Re: [Rd] Verbose output from R CMD check

2013-04-23 Thread Simon Urbanek
On Apr 23, 2013, at 10:51 AM, dpleydell wrote: > 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 the following message > > [START QUOTE] >

Re: [Rd] Verbose output from R CMD check

2013-04-23 Thread Simon Urbanek
On Apr 23, 2013, at 12:43 PM, dpleydell wrote: > Many thanks Simon for your response >>> Identifying the source of the message is a non-trivial problem because >>> there are a large number of calls to printf and fprintf etc in several >>> thousands of lines of code spread over many different *.c

Re: [Rd] Speeding up build-from-source

2013-04-27 Thread Simon Urbanek
On Apr 27, 2013, at 11:34 AM, Adam Seering wrote: > > > On 04/27/2013 09:10 AM, Martin Morgan wrote: >> On 04/26/2013 07:50 AM, Adam Seering wrote: >>> Hi, >>> I've been playing around with the R source code a little; mostly >>> just >>> trying to familiarize myself. I have access to some c

Re: [Rd] Comments in the DESCRIPTION file

2013-05-01 Thread Simon Urbanek
On May 1, 2013, at 6:01 AM, cgenolin wrote: > Hi all, > > Since R 3.0.0, the '#' does no longuer works for comments. > But as noticed above, comments can be introduce by 'anyWord:' or > 'myComment;' or 'toto:'. > > Since '#' can be used to name a field, we can also used '#:' or '###:' (or > eve

Re: [Rd] Windows, format.POSIXct and character encodings

2013-05-01 Thread Simon Urbanek
On May 1, 2013, at 10:06 AM, Hadley Wickham wrote: > Hi all, > > In what encoding does format.POSIXct return its output? It doesn't > seem to be utf-8: > > Sys.setlocale("LC_ALL", "Japanese_Japan.932") > > times <- c("1970-01-01 01:00:00 UTC", "1970-02-02 22:00:00 UTC") > ampm <- format(as.POS

Re: [Rd] Windows, format.POSIXct and character encodings

2013-05-01 Thread Simon Urbanek
On May 1, 2013, at 5:33 PM, Simon Urbanek wrote: > > On May 1, 2013, at 10:06 AM, Hadley Wickham wrote: > >> Hi all, >> >> In what encoding does format.POSIXct return its output? It doesn't >> seem to be utf-8: >> >> Sys.setlocale("LC_AL

Re: [Rd] Comments in the DESCRIPTION file

2013-05-02 Thread Simon Urbanek
On May 2, 2013, at 2:58 AM, cgenolin wrote: > Hi, > > I am not that familiar with the DCF... But R seems to accept # quite easely. The fact that R currently accepts invalid DCF files is not a guarantee that it won't be following the standard more closely in the future. What you are doing is i

Re: [Rd] install.packages from own rpository - depencies

2013-05-02 Thread Simon Urbanek
On May 2, 2013, at 9:58 AM, Knut Krueger wrote: > I am trying to setup a respository for students with a own package. > Its working fine when the depended packages are already installed with: > install.packages("mypackage", > type="source",repos="http://myrepository.example.com";) > > but if the

Re: [Rd] Comments in the DESCRIPTION file

2013-05-02 Thread Simon Urbanek
On May 2, 2013, at 10:17 AM, cgenolin wrote: > So it IS curently accepted, but may NOT be in the futur. Thanks for your > answer. > > So I guess that using > --- 8< - > %1: > %%%2: Section 1 > %%%3 > ... > --- 8< - > > is correct, isn't it? > Yes, that is lega

Re: [Rd] Minimal build of R ...

2013-05-02 Thread Simon Urbanek
On May 2, 2013, at 6:18 PM, Gabriel Becker wrote: > Jony, > > I'm currently writing up the paper for something with a similar result but > very different implementation. The RBrowserPlugin package/browser plugin > (joint with my advisor Duncan Temple Lang) embeds R within the web browser > as an

Re: [Rd] Licence change

2013-05-03 Thread Simon Urbanek
On May 3, 2013, at 10:34 AM, Mauricio Zambrano-Bigiarini wrote: > Dear list, > > For the maintainer of a given package, is it possible to change the licence > of a it from GPL >= 2 to GPL >= 3 ? > In general the maintainer has no such rights. However, if the maintainer is also the author and

Re: [Rd] Minimal build of R ...

2013-05-03 Thread Simon Urbanek
gt; I'll let you know if I make any progress! > > > Jony > > > -- > Centre for Cold Matter, The Blackett Laboratory, > Imperial College London, London SW7 2BW > T: +44 (0)207 5947741 > http://www.imperial.ac.uk/people/jony.hudson > http://www.imperial.ac.uk/

Re: [Rd] Minimal build of R ...

2013-05-03 Thread Simon Urbanek
's neat, but it's a bit hamstrung by > > the lack of javascript libraries to actually do any useful analysis! If you > > could have R running in there though, that would be a much better > > proposition ... > > > > I'll let you know if I make any progre

Re: [Rd] Dependencies of Imports not attached?

