r-devel@r-project.org discussions for October 2012

12	[Rd] concurrent requests (Rook, but I think the question is more general)

This question involves Rook, but I think the answer will be general enough that it pays to post here. At any rate, I don't know enough to know whether this is a Rook only issue or a general R issue ...

Richard D. Morey
Oct 24, 2012 at 6:13 pm
Oct 25, 2012 at 5:44 pm

10	[Rd] Rcmd_environ and R_LIBS_{USER,SITE}

Is there a fundamental reason why I cannot set either one of ## add local library path -- doesn't work either R_LIBS_USER="c:/opt/R-library" R_LIBS_SITE="c:/opt/R-library" in $R_HOME/etc/Rcmd_environ ...

Dirk Eddelbuettel
Oct 17, 2012 at 2:59 pm
Oct 20, 2012 at 3:52 pm

9	[Rd] suppress specific warnings?

Not desperately important, but nice to have and possibly of use to others, is the ability to suppress specific warnings rather than suppressing warnings indiscriminately. I often know of a specific ...

Ben Bolker
Oct 21, 2012 at 7:28 pm
Oct 26, 2012 at 12:20 pm

9	[Rd] How to build a list with missing values? What is missing, anyway?

This is tangentially related to Hadley's question. Suppose I'm building a function programmatically; I have assembled an expression for the body and I know the names of the arguments it wants to ...

Peter Meilstrup
Oct 4, 2012 at 2:37 am
Oct 7, 2012 at 7:54 pm

9	[Rd] Creating functions programmatically

Hi all, A function has three components: arguments, body and environment. Is there no base function that allows us to create a function from those three components? The best I could come up with is ...

Hadley Wickham
Oct 3, 2012 at 2:16 pm
Oct 3, 2012 at 10:55 pm

6	[Rd] Retrieving data from aspx pages

Hi. I'm trying to write an application to retrieve financial data (specially bonds data) from FINRA. The web page is served dynamically from an asp.net application ...

Jose ramon mazaira
Oct 29, 2012 at 8:11 pm
Oct 30, 2012 at 7:14 pm

6	[Rd] Fastest non-overlapping binning mean function out there?

Hi, I'm looking for a super-duper fast mean/sum binning implementation available in R, and before implementing z = binnedMeans(x y) in native code myself, does any one know of an existing ...

Henrik Bengtsson
Oct 3, 2012 at 12:19 am
Oct 4, 2012 at 8:45 pm

5	[Rd] R CMD SHLIB error bad value (core2) for -mtune= switch

Hi there, I'm having trouble to compile the R + C/C++ codes for this project from Yahoo folks on latent factor models: https://github.com/yahoo/Latent-Factor-Models#readme After downloading the ...

Smzyij
Oct 11, 2012 at 10:56 pm
Nov 15, 2013 at 11:36 am

5	[Rd] install.packages() fails if .libPaths() set

Reproducible example: dir.create("test") .libPaths("test") install.packages("relations", type = "source") Fails with: ... * installing *source* package ?relations? ... ... ** testing if installed ...

Hadley Wickham
Oct 29, 2012 at 10:35 pm
Oct 31, 2012 at 12:12 am

5	[Rd] Capturing environment associated with a promise

Hi all, It's possible to capture the expression associated with a promise (using substitute). Is there any way to capture the environment associated with a promise? Similarly, is there any way to ...

Hadley Wickham
Oct 8, 2012 at 1:22 pm
Oct 9, 2012 at 3:58 pm

5	[Rd] identical() fails to compare isS4(<S4 instance>) to TRUE

[1] FALSE R Under development (unstable) (2012-10-04 r60876) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 ...

Martin Morgan
Oct 4, 2012 at 8:57 pm
Oct 5, 2012 at 12:24 pm

4	[Rd] There is pmin and pmax each taking na.rm, how about psum?

Hi, Please consider the following : x = c(1,3,NA,5) y = c(2,NA,4,1) min(x,y,na.rm=TRUE) # ok [1] 1 max(x,y,na.rm=TRUE) # ok [1] 5 sum(x,y,na.rm=TRUE) # ok [1] 16 pmin(x,y,na.rm=TRUE) # ok [1] 1 3 4 1 ...

Matthew Dowle
Oct 30, 2012 at 11:03 am
Oct 30, 2012 at 2:40 pm

4	[Rd] malloc error in tab-completion: OS X

I've just built R-devel (r60889) from source on my Mac OS X 10.6.8 using gcc from Xcode and gfortran from Simon. I didn't use all the recommended configuration flags only ./configure && make Still, I ...

