Re: [Rd] defining r audio connections

2020-05-07 Thread Simon Urbanek
is solely at CRAN's discretion to decide what gets published, so it may be worth raising it with the team, ask for the reasons and what it would take for them to accept packages using that API. Cheers, Simon > On 8/05/2020, at 1:02 AM, Jim Hester wrote: > > https://github.com/j

Re: [Rd] GCC warning

2020-05-22 Thread Simon Urbanek
don't see any link to what you submitted so can’t look at the code involved. Cheers, Simon > On May 22, 2020, at 7:25 PM, Adrian Dușa wrote: > > I am trying to submit a package on CRAN, and everything passes ok on all > platforms but Debian, where CRAN responds with an autom

Re: [Rd] C Interface

2010-06-18 Thread Simon Urbanek
f("The value is %f", *ptr); > UNPROTECT(1); > return result; > } > > }; > > It is compiled with > > R CMD SHLIB OrthoFunctions.c > > with flag > > MAKEFLAGS="CC=g++" > That is entirely wrong - g++ is not a C compiler. Cheers,

Re: [Rd] How to debug: Cons memory exhausted

2010-06-24 Thread Simon Urbanek
Does anybody have an advice on debugging this particular > error? > You can set a breakpoint on mem_err_cons. In general it means that you are simply running out of memory. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] accessing underlying code

2010-07-06 Thread Simon Urbanek
On Jul 6, 2010, at 11:04 AM, Hodgess, Erin wrote: > Dear R Developers: > > Is there a way to look at the underlying code from such items as > R_setup_starma, please? > Yes, of course, they are in the R sources (src/library/stats/src/pacf.c) - that's the beauty of open so

Re: [Rd] Strange R object

2010-07-09 Thread Simon Urbanek
t; attr(,"class") >>> [1] "X" >>>> x >>> [1] "print.X" >>>> xx <- 1*x >>> [1] "Ops.X" >>>> class(xx) <- class(xx) >>>> xx >>> [1] "print.X" >> >> Or, to minimize it further: >> >>> x <- structure(1, class="y") >>> is.object(x) >> [1] TRUE >>> is.object(x*1) >> [1] TRUE >>> is.object(1*x) >> [1] FALSE >>> class(x*1) >> [1] "y" >>> class(1*x) >> [1] "y" >> >> Yup, that looks like a bug. > > I recently came across the following surprising behaviour which turns > out to be the same issue. I had been meaning to ask for an > explanation. > >> x <- 1:20 >> class(x) > [1] "integer" >> is.object(x) > [1] FALSE >> print.integer <- function(x) print(x %% 5) >> print(x) > [1] 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 1 2 3 4 0 >> x > [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 > ... that is an entirely different issue. x is still not an object because it doesn't have any explicit S3 class so it has nothing in common with the case discussed. This is about P in REPL which uses PrintValueEnv which is turn dispatches to print() only for objects (see main and print). Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R-2.11.1 build and 'so' libraries withouth the 'lib' prefix

2010-07-12 Thread Simon Urbanek
e defaults > were. I ended up with shared-libraries which are as follows:- > > $R_HOME/lib/{libRblas.so,libRlapack.so } i.e. with the prefix 'lib' > and the following shared-libraries without the 'lib' prefix. > Those are not shared libraries - they are shared o

Re: [Rd] R-2.11.1 build and 'so' libraries withouth the 'lib' prefix//update

2010-07-12 Thread Simon Urbanek
-shlib \ > --enable-BLAS-shlib > in the configure options of the downloaded R-2.11.1 source prior to > compilation. > > I am compiling R-2.11.1 as an optional dependency of kdeedu-4.4.5. > This > asks for R-shlib )which I noticed it is disable by the default in the > configure script.) > > After compile and install of R-2.11.1, I am only able to start R from the > command line How are you starting it? The R start script does setup everything so that you should never touch anything inside. > when I move the generated libRblas.so to libRblas.soDUFF and > symlink libacml.soto libRblas.so and update $R_HOME/etc/ldpaths > accordingly. I am unable to start R with the compiled-in $R_HOME/libR.so > and $R_HOME/libRblas.so. > > QUESTIONS: > A) How does one start R with the the generated libR.so and libRblas.so? bin/R > B) is the generated libR.so interchangable with libRblas.so (i.e. R > library > without blas enhanced algebra capabilities?) > No - those are two entirely different libraries. The libRblas can be interchanged with a suitably complete BLAS implementation, but please do read the manuals for details. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R-2.11.1 build and 'so' libraries withouth the 'lib' prefix//update

