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

19	[Rd] iterated lapply

Hi everybody, with the following code I generate a list of functions. Each function reflects a "condition". When I evaluate this list of functions by another lapply/sapply, I get an unexpected ...

Daniel Kaschek
Feb 23, 2015 at 8:57 pm
Mar 1, 2015 at 11:52 pm

8	[Rd] Native characterset is wrong for unicode builds for Windows

When I send some outlandish characters through enc2native (or format) in R 3.1.2 on Ubuntu trusty it works quite well: [1] "UTF-8" In Windows the result is different: [1] "latin1" And this is wrong ...

Maillist
Feb 26, 2015 at 8:09 pm
Feb 27, 2015 at 8:01 pm

7	[Rd] Different serialization of functions in interactive vs. batch mode

Hi, I posted this question to the regular help list, but it seems to be this is probably a question that is better addressed on r-devel. Sorry for the double posting. I am using hash-values to cache ...

Holger Hoefling
Feb 18, 2015 at 10:16 am
Feb 18, 2015 at 3:03 pm

7	[Rd] error code 1 from Lapack routine 'dsyevr'

The help page for eigen says Source: By default ?eigen? uses the LAPACK routines ?DSYEVR?, ?DGEEV?, ?ZHEEV? and ?ZGEEV? LAPACK is from <URL: http://www.netlib.org/lapack and its guide is listed in ...

Prof Brian Ripley
Feb 1, 2015 at 7:53 am
Feb 14, 2015 at 5:54 pm

6	[Rd] Proper way to define cbind, rbind for s4 classes in package

I've implemented the proposed changes in R-devel. Minimally tested, so please try it. It should delegate to r/cbind2 when there is at least one S4 argument and S3 dispatch fails (so you'll probably ...

Michael Lawrence
Feb 2, 2015 at 3:23 am
Feb 21, 2015 at 7:56 am

6	[Rd] Imports problem

I'm testing out a new version of coxme and R CMD check fails with "could not find function ranef" (or random.effects or fixef, or anything from nlme). The NAMESPACE file has the line below ...

Therneau, Terry M., Ph.D.
Feb 15, 2015 at 11:31 pm
Feb 16, 2015 at 2:04 pm

5	[Rd] Recycling memory with a small free list

I'm trying to improve the performance of the update loop within a logistic regression, and am struggling against the overhead of memory allocation and garbage collection. The main issue I'd like to ...

Nathan Kurz
Feb 17, 2015 at 8:51 pm
Feb 19, 2015 at 8:59 pm

4	[Rd] A good way to debug a c++ library embedded to R code

Dear all, I am using R CMD SHLIB to compile a c++ code into a library (.so) and dyn.load to load this library into a R code. I am facing some problems in the c++ code that I can not figure out how to ...

Charles Novaes de Santana
Feb 2, 2015 at 6:59 pm
Feb 2, 2015 at 8:17 pm

3	[Rd] alternatives to do.call() when namespace is attached but not loaded?

Dear R-devel I have a function in a package that essentially provides a wrapper for a group of functions in another Suggested package (it sets appropriate defaults for the context, transforms output, ...

Skye Bender-deMoll
Feb 24, 2015 at 6:29 pm
Feb 24, 2015 at 9:38 pm

3	[Rd] Color Coding in R-devel/NEWS

On this feed, which I think is the place we should monitor upcoming changes: http://developer.r-project.org/blosxom.cgi/R-devel/NEWS What is the significance of the green and pink highlighting? ...

Bryan Hanson
Feb 18, 2015 at 7:44 pm
Feb 18, 2015 at 8:23 pm

3	[Rd] xtabs and NA

Hi I haven't found a way to produce a tabulation from factor data with NA values using xtabs. Please find a minimal example below, it's also on R-pubs [1]. Tested with R 3.1.2 and R-devel r67720. It ...

Kirill Müller
Feb 9, 2015 at 1:52 pm
Feb 14, 2015 at 7:00 pm

3	[Rd] update.packages with ask = FALSE will sometimes ask about updates

Today while running update.packages(ask = FALSE), R stopped to ask me a question: There are binary versions available but the source versions are later: binary source needs_compilation KernSmooth ...

Richard Cotton
Feb 11, 2015 at 10:46 am
Feb 13, 2015 at 7:01 pm

3	[Rd] R CMD check: Uses the superseded package: ‘doSNOW’

Dear list, When I run an R CMD check --as-cran on my package (pROC) I get the following note: The fact that it uses the doSNOW package is correct as I have the following example in an .Rd file: The ...

Xavier Robin
Feb 9, 2015 at 10:08 pm
Feb 11, 2015 at 4:26 pm

3	[Rd] WISH: eval() to preserve the "visibility" (now value is always visible)

Would it be possible to have the value of eval() preserve the "visibility" of the value of the expression? "PROBLEM": # Invisible # Visible [1] 2 "TROUBLESHOOTING": $value [1] 1 $visible [1] FALSE ...

