r-devel@r-project.org discussions for April 2013

36	[Rd] R 3.0, Rtools3.0,l Windows7 64-bit, and permission agony

Having finally found some free time, I was going to use it to update a bunch of R packages from 2.15 to 3.0. I am running Windows 7, 64-bit professional. This is on a brand-new laptop using vanilla ...

Kevin Coombes
Apr 19, 2013 at 9:37 pm
Apr 29, 2013 at 1:08 pm

20	[Rd] Patch proposal for R style consistency (concerning deparse.c)

Hello, everybody. I recognize I'm asking you to deal with a not-very-important problem. But its important to me :) I've noticed a little inconsistency in the print.function() output. I traced the ...

Paul Johnson
Apr 18, 2013 at 3:39 am
May 5, 2013 at 5:37 pm

10	[Rd] how to control the environment of a formula

Dear List I have experienced that objects generated with one of my packages used a lot of space when saved on disc (object.size did not show this!). some debugging revealed that formula and call ...

Thomas Alexander Gerds
Apr 18, 2013 at 5:09 am
Apr 21, 2013 at 6:18 am

8	[Rd] as.name and namespaces

'as.name' doesn't recognize a name with its namespace extension as a name: `stats:::lm` Is there a reason why it shouldn't? Pat -- Patrick Burns pburns at pburns.seanet.com twitter: @burnsstat ...

Patrick Burns
Apr 23, 2013 at 5:23 pm
Apr 24, 2013 at 4:13 pm

7	[Rd] Linux distribution with gcc 4.8 and AddressSanitizer ?

Dear R developers, I've got an information from Prof. Ripley regarding a bug found with AdressSanitizer in one of our packages. It is now fixed, thank you for this information. Now, I would like to ...

Thomas Petzoldt
Apr 18, 2013 at 3:38 pm
Apr 20, 2013 at 5:14 pm

7	[Rd] question re: error message --- package error: "functionName" not resolved from current namespace

hello everyone we are developing a package that has worked up until R3.0 which we just tested. the issue is as above .... when we call a function that works in R 2.15.2 from R 3.0 we get an error ...

Brian avants
Apr 10, 2013 at 5:53 pm
Apr 11, 2013 at 8:34 am

6	[Rd] Verbose output from R CMD check

I've been developing a package called foobar for a couple of years now. It has evolved through various versions, but has always contained compiled C code. Recently, R CMD check has started generating ...

Dpleydell
Apr 23, 2013 at 2:51 pm
Apr 27, 2013 at 1:20 pm

6	[Rd] multiple issues with is.unsorted()

Hi, In the man page for is.unsorted(): Value: A length-one logical value. All objects of length 0 or 1 are sorted: the result will be ?NA? for objects of length 2 or more except for atomic vectors ...

Hervé Pagès
Apr 24, 2013 at 6:09 am
Apr 24, 2013 at 7:06 pm

6	[Rd] vignettes: problems with PDF compaction

[Env: OS: Win Xp; R 2.15.2; IDE: eclipse/StatET] Each time I update my heplots package, I get warnings from R CMD check on R-Forge, * checking sizes of PDF files under ?inst/doc? ... WARNING ...

Michael Friendly
Apr 21, 2013 at 5:28 pm
Apr 23, 2013 at 1:50 pm

6	[Rd] R package with Java source code

Dear All, Are there any plans around that "R CMD INSTALL some_package_containing_java_source code" supports Java source code compiling in future versions of R similar to compiling C/C++ and/or ...

Adrian Trapletti
Apr 16, 2013 at 11:20 am
Apr 16, 2013 at 3:49 pm

6	[Rd] package file permissions problem R 3.0.0/Windows OS

Dear list members, I'm experiencing a file permissions problem with a package built under Windows with R 3.0.0. I've encountered the problem on two Windows computers, one running Windows 7 and the ...

John Fox
Apr 14, 2013 at 9:17 pm
Apr 16, 2013 at 1:20 pm

5	[Rd] windows compile R from source, where do I put the Tcl directory?

Hi, I am trying to compile R from source on Windows. I am following the instructions here 3.1 Building from source 3 Installing R under Windows ...

Andre Mikulec
Apr 10, 2013 at 11:27 pm
Apr 15, 2013 at 5:55 pm

5	[Rd] La_svd compiler error

Dear All, I have been trying to compile a package for windows that we have written. Since R version 3.0.0 the package doesn't compile any more. (On Linux the package compiles without errors). The ...

