 at 9:45 am

3	[Rd] Define replacement functions

Hello I tried to define replacement functions for the class "mylist". When I test them in an active R session, they work -- however, when I put them into a package, they don't. Why and how to fix? ...

Soeren Vogel
May 4, 2015 at 12:52 pm
May 4, 2015 at 6:16 pm

3	[Rd] Print output during long tests?

I am the author of R package animint which uses testthat for unit tests. This means that there is a single test file (animint/tests/testthat.R) and during R CMD check we will see the following output ...

Toby Hocking
May 4, 2015 at 3:52 pm
May 4, 2015 at 5:38 pm

2	[Rd] Installation using iconv from glibc

The R Installation and Administration manual section A.1 states that glibc should provide a suitable iconv function, but I can't get R's configure script to accept/validate iconv on a Linux platform ...

Smith, Virgil
May 15, 2015 at 12:19 am
May 16, 2015 at 8:13 pm

2	[Rd] Installation error with R-devel

I have a local library with functions that interrogates an institution-specific web API, so is not of interest to anyone outside of Mayo. For some reason the R CMD INSTALL command fails. See below ...

Therneau, Terry M., Ph.D.
May 15, 2015 at 7:54 pm
May 15, 2015 at 8:12 pm

2	[Rd] Defining Constant variable in a package

Hi all, In my package, I define some constant. In the previous version of R, I just define then in "/data/constants.R" but it seems that it is no longer possible. Instead, I am asked to "define them ...

Christophe Genolini
May 15, 2015 at 9:32 am
May 15, 2015 at 2:52 pm

2	[Rd] Unexpected failure when calling new() with unnamed arg and

Hi, The man page for new() suggests that if 'a' is an object with slots "slot1" and "slot2" and C is a class that extends the class of 'a', then the 2 following calls should be equivalent: new("C", ...

Hervé Pagès
May 12, 2015 at 10:18 pm
May 13, 2015 at 10:13 pm

1	[Rd] returnValue()

In R devel rev.66393 (2014-08-15) it was possible to do this: trace(optim, exit = quote(str(returnValue()))) but returnValue() does not seem to be available any more. The above was useful to get the ...

Gabor Grothendieck
May 22, 2015 at 10:25 pm
May 23, 2015 at 12:31 am

1	[Rd] \alias{} --> rather \concept{} for conceptual "links" to help pages

I've opened a new thread, moving from R-help to R-devel .. Using \alias{} is not a very good thing here, since as you know they are *key*s that must remain unique if possible and they can be linked ...

Martin Maechler
May 18, 2015 at 12:14 pm
May 18, 2015 at 8:31 pm

1	[Rd] The function cummax() seems to have a bug.

Hi, The function cummax() seems to have a bug. [1] NA 0 The correct result of this case should be NA NA. The mistake in [ https://github.com/wch/r-source/blob/trunk/src/main/cum.c#L130-L136] may be ...

Dongcan Jiang
May 17, 2015 at 11:13 am
May 18, 2015 at 12:22 am

1	[Rd] Error when comparing two variables within a dataframe and print relevant observations

I'm trying to use a nested ifelse condition to compare two lines. Input: Code: Expected Output: Actual Output: Any idea what might be causing this problem? -- View this message in context ...

Bw1984
May 15, 2015 at 4:35 am
May 15, 2015 at 10:54 am

1	[Rd] LDFLAGS defined in R_MAKEVARS_USER file is ignored for R CMD SHLIB on Windows

Example input and output to reproduce this can be found at https://gist.github.com/jimhester/b7f05f50794c88e44b17. I tested this attempting to compile the [digest]( ...

Jim Hester
May 11, 2015 at 4:28 pm
May 13, 2015 at 9:38 pm

1	[Rd] PATCH: library(..., quietly=TRUE) still outputs "Loading required package: ..." (forgot to pass down 'quietly')

Calling library(..., quietly=TRUE) may still output: Loading required package: <other pkg in some cases, e.g. Loading required package: R.methodsS3 [...] I traced this to ...

Henrik Bengtsson
May 9, 2015 at 8:57 pm
May 11, 2015 at 3:53 pm

1	[Rd] Package check error: cannot extract package

Hi Compilation failed for package GUTS for r-oldrel Windows, saying cannot extract package: http://www.r-project.org/nosvn/R.check/r-oldrel-windows-ix86+x86_64/GUTS-00check.html 1. What does that ...