Henrik Bengtsson
Feb 7, 2015 at 5:40 pm
Feb 11, 2015 at 12:44 am

3	[Rd] Which function can change RNG state?

Today I struggled for hours to understand some unexpected package test results. It turned out that this is because package "parallel", buried deep in my dependencies, calls runif() during it's ...

Otoomet
Feb 8, 2015 at 3:52 am
Feb 9, 2015 at 5:03 am

3	[Rd] Testthat and global environments in R packages on CRAN

Hi! Im currently developing an R package to automatically give students feedback on programming assignments in R. I use the testthat package as an engine for the unit testing and do a wrapper to make ...

Måns Magnusson
Feb 8, 2015 at 1:22 pm
Feb 8, 2015 at 8:46 pm

3	[Rd] Rcurl crash in R-devel

Hello, I don't know if the problem originates from R-devel 3.2 or Rcurl itself. I post this message to the R-devel list and to the author of RCurl (duncan at r-project.org). R Under development ...

Marc Girondot
Feb 5, 2015 at 9:42 am
Feb 6, 2015 at 10:07 pm

3	[Rd] invoking R function in C++ in parallel

Nope. And you pretty much just explained why. You can - either work in something like OpenMP and run in multiple threads that remain /completely/ shielded from R, ie no R calls, and not even R data ...

Dirk Eddelbuettel
Feb 1, 2015 at 12:05 am
Feb 1, 2015 at 2:27 am

2	[Rd] static pdf vignette

Dear all, In my package I have a computational expensive Rnw file which can't pass R CMD check. Therefore I set evalúLSE in the Rnw file. But I would like to have the pdf vignette generated by the ...

Wang, Zhu
Feb 27, 2015 at 1:44 am
Feb 27, 2015 at 9:53 pm

2	[Rd] The Environment variables settings in bin/R, why do they ignore environment variables of the same name?

Hello, In installation/R/bin/R i notice 1. R_HOME_DIR is hard coded e.g. R_HOME_DIR=/usr/local/lib64/R 2. It ignores R_HOME_DIR echo "WARNING: ignoring environment value of R_HOME" 3. R_SHARE_DIR, ...

Saptarshi Guha
Feb 27, 2015 at 12:20 am
Feb 27, 2015 at 8:05 am

2	[Rd] Package functioning with R but not R-devel

Hi, I am using an R package which includes C++ code inside. The package is functioning well under latest official R version but not under R-devel. I know that the C++ part is not functioning properly ...

Sarah manderni
Feb 18, 2015 at 5:02 pm
Feb 18, 2015 at 5:53 pm

2	[Rd] Small typo in german translation

Dear developers, I found a small typo in the german translation for the aggregate() function: In the string "keine Zeile f?r die Aggragation" it should be spelled 'Aggregation' instead of ...

Rainer Hurling
Feb 16, 2015 at 8:29 am
Feb 16, 2015 at 4:55 pm

2	[Rd] Invalid read of size 8

Hi, I have a R program that call a C function. I define a vector of pointer as int nLC=3; int pownLC = nLC*nLC double *MatCovExtra[nT+1]; for(k=0;k<K+1;k++) { MatCovExtra[k] = ...

Niandra
Feb 5, 2015 at 12:41 pm
Feb 5, 2015 at 5:35 pm

2	[Rd] Output to "raw console" rather than stdout/stderr?

In R, there's readline(), which is great because you can prompt the user, e.g. ans <- readline("Would you like to install Pandoc? [y/N]: ") without having to worry the message is intercepted by ...

Henrik Bengtsson
Feb 1, 2015 at 7:13 pm
Feb 1, 2015 at 11:23 pm

1	[Rd] RStudio Calling C++ Visual Studio DLL

All, I'm a newbie to R and I am interested in seeing a simple example of calling a 3rd party Visual Studio generated DLL from RStudio. Does anyone have a simple example which also walks through the ...

Alex Restrepo
Feb 21, 2015 at 4:45 pm
Feb 21, 2015 at 5:44 pm

1	[Rd] requireNamespace etiquette

I'm trying to resolve a problem of Namespaces and probably have misunderstood something basic. In my quantreg package the function crq() has as its first argument a formula that typically contains ...

RKoenker
Feb 20, 2015 at 9:15 pm
Feb 21, 2015 at 5:53 am

1	[Rd] Can R for Windows be built outside of the top-level source directory?

The "R-admin" manual describes how to build R from outside of the top-level source directory on a *NIX machine (http://cran.r-project.org/doc/manuals/r-release/R-admin.html#Simple-compilation), but ...