R. Michael Weylandt
Oct 7, 2012 at 3:34 pm
Oct 7, 2012 at 8:54 pm

3	[Rd] contr.sum() and contrast names

Hi! I would like to suggest to make it possible, in one way or another, to get meaningful contrast names when using contr.sum(). Currently, when using contr.treatment(), one gets factor levels as ...

Milan Bouchet-Valat
Oct 27, 2012 at 11:39 am
Oct 30, 2012 at 12:08 pm

3	[Rd] Spurious warning when calling data() ?

Hi, When calling data, a warning seems to have been left behind Warning message: In data(package = "stats", verbose = FALSE) : datasets have been moved from package 'stats' to package 'datasets' ...

Laurent Gautier
Oct 23, 2012 at 7:20 pm
Oct 23, 2012 at 8:08 pm

3	[Rd] Change in the RNG implementation?

Hi, Looks like the implementation of random number generation changed in R-devel with respect to R-2.15.1. With R-2.15.1: [1] 22217252 19661919 24099911 45779422 42043111 25774933 21778053 17098516 ...

Hervé Pagès
Oct 19, 2012 at 11:04 pm
Oct 22, 2012 at 6:02 am

3	[Rd] setting option in function

is it possible to set an option inside a function ((I want to set na.action = na.fail) and have the previous state restored if there is an error so that the function doesn't change the option behind ...

Charles Geyer
Oct 19, 2012 at 9:35 pm
Oct 19, 2012 at 11:18 pm

3	[Rd] Do not pass '...' to NextMethod() - it'll do it for you; missing documentation, a bug or just me?

Hi, although I've done S3 dispatching for more than a decade now, I think I managed to overlook/avoid the following pitfall when using NextMethod(): If you explicitly pass argument '...' to ...

Henrik Bengtsson
Oct 17, 2012 at 1:53 am
Oct 18, 2012 at 11:46 pm

3	[Rd] problem with OSX binary package build?

I noticed that my package BayesFactor (http://cran.r-project.org/web/packages/BayesFactor/index.html) is not available on Mac OS, and the note says to see the check log. The only issue in the check ...

Richard D. Morey
Oct 14, 2012 at 1:33 pm
Oct 15, 2012 at 12:10 pm

3	[Rd] How deep can/should lists be nested?

I started idly wondering how deeply lists could be nested, and couldn't find an explicit limit in the documentation. With this simple test a_list <- list() count <- 0 repeat { a_list[[1]] <- a_list ...

Richard Cotton
Oct 14, 2012 at 11:06 am
Oct 14, 2012 at 1:36 pm

3	[Rd] Problems with install.packages when Ncpus > 1

I have a Ubuntu Linux 12.04.1 machine running R 2.15.1. I'm trying to run tests building packages, so install.packages() is trying to install about about 1000 packages from source. I'm running into ...

Winston Chang
Oct 6, 2012 at 4:42 am
Oct 6, 2012 at 5:02 pm

2	[Rd] Class generator functions for reference classes

As of rev. 61035 in r-devel, setRefClass() now returns a generator function, as setClass() has done since 2.15.0. The convenient style is now: mEdit <- setRefClass("mEdit",......) xx <- mEdit(data = ...

John Chambers
Oct 27, 2012 at 9:07 pm
Oct 30, 2012 at 10:25 pm

2	[Rd] R 2.15.2 make check failure on 32-bit --with-blas="-lgoto2"

Is --with-blas="-lgoto2" a known problem (other than possibly not being the preferred choice)? I thought I had been testing RC with the same setup I regularly use, but I now see there was a slight ...

Paul Gilbert
Oct 26, 2012 at 3:37 pm
Oct 26, 2012 at 6:58 pm

2	[Rd] Getting ordered factor levels from C

I'm working on an R package in C and can't seem to get the same level information about a factor that the R console displays. If I define a factor as: lvls <- ...

Mark Lilback
Oct 24, 2012 at 6:14 pm
Oct 24, 2012 at 9:19 pm

2	[Rd] 12-bit functionality in tiff package

Hi, 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 ...

Joseph Barry
Oct 23, 2012 at 11:10 am
Oct 23, 2012 at 9:26 pm

2	[Rd] R-2.15.1 CMD CHECK output: "Call Sequence"

Hi guRus, i'm running R-2.15.1 and the R CMD CHECK output appears to have changed substantially, in that instead of pointing me to the offending functions or files, I get lots of 'call sequence' ...

