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

15	[Rd] R CMD check returns NOTE about package data set as global variable

I'm developing a package that comes with a data set called RutgersMapB36. One of the package's functions requires this data frame. A toy example is: test<-function() { data(RutgersMapB36) ...

Brad McNeney
Apr 6, 2012 at 6:46 pm
Apr 10, 2012 at 7:00 pm

14	[Rd] R datasets ownership(copyright) and license

Dear R Developers, Recently filed (and dismissed ;) ) law suit by Astrolabe against tz database developers caused a lot of media-press and discussions and created some kind of precedence in the USA ...

Yaroslav Halchenko
Apr 2, 2012 at 10:06 pm
Apr 5, 2012 at 2:20 pm

13	[Rd] I wish xlim=c(0, NA) would work. How about I send you a patch?

I'm looking for an R mentor. I want to propose a change in management of plot options xlim and ylim. Did you ever want to change one coordinate in xlim or ylim? It happens to me all the time. x <- ...

Paul Johnson
Apr 16, 2012 at 5:52 pm
Apr 26, 2012 at 10:21 am

13	[Rd] [patch] giving library() a 'version' argument

I've made a small enhancement to R that would help developers better control what versions of code we're using where. Basically, to load a package in R, one currently does: library(whateverPackage) ...

Ken Williams
Apr 11, 2012 at 3:28 pm
Apr 13, 2012 at 3:22 pm

11	[Rd] Vignette questions

Context: R2.15-0 on Ubuntu. 1. I get a WARNING from CMD check for "Package vignette(s) without corresponding PDF: In this case the vignettes directory had both the pdf and Rnw; do I need to move the ...

Terry Therneau
Apr 11, 2012 at 8:41 pm
Apr 12, 2012 at 9:55 pm

8	[Rd] Column(row)wise minimum and maximum

Hi, Currently, the "base" has colSums, colMeans. It seems that it would be useful to extend this to also include colMin, colMax (of course, rowMin and rowMax, as well) in order to facilitate faster ...

Ravi Varadhan
Apr 19, 2012 at 6:12 pm
Apr 19, 2012 at 10:14 pm

7	[Rd] The constant part of the log-likelihood in StructTS

Dear all, I'd like to discuss about a possible bug in function StructTS of stats package. It seems that the function returns wrong value of the log-likelihood, as the added constant to the relevant ...

Jouni Helske
Apr 30, 2012 at 11:37 am
May 17, 2012 at 11:12 am

7	[Rd] url, readLines, source behind a proxy

Hi, when I run R CMD check with flag --as-cran, the process hangs at stage: * checking CRAN incoming feasibility ... I am pretty sure it is a proxy issue. I looked at the check code in the tools ...

Renaud Gaujoux
Apr 17, 2012 at 8:01 am
May 10, 2012 at 8:25 am

6	[Rd] fast version of split.data.frame or conversion from data.frame to list of its rows

Hi, I was wondering if there is anything more efficient than split to do the kind of conversion in the subject. If I create a data frame as in system.time({fd = data.frame(x=1:2000, y = rnorm(2000), ...

Antonio Piccolboni
Apr 30, 2012 at 11:28 pm
May 4, 2012 at 2:20 am

6	[Rd] delayedAssign changing values

I'm not sure if this is a known peculiarity or a bug, but I stumbled across what I think is very odd behavior from delayedAssign. In the below example x switches values the first two times it is ...

McGehee, Robert
Apr 25, 2012 at 9:18 pm
Apr 26, 2012 at 11:37 pm

5	[Rd] How does .Fortran "dqrls" work?

Hi, all. I want to write some functions like glm() so i studied it. In glm.fit(), it calls a fortran subroutine named "dqrfit" to compute least squares solutions to the system x * b = y To learn how ...

Yangleicq
Apr 26, 2012 at 6:00 am
Apr 30, 2012 at 4:06 am

5	[Rd] "NA" vs. NA

Dear All, I assume this is an R-devel issue, apologies if I missed something obvious. I have a dataframe where the row names are country codes, based on ISO 3166, something like this: ------------ ...

Adrian Dusa
Apr 5, 2012 at 11:03 am
Apr 5, 2012 at 2:04 pm

4	[Rd] Using other peoples packages from within C-based R-extension

Hello, what if I want to write a package mixed R/C-extension and want to use code that is provided by other peoples packages? How for example can I use one of the provided wavelet packages from ...

