[Rd] R_tryEval not properly documented in 'Writing R Extensions' (PR#9524)
Full_Name: Byron Ellis Version: 2.4.1 OS: N/A Submission from: (NULL) (75.55.126.10) R_tryEval is implied to be in the public API by 'Embedding R in Other Applications,' but not documented in 'Writing R Extensions.' This would seem to be an oversight given the dependence of many applications including but not limited to the official OS X GUI on this function. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R_tryEval not properly documented in 'Writing R Extensions' (PR#9524)
On Thu, 22 Feb 2007, [EMAIL PROTECTED] wrote: Full_Name: Byron Ellis Version: 2.4.1 OS: N/A Submission from: (NULL) (75.55.126.10) R_tryEval is implied to be in the public API by 'Embedding R in Other Applications,' but not documented in 'Writing R Extensions.' This would seem to be an oversight given the dependence of many applications including but not limited to the official OS X GUI on this function. It is not an oversight. R_tryEval is as far as the R sources are concerned just part of the test examples for embedding. I think you may be referring to http://developer.r-project.org/embedded.html That does not list R_tryEval in 'Routines for the Embedded R', so makes no such implication (and in any case dates from 2000, before there was a documented interface). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R_tryEval not properly documented in 'Writing R Extensions' (PR#9525)
On Thu, 22 Feb 2007, [EMAIL PROTECTED] wrote: Full_Name: Byron Ellis Version: 2.4.1 OS: N/A Submission from: (NULL) (75.55.126.10) R_tryEval is implied to be in the public API by 'Embedding R in Other Applications,' but not documented in 'Writing R Extensions.' This would seem to be an oversight given the dependence of many applications including but not limited to the official OS X GUI on this function. It is not an oversight. R_tryEval is as far as the R sources are concerned just part of the test examples for embedding. I think you may be referring to http://developer.r-project.org/embedded.html That does not list R_tryEval in 'Routines for the Embedded R', so makes no such implication (and in any case dates from 2000, before there was a documented interface). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] rgl update: please test!
(This is bcc'd to a list of people who have had problems with rgl lately or who are known to be big users; not cc'd, so you don't all get cc'd all the responses on the R-devel list). I've just put together a test build of rgl, and put it on my web site as http://www.stats.uwo.ca/faculty/murdoch/software/rgl_0.70.564.tar.gz (source) and http://www.stats.uwo.ca/faculty/murdoch/software/rgl_0.70.564.zip (Windows binary). This includes a number of changes: - changes to configure script from Laszlo Kajan and Brian Ripley: should now be much more portable - removed deprecated OSX font setting calls - texture properties are now returned by material3d() - allowed normals and texture coordinates to be specified in triangles and quads - normals may be specified in qmesh objects, but (at present) subdivide removes them - material3d() now preserves the values of unspecified parameters (as documented, but not previously functioning) - open3d() now resets all material properties to the defaults. Could people who have been having problems with rgl (or just making use of it) please test this update? Some of the changes are very recent, and may still be buggy: but I'm going offline from late tomorrow until March 4, so I'm not going to have an opportunity to test them myself well enough to want to send this to CRAN. I'm hoping to send this to CRAN soon after I return. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R_tryEval not properly documented in 'Writing R Extensions' (PR#9524)
Considering the lack of embedding documentation until relatively recently, the fact that the function appeared in Rinternals and the Embedding test cases makes it more part of the API that its appearance in any documentation since anyone embedding would have to base their work on those test cases. In any case, my second claim---that the function is used heavily by projects under the official R umbrella as well as outside of it---still stands and should probably serve as sufficient cause to nominate R_tryEval for the public API. On 2/22/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Thu, 22 Feb 2007, [EMAIL PROTECTED] wrote: Full_Name: Byron Ellis Version: 2.4.1 OS: N/A Submission from: (NULL) (75.55.126.10) R_tryEval is implied to be in the public API by 'Embedding R in Other Applications,' but not documented in 'Writing R Extensions.' This would seem to be an oversight given the dependence of many applications including but not limited to the official OS X GUI on this function. It is not an oversight. R_tryEval is as far as the R sources are concerned just part of the test examples for embedding. I think you may be referring to http://developer.r-project.org/embedded.html That does not list R_tryEval in 'Routines for the Embedded R', so makes no such implication (and in any case dates from 2000, before there was a documented interface). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 -- Byron Ellis ([EMAIL PROTECTED]) Oook -- The Librarian __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Patch for units- in datetime.R