2010-07-12 Thread Simon Urbanek
On Jul 12, 2010, at 5:59 PM, lI wrote: > On Monday 12 July 2010 20:52:15 Simon Urbanek wrote: >> On Jul 12, 2010, at 2:50 PM, lI wrote: >>> On Monday 12 July 2010 11:07:23 lI wrote: >>>> On Monday 12 July 2010 10:29:30 lI wrote: >>>>> Greetings, >

Re: [Rd] Precompiled vignette on CRAN

2010-07-14 Thread Simon Urbanek
This gives a warning, as you will see in quite a few CRAN package > checks. > In the case of TripleR R CMD check failed (i.e. error code != 0) because of the vignette. Cheers, Simon * - which reminds me -- what is the correct place to list vignette dependencies? "

[Rd] bug in identical()? [Was: [R-sig-ME] Failure to load lme4 on Mac]

2010-07-17 Thread Simon Urbanek
where it fails ... I'm CCing this to R-devel as the current issue seems more like an R issue so more eyes can have a look ... Cheers, Simon [FWIW this is tested in today's R-devel (with valgrind level 2) on x86_64 OS X 10.6.4 with lme4 from CRAN and Matrix form R-devel Recommende

Re: [Rd] bug in identical()? [Was: [R-sig-ME] Failure to load lme4 on Mac]

2010-07-17 Thread Simon Urbanek
s not shown up on other platforms as that is a global issue... (I hope this is the full story - I didn't try all the combinations to see if setting @env to the same environment will appease identical() for all the models) Cheers, Simon On Jul 17, 2010, at 3:49 PM, Simon Urbanek wrote: > D

Re: [Rd] Non-blocking Eval

2010-07-19 Thread Simon Urbanek
which does not include that -- however, it is trivial to implement (just send a request with CMD_detachedVoidEval as there is nothing to decode). Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Non-blocking Eval

2010-07-20 Thread Simon Urbanek
for the result and only come back later to collect the result. Cheers, Simon PS: please continue the discussion on stat-rosuda-devel as that is the correct place. > Thanks AgainMartin >> Subject: Re: [Rd] Non-blocking Eval >> From: simon.urba...@r-project.org >> Date: Mon

Re: [Rd] Plot window does not update in embedded code

2010-07-21 Thread Simon Urbanek
Use R_CheckUserInterrupt() The code below is very fragile and unix-specific. Cheers, Simon On Jul 21, 2010, at 3:45 PM, Thomas Friedrichsmeier wrote: > Hi, > > On Wednesday 21 July 2010, Jan van der Laan wrote: >> How do I ensure that the windows keep being updated? >

Re: [Rd] Plot window does not update in embedded code

2010-07-21 Thread Simon Urbanek
On Jul 21, 2010, at 4:28 PM, Simon Urbanek wrote: > Use > R_CheckUserInterrupt() > Actually, the above is true but assumes that you're running R's REPL and not your own R_ReadConsole (it will work even in your ReadConsole but unix handlers are not run in that case so on

Re: [Rd] Plot window does not update in embedded code

2010-07-22 Thread Simon Urbanek
On Jul 22, 2010, at 3:31 AM, Jan van der Laan wrote: > Thomas, Simon, > > Thank you for your answers. I will have a look at the code Thomas gave > me and probably also have another look at src/unix/sys-std.c. I'll get > back when I have this working, or, more likely, when I

Re: [Rd] R CMD check - "there is no package called"

2010-07-25 Thread Simon Urbanek
t; with > > R_LIBS_USER="/home/john/lib/R/library" > > I've also tried creating an environment variable "export > R_LIBRARY_DIR=/home/john/lib/R/library/" before running R CMD check. The correct name is R_LIBS Cheers, Simon > That made >

Re: [Rd] Recover source from LazyLoaded installation

2010-07-25 Thread Simon Urbanek
R-2.11.1 if it matters. > ?lazyLoad Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] CRAN updates?

2010-07-27 Thread Simon Urbanek
gt; Is the process automated or is it partially manual for some OS's (like > Windows/w64 > and Mac OS X)? > It is automated on Mac OS X (currently R builds start at midnight and package builds at 2am ET). Cheers, Simon PS: If you see delays (i.e. the check result is not avail

Re: [Rd] DetachedEval Issues

2010-08-17 Thread Simon Urbanek
f the port number. Which is entirely wrong - sessions don't re-attach to the server but to the random port generated on detach by the client. Cheers, Simon > Thus I am in fact using this: > Rsession* testSession = new > Rsession(theSession->host(),6311,theSession->key