Oliver
Apr 24, 2012 at 4:31 pm
Apr 24, 2012 at 6:35 pm

4	[Rd] Problem with args

NULL e.g. + name <- match.fun(name) + base::args(name) + } function (..., na.rm = FALSE) NULL -- Statistics & Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email ...

Gabor Grothendieck
Apr 21, 2012 at 5:03 pm
Apr 21, 2012 at 6:18 pm

4	[Rd] unexpectedly high memory use in R 2.14.0

I recently started using R 2.14.0 on a new machine and i am experiencing what seems like unusually greedy memory use. It happens all the time, but to give a specific example, let's say i run the ...

Andre zege
Apr 11, 2012 at 10:53 pm
Apr 12, 2012 at 2:14 pm

4	[Rd] Display instruction text on package load

I'm currently working on a new package for R that interfaces with an API. Most of the package's functionality requires users to supply an access key that allows the package to work with the API. I ...

Thomas J. Leeper
Apr 7, 2012 at 9:27 pm
Apr 8, 2012 at 1:13 pm

3	[Rd] R CMD check: Sys.getenv("R_GSCMD") cannot contain full pathname (contrary to docs)

Hi, in help("R_GSCMD") it says "R_GSCMD: Optional. The path to Ghostscript, used by dev2bitmap, bitmap and embedFonts. Consulted when those functions are invoked.". However, if 'R_GSCMD' contains a ...

Henrik Bengtsson
Apr 20, 2012 at 9:00 pm
Jun 5, 2012 at 7:28 pm

3	[Rd] A doubt about substitute() after delayedAssign()

Hello, ?delayedAssign presents substitute() as a way to look at the expression in the promise. However, msg <- "old" delayedAssign("x", msg) msg <- "new!" x #- new! substitute(x) #- x (was 'msg' ?) ...

Philippe Grosjean
Apr 29, 2012 at 7:30 am
May 1, 2012 at 8:32 pm

3	[Rd] creating a package in R

Please give me the necessary links that permits me to create my own package inR -- View this message in context: http://r.789695.n4.nabble.com/creating-a-package-in-R-tp4596411p4596411.html Sent from ...

Nossa
Apr 29, 2012 at 2:08 pm
Apr 29, 2012 at 8:15 pm

3	[Rd] C - R integration: Memory Issues

Hi all, I am a PhD student and I am working on a C project that involves some statistical calculations. So, I tried to embed R into C, in order to call R functions from a C program. My program seems ...

Nikolaos Bezirgiannidis
Apr 18, 2012 at 5:40 pm
Apr 20, 2012 at 1:51 pm

3	[Rd] R --debug crashes R on Windows

'R --debug' and 'Rterm --debug' crash R on Windows. Indeed, --debug is not a documented command line option, but it still causes a crash. This occurs with R v2.15.0 patched and R devel - both from ...

Henrik Bengtsson
Apr 17, 2012 at 6:19 am
Apr 17, 2012 at 7:12 pm

2	[Rd] Creating a package which contains stand-alone C code

I would like to create an R package which uses some C code, which in turn uses MPI. At the moment I'm only interested in creating this package for UNIX-like systems. The way I envisage this working ...

Rajen Shah
Apr 27, 2012 at 1:54 pm
Apr 30, 2012 at 7:30 am

2	[Rd] nobs.glm

Hi all, The nobs method of (MASS:::polr class) takes into account of weight, but nobs method of glm does not. I wonder what is the rationale of such design behind nobs.glm. Thanks in advance. Best ...

Wincent
Apr 24, 2012 at 1:36 pm
Apr 26, 2012 at 12:16 am

2	[Rd] Write unix format files on windows and vice versa

I go back and forth between windows and linux, and find myself running into problem with line endings. Is there a way to control the line ending conversion when writing files, such as write and cat? ...

Andrew Redd
Apr 24, 2012 at 5:23 pm
Apr 24, 2012 at 5:56 pm

2	[Rd] combining large list of data.frames

It's normal for me to create a list of data.frames and then use do.call('rbind', list(...)) to create a single data.frame. However, I've noticed as the size of the list grows large, it is perhaps ...

Cole Beck
Apr 19, 2012 at 10:34 pm
Apr 23, 2012 at 5:07 pm

2	[Rd] csv version of data in an R object

For a package, I need to write a csv version of a data set to an R object. Right now, I use: out <- capture.output( write.table(x, sep = ",", na = "?", file = "", quote = FALSE, row.names = FALSE, ...

