Re: [Rd] Mac R spinning wheel with Package Manager (PR#14005)

I suppose expected behavior would be something communicating the issue and perhaps a progress bar; certainly I think avoiding a spinning pizza would be a good think, since that is usually very bad news :) Cheers, James On Oct 14, 2009, at 09:32, Simon Urbanek wrote: > (moving to the proper ma

[Rd] allocation of large matrix failing

Hello, this is probably something silly which I am doing, but I cannot understand why this allocation is not happening. Here is a my C code which tries to allocate a list of size 333559, and then a matrix of size 8*333559 I thought I might be running into memory problems, but R is not even using

[Rd] wchar and wstring.

Hello all, I am writing an R interface to some C++ files which make use of std::wstring classes for internationalization. Previously (when I wanted to make R strings from C++ std::strings), I would do something like this to construct a string in R from the results of the parse. SET_VECTOR_ELT(vals

[Rd] Question about SET_LENGTH

Hello all, thanks for all the help on the other issues. This one should be relatively straightforward. I have a vector of integers which I allocate to be the maximal size possible (meaning I'll never see more than cel.GetNumOutliers, but most likely I'll see less) therefore, I want to resize the ve

Re: [Rd] wchar and wstring. (followup question)

ple i based my code of of in main/character.c used wcstombs. Thanks again for all of the help. jim Prof Brian Ripley wrote: > On Fri, 26 Aug 2005, James Bullard wrote: > >> Hello all, I am writing an R interface to some C++ files which make use >> of std::wstring classes f

Re: [Rd] [R] Debugging R/Fortran in Windows

g the same variable name for a function I was estimating and for my current estimate of that function. Sorry I didn't spend more time checking this myself! Thanks again for your help, James __ R-devel@r-project.org mailing list https://stat.ethz.ch/mai

Re: [Rd] [R] Debugging R/Fortran in Windows

test somewhere else? > > Duncan Murdoch No, I didn't find a version of valgrind that works on Windows. I used it on Linux. Best wishes, James __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] vector labels are not permuted properly in a call to sort() (R 2.1)

Martin Maechler wrote: > > "AndyL" == Liaw, Andy <[EMAIL PROTECTED]> > > on Tue, 4 Oct 2005 13:51:11 -0400 writes: > > AndyL> The `problem' is that sort() does not doing anything special when > given > AndyL> a matrix: it only treat it as a vector. After sorting, it copies >

Re: [Rd] [R-gui] R GUI considerations (was: R, Wine, and multi-threadedness)

fficiently motivated to provide money to employ someone (or multiple people) to do something as big as that. Just my thoughts. Feel free to ignore. Regards, James __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] [R-gui] R GUI considerations (was: R, Wine, and multi-threadedness)

a particular department/institute. Or maybe [horrible thought], some business outside the academic community will provide a very expensive but very good GUI development system for R. Best regards, James __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] [R-gui] R GUI considerations (was: R, Wine, and multi-threadedness)

oinformatics OUP so far - and John Fox has published a full-length article on Rcmdr in the Journal of Statistical Software - great stuff! Does that make sense? James __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] calling fortran from C

Hello, I had a question about calling some of R's fortran routines from C. Specifically, I would like to call: dqrfit from some C code which will be bundled as an R package. I was hoping someone knew of an example in some of R's code which does something like this (any fortran call from R's

Re: [Rd] [R-gui] R GUI considerations (was: R, Wine, and multi-threadedness)

verything in a user-friendly way, and doesn't want to try to do that, because that would mean a completely intimidating collection of menus and buttons (which is how some people feel about Microsoft Office). We may have to agree to disagree about some things, but I hope this has made my point of view a little clearer. Best wishes, James __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] native logistic regression

Hello, thanks for the answers to my last questions and apologies for not seeing the answers staring me down in the manual. At the risk of asking another potentially obvious question ... we are currently using some of the NAG routines for model fitting and I am trying to re-write the relevant po

[Rd] segfault following a detach

Hello, first off, thanks for all of the previous help; hopefully someone will have some insight on this question. I am attempting to track down a segmentation fault which occurs only after a detach(2) is called in the code (I have replaced the detach(2) with detach(package:DSA) and that fails a

[Rd] Using .onUnload() to unload compiled code

month 01 day01 svn rev36947 language R

Re: [Rd] How do you make a formal "feature" request?

