r-devel@r-project.org discussions for July 2014

10	[Rd] [Wishlist] a 'PackageDevelopment' Task View

Hello everybody, as a young/unexperienced R package developer (only a few, mainly for personal use) i was thinking it could be very useful having a "meta" task view for all package-development ...

Luca Braglia
Jul 25, 2014 at 12:05 pm
Jul 29, 2014 at 8:19 pm

7	[Rd] R-3.1.1 - R CMD INSTALL problem

Hello I have recently upgraded R to the newest version. Unfortunately my old (fortran and C) R-package cannot be installed anymore (was built before R 3.0.0: please re-install it). I have tried R CMD ...

Eduardo M. A. M.Mendes
Jul 25, 2014 at 12:37 am
Jul 25, 2014 at 6:56 pm

6	[Rd] Licence for datasets in a R-package

Dear List, I am building a R package which collects ecological data about plant species from both remote (web) databases and locally stored rda files (datasets): these "local rda files" are derived ...

Gionata Bocci
Jul 21, 2014 at 4:17 pm
Jul 22, 2014 at 9:10 am

6	[Rd] Reducing RAM usage using UKSM

Greetings, We've a fairly large dataset (around 60GB) to be loaded and crunched in real time. The kind of data operations that will be performed on this data are simple read only aggregates after ...

Varadharajan Mukundan
Jul 15, 2014 at 3:55 pm
Jul 16, 2014 at 4:18 pm

5	[Rd] single quotes in strings, example block

Dear R-devel, In the example block of the documentation for a package, I need to use a single quote in a string: foo <- "Don't know" After building the package, it gets printed as: foo <- "Dont know" ...

Adrian Dușa
Jul 31, 2014 at 8:27 am
Jul 31, 2014 at 11:23 am

5	[Rd] how to list external dependencies (i.e., non-R packages)?

hi. i'm working on a package which only works if one (or both) of two libraries (Imlib2 and MagickWand) exist on the machine on which the package is compiled and executed. as currently written, the ...

Greg Minshall
Jul 13, 2014 at 7:13 pm
Jul 18, 2014 at 6:37 pm

5	[Rd] cummax / cummin for complex numbers

Dear all, in R 3.1.0, this is happening: Error in cummin(c(1 + (0+1i), 2 - (0+3i), 4 + (0+5i))) : 'cummax' not defined for complex numbers Error in cummax(c(1 + (0+1i), 2 - (0+3i), 4 + (0+5i))) ...

Michael Haupt
Jul 14, 2014 at 2:53 pm
Jul 14, 2014 at 4:17 pm

5	[Rd] reserving a package name

Dear All, While wanting to create a package using the name DDI (which stands for Data Documentation Initiative), I sent an email to the DDI Alliance and ask if they would mind, knowing they are now ...

Adrian Dușa
Jul 10, 2014 at 9:46 pm
Jul 11, 2014 at 2:18 pm

4	[Rd] request of information about creating DLL from R to be used in other languages/programs

Hello My question is the following. I have tried to find a similar subject in archives but not found (perhaps bad search!) and I tried R-help and I was advised that R-devel would perhaps better for ...

Ludovic Brossard
Jul 18, 2014 at 3:29 pm
Jul 19, 2014 at 7:09 am

4	[Rd] DESCRIPTION.in file causes R CMD check to fail?

hi. i'm building a package using autotools. to propagate the package version number from configure.ac to DESCRIPTION, i'm using a DESCRIPTION.in file. both of these files are "shar"'d below. i need ...

Greg Minshall
Jul 4, 2014 at 7:27 pm
Jul 5, 2014 at 5:00 pm

3	[Rd] Is the ISC license acceptable for CRAN?

Good afternoon. The ISC (Internet Software Consortium) license[1] is a permissive, open-source license that is considered "functionally equivalent"[2] to the Simplified (2-clause) BSD[3] and MIT[4] ...

Adler, Avraham
Jul 23, 2014 at 10:13 pm
Jul 24, 2014 at 1:38 pm

3	[Rd] Question: Publishing R/S objects with WebServices (SOAP/WSDL)

Hello, Can anyone tell me if there is a package which will allow me to write a package in R, then publish the package using WebServices? The idea is that I want to be able to pass a data set into R, ...