Max Kuhn
Apr 21, 2012 at 2:28 pm
Apr 22, 2012 at 4:42 pm

2	[Rd] R-2.15 compile error: fatal error: internal consistency failure

I am unable to compile R-2.15.0 source. I configured it without problems with options that i used many times before ./configure --prefix=/home/andre/R-2.15.0 --enable-byte-compiled-packages=no ...

Andre zege
Apr 17, 2012 at 9:24 pm
Apr 18, 2012 at 7:19 am

2	[Rd] eval a SYMSXP from C

Can someone offer some advice on how to properly evaluate a SYMSXP from a .Call ? I have the following in R: variable xn, with an attribute "mu" which references the variable mu in the global ...

Whit Armstrong
Apr 16, 2012 at 9:53 pm
Apr 17, 2012 at 12:48 am

2	[Rd] no carriage returns in BATCH output from 2.15.0

It seems like I must be missing something since I haven't been able to find mention of this. Under Windows 7 I'm not getting carriage returns in the output of BATCH files using 2.15.0 (both 64-bit ...

Patrick Burns
Apr 15, 2012 at 4:55 pm
Apr 15, 2012 at 8:06 pm

2	[Rd] R-2.15.0 and Exporting Methods Converted To S4 Generic

Late to the show on this release, unfortunately. One of our production packages no longer builds under R-2.15.0 with the following message. ** testing if installed package can be loaded Error ...

Roebuck,Paul L
Apr 12, 2012 at 6:41 pm
Apr 13, 2012 at 1:05 pm

2	[Rd] Byte compilation of packages on CRAN

In DESCRIPTION if I set LazyLoad to 'yes' will data.table (for example) then be byte compiled for users who install the binary package from CRAN on Windows? This question is based on reading section ...

Matthew Dowle
Apr 11, 2012 at 7:36 pm
Apr 12, 2012 at 6:54 am

1	[Rd] Unable to install rggobi in R 2.15

I am currently using R 2.15.0 with R Tools 2.15 (in Windows XP). I downloaded the source for RGgobi and extracted it to a folder. Then I tried compiling and installing with the following command and ...

Indrajit Sengupta
Apr 28, 2012 at 1:47 am
Apr 28, 2012 at 2:36 pm

1	[Rd] Strange bug in my package

Dear all, I get a bug in the examples of my AFLP package on R-forge (https://r-forge.r-project.org/R/?group_id27) but only on the Linux version. The windows version compiles. The Mac version skips ...

ONKELINX, Thierry
Apr 25, 2012 at 8:58 am
Apr 26, 2012 at 3:47 pm

1	[Rd] Strange behavior of model.frame() when given subset

Dear R-devel, I recent got a bug report from a locfit user about the use of the subset argument when calling locfit(). Basically the symptom is that the following two calls should produce the same ...

Liaw, Andy
Apr 25, 2012 at 12:34 pm
Apr 25, 2012 at 1:41 pm

1	[Rd] Specifying a function as not being and S3 Class function

I am compiling a library with legacy code which has functions named with periods in the names - but are not S3 class functions. For example for example, summary.agriculture is not an extension of the ...

Matt Pocernich
Apr 24, 2012 at 3:33 pm
Apr 24, 2012 at 4:50 pm

1	[Rd] Sending lists using .C

Hi, I posted around a week ago and I will try this time with a more detailed description. I am converting R code to C code to boost speed as currently it takes a few days to run. Now I will try ...

Chris90nz
Apr 22, 2012 at 12:49 am
Apr 22, 2012 at 10:08 am

1	[Rd] R CMD check -- non S3 method warning

I'm trying to R CMD check a package, and I'm getting the 'checking S3 generic/method consistency' warning. I have written a function 'gamma.dist' which is _not_ an S3 method, but happens to collide ...

Whit Armstrong
Apr 21, 2012 at 1:18 pm
Apr 21, 2012 at 2:49 pm

1	[Rd] R CMD check with non-standard .libPaths

Does anyone have advice on how to instruct R CMD check to use a non-standard set of libraries? Here's the situation: I'm trying to do some automated checking on package dependencies of a package I ...