Antczak, Philipp
Apr 11, 2013 at 11:41 am
Apr 12, 2013 at 4:33 pm

5	[Rd] savePlot() under Windows

Hi, A Windows user asked me a question and I believe this is a bug of R 3.0.0 under Windows: Error in .External(C_savePlot, device, filename, type, restoreConsole) : Incorrect number of arguments ...

Yihui Xie
Apr 8, 2013 at 10:05 pm
Apr 11, 2013 at 9:41 am

5	[Rd] R 3.0.0: wrong MD5 checksums for Windows?

Hello dear R-devel, When installing R 3.0.0 on Windows 7, and then running: require(tools) checkMD5sums(dir=R.home()) I get the following massage: files â€˜etc/Rconsoleâ€™, â€˜etc/Rprofile.siteâ€™ ...

Tal Galili
Apr 4, 2013 at 6:38 pm
Apr 4, 2013 at 8:14 pm

4	[Rd] "Failed to locate the 'texi2pdf' output file"

Hi, Every day a few Bioconductor packages (different ones each day) fail to build, on Windows only, with an error like this: D:\biocbld\bbs-2.13-bioc\meat D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD ...

Dan Tenenbaum
Apr 12, 2013 at 9:34 pm
Apr 25, 2013 at 5:56 pm

4	[Rd] Rebuild package on R 3.0.0 without source code?

R-developers, I have a binary R package built using R 2.14.1 that I would like to run on R 3.0.0. Unfortunately, the original source code is unavailable, so I cannot rebuild the package as R 3.0.0 ...

McGehee, Robert
Apr 18, 2013 at 3:07 pm
Apr 18, 2013 at 5:42 pm

4	[Rd] missing exported methods when compiling vignettes in R 3.0.0 RC

A new problem has cropped up with compiling vignettes for my package BayesFactor. I'm not sure when it started, but I can tell you it didn't occur on R 2.15.3, and it does on 3.0.0 RC (2013-03-31 ...

Richard D. Morey
Apr 1, 2013 at 11:52 pm
Apr 2, 2013 at 1:12 pm

4	[Rd] Timing of SET_VECTOR_ELT

Assume a C program invoked by .Call, that returns a list. Near the top of the program we allocate space for all the list elements. (It is my habit to use "xyz2" for the name of the R object and "xyz" ...

Terry Therneau
Apr 1, 2013 at 5:10 pm
Apr 1, 2013 at 7:11 pm

3	[Rd] Speeding up build-from-source

Hi, I've been playing around with the R source code a little; mostly just trying to familiarize myself. I have access to some computers on a reservation system; so I've been reserving a computer, ...

Adam Seering
Apr 26, 2013 at 2:50 pm
Apr 27, 2013 at 10:50 pm

3	[Rd] Lubuntu 13.04 raring ringtail: Problems installing pnmath_0.0-4

Hola! This is 64bit Lubuntu 13.04, with R-3.0.0 installed from deb http://ppa.launchpad.net/marutter/rrutter/ubuntu raring main via synaptic. gcc --version gcc (Ubuntu/Linaro 4.7.3-1ubuntu1) 4.7.3 R ...

Kjetil Halvorsen
Apr 26, 2013 at 6:39 pm
Apr 27, 2013 at 5:51 pm

3	[Rd] extracting tables from web pages?

Hello: What tools would you recommend for extracting the table of members of the US House of representatives from "http://house.gov/representatives/" and ...

Spencer Graves
Apr 25, 2013 at 8:00 pm
Apr 26, 2013 at 6:42 pm

3	[Rd] is.vector(as.vector(x, m), m) not always TRUE

In the man page for as.vector() (same as man page for vector()): Writers of methods for ?as.vector? need to take care to follow the conventions of the default method. In particular ? Argument ?mode? ...

Hervé Pagès
Apr 23, 2013 at 11:48 pm
Apr 24, 2013 at 11:15 pm

3	[Rd] Problem with S3 method dispatch and NAMESPACE

I have updated the rms package to extensively use NAMESPACE. I cannot get certain S3 methods to dispatch. For example I have in NAMESPACE S3method(anova, rms) S3method(latex, anova.rms) anova.rms ...

Frank Harrell
Apr 24, 2013 at 3:22 am
Apr 24, 2013 at 3:00 pm

3	[Rd] Publishing my Package on CRAN

Hi, I have a simple package with two functions. It essentially implements estimators and data simulation for a paper I am writing for immunology (and in some sense, ecology). How long is the typical ...