Index: src/library/base/R/datetime.R === --- src/library/base/R/datetime.R (revision 40781) +++ src/library/base/R/datetime.R (working copy) @@ -381,7 +381,7 @@ if (from == value) return(x) if (!(value %in% c(secs, mins, hours, days, weeks))) stop(invalid units specified) -sc - cumprod(c(sec=1, mins=60, hours=60, days=24, weeks=7)) +sc - cumprod(c(secs=1, mins=60, hours=60, days=24, weeks=7)) newx - as.vector(x)*sc[from]/sc[value] structure(newx, units=value, class=difftime) } Cheers, Jeff -- http://biostat.mc.vanderbilt.edu/JeffreyHorner __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Bug in httpget function for internet.Rout test (PR#9509)
Full_Name: Paul Lynch Version: 2.4.1 OS: RedHat EL4 Submission from: (NULL) (130.14.254.25) The httpget function used for the test that produces the internet.Rout file (or in my case, the internet.Rout.fail file) checks for a Content-Length header returned from a webserver in response to the URL: http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat. When I attempt to access that URL either via the make check in R or via curl --head http://www.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat; via the command line, the header I receive is Content-length with a lower case l. Another user on r-help reports that he gets it with an upper case L, so the problem appears to be only visible from certain IP addresses. It seems likely that the web server at www.stats.ox.ac.uk is doing some load balancing based on the incoming IP address, so that some users with get a response from a web server that returns Content-length while others will get a response from a different web server that returns Content-Length. Whatever the cause is, it seems reasonable that the test for internet.Rout in httpget should not particular about whether the upper or lower case L is used. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] text.rpart for the class method doesn't act on label=yprob
Hello All, Am I misreading the documentation? The text.rpart documentation says: label a column name of x$frame; values of this will label the nodes. For the class method, label=yval results in the factor levels being used, yprob results in the probability of the winning factor level being used, and ‘specific yval level’ results in the probability of that factor level. However, yprob doesn't seem to do this: pred = rep(letters[1:6],5) resp = rep(letters[1:3],10) ex.rp - rpart(resp~pred) plot(ex.rp) text(ex.rp,label=yval) # works as advertised plot(ex.rp) text(ex.rp,label=yprob) Error in text.rpart(ex.rp, label = yprob) : Label must be a column label of the frame component of the tree If I try to fake it, by making an element of the frame, like this: ex.rp$frame$yprob = (ex.rp$frame$n-ex.rp$frame$dev)/ex.rp$frame$n The text command does add text to the plot, but adds the class labels (i.e. yval), not the probabilities text(ex.rp,label=yprob) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] How to override functions in namespaces?
In package A I have askForString(), which asks the user for a string. Also in package A I have defined ssh(), which calls askForString(). Package B has package A as a prerequisite. In package B I redefine askForString() to take advantage of a nicer user interface made available by B, namely the Emacs mini-buffer prompt. Packages B and A are both on the search path, with B ahead of A. If I call askForString() at the command prompt, I get the version from B. But the version used by ssh() depends on whether or not package A has a namespace. If so, ssh() (defined in A) always uses the A version of askForString(). How can I get ssh() to use the B version of askForString()? Or am I going about this all wrong? Jeff __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] dyn.load (PR#9364)