Re: [Rd] c.POSIXct

2010-08-18 Thread Simon Urbanek
us stripping is very plausible and consistent) Cheers, Simon > On Thu, Aug 12, 2010 at 11:33 AM, Gabor Grothendieck > wrote: >> Currently if x1 and x2 are POSIXct then c(x1, x2) will not have a >> tzone attribute even if x1 or x2 or both do but it should. >> >> Thi

Re: [Rd] C or Java code generation

2010-08-20 Thread Simon Urbanek
erve, R[D]COM, JRI, ... all embed R which was that his point, rightly so. There is no way I know of to turn R code into something that can run on its own without R present (save for a tiny subset of Rmath). Cheers, Simon > RInside delivers what it promises: an embedded R instance for your C

Re: [Rd] segfault in embedded r after call to repldlldo1

2010-08-20 Thread Simon Urbanek
eep in mind is that R_ReplDLLinit uses setjmp to setup the top-level context so you have to make sure you're not using any local variables that could be on the stack from R_ReplDLLdo1 as it will get lost (and function calls of course). Cheers, Simon > can anyone please help

Re: [Rd] Rserve graphics output [was Re: C or Java code generation]

2010-08-20 Thread Simon Urbanek
nstalled software, not even java (I >> don't like applets). I thought R would be excellent for this but I need >> some issues cleared up before I invest a lot of time working with it. >> > > Well, Simon is the one who create Rserve. However, if you have questions > a

Re: [Rd] C or Java code generation

2010-08-20 Thread Simon Urbanek
use it. > FWIW: FastRWeb uses Rserve as back-end and is in active development since we use it internally (it's wicked fast, scalable and supports data pre-loading and AJAX). Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Rserve graphics output [was Re: C or Java code generation]

2010-08-20 Thread Simon Urbanek
can perform exploratory data >>> analysis with their browser with no installed software, not even java (I >>> don't like applets). I thought R would be excellent for this but I need >>> some issues cleared up before I invest a lot of time working with it. >>>

Re: [Rd] R-devel Digest, Vol 90, Issue 20

2010-08-21 Thread Simon Urbanek
R extensions, just Python). > Beside other niceties, it will allow working around the lack of > connection API in R for graphics. > Since Python makes the use of file-like objects straightforward, we plan > providing devices that are streams (nice for serving graphics from web >

Re: [Rd] R-devel Digest, Vol 90, Issue 20

2010-08-22 Thread Simon Urbanek
On Aug 22, 2010, at 3:32 AM, Laurent wrote: > On 21/08/10 23:31, Simon Urbanek wrote: >> >> On Aug 21, 2010, at 8:46 AM, Laurent wrote: >> >>> On 21/08/10 12:00, r-devel-requ...@r-project.org wrote: >>>> >>>> On Aug 20, 2010, at 1:59 PM, M

Re: [Rd] Handle RAWSXP in inspect.c:typename()

2010-08-23 Thread Simon Urbanek
RAW support to inspect in R-devel now. Thanks, Simon > Index: src/main/inspect.c > === > --- src/main/inspect.c(revision 52221) > +++ src/main/inspect.c(working copy) > @@ -63,6 +63,7 @@ > cas

Re: [Rd] Speeding up sum and prod

2010-08-23 Thread Simon Urbanek
system elapsed 2.473 0.001 2.474 ... and the "optimal" version above (3rd) with the same optimization settings: > a <- seq(0,1,length=1000) > system.time({for (i in 1:100) b <- sum(a)}) user system elapsed 1.670 0.003 1.673 > system.time({for (i

Re: [Rd] Internal state indicating if a data object has NAs/no NAs/not sure (Was: Re: Speeding up matrix multiplies)

2010-08-23 Thread Simon Urbanek
lelization where you can gain much more ... Luke Tierney did some great work in that direction that could be extended and gives you speed up of orders of magnitude, not just a few percent ...) Cheers, Simon > Then different computational algorithms are free to set the state, if > they kno

Re: [Rd] Speeding up matrix multiplies

2010-08-23 Thread Simon Urbanek
S on a multi-core machine and large matrices. > Of course, the real solution is to change the Fortran routine (which > seems to be in src/extra/blas/blas.f, and isn't all that complicated) Nope - it can be external and BLAS standard doesn't handle NAs. Cheers, Simon >

Re: [Rd] RCMD CHECK and non-methods

2010-08-26 Thread Simon Urbanek
nd t.test() > pre-dated S3} > However, one would hope that S3 will be replaced by S4 (or R5? ;)) eventually so requiring such an arcane rule seems little strong. Personally, I prefer the use of . to that of camelCase [I find it more readable and faster to type] and thus I'm with M

Re: [Rd] Incorrect formatted output after subtracting non-integer seconds from POSIXt origin

