r-devel@r-project.org discussions for December 2011

17	[Rd] bug in sum() on integer vector

Hi, x <- c(rep(1800000003L, 10000000), -rep(1200000002L, 15000000)) This is correct: [1] 0 This is not: [1] 4996000 Returning NA (with a warning) would also be acceptable for the latter. That would ...

Hervé Pagès
Dec 9, 2011 at 6:40 pm
Dec 15, 2011 at 11:32 pm

13	[Rd] bug in rank(), order(), is.unsorted() on character vector

Hi, This looks OK: [1] 1 2 3 But this does not: [1] 2 1 3 Cheers, H. R version 2.14.0 (2011-10-31) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C [3] ...

Hervé Pagès
Dec 7, 2011 at 9:41 am
Dec 8, 2011 at 6:26 pm

11	[Rd] problems with iconv

I'm at wit's ends here and need some help. I've downloaded and compiled iconv versions 1.13 and 1.14 - libiconv.so.2.5.0 and libiconv.so.2.5.1 and copied the iconv all over, replacing the native ...

RogerP
Dec 13, 2011 at 5:12 pm
Dec 15, 2011 at 1:56 pm

8	[Rd] S4 NAMESPACE method imports and exports do not include (promoted?) generics

In [1] "R Under development (unstable) (2011-12-15 r57901)" section 1.6.6 of 'Writing R Extensions' says Note that exporting methods on a generic in the namespace will also export the generic, and ...

Martin Morgan
Dec 15, 2011 at 11:34 pm
Dec 24, 2011 at 5:29 pm

6	[Rd] latest Rtools missing "inconsolita.sty"

Hello: What do you suggest I do to overcome "LaTeX Error: File 'inconsolata.sty' not found", which I got running "R CMD check" on a package using Rtools I downloaded yesterday? I found a similar ...

Spencer Graves
Dec 17, 2011 at 6:43 am
Dec 24, 2011 at 3:00 am

6	[Rd] Debugging namespace problems

Hi all, I frequently find that I've failed to export something in my NAMESPACE and hence my package doesn't work when it's imported into another package. Does anyone have suggestion for debugging ...

Hadley Wickham
Dec 23, 2011 at 7:50 pm
Dec 23, 2011 at 10:56 pm

6	[Rd] Undocumented functions

Hi! I am building a package. This package will not submitted to CRAN. I write the help files for the most important functions of my package, I cannot write it for all functions. This may sounds ...

Nicola Sturaro Sommacal
Dec 15, 2011 at 12:01 pm
Dec 16, 2011 at 11:11 am

5	[Rd] CRAN link broken

The packages link on CRAN (http://cran.at.r-project.org/) seems to be broken. Paul Object not found! The requested URL was not found on this server. The link on the referring ...

Paul Gilbert
Dec 30, 2011 at 9:32 pm
Jan 2, 2012 at 2:57 pm

5	[Rd] secure password token management method in R

hi, r developers, I am now working on a R function/package to handling online request with username and token/password. For security reasons, it's not so safe to store the username & token in ...

Ni Wang
Dec 14, 2011 at 9:54 pm
Dec 18, 2011 at 9:34 pm

4	[Rd] Saving nothing with save()

Scenario: Here I am working away in R. I've got results that prove global warming is anthropogenic and also the solution for producing limitless carbon-neutral energy from nuclear fusion. Its been a ...

Barry Rowlingson
Dec 18, 2011 at 1:32 am
Dec 22, 2011 at 9:29 am

4	[Rd] error starting R-devel with --arch ppc -- "an unusual circumstance has arisen"

When I try and start R-devel as follows: R --vanilla --arch ppc I see this, over and over again, ^C does not interrupt it and I have to close the terminal window: not a BUILTIN function In addition ...

Dan Tenenbaum
Dec 15, 2011 at 9:56 pm
Dec 20, 2011 at 4:44 am

4	[Rd] R package BibTex entries: looking for a more general solution

Back in 2010 I raised this issue, and there was some discussion, https://stat.ethz.ch/pipermail/r-devel/2010-November/058987.html The goal, then, as now is to have a way to produce a bibtex-clean ...

Michael Friendly
Dec 16, 2011 at 1:46 pm
Dec 19, 2011 at 2:09 pm

4	[Rd] Problems in building a DLL in 64-bit Windows

I am trying to build a C language DLL and it works well with i386 but when I compile with it substituted by x64, like the FAQ page says, the result is an error message ...