Kurt Schallitz
Jul 22, 2014 at 2:21 pm
Jul 22, 2014 at 8:13 pm

3	[Rd] create R package include Fortran source code.

Hello, all I am building a R package using Fortran source code. The Fortran code is a subroutine. I can use "R CMD SHLIB bar.f -o bar.o" to create the shared library. For the R package, I put the ...

Yiqun yang
Jul 21, 2014 at 4:10 pm
Jul 22, 2014 at 4:13 am

3	[Rd] grouping list of objects in the help system

Dear list, I've noticed for some packages the Index file in the help system has a single list of objects (arranged alphabetically), while for other packages this list is offered separately by ...

Adrian Dușa
Jul 11, 2014 at 4:11 pm
Jul 11, 2014 at 8:07 pm

3	[Rd] arguments to .Call(), .External should be read-only?

hi. if i'm reading correctly, "Writing R Extensions" appears to be inconsistent on the question of whether the arguments passed to a routine called via .Call() or .External() should considered ...

Greg Minshall
Jul 8, 2014 at 2:05 pm
Jul 9, 2014 at 7:31 pm

2	[Rd] listof

Dear R developers A question about the class 'listof', defined in package 'stats'. Other than its definition and use in the code for 'anova', we can't see that the class 'listof' is used for anything ...

Adrian Baddeley
Jul 30, 2014 at 3:20 am
Aug 3, 2014 at 9:15 pm

2	[Rd] Question on Code snippet semantics

I came across this code in library.R package <- as.character(substitute(package)) where package is the first argument to the "library" function. I've been racking my brains to understand why this is ...

Mick Jordan
Jul 21, 2014 at 3:07 pm
Jul 21, 2014 at 3:20 pm

2	[Rd] patch about mingwbuild 4.9.1

recently I used gcc 4.9.1 (http://sourceforge.net/projects/mingw-w64/files/Toolchains targetting Win64/Personal Builds/mingw-builds/)on windows to build R,but failed when link R.dll ,it report linker ...

Yu Gong
Jul 19, 2014 at 6:52 am
Jul 20, 2014 at 1:53 pm

2	[Rd] C-API: removing key-value pairs in an environment

Hi, I am trying to remove key-value pairs from an environments (using C). While adding seems straightforward with `Rf_defineVar()`, I cannot find a function to remove objects from a given ...

Laurent Gautier
Jul 16, 2014 at 2:24 am
Jul 16, 2014 at 3:18 am

2	[Rd] Namespaces and S4 Generics

I've installed R-devel R Under development (unstable) (2014-07-09 r66111) Platform: x86_64-apple-darwin13.1.0 (64-bit) and am trying to resolve some problems that I am seeing with my SparseM ...

Roger Koenker
Jul 11, 2014 at 6:27 pm
Jul 13, 2014 at 7:32 pm

2	[Rd] Depot for S3 to S4 generics (as in stats4)?

Dear developers, the implementation of S4 generics for existing S3 ones in the base package is concerned to be a threat to quick startup times [1]. But since S4 is promoted, and S3/S4 ...

Sven E. Templer
Jul 6, 2014 at 10:23 am
Jul 9, 2014 at 12:30 pm

2	[Rd] a question about optim.R and optim.c in R

Hi, I am learning R by reading R source code. Here is one question I have about the optim function in R. The context : In the optim.R, after all the prep steps, the main function call call is made ...

Zhiyuan Dong
Jul 7, 2014 at 8:34 pm
Jul 7, 2014 at 9:36 pm

2	[Rd] Rtools -- compiling C dll for 64-bit

I've seen that many people have had trouble using Rtools for a 64-bit compile of C functions. For some, a quick change in path statement seems to corrects the problem; for others, apparently not. For ...

Dalthorp, Daniel
Jul 3, 2014 at 11:53 pm
Jul 4, 2014 at 2:34 pm

2	[Rd] creating a package from a development source tree

hi. this is sort of a software methodology question. i'm working on developing a package (with C source code). developing it, i use autotools, git, make, and such like. as a result, there are random ...

Greg Minshall
Jul 1, 2014 at 3:26 pm
Jul 2, 2014 at 3:34 am

1	[Rd] [patch] Rscript off-by-one error in output

Rscript eats up the last argument when reporting the command it runs: $ Rscript --verbose "/tmp/test.R" one two three running '/usr/local/lib/R-devel/lib/R/bin/R --slave --no-restore ...