I use the summary function. Being unfamiliar with the SAS report function, it is difficult to answer more completely. jim On Aug 21, 2010, at 8:41 AM, Donald Winston wrote: > Who decides what features are in R and how they are implemented? If there is > someone here who has that authority I ha

Re: [Rd] Speeding up matrix multiplies

n: union rd { double d; uint64_t l; }; union rd u; then: u.d is an R NA iff both of: u.l & 0x7ff0 == 0x7ff0 u.l & 0x == 1954; are true. -- James Cloos

[Rd] R project testers - how to help out

things and "R" is my tool of choice. Any help is much appreciated. James Goss Los Angeles, CA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] S4 plus

n deliberately disabled in order to allow someone to set a number of different methods with method specific arguments with a single generic? Many thanks, Jim -- James Perkins, PhD student Institute of Structural and Molecular Biology Division of Biosciences University College London Gower Steet Lond

[Rd] self-referential representations in S4

I'm trying to do the following: > setClass("MyNode", representation(parent = "MyNode")) [1] "MyNode" Warning message: undefined slot classes in definition of "MyNode": parent(class "MyNode") I scanned the docs, but found nothing. The representation function has no problem, it's the setClass func

[Rd] External pointers and an apparent memory leak

I'm using external pointers and seemingly leaking memory. My determination of a memory leak is that the R process continually creeps up in memory as seen by top while the usage as reported by gc() stays flat. I have isolated the C code: void h5R_allocate_finalizer(SEXP eptr) { Rprintf("Calli

Re: [Rd] External pointers and an apparent memory leak

by 0x4EE17E4: do_dotcall (dotcode.c:837) ==22098==by 0x4F18D02: Rf_eval (eval.c:508) ==22098==by 0x4F1A7FD: do_begin (eval.c:1420) ==22098==by 0x4F18B1A: Rf_eval (eval.c:482) ==22098==by 0x4F1B7FC: Rf_applyClosure (eval.c:838) ==22098==by 0x4F189F7: Rf_eval (eval.c:526) ==22098=

[Rd] bug in nlme::getVarCov

, function(g) getVarCov(gls_sorted, individual = g)) all.equal(gls_raw$modelStruct, gls_sorted$modelStruct) all.equal(V_raw, V_sorted) See here for more details and a simple patch: http://jepusto.github.io//Bug-in-nlme-getVarCov Or here for just the R code: https://gist.github.com/jepusto/5477dbe3efa992a3

[Rd] CC on Bug 16932?

uvic.ca) didn't pass our syntax checking for a legal email address. New accounts are disabled. Please post bug reports to R-devel@r-project.org; if they are reasonable, we will whitelist you. It also must not contain any illegal characters." Could I please be whitelisted

[Rd] allocation error and high CPU usage from kworker and migration: memory fragmentation?

move <- merge(move, upc, by=c('upc')) # adds is_PL column, a boolean move <- merge(move, parent, by=c('store', 'year') # adds parent column, an integer setkeyv(move, by) # this reduces move to a data.table with at most 6000 rows, but always 4 colum

[Rd] Question about fifo behavior on Linux between versions 3.0.3 and 3.1.0

of connections.c that doesn't get compiled on Linux (i.e., the code given is Unix only). I also couldn't find any references to fifo behavior changes under Linux in any of R's documentation. My platform is Fedora 20 (64-bit) and I have built and installed R from source. Th

Re: [Rd] Development version of R: Improved nchar(), nzchar() but changed API

>>>>> "GC" == Gábor Csárdi writes: GC> You can get an RSS/Atom feed, however, if that's good: GC> https://github.com/wch/r-source/commits/master.atom That is available in gwene/gmane as: gwene.com.github.wch.r-source.commits.trunk -J