Hi, I have exactly the same problem with R 2.4.1 on an Intel MacBook with Mac OS X 10.4.8. Please find below the output of the test. Christophe --- source(/Users/Christophe/Desktop/Rdynunload/run.R) WARNING: ignoring environment value of R_HOME gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=nocona -c code.c -o code.o gcc-4.0 -arch i386 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 - undefined dynamic_lookup -single_module -multiply_defined suppress -L/ usr/local/lib -o foo.so code.o -L/Library/Frameworks/R.framework/ Resources/lib/i386 -lR -dylib_file libRblas.dylib:/Library/Frameworks/ R.framework/Resources/lib/i386/libRblas.dylib [1] Failed loaded DLL/SO WARNING: ignoring environment value of R_HOME gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/ include -I/Library/Frameworks/R.framework/Resources/include/i386 - msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=nocona -c other.c -o other.o gcc-4.0 -arch i386 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 - undefined dynamic_lookup -single_module -multiply_defined suppress -L/ usr/local/lib -o foo.so other.o -L/Library/Frameworks/R.framework/ Resources/lib/i386 -lR -dylib_file libRblas.dylib:/Library/Frameworks/ R.framework/Resources/lib/i386/libRblas.dylib first attempt loaded DLL/SO first attempt --- __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] MCMC Pack Crashes R-GUI session (PR#9516)
Full_Name: Lloyd Lubet Version: 2.4.1rc OS: XP Submission from: (NULL) (65.19.17.17) Dear Andrew, I am trying to learn gibbs sampling and Metropolis. When I run your gibbs version of multiple linear regression my session crashes. I have trimmed the dataframe and set my object.size = 1 gigB. Despite my best efforts it still crashes while advising me to contact the MCMC Pack developement team. I am running windows XP with R version 2.4.1.c (the latest). Here's the offending instruction in R: mcmcReg-MCMCSVDreg( jpMorganChase.Adj.Close ~ exxon.Oil.Volume+usSteel.Volume, data=yy.lo.res.scaled[ 2000:2274, ], burnin = 100, mcmc = 1000, thin=1, verbose = 1, seed = NA, tau2.start = 1, g0 = 0, a0 = 0.01, b0 = 0.01, c0=2, d0=2, w0=1, beta.samp=TRUE, intercept=TRUE ) Here's the error msg: Runtime Error! Program ... \R\R-2.4.1rc\bin\Rgui.exe This application has requested the Tuntime to terminate it in an unusual way. Please contact the applications support team for more information R Console - Rgui.exe - Application Error The instruction at 0x5ad71531 referenced memory at 0x0014. Memory could not be read. Then, it crashes. Sincerely, Lloyd Lubet __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Windows EPS format error (PR#9518)
This bug can be reproduced using R version 2.4.1 for Windows, where WinAnsiEncoding is used. To reproduce this bug, start a Windows R session, and run: postscript(first.eps, width=6, height=6, horizontal=FALSE, onefile=FALSE, paper=special) plot(1:5) dev.off() q(no) Now, start a new R session, and run: pdf(second.pdf) plot(1:5) dev.off() postscript(third.eps, width=6, height=6, horizontal=FALSE, onefile=FALSE, paper=special) plot(1:5) dev.off() q(no) The differences between first.eps and third.eps are shown to be: $ diff first.eps third.eps 40d39 /WinAnsiEncoding [ 73d71 ] The file third.eps is an invalid format, and Vhostview reports: Error: /undefined in WinAnsiEncoding Operand stack: .notdef .notdef .notdef ... etc ... I've also tested for this peculiar behavior with R 2.4.1 for Debian, however it checked clean. +mt __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Graphical device questions
Dear all, I have posted these questions in r-help list but since I am getting no reply, I concluded that I must asked my question in the wrong list so here I am! Here is my questions: 1- Under a WINDOWS installation of R-2.4.1, can we change the naming of a new ploting device open by the command windows()?. Instead of the default name e.g.: Device 2 I would like to use something like Density plot or whatever! 2- Under a MAC OS X installation of R-2.4.1, using quartz devices, is there a way to perform bringToTop operation like the one available under WINDOWS using bringToTop function. Thank you very much for your time. Cheers Sébastien -- Dans le Ssu Ma Fa on lit: Celui qui place la vie au dessus de toute chose sera paralysé par l'irrésolution __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Request: make as.POSIXlt generic
In the base package, as.POSIXct() is an S3 generic function, but
as.POSIXlt() is not. As shown below, the current implementation is
already crying out to be refactored into a generic function with methods
for various classes. It calls inherits five times. Not only is this
bad style, it also disallows me or anyone else from making as.POSIXlt()
work with other kinds of time-ish objects, such as the 'ti' (Time Index)
class in my fame package.
I would also like to see three other functions made generic: rowSums(),
rowMeans(), and filter(). This would enable Gabor to create methods for
his 'zoo' series, and let me create methods for my 'tis' (Time Indexed
Series). But these are not as urgent as cleaning up as.POSIXlt().