Mark Cowley
Oct 20, 2012 at 11:01 am
Oct 21, 2012 at 10:17 am

2	[Rd] Mac and Windows binaries of rJava broken for R-devel?

Hi, Here is a problem we see with the Mac and Windows binaries of rJava (0.9-3) currently available on CRAN for R-devel (i.e. under bin/macosx/leopard/contrib/2.16/ and bin/windows/contrib/2.16/) ...

Hervé Pagès
Oct 19, 2012 at 5:52 am
Oct 19, 2012 at 10:30 pm

2	[Rd] R CMD check --force-biarch

I'm having problems getting R CMD check to work correctly on Windows 7 (64 bit) in a package that uses C code. What I want to do is to be able to pass the equivalent of the "--force-biarch" option to ...

Russell G. Almond
Oct 18, 2012 at 4:17 pm
Oct 19, 2012 at 2:58 pm

2	[Rd] Licensing concerns in porting S-Plus code to R libraries

I used S-Plus for many years, and developed lots of code for my research. When I switched to R a few years ago, I ported most of my S-Plus code over to R for my own use. Now that some of this code is ...

Chris Green
Oct 16, 2012 at 12:38 am
Oct 18, 2012 at 2:47 am

2	[Rd] Multithreaded code in .Call interface

Hi, I was wondering if it is safe to call R functions and/or R BLAS functions from within multithreaded C/C++ code(.Call interface)? It is not in case with MATLAB. I was experimenting using pthreads ...

Rob Anderson
Oct 13, 2012 at 7:09 am
Oct 15, 2012 at 11:02 pm

2	[Rd] as.data.frame.matrix() returns an invalid object

Hi, Two ways to create what should normally be the same data frame: [1] a b <0 rows (or 0-length row.names) [1] a b <0 rows (or 0-length row.names) unique() works as expected except that I get a ...

Hervé Pagès
Oct 11, 2012 at 6:22 am
Oct 13, 2012 at 7:10 am

2	[Rd] False positive note about ambiguous dispatch

Hi, In the situation below the note issued by the dispatch algo doesn't seem right: setClass("A", representation(stuff="complex")) setAs("ANY", "A", function(from) new("A", stuff=as.complex(from))) ...

Hervé Pagès
Oct 1, 2012 at 10:20 pm
Oct 2, 2012 at 9:24 pm

1	[Rd] R 2.15.2 still missing two files useful with the X11 icon patch

Congrats on getting 2.15.2 out on schedule. Debian builds have been uploaded. It is my understanding that Phil's patch for the X11 logo -- so promimently featured as the first item in the NEWS file ...

Dirk Eddelbuettel
Oct 26, 2012 at 2:07 pm
Oct 26, 2012 at 3:20 pm

1	[Rd] trivial typo in relist.Rd

in src/library/utils/man/relist.Rd, line 50: objects into a vector representation. \code{relist()}, it's methods and spurious apostrophe ... Ben Bolker

Ben Bolker
Oct 25, 2012 at 11:18 pm
Oct 25, 2012 at 11:51 pm

1	[Rd] Addition of plot=F argument to termplot

I have a suggested addition to termplot. We have a local mod that is used whenever none of the termplot options is quite right. It is used here almost daily for Cox models in order to put the y axis ...

Terry Therneau
Oct 19, 2012 at 5:15 pm
Oct 19, 2012 at 5:20 pm

1	[Rd] R 64bit for Windows on Windows 2012 server running Microsoft’s Hyper-V 2012?

Seeking confirmation/disconfirmation that R 64bit for Windows will run on Windows 2012 server running Microsoft?s Hyper-V 2012 server virtualization software and advice on building this on AMD 16 ...

Matthew Schall
Oct 18, 2012 at 11:24 pm
Oct 19, 2012 at 5:00 pm

1	[Rd] simplify2array edge case

Should simplify2array(higher=TRUE) treat 1 by 1 matrices differently than others? I expected a 3-dimensional array from all of the following 3 examples, not just the last 2. int [1, 1:3, 1:2] 11 12 ...

William Dunlap
Oct 11, 2012 at 6:59 pm
Oct 19, 2012 at 9:09 am

1	[Rd] S4 fails to initialize linear hierarchies with intermediate VIRTUAL classes

Initialization of this simple hierarchy A = setClass("A", representation(x="numeric")) setClass("B", contains=c("VIRTUAL", "A")) C = setClass("C", contains="B") fails (neat that setClass returns ...