Liuyipei
Apr 19, 2013 at 4:38 am
Apr 21, 2013 at 4:09 am

3	[Rd] Suppress specific warnings

Hello, is there a convenient way to suppress only *specific* warnings? (I know about ?suppressWarnings) I depend on another package, from which I want to suppress only some warnings, but not others ...

Felix Schönbrodt
Apr 18, 2013 at 11:31 am
Apr 18, 2013 at 4:12 pm

3	[Rd] R 3.0.0 memory use

I did some benchmarking of data frame code, and it appears that R 3.0.0 is far worse than earlier versions of R in terms of how many large objects it allocates space for, for data frame operations - ...

Tim Hesterberg
Apr 14, 2013 at 10:22 pm
Apr 15, 2013 at 4:07 am

3	[Rd] Empty package skeleton

Hi, I know this has been reported/asked before ( http://tolstoy.newcastle.edu.au/R/e15/devel/11/10/0831.html) but it would still be just nice to have a fix for the not user-friendly fact that one ...

Renaud Gaujoux
Apr 14, 2013 at 11:10 am
Apr 14, 2013 at 7:11 pm

3	[Rd] Trying to make DEBUG=T a debug version of R

Hi, I am trying to make a debug version of R ( for use with gdb later ) on windows. I am executing the following. src\gnuwin32 make clean src\gnuwin32 make DEBUG=T? In the output, I see many -O3 ...

Andre Mikulec
Apr 11, 2013 at 12:02 am
Apr 14, 2013 at 2:14 am

2	[Rd] dyn.load inside a package in R >= 3.0

Hello, I am trying to port a package that was built for R 2.15 over to R 3.0. This package has an Initialize method that uses dyn.load to load a dll that was built separately, and then uses .C() to ...

Adrian Mejia
Apr 24, 2013 at 5:55 pm
May 2, 2013 at 12:57 pm

2	[Rd] lsfit: Error in formatting error message

Hi, in R-3.0 I get the following error when calling lsfit with more observations than variables, which seems to come from an error in the formatting of the error message (note that this was not ...

Renaud Gaujoux
Apr 25, 2013 at 11:29 am
Apr 29, 2013 at 11:11 am

2	[Rd] Error Message while Package creation

Hello Guys, I wanted to build a new R package from the R code. I installed all the required software and made all the path settings. When i tried running, cmd RCMD check SamplePackageName while ...

Crish..
Apr 25, 2013 at 5:21 am
Apr 25, 2013 at 9:58 am

2	[Rd] about the 'length' arg of vector()

Hi, In the man page for vector(): length: A non-negative integer specifying the desired length. Double values will be coerced to integer: supplying an argument of length other than one is an error ...

Hervé Pagès
Apr 23, 2013 at 11:20 pm
Apr 24, 2013 at 3:39 pm

2	[Rd] httpd error with and help_type = 'html', package = NULL

Having loaded a package that masks an object from another package, calling help(conflictedname, help_type = 'html') instead of producing a page giving the choices of help page available The page ...

Michael Nelson
Apr 23, 2013 at 6:32 am
Apr 23, 2013 at 6:01 pm

2	[Rd] parallel::mclapply does not return try-error objects with mc.preschedule=TRUE

Hello, Consider this: 1) library(parallel) res <- mclapply(1:2, stop) #Warning message: #In mclapply(1:2, stop) : # all scheduled cores encountered errors in user code is(res[[1]], 'try-error') #[1] ...

Karl Forner
Apr 11, 2013 at 11:43 am
Apr 23, 2013 at 3:16 pm

2	[Rd] Line breaks in rd files

How can I add a new line in an rd file f.e between references? Knut

Knut Krueger
Apr 23, 2013 at 9:34 am
Apr 23, 2013 at 1:20 pm

2	[Rd] Help: Where can I find the code for 'C_Cdqrls'?

Dear all, Iâ€™m not sure if it is O.K. to ask this question here. But where can I find the code for the function â€˜C_Cdqrlsâ€™ which is called by the R function â€˜lsfitâ€˜. Thank you all. Sorry for ...

赵自强
Apr 23, 2013 at 7:35 am
Apr 23, 2013 at 1:01 pm

2	[Rd] Converting an environment to a list: mget vs. as.list

Hi all, An interesting discovery: if you want to convert an environment to a list, and you already know the names of the objects in the environment, using mget is about twice as fast as using as.list ...