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

f work from the PSO iteration stage. This is, of course, straight forward if I implement the whole thing in a self-contained C program--however, I'd like R to handle the optimization routines, and my shared library to implement the value function. So: what do folks think? Cheers, James

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

tines, and my shared library to implement the value function. So: what do folks think? Cheers, James __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

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

Thanks Duncan, you've unclogged my thinking. For anybody interested, see below a sketch of the solution. Cheers, James --START SKETCH OF SOLUTION-- #include #include static typedef struct { int nrow, ncol; double *data; } _myparticle_data_struct; static _myparticle_data_s

[Rd] Bordered legend icons and Text in plots

ne "fill = fill," to the output list of process.key(), and this seems to have fixed the issue (see legend.R line 216 and Fill.png for results). For Issue 2 there is a workaround in update.trellis.R lines 267-275 (see Text.png for the results). James Hawley Student Ontario Institute for

Re: [Rd] linking hdf5, requires setting LD_LIBRARY_PATH

On Mar 2, 2010, at 17:45, Dirk Eddelbuettel wrote: Unless I am missing something, this has nothing to do with hdf5 per se. See below. No, you are not missing anything. Thank you for the response. This is exactly what I was looking for. Thanks again, Jim On 2 March 2010 at 16:

[Rd] application to mentor syrfr package development for Google Summer of Code 2010

were reasonably excluded. (Show your R transcript.) 4. Explain the relationship between degrees of freedom and correlated independent variables. Best regards, James Salsman jsals...@talknicer.com http://talknicer.com __ R-devel@r-project.org mailing

Re: [Rd] application to mentor syrfr package development for Google Summer of Code 2010

: http://en.wikipedia.org/wiki/F-test#Regression_problems Best regards, James Salsman On Sun, Mar 7, 2010 at 7:35 PM, Chidambaram Annamalai wrote: > It's been a while since I proposed syrfr and I have been constantly in > contact with the many people in the R community and I wasn

Re: [Rd] application to mentor syrfr package development for Google Summer of Code 2010

his fit evaluations. Best regards, James Salsman On Sun, Mar 7, 2010 at 10:39 PM, Chidambaram Annamalai wrote: > >> If I understand your concern, you want to lay the foundation for >> derivatives so that you can implement the search strategies described >> in Schmidt and Lip

Re: [Rd] application to mentor syrfr package development for Google Summer of Code 2010

rwiki.sciviews.org/doku.php?id=developers:projects:gsoc2010:syrfr I've already stepped forward, so you could do as much or as little as you like if you wanted to co-mentor and Dirk agreed to that arrangement. Best regards, James Salsman > On Mon, Mar 8, 2010 at 2:49 AM, James Salsman

Re: [Rd] application to mentor syrfr package development for Google Summer of Code 2010

derivative package necessary for general relation regressions? Thank you for your kind consideration. Best regards, James Salsman On Tue, Mar 9, 2010 at 11:06 AM, Michael Schmidt wrote: > I think it's a great idea worth trying out. We have always done significance > tests just on the fin

[Rd] ranges and contiguity checking

Hi All, I am interfacing to some C libraries (hdf5) and I have methods defined for '[', these methods do hyperslab selection, however, currently I am limiting slab selection to contiguous blocks, i.e., things defined like: i:(i+k). I don't do any contiguity checking at this point, I just grab the

Re: [Rd] ranges and contiguity checking

t: Re: [Rd] ranges and contiguity checking >> >> On 12/05/2010 2:18 PM, James Bullard wrote: >> > Hi All, >> > >> > I am interfacing to some C libraries (hdf5) and I have >> methods defined for >> > '[', these methods do hyperslab sel

[Rd] difficulties with setMethod("[" and ...

Apologies if I am not understanding something about how things are being handled when using S4 methods, but I have been unable to find an answer to my problem for some time now. Briefly, I am associating the generic '[' with a class which I wrote (here: myExample). The underlying back-end allows m

[Rd] R from SVN fails to build on win32

*** [rbuild] Error 2 make: *** [all] Error 2 Best, Jim James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 **

[Rd] Best practices - R CMD check and vignettes

ere Sweave() and texi2dvi() are run. Unfortunately, the above code chunks no longer work. I can certainly hard code the first chunk to find the .Rdata file, but I have to imagine there is a much more elegant way to do this. Any suggestions? Best, Jim -- James W. MacDonald, MS Biostatistician UMCCC cDN

[Rd] Is rcompgen still recommended?