Jeff Hallman
The current as.POSIXlt() implementation:
as.POSIXlt - function(x, tz = ){
fromchar - function(x) {
xx - x[1]
if(is.na(xx)) {
j - 1
while(is.na(xx) (j - j+1) = length(x))
xx - x[j]
if(is.na(xx)) f - %Y-%m-%d # all NAs
}
if(is.na(xx) ||
!is.na(strptime(xx, f - %Y-%m-%d %H:%M:%OS)) ||
!is.na(strptime(xx, f - %Y/%m/%d %H:%M:%OS)) ||
!is.na(strptime(xx, f - %Y-%m-%d %H:%M)) ||
!is.na(strptime(xx, f - %Y/%m/%d %H:%M)) ||
!is.na(strptime(xx, f - %Y-%m-%d)) ||
!is.na(strptime(xx, f - %Y/%m/%d)))
{
res - strptime(x, f)
if(nchar(tz)) attr(res, tzone) - tz
return(res)
}
stop(character string is not in a standard unambiguous format)
}
if(inherits(x, POSIXlt)) return(x)
if(inherits(x, Date)) return(.Internal(Date2POSIXlt(x)))
tzone - attr(x, tzone)
if(inherits(x, date) || inherits(x, dates)) x - as.POSIXct(x)
if(is.character(x)) return(fromchar(unclass(x))) # precaution PR7826
if(is.factor(x))return(fromchar(as.character(x)))
if(is.logical(x) all(is.na(x))) x - as.POSIXct.default(x)
if(!inherits(x, POSIXct))
stop(gettextf(do not know how to convert '%s' to class \POSIXlt\,
deparse(substitute(x
if(missing(tz) !is.null(tzone)) tz - tzone[1]
.Internal(as.POSIXlt(x, tz))
}
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[Rd] supsmu produces segfault when handed all NAs. (PR#9519)
When handed an argument with all NAs, supsmu() causes a sigfault causing termination of R. The following example reproduces the problem (on a linux gentoo system), but I have verified the same behavior on a solaris builds as well as several versions of R. x - (1:100)/10; y - sin(pi*x) + rnorm(length(x)); tmp - supsmu(x,y); # works y[c(2,5,10)] - NA; # a few NAs is OK, warning generated tmp- supsmu(x,y); y- NA + y; # all NAs tmp - supsmu(x,y); # oops *** caught segfault *** address 0xfff8, cause 'memory not mapped' Traceback: 1: .Fortran(R_supsmu, as.integer(leno), as.double(xo), as.double(y[ord]), as.double(wt[o rd]), as.integer(iper), as.double(span), as.double(bass), smo = double(leno), double(n * 7 ), double(1)) 2: supsmu(x, y) Possible actions: 1: abort (with core dump) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: --please do not edit the information below-- Version: platform = i686-pc-linux-gnu arch = i686 os = linux-gnu system = i686, linux-gnu status = major = 2 minor = 4.1 year = 2006 month = 12 day = 18 svn rev = 40228 language = R version.string = R version 2.4.1 (2006-12-18) Locale: LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_US.utf8;LC_MONETARY=en_US.ut f8;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASURE MENT=en_US.utf8;LC_IDENTIFICATION=C Search Path: .GlobalEnv, package:stats, package:graphics, package:grDevices, package:utils, package:datase ts, package:methods, Autoloads, package:base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R crashes in Mac OS
I am running R under Mac OS X (Tiger, v10.4). Unfortunately it keeps crashing while using the editor. One thing that seems to make things worse is having more than one script open at the same time. Can anyone help? The last time it happened I got the following messages error message from R: *** caught segfault *** address 0x89d789d8, cause 'memory not mapped' report: Date/Time: 2007-02-18 18:59:42.108 + OS Version: 10.4.8 (Build 8N1051) Report Version: 4 Command: R Path:/Applications/R.app/Contents/MacOS/R Parent: WindowServer [55] Version: R 2.4.1 GUI 1.18 (4038) PID:235 Thread: 0 Exception: EXC_BAD_ACCESS (0x0001) Codes: KERN_INVALID_ADDRESS (0x0001) at 0x89d789d8 Thread 0 Crashed: __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] lower.tail for plnorm (PR#9520)
Full_Name: Chris Andrews Version: 2.4.1 OS: Windows XP Submission from: (NULL) (128.205.90.25) # CDF works as expected (=0) pnorm(-Inf) # 0 plnorm(0) # 0 # specifying lower.tail=FALSE should give survival function (=1) pnorm(-Inf, lower.tail=FALSE) # 1 plnorm(0, lower.tail=FALSE) # 0 != 1 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] memory problem read.table v array (PR#9526)