2013-05-08 Thread Simon Urbanek
On May 7, 2013, at 11:35 PM, Peter Meilstrup wrote: > Encountered an error in scripting, which can be reproduced using Rscript as > follows: > > $ Rscript -e "library(httr); handle('http://cran.r-project.org')" > > Error in getCurlHandle(cookiefile = cookie_path, .defaults = list()) : > could

Re: [Rd] Dependencies of Imports not attached?

2013-05-08 Thread Simon Urbanek
On May 8, 2013, at 1:52 PM, Martin Morgan wrote: > On 05/08/2013 10:25 AM, Simon Urbanek wrote: >> >> On May 7, 2013, at 11:35 PM, Peter Meilstrup wrote: >> >>> Encountered an error in scripting, which can be reproduced using Rscript as >>> follows: >&

Re: [Rd] call R function from C code

2013-05-09 Thread Simon Urbanek
On May 8, 2013, at 2:24 PM, Matwey V. Kornilov wrote: > Hi, > > I am writing C code for R, but in middle of the routine I want to call > solve(A,b) function. What is the right way to solve linear set inside C code? > Is it ok to just invoke La_solve()? > There is no such thing as La_solve().

Re: [Rd] call R function from C code

2013-05-10 Thread Simon Urbanek
On May 10, 2013, at 5:34 AM, Matwey V. Kornilov wrote: > > Thanks, It is what I was looking for. But now, I poorly understand > environment conception. My initial C function in invoked from R (in some > environment I suppose), how do I know this env, to provide it to eval()? Or, > may I just m

Re: [Rd] setTimeLimit sometimes fails to terminate idle call in R

2013-05-16 Thread Simon Urbanek
Jeroen, On May 16, 2013, at 2:12 PM, Jeroen Ooms wrote: > I would like to use setTimeLimit to abort operations that are stuck > waiting (idle) after n seconds. Below a toy example in which Sys.sleep > is a placeholder call that is idle: > > testlimit <- function(){ > setTimeLimit(elapsed=3, tra

Re: [Rd] Using a shared object without installing a library required by the object.

2013-05-23 Thread Simon Urbanek
On May 23, 2013, at 4:18 PM, Xiao He wrote: > Dear all, > > I have a C++ code. To create a shared object from this particular code, I > had to install a Fortran library on my computer (Mac). The compiled code > runs fine on my computer. However, if I try to dyn.load() said shared > object on a

Re: [Rd] Standalone example to use eval in C (not eval in R)?

2013-05-24 Thread Simon Urbanek
On May 24, 2013, at 6:00 AM, Peng Yu wrote: > 'eval' is used in optim.c, but it is used along with other things. I'm > looking for a standalone example to demonstrate the usage of eval in > C. Does anybody have some a simple example? Thanks. > Try R-exts: "5.11 Evaluating R expressions from C"

Re: [Rd] Assigning NULL to large variables is much faster than rm() - any reason why I should still use rm()?

2013-05-25 Thread Simon Urbanek
On May 25, 2013, at 3:48 PM, Henrik Bengtsson wrote: > Hi, > > in my packages/functions/code I tend to remove large temporary > variables as soon as possible, e.g. large intermediate vectors used in > iterations. I sometimes also have the habit of doing this to make it > explicit in the source c

Re: [Rd] About " Error: C stack usage is too close to the limit"

2009-05-19 Thread Simon Urbanek
On May 19, 2009, at 4:30 AM, goon83 wrote: Hi everyone! I meet one problem when embedding R in C code, when I run the the R code in one child thread , it always print error info: Error: C stack usage is too close to the limit I also try to set R_CStackLimit = (uintptr_t)-1 to disab

Re: [Rd] [R] step by step debugger in R?

2009-05-25 Thread Simon Urbanek
On May 24, 2009, at 10:18 AM, Romain Francois wrote: Robert Gentleman wrote: Hi, I stripped the cc's as I believe that all read this list. Romain Francois wrote: [moving this to r-devel] Robert Gentleman wrote: Hi, Romain Francois wrote: Duncan Murdoch wrote: On 5/22/2009 10:59 AM,

Re: [Rd] [R] step by step debugger in R?

2009-05-25 Thread Simon Urbanek
On May 25, 2009, at 4:54 PM, Romain Francois wrote: Simon Urbanek wrote: [snip] I need to read more about embedding R (as in section 8 of WRE). I know you can supply your own implementation of the REPL, but I am not sure this includes the one that goes on once trapped into the

Re: [Rd] Problems with plot and Quartz device (PR#13744)

2009-06-03 Thread Simon Urbanek
Thomas, rna is not defined in R, can you, please, supply a reproducible example? From your description I think I know roughly what's going on (Quartz attempts to snap rectangles on pixel boundaries to prevent malignant anti-aliasing effects in image plots and this may somehow interact wit

Re: [Rd] Problems with plot and Quartz device

2009-06-03 Thread Simon Urbanek
On Jun 3, 2009, at 4:45 , t...@stat.washington.edu wrote: Full_Name: Thomas Richardson Version: R 2.9.0 GUI 1.28 Tiger build 32-bit (5395) OS: 10.4.11 Submission from: (NULL) (216.254.15.72) I have encountered a problem with points in scatterplots disappearing in a quartz window when it i

Re: [Rd] Problems with plot and Quartz device / What is alpha?