2010-09-03 Thread Simon Urbanek
second later than expected >> format(as.POSIXct("1970-1-1", tz="UTC")-86400, format="%Y-%m-%d > %H:%M:%OS2") > [1] "1969-12-31 00:00:00.00" # OK >> format(as.POSIXct("1970-1-1", tz="UTC")-86400.5, format="%Y-%m-%

Re: [Rd] RJava

2010-09-06 Thread Simon Urbanek
ne API instead: REngine eng = REngine.engineForClass("org.rosuda.REngine.JRI.JRIEngine"); eng.assign("x", "Peter") It is far more flexible and more safe that he direct API. Also it allows you to switch to several back-ends. Cheers, Simon __

Re: [Rd] Is an R sub-session somehow possible?

2010-09-07 Thread Simon Urbanek
ng an R > function that creates the completion. But, while in the middle of user > input, I can't call a function. > Why not? After the "+" prompt you're back in ReadConsole so it's safe. Cheers, Simon > I guess that ESS for emacs has the same problem. when I

Re: [Rd] what is the best way for an external interface to interact with graphics, libraries

2010-09-07 Thread Simon Urbanek
reasonably simple way would be to check the search path - if it changed a package has been loaded. A natural place to do such check would be in a top-level task handler for example. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] what is the best way for an external interface to interact with graphics, libraries

2010-09-07 Thread Simon Urbanek
On Sep 7, 2010, at 3:07 PM, ghostwheel wrote: > > > Simon Urbanek wrote: >> >> >> I don't know the mechanics of the actual "inserting" in TeXmac but it >> would be trivial to simply create a copy of the plot as EPS (or whatever >> is need

Re: [Rd] Is an R sub-session somehow possible?

2010-09-07 Thread Simon Urbanek
On Sep 7, 2010, at 2:43 PM, ghostwheel wrote: > > > Simon Urbanek wrote: >> >> >> On Sep 7, 2010, at 2:06 PM, ghostwheel wrote: >> >>> a<-c(3,4 >>> and then R will respond with '+'. >>> >>> The problem is th

[Rd] Sweave issue; keep.source=TRUE and cacheSweave incompatible?

2010-09-11 Thread Simon Jackman
that code chunks with keep.source=TRUE aren't being parsed correctly; the corresponding Schunk starts at the *very top* of the Rnw file, snippet shown below. The error seems specific to R 2.12.0; cacheSweave + keep.source=TRUE seems to work ok in R 2.11. Many thanks — Simon Version detai

Re: [Rd] Best way to manage configuration for openMP support

2010-09-14 Thread Simon Urbanek
MSG_ERROR here is OpenMP is required fi AC_SUBST(OPENMP_CFLAGS) AC_CONFIG_FILES([src/Makevars]) AC_OUTPUT And your Makevars.in will probably look something like: pkg_cppfla...@openmp_cflags@ pkg_li...@openmp_cflags@ @LIBS@ Cheers, Simon * - compiler version checks are sometime used directly in

Re: [Rd] Problem with WARNING...headers with CRLF line endings

2010-09-14 Thread Simon Urbanek
to be part of the distribution. Cheers, Simon > > On 9/14/10 2:06 AM, William Dunlap wrote: >> >>> -Original Message- >>> From: r-devel-boun...@r-project.org >>> [mailto:r-devel-boun...@r-project.org] On Behalf Of cstrato >>> Sent: Monday, Sept

Re: [Rd] advice on writing/maintaining an R package with a version control system

2010-09-16 Thread Simon Urbanek
od in case you forgot to add files to the VCS). If you have large or complex packages, it may be useful to just change a function at a time in the interactive session -- but that's trivial as you simply send the assignment from your editor. (Some tricks may be needed if namespaces are involve

Re: [Rd] How to set up an own package repository

2010-09-17 Thread Simon Urbanek
,"file:///myRepository") and have the files locally in /myRepository/src/contrib if you're only concerned about your local use. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Is it safe not to coerce matrices with as.double() in .C()?

2010-09-17 Thread Simon Urbanek
m.time(junk <- replicate(reps, f3(x))) > user system elapsed > 0 0 0 > > Perhaps I need to first check and see if the storage mode is as expected > before trying coercion? > Well, the devil is in the details. Although storage.mode<- is a noop itself, t

Re: [Rd] checking user interrupts in C(++) code

2010-09-28 Thread Simon Urbanek
ent loop (otherwise users would have no way of actually triggering it) which in turn could trigger error handing and thus not return to your function, either. BTW: pretty much any call to R can trigger an error, so R_CheckUserInterrupt() is not the only place that requires you to think about cle

Re: [Rd] checking user interrupts in C(++) code

2010-09-29 Thread Simon Urbanek
On Sep 29, 2010, at 11:34 AM, Berwin A Turlach wrote: > G'day Simon, > > since Karl brought up this topic, I thought I might use it to seek > clarification for something that bothered me for some time. > > On Tue, 28 Sep 2010 14:55:34 -0400 > Simon Urbanek wrote: &g

Re: [Rd] checking user interrupts in C(++) code

2010-09-29 Thread Simon Urbanek
ial (you will have a top-level interfacing call anyway). If you have multiple such objects that are hard to track for some reason, you can always use the finalizer approach. As you mentioned yourself the only issue are method-local objects that you cannot move

Re: [Rd] How do I put ldpaths in a specific place?