Full_Name: bill langdon Version: 2.4.1 OS: ubuntu Submission from: (NULL) (155.245.58.159) #WBL 22 Feb 2007 ubuntu R.version #platform i486-pc-linux-gnu #arch i486 #os linux-gnu #system i486, linux-gnu #status #major 2 #minor 4.1 #year 2006 #month 12 #day18 #svn rev40228 #language R #version.string R version 2.4.1 (2006-12-18) #if matrix a is created by array vals is created ok #if matrix a is created by read.table, #peak resource use (CPU, memory) by array() is excessive #a = array(0,dim=c(409600,1));#ok #a = read.table(big.txt,header=FALSE); #all memory used #a = read.table(639x639.txt,header=FALSE); #all memory used #a = read.table(4096.txt,header=FALSE); #all memory used #a = read.table(4096nocomment.txt,header=FALSE);#all memory used #a = read.table(tiny.txt,header=FALSE); #ten lines ok #a = read.table(1000.txt,header=FALSE); #all memory used a = read.table(639.txt,header=FALSE); #uses 1.6047029GB dim(a) dd = 639; vals = array(a,dim=c(dd,dd)); __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Problem with types on 64-bit
Hi Everyone,
I have a problem using some working 32-bit R code with 64-bit machine ( I am
using version R-2.4.1 ). The problem occurs when I am trying to detect a NULL
STRSXP type. ( Perhaps I am doing this detection in the wrong way? )
On 32-bit the following works, and correctly identifies if I am passing NULL
or a valid string object:
if ( v_dta_start != R_NilValue STRING_ELT( v_dta_start, 0 ) != R_NilValue )
{
dta.start = CHAR( STRING_ELT( v_dta_start, 0 ) );
}
Yet on a 64-bit machine I get the following errors:
(1) when I pass NULL it goes into the if clause and then when it tries to set
dta.start it displays:
CHAR() can only be applied to a 'CHARSXP', not a 'NULL'
(2) if I pass a valid string such as hello, I get the following:
CHAR() can only be applied to a 'CHARSXP', not a 'character'
I have tried converting using AS_CHARACTER but that just brings up the same
messages. I have also seen S4 and PROMSXP types come up in these error
messages.
What I don't understand is why this happens - any ideas?
If I can supply any more info let me know, below is the CPU information for
the 64-bit machine.
Many thanks for your help
Tom
64-BIT CPU INFO
===
processor : 0
vendor_id : AuthenticAMD
cpu family : 15
model : 5
model name : AMD Opteron(tm) Processor 144
stepping: 10
cpu MHz : 1794.932
cache size : 1024 KB
fpu : yes
fpu_exception : yes
cpuid level : 1
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat
pse36 clflush mmx fxsr sse sse2 syscall nx mmxext lm 3dnowext 3dnow
bogomips: 3597.08
TLB size: 1024 4K pages
clflush size: 64
cache_alignment : 64
address sizes : 40 bits physical, 48 bits virtual
power management: ts fid vid ttp
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Re: [Rd] rgl update: please test!
Hallo Duncan, your newest version works fine under R-2.5.0 (devel) on FreeBSD 7.0-CURRENT (i386). I made some tests with different types of diagrams and all seems to be ok for me. Thank you very much. I am look forward to the release of this version. Have a nice trip, Rainer Duncan Murdoch wrote: (This is bcc'd to a list of people who have had problems with rgl lately or who are known to be big users; not cc'd, so you don't all get cc'd all the responses on the R-devel list). I've just put together a test build of rgl, and put it on my web site as http://www.stats.uwo.ca/faculty/murdoch/software/rgl_0.70.564.tar.gz (source) and http://www.stats.uwo.ca/faculty/murdoch/software/rgl_0.70.564.zip (Windows binary). This includes a number of changes: - changes to configure script from Laszlo Kajan and Brian Ripley: should now be much more portable - removed deprecated OSX font setting calls - texture properties are now returned by material3d() - allowed normals and texture coordinates to be specified in triangles and quads - normals may be specified in qmesh objects, but (at present) subdivide removes them - material3d() now preserves the values of unspecified parameters (as documented, but not previously functioning) - open3d() now resets all material properties to the defaults. Could people who have been having problems with rgl (or just making use of it) please test this update? Some of the changes are very recent, and may still be buggy: but I'm going offline from late tomorrow until March 4, so I'm not going to have an opportunity to test them myself well enough to want to send this to CRAN. I'm hoping to send this to CRAN soon after I return. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Error in ICC1.CI ? (PR#9528)