I assume I am missing something obvious, but don't know what it is. Any pointers? Best, Jim > sessionInfo() R version 2.7.0 Under development (unstable) (2008-02-18 r44516) i386-apple-darwin8.11.1 locale: C attached base packages: [1] stats graphics grDevices datasets util

[Rd] confusion about evaluation.

Hi All, I am confused about the following code. I thought that the problem stemmed from lazy evaluation and the fact that 'i' is never evaluated within the first lapply. However, I am then confused as to why it gets bound to the final element of the lapply. The environments of the returned

[Rd] NAMESPACE/DESCRIPTION and imports

wanted. I am obviously misunderstanding something but I don't know what. Best, Jim James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662 ** Electronic

[Rd] iconv.dll in Windows

s.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] XML_1.99-0 -- James W. MacDonald, M.S. Biostatistician Douglas Lab 5912 Buhl 12

[Rd] multiple packages using the same native code.

This might fall under the purview of bundles, but I could not find any example bundles which demonstrated what I am after. I would like to construct two packages (A, B) which utilize a number of common C functions. The most straightforward way to do this is just copy the relevant .c and .h file

Re: [Rd] multiple packages using the same native code.

users could download and install packages separately even if it's a bundle) then it seems like there is no way to generally modify the configure file to do this. thanks, jim Seth Falcon wrote: >Hi Jim, > >James Bullard <[EMAIL PROTECTED]> writes: > > >>I

[Rd] write.table and segment fault?

Hi, I'm experiencing R segmentation faults on multiple versions of R when writing out a particular data.frame: ## dd is a 44 by 3 data.frame load(url("http://stat.bell-labs.com/RS-DBI/download/dd.rda";)) write.table(dd, file = "dd.csv", sep = ",", row.names = FALSE) this occurs on > s

[Rd] Segfault with too many menu items on Rgui

2006 month 03 day29 svn rev37607 language R version.string Version 2.3.0 a

[Rd] R CMD check: non source files in src on (2.3.0 RC (2006-04-19 r37860))

Hello, I am having an issue with R CMD check with the nightly build of RC 2.3.0 (listed in the subject.) The problem is this warning: * checking if this is a source package ... WARNING Subdirectory 'src' contains: README _Makefile These are unlikely file names for src files. In fact, they ar

[Rd] Build error/zlib question

svn rev39242 language R version.string R version 2.4.0 alpha (2006-09-10 r39242) TIA, Jim James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Mic

Re: [Rd] Compiling R 2.4.0 in ubuntu/linux

Gavin Simpson wrote: > On Wed, 2006-10-11 at 17:58 -0400, T C wrote: >> I'm not sure if this is the place to post this question, but, I am >> having trouble compiling the source code. I do have a suitable C >> compiler and f2c but I get this error when I run ./configure >> >> configure: error: --

[Rd] Coping with non-standard evaluation in R program analysis

Hello R experts, I plan to develop a tool for dynamic analysis of R programs. I would like to trace function calls at runtime, capturing argument and return values. Following a suggestion made some time ago on this list, my high-level implementation strategy is to rewrite the AST, augmenting c

[Rd] R CMD CHECK doens't run configure when testing install?

I'm trying to get ready to submit a package to CRAN, but in order for the package to install on OS X, I need to temporarily set an environment variable. I put this in the 'configure' script, and 'R CMD INSTALL MyPackage' works fine, but when I do 'R CMD CHECK MyPackage', and it tests installati

[Rd] Nested tracing with custom callback

Hi all, I would like to install a trace function that gets executed whenever *any* R function is called. In Python, for example, this functionality is provided by the `sys.settrace` function. I am not aware of any public interface, at the R or C level, that can accomplish this. The `trace` fu