Sören Vogel
May 7, 2015 at 7:17 pm
May 7, 2015 at 9:11 pm

1	[Rd] Integrate R in perl6

Hi there, perl6 offers with the NativeCall package a great tool to implement other languages into perl scripts. This has already been done with python, C(++) and perl5. For my use cases - lots of ...

Florian Losch
May 5, 2015 at 5:38 pm
May 6, 2015 at 11:16 am

0	[Rd] Compatibility issue between lme4 and kml (operateur "[")

Hi all, There is a compatibility issue between the package 'lme4' and my package 'kml'. I define the "[" operator. It works just fine in my package (1). If I try to use the lme4 package, then it does ...

Cgenolin
May 26, 2015 at 9:31 am
May 26, 2015 at 9:31 am

0	[Rd] foreach hangs when using doMPI on Windows with Microsoft MPI

??I installed Microsoft MPI. Then installed the foreach and Rmpi packages. Then built doMPI from source. mpi.remote.exec works. foreach hangs with the main process and all worker processes idle. I ...

Teller, David
May 25, 2015 at 5:25 pm
May 25, 2015 at 5:25 pm

0	[Rd] The R Foundation announces new mailing list 'R-package-devel'

New Mailing list *** R-package-devel -- User R Packages Development *** At last week's monthly meeting, the R foundation has decided to create a new mailing list in order to help R package authors in ...

Martin Maechler
May 21, 2015 at 8:59 am
May 21, 2015 at 8:59 am

0	[Rd] Is the parallel package the right place for locking functionality?

Hello, Sometime ago I had to solve the problem of writing to common files from parallel R processes. For the synchronization, I created a small package ( ...

Ivan Popivanov
May 20, 2015 at 3:02 pm
May 20, 2015 at 3:02 pm

0	[Rd] install.packages() / update.packages() sometimes outputs to stdout and sometimes to stderr [and menu() & readline()]

I've noticed that install.packages() [https://svn.r-project.org/R/trunk/src/library/utils/R/packages.R] and update.packages() [https://svn.r-project.org/R/trunk/src/library/utils/R/packages2.R] ...

Henrik Bengtsson
May 18, 2015 at 12:13 am
May 18, 2015 at 12:13 am

0	[Rd] WISH: A more informative abor message than "aborting ..."

When R aborts ("core dumps"), it outputs: "aborting ..." This message is rather generic and can be hard to track back to R itself, i.e. it is not always clear whether it is R itself that aborted or ...

Henrik Bengtsson
May 13, 2015 at 12:17 am
May 13, 2015 at 12:17 am

0	[Rd] Windows environmental variables

Hi, I recently had some difficulty getting an embedded R session running on Windows, due to the way that R Sys.getenv works, which I would consider a bug. Even if you do not agree, then you may still ...

Simon Byrne
May 11, 2015 at 1:37 pm
May 11, 2015 at 1:37 pm

0	[Rd] MAX_NUM_DLLS too low ?

Hello, My problem is that I hit the hard-coded MAX_NUM_DLLS (100) limit of the number of loaded DLLs. I have a number of custom packages which interface and integrate a lot of CRAN and Bioconductor ...

Karl Forner
May 8, 2015 at 3:09 pm
May 8, 2015 at 3:09 pm

0	[Rd] capabilities("X11"): Force refresh from within R? (... and minor documentation issue)

Is there a way to refresh capabilities("X11") without restarting R such that it reflects the enabling/disabling of X11? BACKGROUND: If I launch R with X11 server disabled (e.g. ssh -X / ssh -Y to ...

Henrik Bengtsson
May 6, 2015 at 8:37 pm
May 6, 2015 at 8:37 pm

0	[Rd] R SVN server is down

It seems. FYI. Gabor [[alternative HTML version deleted]]

Gábor Csárdi
May 5, 2015 at 9:26 pm
May 5, 2015 at 9:26 pm

0	[Rd] Matlab Program to R

R rounds. Perhaps Matlab avoids doing so here. It's hard to say because your code is too long for anyone to read through. Maybe you could post a smaller reproducible example to pinpoint the result ...

Franknarf
May 4, 2015 at 9:02 pm
May 4, 2015 at 9:02 pm

group	r-devel @
categories	r
discussions	48
posts	242
users	72
website	r-project.org
irc	#r

summaries	on	Hotkey: s
users list	on	Hotkey: d
user style	avatars	Hotkey: a

R > r-devel > May 2015

Search Discussions

48 discussions - 242 posts

72 users for May 2015

Content

People

Support

Translate