Hello, I'm using the function ICC1.CI of the psychometric package. I wonder if there is an error in this function. Because in the paper of McGraw and Wong (Psychol Met, 1, 30) or the one of Shrout Fleiss (Psychol Bult, 86, 420), the Ftab is not calculate in the same manner of the lower and upper bound. According to these articles Ftab for the lower bound is: F(df.row, df.error) and for the upper bound, it is: F(df.error, df.row). So the df are reversed. However, in your function ICC1.CI, the Ftab is calculated in the same way for the upper and lower bound: Ftab - qf(noma/2, df1, df2, lower.tail = F) Fl - Fobs/Ftab Fu - Fobs * Ftab lcl - (Fl - 1)/(Fl + n) ucl - (Fu - 1)/(Fu + n) Is that an error ? Best regards, -- Mathieu d'Acremont, PhD [EMAIL PROTECTED] Maître-Assistanttel/fax +4122 379 98 20/44 Pôle de Recherche National en Sciences Affectives CISA - Université de Genève Rue des Battoirs 7 CH-1205 Genève http://affect.unige.ch/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Problem with types on 64-bit
Neither NULL nor hello are valid values for an element of a STRSXP: only
CHARSXPs are. So your test is not the correct one: you need to test
both isString(v_dta_start) and TYPEOF(STRING_ELT( v_dta_start, 0 )) ==
CHARSXP to be really safe.
Calling STRSXP on a random SEXP is likely to give different results on
different machines: there is no fundamental 32- vs 64-but difference here.
On Tue, 20 Feb 2007, [EMAIL PROTECTED] wrote:
Hi Everyone,
I have a problem using some working 32-bit R code with 64-bit machine ( I am
using version R-2.4.1 ). The problem occurs when I am trying to detect a NULL
STRSXP type. ( Perhaps I am doing this detection in the wrong way? )
On 32-bit the following works, and correctly identifies if I am passing NULL
or a valid string object:
if ( v_dta_start != R_NilValue STRING_ELT( v_dta_start, 0 ) != R_NilValue )
{
dta.start = CHAR( STRING_ELT( v_dta_start, 0 ) );
}
Yet on a 64-bit machine I get the following errors:
(1) when I pass NULL it goes into the if clause and then when it tries to set
dta.start it displays:
CHAR() can only be applied to a 'CHARSXP', not a 'NULL'
(2) if I pass a valid string such as hello, I get the following:
CHAR() can only be applied to a 'CHARSXP', not a 'character'
I have tried converting using AS_CHARACTER but that just brings up the same
messages. I have also seen S4 and PROMSXP types come up in these error
messages.
What I don't understand is why this happens - any ideas?
If I can supply any more info let me know, below is the CPU information for
the 64-bit machine.
Many thanks for your help
Tom
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [Rd] memory problem read.table v array (PR#9526)
There is nothing to reproduce here: we do not have 639.txt. But note that read.table returns a data frame, and ?array has data: a vector (including a list) giving data to fill the array. so I do wonder if this is what you intended: you seem to have tried to create an array list with 639*639 elements. It is certainly not the same sort of object as array(0,dim=c(409600,1)). Had 639.txt contained 639 rows of reals, your 'a' would be about 639*639*639*8 bytes, beyond the address space of your machine. as.matrix(read.table(639.txt, header=FALSE)) might have been what you are looking for. On Thu, 22 Feb 2007, [EMAIL PROTECTED] wrote: Full_Name: bill langdon Version: 2.4.1 OS: ubuntu Submission from: (NULL) (155.245.58.159) #WBL 22 Feb 2007 ubuntu R.version #platform i486-pc-linux-gnu #arch i486 #os linux-gnu #system i486, linux-gnu #status #major 2 #minor 4.1 #year 2006 #month 12 #day18 #svn rev40228 #language R #version.string R version 2.4.1 (2006-12-18) #if matrix a is created by array vals is created ok #if matrix a is created by read.table, #peak resource use (CPU, memory) by array() is excessive #a = array(0,dim=c(409600,1));#ok #a = read.table(big.txt,header=FALSE); #all memory used #a = read.table(639x639.txt,header=FALSE); #all memory used #a = read.table(4096.txt,header=FALSE); #all memory used #a = read.table(4096nocomment.txt,header=FALSE);#all memory used #a = read.table(tiny.txt,header=FALSE); #ten lines ok #a = read.table(1000.txt,header=FALSE); #all memory used a = read.table(639.txt,header=FALSE); #uses 1.6047029GB dim(a) dd = 639; vals = array(a,dim=c(dd,dd)); -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Problem with types on 64-bit
Besides the comments from Prof. Ripley, I am not sure your if statement
is fully correct, because suppose v_dta_start is R_NilValue -- why then
STRING_ELT( R_NilValue, 0 ) should be a valid statement in first place?