2010-10-06 Thread Simon Urbanek
nt!) If it's not then you are entirely on your own as you will have to use the above approach but then also make sure any dependent tools and libraries used by R are also present in the chroot jail. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] long double, C, fortran

2010-10-07 Thread Simon Urbanek
f, dpotri) still work with > long doubles? > No. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] "$<-" fails (invalid subscript type 'language')

2010-10-24 Thread Simon Urbanek
for bad names). > No, as David pointed out the documentation tells you unmistakably: "[...] The main difference is that ‘$’ does not allow computed indices [...]" so you want to use `[[` instead since `$` is defined exactly to not allow just what you're doing: the index argument

Re: [Rd] "$<-" fails (invalid subscript type 'language')

2010-10-25 Thread Simon Urbanek
On Oct 25, 2010, at 3:51 AM, Vitalie S. wrote: > Simon Urbanek writes: > >> On Oct 24, 2010, at 4:21 PM, Vitalie S. wrote: >> >>> David Winsemius writes: >>> >>>> On Oct 24, 2010, at 5:35 AM, Vitalie S. wrote: >>>> >&

Re: [Rd] windows 64-bit package build on 32-bit machine

2010-10-26 Thread Simon Urbanek
t; windows machine. But it doesn't look possible to build a 64-bit > library on a 32-bit windows machine? > Why not? It works for me without problems ... Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] windows 64-bit package build on 32-bit machine

2010-10-27 Thread Simon Urbanek
k regardless since you can't run 64-bit binary of R on 32-bit Windows. The same applies on OS X - you can cross compile for ppc64 (i.e. install multi-arch if the package has no Makefile/configure) but you can't run ppc64 R on Intel Macs (and hence you cannot install packages with config

Re: [Rd] Sections 5.8.1 and 5.8.2 of Writing R Extensions (LinkingTo)

2010-10-27 Thread Simon Urbanek
quot;,...) doesn't do the job these days since it will be missing R_ARCH so you need something like system.file("libs",.Platform$r_arch, package=...) for any more recent R. Cheers, Simon > So > there > is a trade-off of convenience vs efficiency. > > Thanks, > D

Re: [Rd] must .Call C functions return SEXP?

2010-10-27 Thread Simon Urbanek
6)); /* do something ... */ and in order to pass it out you just create a list and return it: SEXP result = PROTECT(allocVector(VECSXP, 2)); SET_VECTOR_ELT(result, 0, result_1); SET_VECTOR_ELT(result, 1, result_2); UNPROTECT(3); return result; Accordingly you get: l = .Call("my_C_func

Re: [Rd] must .Call C functions return SEXP?

2010-10-28 Thread Simon Urbanek
On Oct 28, 2010, at 9:48 AM, Andrew Piskorski wrote: > On Thu, Oct 28, 2010 at 12:15:56AM -0400, Simon Urbanek wrote: > >>> Reason I ask, is I've written some R code which allocates two long >>> lists, and then calls a C function with .Call. My C code writes t

Re: [Rd] list2env() is broken

2010-10-29 Thread Simon Urbanek
nclude a crash report. Also there is no such thing as "timeout" in this context - Herve meant probably hanging R which you should look at by attaching a debugger to get a backtrace to see where it is (on Mac you get an automatic backtrace if you force-quite the app which makes it easier).

Re: [Rd] [R-SIG-Mac] BLAS benchmarks on R 2.12.0

2010-11-03 Thread Simon Urbanek
> Mac Pro, so 32-bit x86 architecture." > The current build flags for i386 are listed in https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R-build/conf.leopard-i386 They did not change recently so they were the same for 2.11.1. The compiler used is gcc-4.2 from Xcode 3.1.4 (R is built on O

Re: [Rd] Calling C in R in Windows 64 bit

2010-11-03 Thread Simon Urbanek
tatic-libgcc -o COXPHmatprod24delta.dll tmp.def > COXPHmatprod24d > elta.o -LC:/PROGRA~1/R/R-212~1.0/bin/i386 -lR > gcc: not found' > You are compiling 32-bit and you don't have the tools installed. If you meant to use 64-bit you

Re: [Rd] SEXPs and slots

2010-11-16 Thread Simon Urbanek
On Nov 16, 2010, at 8:52 PM, Patrick Leyshock wrote: > Revisiting the output below: > > 1. Am I correct in thinking that the @XXX items are addresses? yes > 2. What are the meanings of the gXcX items? you should not worry about those - they are internal flags related to the garbage co

Re: [Rd] R5 reference classes: how to initialize exactly?