2009-06-03 Thread Simon Urbanek
On Jun 3, 2009, at 15:00 , Thomas Richardson wrote: PS Please forgive my ignorance, but when you say: BTW: you may want to use something like pch=19, cex=0.1 (and maybe add some alpha to get a quick density estimation). I don't know what alpha refers to here. alpha = alpha component of

Re: [Rd] Problems with plot and Quartz device (PR#13744)

2009-06-03 Thread Simon Urbanek
ytmp <- mydata[,2] y <- ytmp[(mydata[,3]==i)&(mydata[,4]==j)] plot (x,y,xaxt="n",yaxt="n",ann=FALSE,xlim=c(0,100),ylim=c(0,300),pch=".") } } --- On Wed, 3 Jun 2009, Simon Urbanek wrote: Thom

Re: [Rd] Issues converting from JSON to R

2009-06-12 Thread Simon Urbanek
On Jun 12, 2009, at 6:34 PM, Kynn Jones wrote: When converting from JSON to R it seems logical that a JSON array would correspond to an "unnamed" R list, while a JSON object would correspond to a "named" R list. E.g. JSON: [1, 3.1415927, "foo", false, null] => R: list(1, 3.1415927, "fo

Re: [Rd] R build fails during make when configured with "--with-x=no" (PR#13665)

2009-06-16 Thread Simon Urbanek
On Jun 14, 2009, at 14:16 , kevmac wrote: I still have that same error. Can you be more specific, please (exact errors, config.log, R version ...)? Are you using latest R? Cheers, Simon Do you have the la Simon Urbanek wrote: It should be fixed now. Cheers, Simon On Apr 20

Re: [Rd] Argument as.integer(NA) to a function C

2009-06-18 Thread Simon Urbanek
On Jun 18, 2009, at 9:57 , Christophe Genolini wrote: Hi the list, I am writing a R function that call a C function. The C function needs integers but I do not manage to give a NA integer as argument : --- C code --- void essai(int *t){ Rprintf("\nT0=%i T1=%i T2=%i T3=%i",t[0],t[1],t[2],t

Re: [Rd] R_parseVector and syntax error [was: error messages while parsing with rniParse]

2009-06-18 Thread Simon Urbanek
x27;s not what I'm arguing for]. Or am I missing something? Cheers, S Romain Simon Urbanek wrote: On Jun 15, 2009, at 12:05 , Romain Francois wrote: Hello, In JRI, is there a way to get the error message that is generated by the parser through rniParse For example, if I have th

Re: [Rd] ScalarLong?

2009-06-18 Thread Simon Urbanek
On Jun 18, 2009, at 16:34 , Kynn Jones wrote: I was surprised to see that there is a ScalarInteger function in Rinlinedfuns.h, but nothing like ScalarLong. How can one create an R-integer from a C long? There is no such thing as "long" in R (*), so one cannot make a "scalar long" vector i

Re: [Rd] Memory management issues

2009-07-05 Thread Simon Urbanek
On Jul 5, 2009, at 10:54 AM, Yuri D'Elia wrote: Hi everybody, I have been interfacing some C++ library code into an R package but ran into optimization issues specific to memory management that require some insight into the GC. One of the C++ libraries returns simple vectors of integers, d

Re: [Rd] Any workaround for CRAN Mac OS X compiler switch to R 2.10.0?

2009-07-18 Thread Simon Urbanek
On Jul 17, 2009, at 8:55 PM, Kasper Daniel Hansen wrote: This has been discussed on the R-sig-mac email list. The short answer is that something bad happened (bad = R-devel was used to compile CRAN packages) and Simon (who is maintaining this) was traveling. He is working on the problem no

Re: [Rd] destructor for S4 class objects in analogy to C++

2009-07-21 Thread Simon Urbanek
David, On Jul 21, 2009, at 13:00 , David Scherrer wrote: I'm wondering if there is a way to define a destructor function (to free memory) for S4 class objects in analogy to C++? The analogy doesn't work, because in C++ you have pass-by-reference semantics, but in R you have pass-by-value.

Re: [Rd] Rcmd check fails on Windows Samba network path in R 2.9.1

2009-07-22 Thread Simon Urbanek
On Jul 22, 2009, at 10:28 , Duncan Murdoch wrote: On 7/22/2009 9:10 AM, Kevin R. Coombes wrote: Hi, Thanks; that confirms that the problem originates where I thought it did, and provides a fix from within R. However, the original problem was that running "Rcmd check" from a Windows/DOS com

Re: [Rd] Checking package on Windows (and seemingly irreproducible errors in CRAN checks)

2009-07-30 Thread Simon Urbanek
On Jul 30, 2009, at 7:33 , Carlos J. Gil Bellosta wrote: Dear Uwe, The thing that I find funny is that the check of the package on Windows for R 2.10.x works on r-forge as you can see here: http://r-forge.r-project.org/R/?group_id=426&log=check_x86_32_windows&pkg=colbycol&flavor=devel May I