Scott Kostyshak
Jul 9, 2014 at 11:26 pm
Sep 20, 2014 at 12:53 pm

1	[Rd] capture.output on S4 slot

Hello, capture.output produces a different result if the S4 object was created with a constructor than if the body of the constructor is copied and pasted. setClass("TransformParams", representation( ...

Dario Strbenac
Jul 18, 2014 at 4:00 am
Aug 19, 2014 at 8:01 pm

1	[Rd] Parsing and deparsing of escaped unicode characters

In both R and JSON (and many other languages), unicode characters can be escaped using a backslash followed by a lowercase "u" and a 4 digit hex code. However when deparsing a character vector in R ...

Jeroen Ooms
Jul 28, 2014 at 8:47 am
Aug 3, 2014 at 7:30 pm

1	[Rd] Interface between R and a Open Load Flow tool (Gridlabd or OpenDSS)

Dear all, I want to know if it would be possible to have an interface between R and an electrical load flow tool. It would be interesting with Gridlab-D, an open-source tool that works in C++. The ...

Yamshid
Jul 30, 2014 at 8:42 am
Jul 31, 2014 at 9:41 pm

1	[Rd] Multiple -g flags in R CMD SHLIB

Does anybody know why two "-g" flags appear in the call to gcc in R CMD SHLIB Example: gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic *-g* -O2 -fstack-protector --param=ssp-buffer-size=4 ...

Alan Benson
Jul 25, 2014 at 2:30 pm
Jul 25, 2014 at 3:32 pm

1	[Rd] Problems with building a private R-package with Fortran source under Windows

Hi, I recently managed to port the slicot library (http://slicot.org/) to R. I created a new package, put the fortran libs into the src directory together with a Makevars file that include the line ...

Alexander Braumann
Jul 22, 2014 at 1:57 pm
Jul 22, 2014 at 6:42 pm

1	[Rd] Multiple versions of data in a package

Dear R-devel, I am writing for help on how I should include parallel sets of data in my package. Brief summary: I am new to using data within packages. I want a user to be able to specify one of two ...

Chris Wallace
Jul 21, 2014 at 1:58 pm
Jul 22, 2014 at 7:40 am

1	[Rd] proposed change of check message when VIgnetteBuilder package is not declared as a dependency

Hi, I notice in R-3.1.1, if a package specifies a VignetteBuilder (such as knitr) in its DESCRIPTION file, but does not also depend on the specified package (in either Depends, Imports, or Suggests), ...

Dan Tenenbaum
Jul 11, 2014 at 11:49 pm
Jul 14, 2014 at 3:07 pm

1	[Rd] Error in compactPDF/find_gs_cmd or documentation?

I am using tools::compactPDF for reducing the size of some pdf-files with GhostScript. I had some trouble in the beginning as the documentation seems not to match the usage of the function. For ...

Jon Olav Skoien
Jul 14, 2014 at 8:43 am
Jul 14, 2014 at 9:22 am

1	[Rd] a question about optim.R and optim.c in R

As you dig deeper you will find vmmin.c, cgmin.c and (I think) nmmin.c etc. Those were, as I understand, converted by p2c from my Pascal codes that you can find in the pascal library on netlib.org ...

Prof J C Nash (U30A)
Jul 8, 2014 at 12:41 pm
Jul 8, 2014 at 12:56 pm

1	[Rd] using R functions in a C loop

I would like to write a fast version of a function which contains slow loops that I cannot vectorize. I would like to rewrite it in C, but in the loops I need to call a few (two) R functions. Which ...

Enrico Bibbona
Jul 8, 2014 at 8:33 am
Jul 8, 2014 at 10:56 am

1	[Rd] Error when compiling R with openblas

Hi, I tried to compile R with openblas on a ubuntu 12.04 machine. I have to say that I normally use the package system and that I have no experience with compiling R. I did the following: ./configure ...

Alexander Braumann
Jul 1, 2014 at 10:00 am
Jul 1, 2014 at 1:33 pm

0	[Rd] making cuda-based R package CRAN friendly

Dear R-devel, We are planning a package that provides R interface to cuBLAS (CUDA accelerated BLAS). Due to CUDA's requirement, we are wondering if anyone can provide some guidance and suggestions on ...