In my code I often use R_NilValue to check for R-NULL, but it always
works fine on both 32 and 64 bits, moreover on Linux, Mac and Windows as
well... Oleg
[EMAIL PROTECTED] wrote:
Hi Everyone,
I have a problem using some working 32-bit R code with 64-bit machine ( I am
using version R-2.4.1 ). The problem occurs when I am trying to detect a NULL
STRSXP type. ( Perhaps I am doing this detection in the wrong way? )
On 32-bit the following works, and correctly identifies if I am passing NULL
or a valid string object:
if ( v_dta_start != R_NilValue STRING_ELT( v_dta_start, 0 ) != R_NilValue )
{
dta.start = CHAR( STRING_ELT( v_dta_start, 0 ) );
}
Yet on a 64-bit machine I get the following errors:
(1) when I pass NULL it goes into the if clause and then when it tries to set
dta.start it displays:
CHAR() can only be applied to a 'CHARSXP', not a 'NULL'
(2) if I pass a valid string such as hello, I get the following:
CHAR() can only be applied to a 'CHARSXP', not a 'character'
I have tried converting using AS_CHARACTER but that just brings up the same
messages. I have also seen S4 and PROMSXP types come up in these error
messages.
What I don't understand is why this happens - any ideas?
If I can supply any more info let me know, below is the CPU information for
the 64-bit machine.
Many thanks for your help
Tom
64-BIT CPU INFO
===
processor : 0
vendor_id : AuthenticAMD
cpu family: 15
model : 5
model name: AMD Opteron(tm) Processor 144
stepping : 10
cpu MHz : 1794.932
cache size: 1024 KB
fpu : yes
fpu_exception : yes
cpuid level : 1
wp: yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat
pse36 clflush mmx fxsr sse sse2 syscall nx mmxext lm 3dnowext 3dnow
bogomips : 3597.08
TLB size : 1024 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 40 bits physical, 48 bits virtual
power management: ts fid vid ttp
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Re: [Rd] How to override functions in namespaces?
On Mon, 12 Feb 2007, [EMAIL PROTECTED] wrote: In package A I have askForString(), which asks the user for a string. Also in package A I have defined ssh(), which calls askForString(). Package B has package A as a prerequisite. In package B I redefine askForString() to take advantage of a nicer user interface made available by B, namely the Emacs mini-buffer prompt. Packages B and A are both on the search path, with B ahead of A. If I call askForString() at the command prompt, I get the version from B. But the version used by ssh() depends on whether or not package A has a namespace. If so, ssh() (defined in A) always uses the A version of askForString(). How can I get ssh() to use the B version of askForString()? Or am I going about this all wrong? That is one of the main purposes of a namespace, but you can defeat it. In the scenario you paint, B::askForString() should work (whether or not B has a namespace). If (I am guessing) you want the version that would be gotten at the top level (the prompt) whether or not B is in use, use get(askForString, pos=1)(). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] (PR#9523) avoiding a needless function evaluation in optimize()
This is very far from easy, as the C code used does not return the
function value.
If you would like to rewrite it and the interface and submit a patch it
will be considered.
It's hard to imagine an application where this would matter, and you have
not given one to encourage us to give this more than the lowest priority
on the wishlist.
On Wed, 21 Feb 2007, [EMAIL PROTECTED] wrote:
Full_Name: Jelle Goeman
Version: 2.4.0
OS: windows XP
Submission from: (NULL) (145.88.209.33)
Hi,
I like to use optimize() to optimize functions whose evaluation is costly in
terms of computation time. The Brent algorithm which is implemented in
optimize
was designed to optimize a function with as few function evaluations as
possible. Therefore it bothers me that optimize() always evaluates the
function
twice at the optimal value. This can be seen for example by saying:
square - function(x) {
print(x)
x*x
}
opt - optimize(square, c(-5,1), tol=0.1)
Looking at the code of optimize(), I see that the extra function evaluation
comes when optimize returns
list(minimum = val, objective = f(val, ...))
f(val, ...) is calculated, but f(val, ...) has already been calculated at some
point during the algorithm.