Re: [Rd] identical(0, -0)

2009-08-10 Thread Simon Urbanek
On Aug 10, 2009, at 5:47 , Duncan Murdoch wrote: Petr Savicky wrote: On Sat, Aug 08, 2009 at 10:39:04AM -0400, Prof. John C Nash wrote: I'll save space and not include previous messages. My 2 cents: At the very least the documentation needs a fix. If it is easy to do, then Ted Harding's s

Re: [Rd] multicore mclapply hangs

2009-08-10 Thread Simon Urbanek
On Aug 10, 2009, at 6:17 , Markus Schmidberger wrote: Hello Rune, please use the mailinglist 'R-sig-hpc' (https://stat.ethz.ch/mailman/listinfo/r-sig-hpc , do not forget to register!) for this topic. .. or even better ask the package maintainer (with more precise details such as the exa

Re: [Rd] 10x slower merge in mac 2.9.1 vs. 2.9.0 (PR#13890)

2009-08-13 Thread Simon Urbanek
Rick, I'm sorry, but I cannot reproduce it. You didn't supply sessionInfo() and the actual data, so all I can do is guess, but according to your description this test case shows no difference: set.seed(1) n=1 d1 = data .frame (seqn = as .integer (runif (n )*n ),a = rnorm (

Re: [Rd] memory management

2009-08-13 Thread Simon Urbanek
Yuri, I'm not convinced that what you propose is a good idea. First, I don't quite understand why you would want to use an existing SEXP - if you had a valid SEXP for the current R instance, then there is no need for R_RegisterObject. If the SEXP is from a different R instance then you ca

Re: [Rd] Calling C functions with value parameters

2009-08-18 Thread Simon Urbanek
Jeff, On Aug 17, 2009, at 10:23 , Jeffrey J. Hallman wrote: One hassle I could do without is the necessity of writing C wrapper functions like this: void fameInit(int *status){ cfmini(status); return; } when I want to call a library function (cfmini, in this case) that takes an int argu

Re: [Rd] trouble building 2.10?

2009-08-18 Thread Simon Urbanek
On Aug 18, 2009, at 17:06 , Ben Bolker wrote: Should I expect to be able to build 2.10 at the moment? Yes (it works on my system) - when in doubt pull a fresh checkout (in general you cannot expect svn updates to build without full cleanup due to possible changes in the build process).

Re: [Rd] Problem using findVar( ) in combination with R's lazy evaluation

2009-08-20 Thread Simon Urbanek
Marcel, On Aug 20, 2009, at 8:41 , MarcelK wrote: I have a few small questions about the usage of the C findVar( ) function when used in C code called with '.Call'. In my case I create an R function with an argument. This function calls some C code in which I use findVar( ) to retrieve the

Re: [Rd] Cannot make 3 different R installations for 3 different valgrind-instrumentation levels

2009-08-25 Thread Simon Urbanek
On Aug 25, 2009, at 12:31 PM, pleyd...@supagro.inra.fr wrote: "R Installation and Administration", section 2.5 "Sub-architectures" describes calling specific builds of R using the call "R --arch=name". I am trying to build and install three versions of R-2.9.1, each configured with a diffe

Re: [Rd] Cannot make 3 different R installations for 3 different valgrind-instrumentation levels

2009-08-26 Thread Simon Urbanek
On Aug 26, 2009, at 6:47 , pleyd...@supagro.inra.fr wrote: You're confusing rhome and arch - the above makes no sense. Let rhome alone and you should be fine. (And make sure you're not building in the source tree - you should be using something like mkdir obj_vg0 && cd obj_vg0 && ../R-2

Re: [Rd] Cannot make 3 different R installations for 3 different valgrind-instrumentation levels

2009-08-26 Thread Simon Urbanek
On Aug 26, 2009, at 10:43 , pleyd...@supagro.inra.fr wrote: ^^-- this is really bad form - you should never build/compile software as root. The location of the build directory is irrelevant so use /tmp or you home or something like that ... (usualy the fastest disk ;)) OK, thanks for

Re: [Rd] Clarifications please.

2009-08-26 Thread Simon Urbanek
On Aug 26, 2009, at 12:55 , Martin Morgan wrote: Hi Abhijit -- Abhijit Bera wrote: Hi Martin Thanks. I think I got it! Read the R extensions documentation again. I don't even need to convert to a list. This is what I did (just a demo): #include #include #include #include int main

Re: [Rd] ARM v7/Linux Port/cross-compile?

2009-08-27 Thread Simon Urbanek
On Aug 27, 2009, at 5:37 PM, Jonathan Wilner wrote: Hi, Has anyone succeeded in cross-compiling R to Linux on an ARM CPU? Yes (although that questions leaves a lot of room for interpretation). If so, can you share a little about your toolchain & build process? It was fairly straight-fo

Re: [Rd] Clarifications please.