Re: [Rd] Nested tracing with custom callback

Hi Jeroen, That was exactly what I was looking for. Thanks! Evan From: jeroeno...@gmail.com on behalf of Jeroen Ooms Sent: Wednesday, July 13, 2016 4:04 AM To: Evan James Patterson Cc: r-devel@r-project.org Subject: Re: [Rd] Nested tracing with custom callback   On Wed, Jul 13, 2016 at 5

[Rd] Process to Incorporate Functions from {parallely} into base R's {parallel} package

Hi all, Henrik Bengtsson has done some fantastic work with {future} and, more importantly, greatly improved constructing and deconstructing a parallelized environment within R. It was with great joy that I saw Henrik slowly split off some functionality of {future} into {parallelly} package. Rea

[Rd] Preferred way to include internal data in package?

surface, without the users awareness. Many thanks, James __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Preferred way to include internal data in package?

I saw that, but actually I was wondering if there was a more general method. I’d like to use plain text files if I can, instead of Rda files, since they’re easier to maintain (and it’s a small file). On 4 Aug 2014, at 16:30, Jeroen Ooms wrote: >> I’m developing a package and would like to inc

Re: [Rd] R from SVN fails to build on win32

ude work? > > > I am also having no problems with > > [d:/R/svn/trunk/src/gnuwin32]% windres --version > GNU windres 2.17.50 20070129 You were correct. I updated to binutils-2.17.50-20060824 and the compilation is now proceeding without error. Thank you for the help!

Re: [Rd] xlsReadWrite Pro and embedding objects and files in Excel worksheets

me and >>hopefully a lot of people. R developers tend to think that all >>scientists are running Linux on 64-bit computers, but most biomedical >>researches still store date in Excel files. This won't solve everybody's >>needs, but it could be a start. &g

[Rd] rm error on Windows after R CMD INSTALL

7;t have Cygwin installed. Any suggestions? Best, Jim -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 __ R-dev

Re: [Rd] suggesting \alias* for Rd files (in particular for S4 method documentation)

her, substituting them with pairs of >> >> \section{Usage}{\preformatted{ >> }} >> \section{Arguments}{ >> } >> >> and putting all aliases marked above with * into internals, which is >> definitely not the best way of going around documentation and >

Re: [Rd] Best practices - R CMD check and vignettes

;, package = "PkgName")) > > Max > > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of James MacDonald > Sent: Monday, September 17, 2007 11:07 PM > To: [EMAIL PROTECTED] > Subject: [Rd] Best practices - R CMD

Re: [Rd] Package Building and Name Space

;MyPackage' has no name space and is not on the search path >> Calls: ... -> switch -> sys.source -> eval -> >> eval -> :: >> Execution halted >> >> 'MyFunction' contains 'strapply' from gsubfn. >> >> Please tell me wher

[Rd] R CMD build question

al to the package is off? R CMD check does issue a warning that the vignette is missing, so maybe that is the intended result. Best, Jim -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCG

Re: [Rd] Build error/zlib question

Prof Brian Ripley wrote: > On Fri, 29 Sep 2006, Uwe Ligges wrote: > >> >> >> James MacDonald wrote: >> >>> Hi, >>> >>> I am unable to build a package I maintain using a relatively >>> current build of R-2.4.0 alpha, whereas th

Re: [Rd] x86_64, acml-3.5.0-gfortran64 and lme4

ith Atlas and/or Goto's BLAS. > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > ______ > R-devel@r-project.org mailing list > https://stat.ethz.

Re: [Rd] rm() deletes 'c' if c('a','b') is the argument (PR#9399)

uot;last.warning" "myfun" > > > Steven McKinney > > Statistician > Molecular Oncology and Breast Cancer Program > British Columbia Cancer Research Centre > > email: [EMAIL PROTECTED] > > tel: 604-675-8000 x7561 > > BCCRC > Molecular Oncology > 675 West 10

Re: [Rd] [R] HTTP User-Agent header

On 7/28/06, Seth Falcon <[EMAIL PROTECTED]> wrote: > I have a rough draft patch, see below, that adds a User-Agent header > to HTTP requests made in R via download.file. If there is interest, I > will polish it. It looks right, but I am running under Windows without a compile