Would it be possible to let optimize() store its previous function evaluations
to avoid this unnecessary function evaluation?
Kind regards,
Jelle
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Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [Rd] How to override functions in namespaces?
On 2/12/2007 1:13 PM, [EMAIL PROTECTED] wrote: In package A I have askForString(), which asks the user for a string. Also in package A I have defined ssh(), which calls askForString(). Package B has package A as a prerequisite. In package B I redefine askForString() to take advantage of a nicer user interface made available by B, namely the Emacs mini-buffer prompt. Packages B and A are both on the search path, with B ahead of A. If I call askForString() at the command prompt, I get the version from B. But the version used by ssh() depends on whether or not package A has a namespace. If so, ssh() (defined in A) always uses the A version of askForString(). How can I get ssh() to use the B version of askForString()? Or am I going about this all wrong? There are several ways. If package A knows that some users will want to replace askForString(), then it should allow the user to tell it what to use for that function, and fall back to its own definition as a default. It could do this by explicitly looking for askForString in the global environment (which will fall back to the search list if not found), or it could get the function from an option() setting, etc. If package A doesn't expect askForString() to be changed, then you shouldn't change it: you might break something else in A. You should write to the author of A (which sounds as though it's yourself), and ask for some improvements to the package. There are dirty methods to modify the contents of a namespace, but you shouldn't use those. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Writing a package in which files must be sourced in a specific order
Put all loadings into functions and call the functions in .onLoad or
.FirstLib, whatever you have there. I would simply advise not to put any
code outside of functions or class methods. In this way the order of
loading will not matter, it will not depend on system or alphabet and
you will also be able to save the loaded image of the package for faster
loading.
Best
Oleg
hadley wickham wrote:
Dear all,
I have been using the proto package to create objects with mutable
state for my ggplot package. This has been very successful so far,
but I have run into a problem when building/installing the package,
because the source files need to be loaded in a specific order so that
dependencies are initialised correctly.
I have named the files so that dependencies are loaded before they are
needed, so that
lapply(dir(~/documents/ggplot/ggplot/R, full.name=T), source)
runs without error, but when installing the package I get an error
than indicates that the files aren't being loaded in alphabetical
order:
Error in proto(Geom, { : object Geom not found
Error: unable to load R code in package 'ggplot'
Error: package/namespace load failed for 'ggplot'
Can anyone suggest how I could get around this?
Regards,
Hadley
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Re: [Rd] Writing a package in which files must be sourced in a specific order
What 'alphabetical order' is depends on the locale. In en_NZ g G, in C
G g. So it is a rather slippery concept (and gets worse in non-English
locales: 'aa' sorts after z in Danish).
You don't tell us quite what you are doing, but R CMD INSTALL is
working in C when concatenating the files in the R directory to ensure
consistency across R installations.
My guess is that you need to give a collation order in the DESCRIPTION
file (see 'Writing R Extensions'), if I am interpolating your
comments correctly.
On Thu, 22 Feb 2007, hadley wickham wrote:
Dear all,
I have been using the proto package to create objects with mutable
state for my ggplot package. This has been very successful so far,
but I have run into a problem when building/installing the package,
because the source files need to be loaded in a specific order so that
dependencies are initialised correctly.
'loaded'? Do you mean sourced during INSTALL?
I have named the files so that dependencies are loaded before they are
needed, so that
lapply(dir(~/documents/ggplot/ggplot/R, full.name=T), source)
runs without error, but when installing the package I get an error
than indicates that the files aren't being loaded in alphabetical
order:
Error in proto(Geom, { : object Geom not found
Error: unable to load R code in package 'ggplot'
Error: package/namespace load failed for 'ggplot'
Can anyone suggest how I could get around this?
Regards,
Hadley
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Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [Rd] Writing a package in which files must be sourced in a specific order
What 'alphabetical order' is depends on the locale. In en_NZ g G, in C G g. So it is a rather slippery concept (and gets worse in non-English locales: 'aa' sorts after z in Danish). I only used characters a-z, so I didn't think that would be a problem. However, it turns out I had misnamed one of my files so that it wasn't sorting correctly, and renaming it fixed the problem. (Previously I had manully included that file first and I had forgotten to remove it) Thanks for the help. Hadley __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