2009-08-28 Thread Simon Urbanek
On Aug 28, 2009, at 7:41 AM, Abhijit Bera wrote: Hi Martin Here's the code. I'm stuck at one point. I cannot figure out how to print the dimnames. I've commented it in my code: int main (int argc, char** argv) { SEXP e,t1,t2,val; int errorOccurred,nx,ny,i,j; double *v; char x[

Re: [Rd] Clarifications please.

2009-08-28 Thread Simon Urbanek
On Aug 28, 2009, at 9:42 AM, Abhijit Bera wrote: Hi Simon Thanks. All the confusion between CHAR and STRING. First I read this : http://www1.cuni.cz/~obo/r_surprises.html Uh, oh, that doc confuses things even more and is not really correct (well, the author admits that he has no idea, bu

Re: [Rd] ARM v7/Linux Port/cross-compile?

2009-08-28 Thread Simon Urbanek
On Aug 28, 2009, at 11:18 , Andrew Piskorski wrote: On Thu, Aug 27, 2009 at 06:36:38PM -0400, Simon Urbanek wrote: It was fairly straight-forward to build R (like any other cross- compilation). The tricky part is to install packages (if you are truly cross-compiling on another architecture

Re: [Rd] Installing rJava RJDBC bad interpreter: Permission denied

2009-09-02 Thread Simon Urbanek
On Sep 1, 2009, at 21:05 , Matias Silva wrote: Trying to install the above two packages via the "install.packages("package_name")" command and the "R CMD INSTALL file.tar.gz". I receive the following error either way "sh: ./configure: /bin/sh: bad interpreter: Permission denied". I have tr

Re: [Rd] Dependencies of packages' CHECK....

2009-09-02 Thread Simon Urbanek
Allen, On Sep 2, 2009, at 2:53 , Allen S. Rout wrote: I'm working to automate the building of RPM packages for CRAN &c. In the process, I'm trying to get a sense of the correct dependencies. It's my sense that R CMD CHECK is the Right Way to check to see if a package is built properly. B

Re: [Rd] Including a binary Python Interpreter into a binary R-package for MS Windows

2009-09-02 Thread Simon Urbanek
On Sep 1, 2009, at 17:41 , gvst...@yahoo.com wrote: 2009/8/30 Uwe Ligges : [snip] Guido van Steen wrote: [snip] Something that interests me too: What about R's policy with respect to including binary files? I saw that developers should include a file [snip] Please do not include binary fil

Re: [Rd] Depth of protection stack?

2009-09-03 Thread Simon Urbanek
On Sep 2, 2009, at 22:28 , Saptarshi Guha wrote: Hello, Is there a way, in C, to find how deep my current protection stack is(apart from keeping a count). I know the default nested size is 50,000 and because of some coding error i think i'm reaching it. Is there a way to find out the curr

Re: [Rd] Running an expression 1MN times using embedded R

2009-09-03 Thread Simon Urbanek
On Sep 3, 2009, at 7:15 PM, Saptarshi Guha wrote: Hello, I'm evaluating this expression expression({ for(x in 1:5){ .Call('rh_status','x') }}) a million times from a program with R embedded in it. I have attached reproducible code that crashes with Program received signal SIGSEGV, Segmenta

Re: [Rd] Rscript and default packages

2009-09-04 Thread Simon Urbanek
On Sep 3, 2009, at 13:52 , Romain Francois wrote: On 09/03/2009 05:23 PM, Duncan Murdoch wrote: On 03/09/2009 9:53 AM, Romain Francois wrote: Hi, Is is possible to embed inside an R script, the name of the default packages to be loaded when the script is invoked with Rscript. I know about

Re: [Rd] Rscript and default packages

2009-09-04 Thread Simon Urbanek
On Sep 4, 2009, at 10:20 , Simon Urbanek wrote: On Sep 3, 2009, at 13:52 , Romain Francois wrote: On 09/03/2009 05:23 PM, Duncan Murdoch wrote: On 03/09/2009 9:53 AM, Romain Francois wrote: Hi, Is is possible to embed inside an R script, the name of the default packages to be loaded

Re: [Rd] enabling core dumps

2009-09-04 Thread Simon Urbanek
On Sep 4, 2009, at 12:11 , pleyd...@supagro.inra.fr wrote: not really answering your question, but I find it more useful to R -d gdb or R -d gdb -f test.R where test.R reproduces the bug in some minimal code. A variant is R -d valgrind -f test.R if the memory problem is not easy to spot.

Re: [Rd] asking for suggestions: interface for a C++ class

2009-09-04 Thread Simon Urbanek
Yurii, On Sep 4, 2009, at 16:54 , Yurii Aulchenko wrote: Dear All, I would like to have an advice for designing an R library, and thought that R-devel may be the best place to ask given so many people who are highly expert in R are around. We are at an early stage of designing an R libra

Re: [Rd] Running two R instances at the same time

2009-09-05 Thread Simon Urbanek
On Sep 5, 2009, at 2:31 PM, Peter Juhasz wrote: Reposting from R-help: Dear R experts, please excuse me for writing to the mailing list without subscribing. I have a somewhat urgent problem that relates to R. I have to process large amounts of data with R - I'm in an international collaborat