Liaw, Andy
Jul 29, 2014 at 9:10 pm
Jul 29, 2014 at 9:10 pm

0	[Rd] combining generics/methods from multiple packages

I?m wondering if there is any way for me to create a generic function in a package that merges the generics and methods from two or more packages that each define a generic with the same name, but ...

Randall Pruim
Jul 29, 2014 at 3:56 am
Jul 29, 2014 at 3:56 am

0	[Rd] R-devel Digest, Vol 137, Issue 25

Finding and not unnecessarily duplicating existing functionality is important also from a user perspective. Negative binomial regression provides a somewhat extreme example of existing overlap ...

John Maindonald
Jul 28, 2014 at 11:08 am
Jul 28, 2014 at 11:08 am

0	[Rd] Removed 'extern' on R_running_as_main_program in Rinterface.h -- intentional?

Hi R-devel, In this commit: https://github.com/wch/r-source/commit/c67a107dd7b0f074cec9359b8e2ca07c6243283c R_running_as_main_program was moved from Rmain.c to Rinterface.h, and lost its 'extern' ...

Kevin Ushey
Jul 22, 2014 at 10:27 pm
Jul 22, 2014 at 10:27 pm

0	[Rd] Byte Order Mark in ?connections

Hi, There seems to be a couple of typos in the documentation of connections about the Byte Order Mark, e.g. 0xFFFE should be 0xFEFF, and c(0xef, 0xbb, 0xff) should be c(0xef, 0xbb, 0xbf) ...

Yihui Xie
Jul 22, 2014 at 8:40 pm
Jul 22, 2014 at 8:40 pm

0	[Rd] Displaying database records returned from postgresql to R through Java

Hi All, I have a R script which returns a set of records from the postgresql to the Java program and I want to print those records in Java.My script is like this: library(RPostgreSQL) fnct1 <- ...

Jason Donnald
Jul 21, 2014 at 3:08 am
Jul 21, 2014 at 3:08 am

0	[Rd] Unlisting Nested Lists of Factors

Hello, I rediscovered an old bug https://bugs.r-project.org/bugzilla/show_bug.cgi?id572 It was reported six years ago, but hasn't been accepted or rejected. Is there a plan to address it soon ? R ...

Dario Strbenac
Jul 21, 2014 at 3:00 am
Jul 21, 2014 at 3:00 am

0	[Rd] How to access a return value of a function that is being traced

Is there any way of accessing return value of a function that is being traced by a function specified as exit param to trace? That sounds hard to understand, but I was not able to simplify the ...

Roman Tsegelskyi
Jul 16, 2014 at 2:46 am
Jul 16, 2014 at 2:46 am

0	[Rd] checking whether 'INDEX' is up-to-date ... NO

Dear List, does the warning "checking whether 'INDEX' is up-to-date ... NO" while building a package appear due to missing definitions of functions that are in the NAMESPACE but not INDEX file? Do ...

Sven E. Templer
Jul 11, 2014 at 8:42 am
Jul 11, 2014 at 8:42 am

0	[Rd] useDynLib

I would like to be able to load two versions of a package at once and to do that was thinking of giving each version a different package name in the DESCRIPTION file and the building and installing ...

Gabor Grothendieck
Jul 6, 2014 at 12:36 pm
Jul 6, 2014 at 12:36 pm

0	[Rd] request for "minor" fix to src/library/tools/QC.r

hi. i was hoping to automatically set the Version: number in my package description file (image2k-package.Rd) in the man directory by using a .in file in the same directory. "R CMD build" excludes ...

Greg Minshall
Jul 6, 2014 at 11:34 am
Jul 6, 2014 at 11:34 am

0	[Rd] USE_CXX1X, Snow Leopard R binaries + Mavericks

Hi R-devel, I'm noticing the following behaviour: writeLines("#include <Rcpp.h ", file = "test.cpp") Rcpp::sourceCpp("~/test.cpp") ## succeeds at trivial compile Sys.setenv("USE_CXX1X" = "yes") ...

Kevin Ushey
Jul 1, 2014 at 6:15 pm
Jul 1, 2014 at 6:15 pm

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