Ben Bolker
Apr 15, 2012 at 12:45 am
Apr 15, 2012 at 1:49 am

1	[Rd] Add DUP = FALSE when tabulate() calls .C("R_tabulate"

In base/R/tabulate.R, tabulate() calls .C("R_tabulate"; I suggest adding DUP = FALSE to that call.

Tim Hesterberg
Apr 8, 2012 at 6:37 pm
Apr 9, 2012 at 8:48 am

1	[Rd] issue with base:::namespaceImportMethods

Hi, I've noticed an issue with S4 methods and namespaces which only arises in particular, difficult to reproduce configurations. One example is the ggbio package in Bioconductor, which currently ...

Michael Lawrence
Apr 5, 2012 at 10:35 pm
Apr 7, 2012 at 7:11 pm

1	[Rd] Compatibility problem with R-2.9.0 and R-2.14.0

Hello all, Using classical glm function with binomial family, I experienced a problem when using predict() over a glm object. I found that family objects built on R-2.14.0 contain elements like ...

Harold.petithomme
Apr 6, 2012 at 11:05 am
Apr 6, 2012 at 2:32 pm

0	[Rd] file.copy(src, src, recursive=TRUE) causes a segfault (Was: Re: R CMD check . segfault on re-building vignettes)

It appears that file.copy() does not protect against the case when one copies one directory to a subdirectory of itself resulting in it trying to create and endless recursive copy of itself ...

Henrik Bengtsson
Apr 30, 2012 at 5:14 pm
Apr 30, 2012 at 5:14 pm

0	[Rd] R CMD check . segfault on re-building vignettes

(Warning: There is some potential that this message is redundant.) I think that i have spotted an issue with R CMD check that does not trace back to a rare case, so it must have been reported already ...

Sebastian Meyer
Apr 30, 2012 at 3:48 pm
Apr 30, 2012 at 3:48 pm

0	[Rd] globalVariables()

There have been several threads on this list about the Notes generated in the check process regarding "global variables" with no visible definition. These can be useful but false positives tend to ...

John Chambers
Apr 28, 2012 at 12:02 am
Apr 28, 2012 at 12:02 am

0	[Rd] Some graphical parameters don't works in plot.table and plot.TukeyHSD.

Hello all, I would like to relate this behaviour of: plot.table & plot.TukeyHSD. They don't work with some graphical parameters. Thanks for your attetion. Cleber Error in plot.default(c(xi[, "lwr"], ...

Cleber N.Borges
Apr 26, 2012 at 4:36 pm
Apr 26, 2012 at 4:36 pm

0	[Rd] checkPoFiles function added to R-devel

I've just added a couple of functions to the tools package to check for bad format strings in the .po files that translators produce. See ?tools::checkPoFiles for the docs. They detect cases where ...

Duncan Murdoch
Apr 25, 2012 at 6:55 pm
Apr 25, 2012 at 6:55 pm

0	[Rd] Creating model frame from R formula inside compiled code

I am developing a custom regression package, which accepts a formula object as way of setting up the model matrix and response variable from a data frame. For large data sets, I expect that going ...

Alireza Mahani
Apr 24, 2012 at 4:41 pm
Apr 24, 2012 at 4:41 pm

0	[Rd] Where to store and how to load support data ?

Dear R developers, I am writing a R module, which contains a function that needs support data (a table with two columns). I wonder how to make sure the data is available to the function, without ...

Charles Plessy
Apr 24, 2012 at 1:00 pm
Apr 24, 2012 at 1:00 pm

0	[Rd] Method=df for coxph in survival package

In that particular example the value of "4" was pulled out of the air. There is no particular justification. There is a strong relationship between the "effective" degrees of freedom and the variance ...

Terry Therneau
Apr 18, 2012 at 1:02 pm
Apr 18, 2012 at 1:02 pm

0	[Rd] Setting up the NAMESPACE file "automatically" during R CMD build?

Hi, I'd like to compile the NAMESPACE file from a template where things such as S3method() statements are automatically inserted based on code inspection, because doing it by hand is too error ...

Henrik Bengtsson
Apr 17, 2012 at 9:20 pm
Apr 17, 2012 at 9:20 pm

group	r-devel @
categories	r
discussions	57
posts	215
users	91
website	r-project.org
irc	#r

summaries	on	Hotkey: s
users list	on	Hotkey: d
user style	avatars	Hotkey: a

R > r-devel > April 2012

Search Discussions

57 discussions - 215 posts

91 users for April 2012

Content

People

Support

Translate