Re: [Rd] Reissue: Base "Object" class to use in S4 slot specification

2009-09-08 Thread Simon Urbanek
On Sep 8, 2009, at 12:39 , Simon Urbanek wrote: On Sep 8, 2009, at 12:14 , Patrick Aboyoun wrote: This is a reissue of a question I had asked a few weeks ago to see if anyone had any thoughts on the matter. I am looking to have slot in an S4 class definition that can take any (S3 or S4

Re: [Rd] Reissue: Base "Object" class to use in S4 slot specification

2009-09-08 Thread Simon Urbanek
On Sep 8, 2009, at 12:14 , Patrick Aboyoun wrote: This is a reissue of a question I had asked a few weeks ago to see if anyone had any thoughts on the matter. I am looking to have slot in an S4 class definition that can take any (S3 or S4) object. The ANY class seemed to be a good candidat

Re: [Rd] Finding the environment of a promise

2009-09-09 Thread Simon Urbanek
On Sep 9, 2009, at 9:40 , Henrique Dallazuanna wrote: If I understand your question, you can get the environment with sys.frame: f <- function(code){ print(sys.frame()) ^-- this will always return R_GlobalEnv (see ?sys.frame - which = 0 by default) regardless of the function and promi

Re: [Rd] Non-GPL packages for R

2009-09-11 Thread Simon Urbanek
John, On Sep 11, 2009, at 9:07 , Prof. John C Nash wrote: The responses to my posting yesterday seem to indicate more consensus than I expected: 1) CRAN should be restricted to GPL-equivalent licensed packages I would definitely vote against that - I think this is not what the most people

Re: [Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze

2009-09-16 Thread Simon Urbanek
Mark, On Sep 16, 2009, at 15:51 , Mark Kimpel wrote: I just downloaded R-devel and when loaded it immediately segfaults. I'm not sure how much or what sort of diagnostic info and can provide, At the very least something like R -d gdb and the output of bt would be helpful. Then in general th

Re: [Rd] Windows Source Install Without Rtools

2009-09-17 Thread Simon Urbanek
On Sep 17, 2009, at 12:43 , Gabor Grothendieck wrote: Thanks. Perhaps someone in the core group can still provide explicit information on how to install such a package. R CMD INSTALL (see R --help and it has been *the* way to install packages for quite a while so I'm not sure how more exp

Re: [Rd] Windows Source Install Without Rtools

2009-09-17 Thread Simon Urbanek
e) sources, or to gzipped package 'tar' archives. The library tree [...] Cheers, S On Thu, Sep 17, 2009 at 3:58 PM, Simon Urbanek wrote: On Sep 17, 2009, at 12:43 , Gabor Grothendieck wrote: Thanks. Perhaps someone in the core group can still provide explicit information on h

Re: [Rd] basename returns "." not in filename (PR#13958)

2009-09-18 Thread Simon Urbanek
On Sep 18, 2009, at 12:11 , Peter Dalgaard wrote: jo...@web.de wrote: Full_Name: Jens Oehlschlägel Version: 2.9.2 OS: Win32 Submission from: (NULL) (85.181.152.156) # Obviously an empty basename is allowed (if the filepath is a pure path) basename("/") [1] "" # but here we get the dot f

Re: [Rd] basename returns "." not in filename (PR#13958)

2009-09-18 Thread Simon Urbanek
Jens, On Sep 18, 2009, at 15:08 , Jens Oehlschlägel wrote: Mmh, Point is, I gather, that trailing slashes are removed, e.g., viggo:~/>basename foo/ foo So, not a bug. This unfortunately means that we cannot distinguish between 1) a path with a filename 2) a path without a filename Of c

Re: [Rd] basename returns "." not in filename (PR#13958)

2009-09-18 Thread simon . urbanek
Jens, On Sep 18, 2009, at 15:08 , Jens Oehlschl=E4gel wrote: > Mmh, > >>> Point is, I gather, that trailing slashes are removed, e.g., >>> >>> viggo:~/>basename foo/ >>> foo >>> >>> So, not a bug. > > This unfortunately means that we cannot distinguish between > 1) a path with a filename > 2) a p

Re: [Rd] R with Java

2009-09-21 Thread Simon Urbanek
On Sep 21, 2009, at 5:27 , Nadine Bethke wrote: Hey, I´m a newbie in R and have a big problem. I hope, I´m in the right mailinglist, if not, sorry for this. Please use the stats-rosuda-devel mailing list: http://mailman.rz.uni-augsburg.de/mailman/listinfo/stats-rosuda-devel You may want to

Re: [Rd] Snow leopard ./configure "cannot compile a simple Fortran program"

2009-09-22 Thread Simon Urbanek
Jeff, On Sep 22, 2009, at 6:12 PM, Jeff Hamann wrote: I hope this is the place for this... Yes, indeed. I have to rebuild from scratch under Snow Leopard, and when I attempted to build R-2.9.1, I get the following results from ./ configure: checking how to get verbose linking output

Re: [Rd] How do I access class slots from C?