Josh O'Brien
Feb 20, 2015 at 5:30 pm
Feb 20, 2015 at 5:37 pm

1	[Rd] save.image Doesn't Save Objects When Browsing

The documentation states that "save.image() is just a short-cut for save(list = ls(all = TRUE), file = ".RData")". However, if I do Browse[1] ls(all=TRUE) [1] "expression" "orderedFeatures" ...

Dario Strbenac
Feb 20, 2015 at 1:00 am
Feb 20, 2015 at 6:11 am

1	[Rd] How to unload R.dll successfully by FreeLibrary

hi, I've some C++ code which try to load R.dll and execute some R command, then unload R.dll, yet it seems fail to unload it, so second time to call the function hangs since it is trying to ...

暮如雪
Feb 5, 2015 at 8:09 am
Feb 9, 2015 at 3:56 am

1	[Rd] Documentation for reg.finalizer

Documentation says (emphasis mine): "Registers an R function to be called upon garbage collection of object OR (optionally) at the end of an R session." Should this say "and" and not "or"? THK -- ...

Tim Keitt
Feb 6, 2015 at 8:46 pm
Feb 6, 2015 at 11:22 pm

1	[Rd] BinaryFiles format

Hello, after many failed attempts to correctly write BinaryFiles file "R CMD check will warn about them unless they are listed (one filepath per line) in a file BinaryFiles at the top level of the ...

Teodor Krastev
Feb 2, 2015 at 11:40 am
Feb 2, 2015 at 1:17 pm

1	[Rd] libcurl support and curlGetHeaders warning message in R CMD check

Is this a recent version of R-devel? Which svn? The check is rather new and may have changed the days before you wrote. Best, Uwe Ligges

Uwe Ligges
Feb 1, 2015 at 8:26 am
Feb 2, 2015 at 4:28 am

0	[Rd] smoothScatter() and the KernSmooth package

Dear R-devel, my Bioconductor EDASeq package has a function MDPlot that uses the smoothScatter() function from the graphics package. When I test this package on travis-ci.org (R CMD check) I get the ...

Davide risso
Feb 18, 2015 at 8:19 pm
Feb 18, 2015 at 8:19 pm

0	[Rd] Release plans for R versions 3.1.3 and 3.2.0

The upcoming wrap-up release 3.1.3 is scheduled for March 9. The start of the next series, 3.2.0 is scheduled for April 16. Detailed schedules will be published on developer.r-project.org. Package ...

Peter Dalgaard
Feb 12, 2015 at 10:29 am
Feb 12, 2015 at 10:29 am

0	[Rd] CRAN check fails on Solaris, any hints why?

Dear all, I recently uploaded a new package Rlibeemd to CRAN (http://cran.r-project.org/web/packages/Rlibeemd/index.html, and in github: https://github.com/helske/Rlibeemd), and simple example in ...

Helske, Jouni
Feb 11, 2015 at 6:37 am
Feb 11, 2015 at 6:37 am

0	[Rd] How to deal with functions detected as apparent S3 methods

Dear list, I am trying to clear the following note that is generated by an R CMD check --as-cran on my package (pROC): However, these functions are (at least intended to be) actual functions, not ...

Xavier Robin
Feb 10, 2015 at 2:25 pm
Feb 10, 2015 at 2:25 pm

0	[Rd] as.factor -> S3 generic

Would it be possible to turn as.factor into an S3 generic? It seems to be one of the few coercion methods that aren't already generic. Hadley -- http://had.co.nz/

Hadley Wickham
Feb 6, 2015 at 6:43 pm
Feb 6, 2015 at 6:43 pm

0	[Rd] Seed in 'parallel' vignette

Hi, This is most likely only a minor technicality, but I saw the following: On page 6 of the 'parallel' vignette (http://stat.ethz.ch/R-manual/R-devel/library/parallel/doc/parallel.pdf), the ...

Marius Hofert
Feb 3, 2015 at 3:39 pm
Feb 3, 2015 at 3:39 pm

0	[Rd] R CMD check: Locale not set to C?

I just wanted to share my findings on this topic with you: Custom variables for checking and building can be set through "~/.R/check.Renviron" and " ~/.R/build.Renviron". But not the "LANGUAGE" ...

Tobias Setz
Feb 3, 2015 at 10:08 am
Feb 3, 2015 at 10:08 am

0	[Rd] updated R-cairo bridge, official R-3.1.*-mavericks.pkg crippled, snpMatrix 1.19.0.20

The windows replacement is R-library-grDevices-libs-winCairo_20150122.zip in http://sourceforge.net/projects/outmodedbonsai/files/R/ The cairo replacements are just two bundles, windows or OS X - ...

Hin-Tak Leung
Feb 2, 2015 at 2:58 am
Feb 2, 2015 at 2:58 am

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