Ruipbarradas
Dec 12, 2011 at 1:12 pm
Dec 12, 2011 at 8:28 pm

3	[Rd] Subsetting a data frame vs. subsetting the columns

Hi all, There seems to be rather a large speed disparity in subsetting when working with a whole data frame vs. working with just columns individually: df <- as.data.frame(replicate(10, runif(1e5))) ...

Hadley Wickham
Dec 28, 2011 at 3:37 pm
Dec 28, 2011 at 7:48 pm

3	[Rd] Initializing a large data structure to be accessed strictly within a shared C library

Dear R-devel members, The question: Is it possible to initialize and later free a large data structure strictly within a shared C library, to be used by a function in the C library that I'll call ...

James Muller
Dec 27, 2011 at 10:58 pm
Dec 28, 2011 at 1:36 am

3	[Rd] Issues with building package with C src on windows [R CMD INSTALL ignoring makefile]

I've written a rather complex package that requires overriding the default compilation behavior for the C code component. In the src dir I have a Makefile that is used correctly on OSX and Linux ...

Jonathan Shore
Dec 19, 2011 at 3:30 pm
Dec 19, 2011 at 3:43 pm

3	[Rd] R CMD check fails to warn about undocumented classes and methods

In [1] "R Under development (unstable) (2011-12-15 r57901)" PkgA promotes 'unique' to a generic and exports that DESCRIPTION: Imports: methods R/f.R: setGeneric("unique") NAMESPACE: export(unique) ...

Martin Morgan
Dec 15, 2011 at 11:40 pm
Dec 16, 2011 at 2:05 pm

3	[Rd] RcppArmadillo compilation error: R CMD SHLIB returns status 1

Dear all, running the example by D. Eddebuettel (http://dirk.eddelbuettel.com/blog/2011/04/23/) I get an error message. Specifically, the R code I was taking from the above example is ### BEGIN ...

Paul Viefers
Dec 5, 2011 at 6:22 pm
Dec 8, 2011 at 7:36 am

2	[Rd] Cholesky update/downdate

Dear R-devel members, I am looking for a fast Cholesky update/downdate. The matrix A being symmetric positive definite (n, n) and factorized as A = L %*% t(L), the goal is to factor the new matrix A ...

Yves Deville
Dec 29, 2011 at 2:05 pm
Dec 30, 2011 at 10:47 am

2	[Rd] Crashing R with readline()

I get the following with R v2.14.1 patched on Windows 7: % Rterm --vanilla --silent R version 2.14.1 Patched (2011-12-26 r58001) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] ...

Henrik Bengtsson
Dec 29, 2011 at 2:49 pm
Dec 29, 2011 at 10:50 pm

2	[Rd] rgeos on Linux requires GEOS 3.2.3, not 3.3.1

Some notes on installing rgeos in R 2.14.0 on a Linux Mint 11 (x86_64-pc-linux-gnu) machine 1. rgeos 0.1-15 will not run with GEOS 3.2.0-1, which is the version currently available on Synaptic ...

Dan Bebber
Dec 20, 2011 at 11:49 am
Dec 21, 2011 at 8:56 pm

2	[Rd] Possible bug in edit(x) for editing matrices [tested on a Mac]

Hi, it seems there's a possible bug in edit(x) if x is a matrix filled with NA only. To reproduce please do the following: a <- matrix() edit(a) change e.g. the cell value to 1 and close the ...

Hans-Jörg Bibiko
Dec 19, 2011 at 9:48 am
Dec 19, 2011 at 11:43 am

2	[Rd] last message -- I've answered my own question

Yes, it was glaring and obvious: I had the label "description" a second time when I really meant "details". Still, I had to delete sections of the file 1 by 1 until it slapped me in the face. Sorry ...

Terry Therneau
Dec 16, 2011 at 10:29 pm
Dec 17, 2011 at 10:02 pm

2	[Rd] Rcpp too good to be true?

Hello all, I've been working on a package to do various things related to the Conway-Maxwell-Poisson distribution and wanted to be able to make fast random draws from the distribution. My R code was ...

Jeffrey Pollock
Dec 13, 2011 at 11:48 pm
Dec 14, 2011 at 1:07 am

2	[Rd] warning for inefficiently compressed datasets

Hi, Recently added to doc/NEWS.Rd: 'R CMD check' now gives a warning rather than a note if it finds inefficiently compressed datasets. With 'bzip2' and 'xz' compression having been available since R ...