2010-11-17 Thread Simon Urbanek
capability to do so technically). Reference classes are just an addition to S4. Cheers, Simon On Nov 16, 2010, at 12:30 AM, Janko Thyson wrote: > Sorry, I was stupid: > > > > MyRefObj <- setRefClass("Blabla", .) > > > > One can always get the genera

Re: [Rd] JRI and error message from R_isMethodsDispatchOn

2010-11-19 Thread Simon Urbanek
allel instances. BTW: please use stats-rosuda-devel mailing list of questions related to rJava, JRI or Rserve. It's also worth scanning the archives as those issues have been raised before. Cheers, Simon > R version: 2.11.1 > rJava version: 0.8-4 > OS: Arch Linux > > Best, &g

Re: [Rd] how to store package options over sessions?

2010-11-22 Thread Simon Urbanek
when not expected is impolite to say the least. Cheers, Simon On Nov 20, 2010, at 11:12 AM, Mark Heckmann wrote: > Hi, > I posted this a week ago on r-help but did not get an answer. So I hope that > someone here can help me: > I want to define some options for my package the user may cha

Re: [Rd] R-.12.0 atlas lapack

2010-11-22 Thread Simon Urbanek
use). > b) if one now links libR.so to lib{atlas,lapack}.so (or .a) > You can do either -- or you can use shared BLAS - it's entirely up to you. Nothing really changed in recent R - the above applies for quite some time (ever since shared BLAS support was added) so it's very likely that any differences you see are entirely due to your setup, not due to R. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] segfault interest?

2010-12-02 Thread Simon Urbanek
Matt, please use R -d gdb and then "bt" for a more useful trace. Thanks, Simon On Dec 2, 2010, at 4:06 PM, Matt Shotwell wrote: > On Wed, 2010-11-24 at 12:12 -0500, ivo welch wrote: >> I just figured out what is happening. The root drive (presumably OSX >> virtual

Re: [Rd] Wait for user input with readline()

2010-12-07 Thread Simon Urbanek
You can't tell R code and input apart in cases like R < myScript.R but you can if you use source() or Rscript -- and you can treat them differently. I assume what Alexandre wants is something like: input=file("stdin") print(readLines(input,1)) which works both in interactive and non-i

Re: [Rd] Namespace File

2010-12-15 Thread Simon Urbanek
> } > Well, that's shooting at a clay pigeon with a missile ;). You could have done the same simply using useDynLib(Bayesthres) in the NAMESPACE. Your issue is very likely just a mixup of cases as there is no "vuA" symbol in Fortra

Re: [Rd] Namespace File

2010-12-15 Thread Simon Urbanek
On Dec 15, 2010, at 1:31 PM, Fabio Mathias Corrêa wrote: > Dear Simon > > By using useDynLib (Bayesthres) in NAMESPACE file. Appeared another error: > > Error in dyn.load("Bayesthres.so") : > unable to load shared object '/home/fmc/Bayesthres/Bayest

Re: [Rd] Namespace File

2010-12-15 Thread Simon Urbanek
ectories: inst, man, R and src > What is in inst? Make sure you have no binaries there. Cheers, Simon > > ... but that's an entirely wrong place - I suspect you have some real issues > in > the way your package is constructed. Are you sure you have the correct layout &g

Re: [Rd] Namespace File

2010-12-15 Thread Simon Urbanek
g copy. Cheers, Simon BTW: in order to avoid us having to guess what you did wrong it would be much easier if you simply put the package somewhere so we can check it - that would save us and you quite a bit of time. On Dec 15, 2010, at 3:34 PM, Fabio Mathias Corrêa wrote: > See the c

Re: [Rd] Rcmd SHLIB error

2010-12-19 Thread Simon Urbanek
t;> >>>> Duncan Murdoch >>>> >>> >>> Where in the sources is the C:\PROGRA~1\R\R-212~1.X\etci386 [sic] path >>> set? >> >> I don't know. Possibilities include src/gnuwin32/fixed/Makefile line 31 >> (where a bad R_ARCH woul