2009-09-29 Thread Simon Urbanek
Abhijit, as for your subject - it's GET_SLOT, but why don't you just use ParseVector and eval instead of hand- crafting C code that calls the evaluator? That latter is way more error prone and the error-handling is a nightmare (your current code is inefficient anyway so you don't gain anythi

Re: [Rd] How do I access class slots from C?

2009-09-29 Thread Simon Urbanek
MArtin, On Sep 29, 2009, at 12:17 , Martin Morgan wrote: Simon Urbanek wrote: Abhijit, as for your subject - it's GET_SLOT, but why don't you just use ParseVector and eval instead of hand- crafting C code that calls the evaluator? That latter is way more error prone and the erro

Re: [Rd] Problems connecting to httpd help server with some browsers

2009-09-29 Thread Simon Urbanek
Thomas, On Sep 29, 2009, at 15:15 , Thomas Friedrichsmeier wrote: Hello, sorry to provide only very little testing, but with the release date nearing, I thought it better to report this quickly than to wait for an uncertain period until I find more time. Yes, good thinking :). I'm ob

Re: [Rd] Problems connecting to httpd help server with some browsers

2009-09-30 Thread Simon Urbanek
Thanks, Jeff, good catch. Now committed. Simon On Sep 29, 2009, at 18:27 , Jeff Horner wrote: Simon Urbanek wrote: [...] I don't have konqueror at hand, so I have tested and fixed the lynx case (lynx is acting as an HTTP/1.0 client and expects non- persistent connection). With some luc

Re: [Rd] R 2.9.2 crashes when sorting latin1-encoded strings

2009-09-30 Thread Simon Urbanek
Stefan, On Sep 30, 2009, at 5:11 , Stefan Evert wrote: Hi everyone! I think I stumbled over a bug in the latest R 2.9.2 patched for OS X: R version 2.9.2 Patched (2009-09-24 r49861) i386-apple-darwin9.8.0 When I try to sort latin1-encoded character vectors, R sometimes crashes with a se

Re: [Rd] How to compile R with command completion?

2009-09-30 Thread Simon Urbanek
On Sep 30, 2009, at 10:13 , Peng Yu wrote: I compiled R-2.9.2 from source on Cent OS. But the compile R program does not support command completion. I get the following configure output that is related to readline. Why 'rl_completion_matches' doesn't exist? Maybe your readline is too old? Ma

Re: [Rd] How to compile R with command completion?

2009-09-30 Thread Simon Urbanek
b64 -- did you build it just in 32-bit?) Cheers, Simon On Sep 30, 2009, at 16:30 , Peng Yu wrote: On Wed, Sep 30, 2009 at 9:58 AM, Simon Urbanek wrote: On Sep 30, 2009, at 10:13 , Peng Yu wrote: I compiled R-2.9.2 from source on Cent OS. But the compile R program does not support command

Re: [Rd] creating environments in package's C code

2009-10-01 Thread Simon Urbanek
On Oct 1, 2009, at 11:33 , Martin Becker wrote: Dear developers, is it possible to create environments in C code of packages? Simply using SEXP env; PROTECT (env = allocSExp(ENVSXP)); and assigning the enclosing environment with SET_ENCLOS seems to be insufficient. Rf_NewEnvironment is

Re: [Rd] creating environments in package's C code

2009-10-01 Thread Simon Urbanek
Jeff, On Oct 1, 2009, at 12:37 , Jeff Horner wrote: Jeff Horner wrote: Martin Becker wrote: Dear developers, is it possible to create environments in C code of packages? Simply using SEXP env; PROTECT (env = allocSExp(ENVSXP)); and assigning the enclosing environment with SET_ENCLOS seems t

Re: [Rd] Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'character' & 'getEncChar' must be called on a CHARSXP

2009-10-01 Thread Simon Urbanek
Saptarshi, how did you create those lists? Can you send us the code? If not, can you put up the .RData file? Without a reproducible example this is hard to debug ... Thanks, Simon On Oct 1, 2009, at 14:26 , Saptarshi Guha wrote: Hello, I have list of 600K lists, each sublist a list of t

Re: [Rd] Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'character' & 'getEncChar' must be called on a CHARSXP

2009-10-01 Thread Simon Urbanek
r to code in R src/main rv = CDR(rv); SEXP rval; PROTECT(rval = Rf_allocVector(VECSXP, Rf_length(rv))); for (int n = 0 ; n < LENGTH(rval) ; n++, rv = CDR(rv)){ SET_VECTOR_ELT(rval, n, CAR(rv)); } UNPROTECT(2); //rval and rv return(rval) On Thu, Oct 1, 2009 at 5:36 PM, Simon Urbanek wrote: Saptars

Re: [Rd] Compiling with High Performance Fortran

2009-10-02 Thread Simon Urbanek
On Oct 2, 2009, at 2:35 PM, Fabio Mathias Corrêa wrote: Dear, I looked in the list something on as to compile a code with access the High Performance FORTRAN using R CMD SHLIB, but I did not find. Would like to know if the accepted R this type of language? R supports systems with FORTR