Hervé Pagès
Dec 6, 2011 at 10:28 pm
Dec 14, 2011 at 12:09 am

2	[Rd] Unable to collate and parse R files with R CMD check

Hi all, I'm trying to build a package on Windows 7 (64 bit) and although R cmd build worked fine and I got pkg.tar.gz with no errors, but when I tried doing R CMD check everything turns out ok except ...

Sumukh Sathnur
Dec 6, 2011 at 7:05 pm
Dec 8, 2011 at 8:33 pm

2	[Rd] unserialize and eager execution

Hi, While debugging a network server I'm developing I noticed something unusual - call to unserialize() resulted in an error about loading a namespace. I was a bit taken back by this - why should ...

Tyler Pirtle
Dec 6, 2011 at 5:29 am
Dec 6, 2011 at 7:00 am

2	[Rd] Vignette using parallel's makeCluster function has trouble building on Windows 7

Hi, all-- I've been working on a doParallel package to provide a foreach parallel backend for the new parallel package, but I am having trouble building the vignette. On my system, if I use the ...

Rich Calaway
Dec 6, 2011 at 12:19 am
Dec 6, 2011 at 1:10 am

2	[Rd] class extension and documentation

I've added a "backsolve" method to the bdsmatrix library. Per the Extending manual section 7.1 I've also added the following 3 lines along with my setMethod definitions for 2 classes. backsolve <- ...

Terry Therneau
Dec 5, 2011 at 5:11 pm
Dec 5, 2011 at 8:34 pm

2	[Rd] HDF5 compound data types and h5r/hdf5 R packages

Hi there, I have a Java process that writes HDF5 files with the following approximate structure: group "xxx" { group "yyy" { dataset {} dataset {} } group "zzz" { dataset {} dataset {} } } where ...

Jeremy Reeve
Dec 1, 2011 at 6:22 am
Dec 2, 2011 at 7:48 am

1	[Rd] Reference class finalize() fails with 'attempt to apply non-function'

This bug appears intermittently in R CMD check when reference classes have finalize methods. The problem is that garbage collection can be run after the methods package is no longer available. It ...

Martin Morgan
Dec 8, 2011 at 10:52 pm
Dec 29, 2011 at 7:35 pm

1	[Rd] external pointers

I have an external pointer object that I'd like to pass from my R code to some C code. Per Section 5.13 of "Writing R Extensions", I've noted that "external pointers should only be used as part of an ...

Patrick Leyshock
Dec 28, 2011 at 5:07 am
Dec 28, 2011 at 3:09 pm

1	[Rd] adding packages R 2.14.0

Well, I was able to build R 2.14.0 on my Solaris x86 machine, with a lot of work and some help. Thanks! At first the update.packages() would not work because some of the .so files that came with R ...

RogerP
Dec 22, 2011 at 6:13 pm
Dec 23, 2011 at 1:38 pm

1	[Rd] attach 'name' argument ignored with a file?

Dear experRts, I have the feeling that the 'name' argument to the attach function is ignored when 'what' is a file name. Here is an example: save(letters, file="letters.RData") letters.env <- ...

Xavier Robin
Dec 22, 2011 at 1:39 pm
Dec 23, 2011 at 11:22 am

1	[Rd] Why is the 64bit Windows version of package RSVGTipsDevice not available on CRAN?

On CRAN, the package RSVGTipsDevice is only installed for 32bit Windows, and is not available as a 64bit package for Windows. The file linked to in the package check summary on CRAN says "NB: this ...

Tony Plate
Dec 20, 2011 at 2:59 am
Dec 20, 2011 at 2:17 pm

1	[Rd] Speed issue when writing to RGui console from tcl/tk GUI

It seems that there are speed issues when printing to the R console from a tcl/tk GUI. Here are functions to write a lot of output, and to display how long it takes. printsalot <- function(n) { for(i ...

Richard Cotton
Dec 19, 2011 at 10:34 am
Dec 20, 2011 at 12:54 pm

1	[Rd] makeNamespace and rdyncall

Dear R Core Team, I have a question related to the programming interface for namespace object creation at run-time. This is something that I need in the rdyncall package: During the dynamic linkage ...

Daniel Adler
Dec 16, 2011 at 12:36 pm
Dec 16, 2011 at 1:11 pm

1	[Rd] DESCRIPTION Suggests entry help

How should the Suggests entry be written in this case? Have package that supports parallel processing available for multiple R versions. Original package DESCRIPTION Suggests entry only listed ...