Hadley Wickham
Apr 22, 2013 at 1:14 pm
Apr 22, 2013 at 2:41 pm

2	[Rd] stack imbalance in max.col for non-real matrices

It's tough to reliably reproduce, but I often get stack imbalance warnings when calling max.col() on non-real/double matrix. The code is conditionally PROTECTing but not incrementing its nprot ...

Michael Lawrence
Apr 17, 2013 at 8:25 pm
Apr 19, 2013 at 1:20 pm

2	[Rd] support for POSIXct classes in image.default axes

Hello, I would like to suggest the following change to image.default in src\library\graphics\R\image.R: 98c98 < plot(NA, NA, xlim = xlim, ylim = ylim, type = "n", xaxs = xaxs, --- This provides all ...

Michael Sumner
Apr 12, 2013 at 11:27 am
Apr 17, 2013 at 12:09 pm

2	[Rd] parallel: Race-condition concern regarding graphics devices in a multi-thread environment

Hi, I'm trying to figure out how to safely make sure that I close the same graphics device that I opened earlier in a thread (and not one opened by a parallel thread). In a *single-thread* ...

Henrik Bengtsson
Apr 5, 2013 at 7:23 pm
Apr 6, 2013 at 9:09 pm

2	[Rd] Non-vignette sweave file in package

Dear all, I'm documenting an elaborate analysis as a private package. The package writes all required output to a database. I use a Sweave file to transform all the results from the database into a ...

ONKELINX, Thierry
Apr 4, 2013 at 2:55 pm
Apr 5, 2013 at 12:01 pm

2	[Rd] R-3.0.0 reg-tests-3.R / survival

"make check" is failing on reg-test3.R with a message that survival was built with an older version of R. (On my Ubuntu 32 bit and Ubuntu 64 bit machines). Why would "make check" be looking anywhere ...

Paul Gilbert
Apr 3, 2013 at 3:00 pm
Apr 3, 2013 at 4:10 pm

2	[Rd] R-package preparation --as-cran behaving unexpectedly

Dear all, I am trying to submit an R-package to CRAN. In preparation I do run R_INSTALL_TAR=/bin/tar R CMD check --as-cran parallelize.dynamic_0.9.tar.gz and the command finishes without warnings or ...

Stefan Boehringer
Apr 3, 2013 at 11:25 am
Apr 3, 2013 at 3:36 pm

1	[Rd] Loss of identified points

Minimizing and then restoring a window that contains identified points leads to an error on my linux box. R version 3.0.0 (2013-04-03) Platform: i686-pc-linux-gnu (32-bit) locale: [1] ...

Terry Therneau
Apr 29, 2013 at 1:54 am
Apr 29, 2013 at 8:55 am

1	[Rd] cause 'invalid permissions'

Hi folks, I am writing a package in C. It works most of the time, but fails occasionally by the segfault looking like: address 0x7f55302e2700, cause 'invalid permissions' Possible actions: 1: abort ...

Maxpar Lin
Apr 28, 2013 at 4:00 pm
Apr 29, 2013 at 8:52 am

1	[Rd] RFC: R_data_class as part of the C-API

Hi, In src/attrib.c, the comment for the function R_data_class is: ``` /* the S4-style class: for dispatch required to be a single string; for the new class() function; if(!singleString) , keeps ...

Laurent Gautier
Apr 26, 2013 at 7:07 pm
Apr 28, 2013 at 4:51 pm

1	[Rd] POSIXt oddness at end of 1969

A user here noticed the following difference between Linux and Windows versions of R-2.15.3 (and R-3.0.0, I think) when using times within a second of the end of 1969: f <- function (sec = -1) { x1 ...

William Dunlap
Apr 17, 2013 at 8:10 pm
Apr 17, 2013 at 9:16 pm

1	[Rd] [R] Question on Stopword Removal from a Cyrillic (Bulgarian)Text

Thanks for the pointer. Indeed, this allowed me to discover the existence of the PCRE_UCP (Unicode Character Properties) flag, which changes matching behavior so that Unicode alphanumerics are not ...

Milan Bouchet-Valat
Apr 10, 2013 at 6:43 pm
Apr 10, 2013 at 8:31 pm

1	[Rd] Issue with Control-Z in a text file on Windows - readLines() appears to truncate

Working on Windows I have had to deal with CSV files that, unfortunately, contain embedded Control-Zs, i.e. ASCII character 26 in decimal, and the readLines() function in R on Windows (2.15.2 and ...

Sean O'Riordain
Apr 10, 2013 at 2:20 pm
Apr 10, 2013 at 7:47 pm

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