Re: [Rd] Bug filed on unzip() function

2010-12-23 Thread Simon Urbanek
el readership would say... Comments are welcome. Cheers, Simon > > On 21.12.2010 18:50, Ken Williams wrote: >> Hi, >> >> A few days ago I filed a bug report on the unzip() function: >> >> https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14462 >>

[Rd] Bugs e-mails and R-devel [Was: Bug filed on unzip() function]

2010-12-24 Thread Simon Urbanek
On Dec 24, 2010, at 12:22 AM, Marc Schwartz wrote: > On Dec 23, 2010, at 8:24 PM, Simon Urbanek wrote: > >> On Dec 23, 2010, at 7:44 AM, Uwe Ligges wrote: >> >>> This message contains a good question: >>> >>> Is there any reason why the bug report

Re: [Rd] Bug filed on unzip() function

2010-12-24 Thread Simon Urbanek
t that was just my personal rationalization for not looking into it if you want to know ;)] And as I mentioned there are reminders of open bugs to the assignees twice a week (R-core for most bugs), so the chance of a bug report being unnoticed is close to zero. Cheers, Simon ___

Re: [Rd] Bugs e-mails and R-devel

2010-12-24 Thread Simon Urbanek
t; the earliest 100 entries, starting Jan 28, 2000. Actually, the "recommended" link (first on the page) leads to a new-to-old open bugs query -- that's at least what I use most of the time -- and the feed link from there does work as expected. Cheers, Simon > I have had good

Re: [Rd] rJava question

2010-12-28 Thread Simon Urbanek
(other than using the J/$ API). That's why I was hesitant so far to fix the bug, but I really should -- which is why the behavior your discovered will change. However, then I need to add some API to be able to convert a reference in the same way that rJava:::newArray provides and expose it -

Re: [Rd] key-value mapping in C inside R?

2010-12-30 Thread Simon Urbanek
unction or some other approach already used inside the R > core for key-value mappings? > environment created with hash=TRUE, e.g.: e = new.env(TRUE, emptyenv()) e[["foo"]] = "bar" You can even set "size" with the expected size if you know it in advance. Cheer

Re: [Rd] key-value mapping in C inside R?

2010-12-30 Thread Simon Urbanek
On Dec 30, 2010, at 11:25 AM, Matteo Bertini wrote: > Il giorno 30/dic/2010, alle ore 16.03, Simon Urbanek ha scritto: > >> On Dec 30, 2010, at 7:50 AM, Matteo Bertini wrote: >> >>> I'm testing some modifications in arima.c. >>> I've noticed

Re: [Rd] C code hanging and printing everything at the end

2011-01-04 Thread Simon Urbanek
ny > way to print out as the program is running? > You want to add R_CheckUserInterrupt(); so that the system has a chance to run the event loop and thus display the result. But the implication is that you may be interrupted so make sure R controls any memory allocations you have made.

Re: [Rd] as.environment.list provides inconsistent results under torture

2011-01-11 Thread Simon Urbanek
Interesting, I'd argue that the bug is in eval() not protecting its arguments since the usual convention is for functions to protect its arguments... On Jan 11, 2011, at 2:33 PM, Romain Francois wrote: > Hello, > > Using R-devel (rev 53950), I get inconsistent results with as.environment( > VE

Re: [Rd] as.environment.list provides inconsistent results under torture

2011-01-11 Thread Simon Urbanek
(partly because one of them is mine ;)). Unfortunately all the examples in R-ext use implicitly protected arguments (as function arguments or parts of larger already protected constructs) so it's not obvious from that, either. Thanks, Simon > > > On Tue, 11 Jan 2011, Simon Urban

[Rd] naresid.exclude query

2011-01-14 Thread Simon Wood
ether I should just code up a work-around for predict.gam? Simon -- > Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK > +44 1225 386603 www.maths.bath.ac.uk/~sw283 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] isoreg memory leak?

2011-01-17 Thread Simon Wotherspoon
n/gc works is a bit off here, but I can't see how else the leak may occur. Hope this is more use than nuisance. Simon. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] isoreg memory leak?