Martin Morgan
Oct 18, 2012 at 1:31 pm
Oct 18, 2012 at 7:03 pm

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

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 ...

Xiaobo Gu
Oct 17, 2012 at 4:46 am
Oct 17, 2012 at 3:37 pm

1	[Rd] Effect of the R framework on ctype.c

Dear all, I'm facing a strange behavior in the the C code of a R package. This package, "rcqp", is a wrapper on an existing program that I did not write, "CWB". In this package, on a linux (ubuntu ...

Sylvain Loiseau
Oct 8, 2012 at 2:11 pm
Oct 8, 2012 at 3:17 pm

1	[Rd] Minor edit to R-ints doc will be needed for R-2.15.2: axis() no longer uses .Internal()

Hello, The second paragraph of Chapter 2: .Internal vs .Primitive of R-ints uses axis() as an example of a function that uses .Internal(). Here's the quote: As of R-2.15.2, though, this will no ...

Josh O'Brien
Oct 2, 2012 at 9:17 pm
Oct 3, 2012 at 6:33 am

0	[Rd] data.frame() args in transform()

Starting in SVN revision 47035 (which shows up in the R-2-9-0 line), transform.data.frame() started accepting arguments like 'row.names' and 'stringsAsFactors' to be passed through to the ...

Ken Williams
Oct 29, 2012 at 4:20 pm
Oct 29, 2012 at 4:20 pm

0	[Rd] Namespace Dependencies not required

Hi, I am trying to build an R package so reading the manual on CRAN. I could figure out that using imports to load functions in your namespace would be the best bet to use in the Description file ...

Mayank Bansal
Oct 26, 2012 at 11:01 am
Oct 26, 2012 at 11:01 am

0	[Rd] parallel::pvec FUN types differ when v is a list; code simplifications?

In pvec(list(1, 2), FUN, mc.cores=2) FUN sees integer() arguments whereas pvec(list(1, 2, 3), FUN, mc.cores=2) FUN sees list() arguments; the latter seems consistent with pvec's description. This ...

Martin Morgan
Oct 26, 2012 at 4:35 am
Oct 26, 2012 at 4:35 am

0	[Rd] Shouldn't the \usage section tell the truth?

Hi, The signature of mget() changed between R-2.15.1 and recent R-devel. In R-2.15.1: function (x, envir, mode = "any", ifnotfound = list(function(x) stop(paste0("value for '", x, "' not found"), ...

Hervé Pagès
Oct 24, 2012 at 8:12 pm
Oct 24, 2012 at 8:12 pm

0	[Rd] Typos/omissions/inconsistencies in man page for clusterApply

Hi, Here are the issues I found: Typos ----- (a) Found: It a parallel version of ?evalq?, "is" missing. (b) Found: 'parLapplyLB', 'parSapplyLB' are load-balancing versions, intended for use when ...

Hervé Pagès
Oct 23, 2012 at 10:33 pm
Oct 23, 2012 at 10:33 pm

0	[Rd] customize building package vignettes

Hi, I mentioned this at useR! 2012 but I guess the relevant R core members were not there (presumably Fritz, Duncan and Brian), so I'm making this wishlist again: Currently package vignettes have to ...

Yihui Xie
Oct 19, 2012 at 6:22 pm
Oct 19, 2012 at 6:22 pm

0	[Rd] --enable-R-shlib and external BLAS/LAPACK libraries

A couple of years ago (in 2008, using R 2.7.x, I believe) I noted that using the configure switch --enable-R-shlib when buildig R made configure ignore any specified external LAPACK library and use ...

Bjørn-Helge Mevik
Oct 19, 2012 at 7:53 am
Oct 19, 2012 at 7:53 am

0	[Rd] possible bug in print.bibentry

bsseq is a Bioconductor package. I think the main issue here is that CITATION has a volume field, like bibentry("Article", title = "{BSmooth: from whole genome bisulfite sequencing reads to ...

Kasper Daniel Hansen
Oct 16, 2012 at 8:27 pm
Oct 16, 2012 at 8:27 pm

0	[Rd] Translations in R 2.15.2-to-be

This year we have done a refresh of the translations mid-cycle: all the updates are now in R-patched for release in R 2.15.2 on the 26th. This includes several of the recommended packages. If you use ...

Prof Brian Ripley
Oct 15, 2012 at 8:29 am
Oct 15, 2012 at 8:29 am

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