Roebuck,Paul L
Dec 15, 2011 at 6:53 pm
Dec 15, 2011 at 9:08 pm

1	[Rd] termplot & predict.lm. some details about calculating predicted values with "other variables set at the mean"

I'm making some functions to illustrate regressions and I have been staring at termplot and predict.lm and residuals.lm to see how this is done. I've wondered who wrote predict.lm originally, because ...

Paul Johnson
Dec 14, 2011 at 6:30 am
Dec 14, 2011 at 6:39 am

1	[Rd] Detecting typo in function argument

With some chagrin after spending a couple of hours trying to debug a script, I realized I had typed in something like ans<-optimx(start, myfn, mygr, lower<-lo, upper=up) that is, the "<-" rather than ...

John C Nash
Dec 12, 2011 at 9:10 pm
Dec 12, 2011 at 9:24 pm

1	[Rd] Graphics device hook to manipulate plotmath

Is there a hook that allows a graphics device to apply transformations to plotmath expressions *before* they are rendered? If there isn't one yet, would it be feasible to add one? The motivation for ...

Zack Weinberg
Dec 6, 2011 at 8:34 pm
Dec 11, 2011 at 9:17 pm

1	[Rd] Possible bug in 'new()' for Reference Classes

Dear list, I think I stumbled across a little bug with respect to the standard initialization routine for Reference Classes. It seems that a field 'self' is treated as if it's name would be '.self' ...

Janko Thyson
Dec 7, 2011 at 3:36 pm
Dec 7, 2011 at 11:19 pm

1	[Rd] 1.6x speedup for requal() function (in R/src/main/unique.c)

Hi, FWIW: /* Taken from R/src/main/unique.c */ static int requal(SEXP x, int i, SEXP y, int j) { if (i < 0 || j < 0) return 0; if (!ISNAN(REAL(x)[i]) && !ISNAN(REAL(y)[j])) return (REAL(x)[i] == ...

Hervé Pagès
Dec 2, 2011 at 1:40 am
Dec 2, 2011 at 3:13 am

1	[Rd] Standardizing included packages

It seems that R is mostly distributed with the tcltk package but not always. Is there some reason for this inconsistency? It would be nice if one could count on those packages that are distributed on ...

Gabor Grothendieck
Dec 1, 2011 at 12:56 am
Dec 1, 2011 at 7:42 am

0	[Rd] Chi-squared test p-value based on simulation.

Prompted by a (fairly!) recent question from Michael Fuller, I got to thinking about the issue of goodness-of-fit testing via chisq.test() using p-values obtained via simulation. I believe that such ...

Rolf Turner
Dec 23, 2011 at 6:16 am
Dec 23, 2011 at 6:16 am

0	[Rd] Small inconsistency in help page unique - duplicated doesn't return indices.

I read this in the help page of unique in 2.14.0, but I reckon it's not changed yet in 2.14.1 Under the section 'see also' is mentioned : duplicated which gives the indices of duplicated elements ...

Joris Meys
Dec 22, 2011 at 3:59 pm
Dec 22, 2011 at 3:59 pm

0	[Rd] Rd error message

I get the following error from one of my Rd files in R CMD check (R 2-14.0) * checking Rd files ... WARNING Error in switch(attr(block, "Rd_tag"), TEXT = if (!grepl("^[[:space:]]* $", : EXPR must be ...

Terry Therneau
Dec 16, 2011 at 10:12 pm
Dec 16, 2011 at 10:12 pm

0	[Rd] paste0 bug in install.packages() - leopard installer?

Hello, I get the following: trying URL 'http://cran.fhcrc.org/src/contrib/abind_1.4-0.tar.gz' Content type 'application/x-gzip' length 19642 bytes (19 Kb) opened URL ...

Dan Tenenbaum
Dec 13, 2011 at 9:58 pm
Dec 13, 2011 at 9:58 pm

0	[Rd] Proper use of suppressPackageStartupMessages in package building

All, When building a package, how can I suppress startup messages of package imports? I know you can use suppressPackageStartupMessages() around library or require when loading a package, but can I ...

Scott Chamberlain
Dec 12, 2011 at 3:23 pm
Dec 12, 2011 at 3:23 pm

0	[Rd] clusterSetRNGStream() question

In a vanilla R 2.14.0 GUI session (on Windows XP SP3): Is it intentional that clusterSetRNGStream() changes the RNG kind in the master process? The code of clusterSetRNGStream() suggests that it is ...

J. R. M. Hosking
Dec 10, 2011 at 9:00 pm
Dec 10, 2011 at 9:00 pm

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