2011-01-17 Thread Simon Urbanek
On Jan 16, 2011, at 10:41 PM, Simon Wotherspoon wrote: > > I believe there is a memory leak in isoreg in the current version of R, as I > believe the following shows > > > gc() > used (Mb) gc trigger (Mb) max used (Mb) > Ncells 120405 3.3 35 9.4 350

[Rd] Possible bug in Spearman correlation with use="pairwise.complete.obs"

2011-01-22 Thread Simon Anders
ank(x)[goodobs] [1] 10 6 8 7 4 5 1 9 2 Would you hence agree that 'method="spearman"' with 'use="pairwise.complete.obs"' is incorrect? Cheers Simon sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_

Re: [Rd] Windows script editor and locale

2011-01-23 Thread Simon Urbanek
ere are a few loose ends I want to tackle later next week and document re-interpretation code is included but without a GUI yet (the idea is that if you fall-back to MacRoman you can re-interpret it in any other of the 8-bit character encodings like latin1 if you wish). Cheers, Simon

Re: [Rd] feature request: additional hook in plot.new()

2011-01-23 Thread Simon Urbanek
tps://r-forge.r-project.org/projects/tabbedplots/ ), having this hook > would enable it to operate in a mode where a new tab is automatically created > for each new plot. > Just note on the latter: I would expect this to be usually better handled by the device/UI as you will be i

Re: [Rd] match function causing bad performance when using tablefunction on factors with multibyte characters on Windows

2011-01-25 Thread Simon Urbanek
20 0.024 1.263158 0.020 0 0 0 1 tabulate(x.num) 20 0.019 1.00 0.020 0 0 0 Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Memory Leak

2011-02-01 Thread Simon Urbanek
s. I you want to lean more, you'll have to grab the tools available for your platform to find out who's allocating what. Since you didn't even mention your platform I can't really help you with the specifics, though. Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Using MathJax in R's help system

2011-02-02 Thread Simon Urbanek
On Feb 2, 2011, at 12:08 PM, Gong-Yi Liao wrote: > > I think your "another CRAN package for mathjax" approach is better > > than modifying the base R's code. I am trying to find the possible > > way to implement it. > Note that R has already an extensible http server included (it's used for

Re: [Rd] [.raster bug {was "str() on raster objects fails .."}

2011-02-02 Thread Simon Urbanek
her non-standardness to try >>> to ensure that the subset of a raster image always produces a sensible >>> image. A simple solution would be just to outlaw r[i] for raster objects >>> and force the user to write r[i, ] or r[, j], depending on what they want. >>

Re: [Rd] [.raster bug {was "str() on raster objects fails .."}

2011-02-02 Thread Simon Urbanek
On Feb 2, 2011, at 7:00 PM, Paul Murrell wrote: > Hi > > Martin Maechler wrote: >> On Wed, Feb 2, 2011 at 23:30, Simon Urbanek >> wrote: >>> On Feb 1, 2011, at 8:16 PM, Paul Murrell wrote: >>> >>>> Hi >>>> >>>> On

Re: [Rd] dependencies on system packages

2011-02-03 Thread Simon Urbanek
ns already come with a large set of R packages resolving all dependencies. Hence I don't see any reason why this should have anything to do with the DESCRIPTION file. The improvements I could think of would be a parseable entry or a canonical pointer to dependency sources, but that

Re: [Rd] dependencies on system packages

2011-02-04 Thread Simon Urbanek
the instructions as far as the developer knows. And as a package developer you'll learn soon enough when people start complaining ;). Thanks, Simon > Giving the package name for specific distributions is of course polite (if > the developer knows it). As developer you may also pu

Re: [Rd] dependencies on system packages

2011-02-04 Thread Simon Urbanek
On Feb 4, 2011, at 1:24 PM, Dirk Eddelbuettel wrote: > > Simon, > > On 4 February 2011 at 10:01, Simon Urbanek wrote: > | Claudia, > | > | thanks for you comments . > | > | On Feb 4, 2011, at 3:18 AM, Claudia Beleites wrote: > | > | > Dear all, >

Re: [Rd] [.raster bug {was "str() on raster objects fails .."}

2011-02-06 Thread Simon Urbanek
On Feb 6, 2011, at 8:10 PM, Paul Murrell wrote: > Hi > > On 3/02/2011 1:23 p.m., Simon Urbanek wrote: >> >> On Feb 2, 2011, at 7:00 PM, Paul Murrell wrote: >> >>> Hi >>> >>> Martin Maechler wrote: >>>> On Wed, Feb 2, 2011 at

Re: [Rd] Compiling a Tcl extension for an R package

2011-02-08 Thread Simon Urbanek
lo a small bug in R (x64/Makeconf has wrong TCLTK_LIBS - it should point to bin64 instead of bin) and the fact that Tcl doesn't like paths with spaces (I suppose you can escape it somehow) it actually works on Windows as well. Cheers, Simon > Thanks, > > Adrian Waddell &g

Re: [Rd] manipulating the Date & Time classes

2011-02-08 Thread Simon Urbanek
t; in order to > create a "max" & "min" for times, but it would be nice to have something > vetted & official. > >If others could chime in with any strange behaviors they've seen in > working with times, maybe we could get a critical

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