Re: [Rd] compiling packages without Framework and CoreFoundation options on OSX

2009-10-08 Thread Simon Urbanek
Jeff, On Oct 7, 2009, at 18:48 , Jeff Hamann wrote: I've been trying to get R+PostgreSQL+PL/R to work together on a OSX machine without the Framework and CoreFoundation options and have noticed some suspicious switches when compiling packages. I've installed R (on OSX) with the following ./con

Re: [Rd] [R-SIG-Mac] rnorm.halton

2009-10-10 Thread Simon Urbanek
Christophe, you're looking at the wrong docs -- normally there is nothing you need to change FORTRAN code when switching between 32-bit and 64-bit. There is no separate "64-bit code" or "32-bit code". None of the scalar types used by R in interfaces changes (int, double and INTEGER, REAL*8

Re: [Rd] [R-SIG-Mac] rnorm.halton

2009-10-10 Thread Simon Urbanek
Christophe, I forgot to answer the second part of your e-mail -- see below. On Oct 10, 2009, at 12:04 PM, Christophe Dutang wrote: Hi all, I need to transform classic 32bit Fortran code to 64bit Fortran code, see the discussion [R-SIG-Mac] rnorm.halton. But I'm clearly a beginner in Fortr

Re: [Rd] Help with OCaml bindings for R interpreter.

2009-10-10 Thread Simon Urbanek
On Oct 10, 2009, at 3:53 PM, Guillaume Yziquel wrote: Hello. I've made out a Debian package out of Maxence Guesdon's OCaml/R bindings: http://yziquel.homelinux.org/topos/debian-ocamlr.html http://yziquel.homelinux.org/debian/pool/main/o/ocaml-r/ The upstream software itsel

Re: [Rd] R on Google Android

2009-10-11 Thread Simon Urbanek
Mikkel, On Oct 11, 2009, at 6:38 AM, Mikkel Meyer Andersen wrote: As a follow-up on [1], I'd like to raise the question of whether it's practically possible to compile R to the Google Android mobile platform? The best way would probably be to use the Native Developer Kit [2], NDK, and in that

Re: [Rd] R on Google Android

2009-10-11 Thread Simon Urbanek
A description would help me trying to do it with Android. I've done some searching, but the only relevant hit I've found is http://ephphatharesearch.com/Eph_Blog_Post.aspx/Show/41. Cheers, Mikkel. 2009/10/12 Simon Urbanek : Mikkel, On Oct 11, 2009, at 6:38 AM, Mikkel Meyer Andersen

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

2009-10-14 Thread simon . urbanek
(moving to the proper mailing list: R-SIG-Mac - this is not a bug so far!) James, this look like your internet access is stalling R -- it's not really R freezing but your internet. Try using a different mirror and/or check your internet connection. Cheers, Simon On Oct 13, 2009, at 10:45

Re: [Rd] Question when compiling source code with VC++

2009-10-16 Thread Simon Urbanek
On Oct 15, 2009, at 17:01 , cstrato wrote: Dear Duncan, In your document "readme.packages.txt" you have a very helpful chapter on "Using Visual C++". Please allow me to ask you one question: Why do you propose the option "/MT" instead of option "/MD"? (To my knowledge usually option "/MD"

Re: [Rd] Fixing html help port in 2.10

2009-10-16 Thread Simon Urbanek
Dieter, On Oct 16, 2009, at 11:01 , Dieter Menne wrote: Duncan Murdoch-2 wrote: On 10/16/2009 10:39 AM, Dieter Menne wrote: I noted that the new html-help in 2.10 under Windows uses a random port on my computer. This cause a problem, because when I create a link such as: http://127.0.0.1

Re: [Rd] Confusion regarding allocating Matrices.

2009-10-24 Thread Simon Urbanek
On Oct 24, 2009, at 2:58 PM, Abhijit Bera wrote: Ok I get it. So everytime it does a alloc and copy. I haven't finished the design yet. I'm just thinking about how randomly the data might arrive; its real time data. So I will allocate a large chunk of memory and keep track of when it fills

Re: [Rd] R on maemo

2009-10-27 Thread Simon Urbanek
On Oct 27, 2009, at 12:13 , Juha Vierinen wrote: Has anyone tried to compile R on the Nokia maemo platform? I've been thinking about buying the n900 phone when it comes out, but I guess the main selling point would be a possibility to run R on it. I've read some rumors that it is based on

Re: [Rd] Help with lang4

2009-10-29 Thread Simon Urbanek
On Oct 29, 2009, at 13:56 , Seth Falcon wrote: On 10/29/09 7:38 AM, Abhijit Bera wrote: Can't find the source to Rf_lang* series of functions. :| But I'm thinking it should be like this correct me if I'm wrong: PROTECT(e=lang4(install("myfunction"),arg1,arg2,arg3); PROTECT(SETCAR(CDR(e),port

Re: [Rd] R 2.10.0 Mac OS X 10.6 (PR#14058)

2009-11-11 Thread simon . urbanek
Stephen, I cannot reproduce it (using Leopard build). Please supply full information (including sessionInfo() and version of the GUI used) as required by the posing guide. Thanks, Simon On Nov 11, 2009, at 7:50 , step...@prollenium.com wrote: > > --Apple-Mail-56-463481941 > Content-Transf

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