Re: [Rd] (PR#11484) On WinXP, R CMD config needs sh (and breaks
Where is the bug here? It also does on a Unix-alike. Anything involving R CMD potentially needs the Rtools set in the path. R CMD config is primarily intended to be used in configure scripts in packages. On Sun, 18 May 2008, [EMAIL PROTECTED] wrote: Full_Name: Laurent Gautier Version: R-2.7.0patched (r45712) OS: WinXP Submission from: (NULL) (90.15.141.247) On a WinXP box (that does not has sh in the %Path%, R CMD config appears to break: C:\R CMD config 'sh' is not recognized as an internal or external command, operable program or batch file. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- 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] predict.prcomp: wrong check for matrix dimensions (PR#11482)
Full_Name: Gad Abraham Version: 2.7.0 OS: Ubuntu Linux Submission from: (NULL) (59.167.148.182) Description: x1 - matrix(rnorm(100), 5, 20) x2 - matrix(rnorm(100), 5, 20) p - prcomp(x1) predict(p, x2) Error in predict.prcomp(p, x2) : 'newdata' does not have the correct number of columns dim(x2) [1] 5 20 dim(p$rotation) [1] 20 5 All predict.prcomp really does is x2 %*% p$rotation, which is a perfectly legal operation that should yield a 5x5 matrix: dim(x2 %*% p$rotation) [1] 5 5 Solution: = Change p - NCOL(object$rotation) to p - NROW(object$rotation) This bug is still present in R-patched_2008-05-16. sessionInfo() R version 2.7.0 (2008-04-22) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] (PR#11484) On WinXP, R CMD config needs sh (and breaks without it)
2008/5/19 Prof Brian Ripley [EMAIL PROTECTED]: Where is the bug here? It also does on a Unix-alike. Then R CMD config --help could at least spit out an error stating what should be installed (rather than die with an execution error straight from the DOS). Setting an sh in the %Path% (sh coming from cygwin) does not seem to lead to something working under winXP (various error messages). Anything involving R CMD potentially needs the Rtools set in the path. I guess that I have been lucky with the potential aspect of the requirements so far. Is there a documentation of what is needed by the respective R CMD flavors ? R CMD config is primarily intended to be used in configure scripts in packages. On Sun, 18 May 2008, [EMAIL PROTECTED] wrote: Full_Name: Laurent Gautier Version: R-2.7.0patched (r45712) OS: WinXP Submission from: (NULL) (90.15.141.247) On a WinXP box (that does not has sh in the %Path%, R CMD config appears to break: C:\R CMD config 'sh' is not recognized as an internal or external command, operable program or batch file. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- 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#11484) On WinXP, R CMD config needs sh (and breaks without it)
Note that if you place Rcmd.bat andor R.bat from http://batchfiles.googlecode.com anywhere in your path and install the latest rtools from http://www.murdoch-sutherland.com/Rtools/ then you don't have to change your PATH. On Mon, May 19, 2008 at 5:40 AM, [EMAIL PROTECTED] wrote: 2008/5/19 Prof Brian Ripley [EMAIL PROTECTED]: Where is the bug here? It also does on a Unix-alike. Then R CMD config --help could at least spit out an error stating what should be installed (rather than die with an execution error straight from the DOS). Setting an sh in the %Path% (sh coming from cygwin) does not seem to lead to something working under winXP (various error messages). Anything involving R CMD potentially needs the Rtools set in the path. I guess that I have been lucky with the potential aspect of the requirements so far. Is there a documentation of what is needed by the respective R CMD flavors ? R CMD config is primarily intended to be used in configure scripts in packages. On Sun, 18 May 2008, [EMAIL PROTECTED] wrote: Full_Name: Laurent Gautier Version: R-2.7.0patched (r45712) OS: WinXP Submission from: (NULL) (90.15.141.247) On a WinXP box (that does not has sh in the %Path%, R CMD config appears to break: C:\R CMD config 'sh' is not recognized as an internal or external command, operable program or batch file. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] k means
On Sat, 17 May 2008 00:54:55 +0200,
cgenolin (c) wrote:
Hi the list
I try the flexclust, but I do not manage to see what is wrong in my
(very simple) code...
Will you have few minutes to check it?
Thanks for your help.
Christophe
--- 8
data - rbind(c(1,2 ,NA,4 ),
c(1,1 ,NA,1 ),
c(2,3 ,4 ,5 ),
c(2,2 ,2 ,2 ),
c(3,NA,NA,6 ),
c(3,NA,NA,3 ),
c(2,4 ,4 ,NA),
c(2,3 ,2 ,NA))
distTest - rbind(c(0,0,0,0),
c(1,1,1,1))
distNA - function(x,centers){
z - matrix(0,nrow=nrow(x),ncol=nrow(centers))
for(k in 1:nrow(centers)){
z[,k]- apply(x,1,function(x){dist(rbind(x,centers[k,]))})
}
z
}
distNA(data,distTest)
km - kccaFamily(dist=distNA,cent=colMeans)
kcca(x=data,k=2,family=km)
kcca(x=data,k=3,family=km)
I don't think this is really appropriate for r-devel, you should
either ask the package author (me), or r-help.
Anyway, colMeans will not remove the missing values by default, so you
need also a special function for centroid computation:
R centNA - function(x) colMeans(x, na.rm=TRUE)
R km - kccaFamily(dist=distNA,cent=centNA)
R kcca(x=data,k=2,family=km)
kcca object of family ??distNA??
call:
kcca(x = data, k = 2, family = km)
cluster sizes:
1 2
5 3
Hope this helps,
Fritz
--
---
Prof. Dr. Friedrich Leisch
Institut für Statistik Tel: (+49 89) 2180 3165
Ludwig-Maximilians-Universität Fax: (+49 89) 2180 5308
Ludwigstraße 33
D-80539 München http://www.statistik.lmu.de/~leisch
---
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Münchner R Kurse --- http://www.statistik.lmu.de/R
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[Rd] as.POSIX{ct,lt} fail on class AsIs
(I think this is probably appropriate for r-devel -- if my diagnosis
is correct, that is)
I have a script that I run infrequently (i.e., quarterly) that has
been working for several years. I re-ran it this morning for the
first time since updating R from 2.6.2 to 2.7.0, and encountered an
error.
I found a simple example that shows the problem:
as.POSIXct( I( '2008-01-01' ) )
Error in as.POSIXlt.default(x, tz, ...) :
do not know how to convert 'x' to class POSIXlt
traceback()
6: stop(gettextf(do not know how to convert '%s' to class \POSIXlt\,
deparse(substitute(x
5: as.POSIXlt.default(x, tz, ...)
4: as.POSIXlt(x, tz, ...)
3: as.POSIXct(as.POSIXlt(x, tz, ...), tz, ...)
2: as.POSIXct.default(I(2008-01-01))
1: as.POSIXct(I(2008-01-01))
class( I('2008-01-01') )
[1] AsIs
is.character( I('2008-01-01') )
[1] TRUE
It looks to me as though as.POSIXlt() does not recognize the object
as being also a character object
because it calls as.POSIXlt.default() instead of as.POSIXlt.character().
sessionInfo()
R version 2.7.0 (2008-04-22)
powerpc-apple-darwin8.10.1
locale:
C
attached base packages:
[1] utils stats graphics grDevices methods base
I have done some searching in r-help, r-devel, and NEWS through 2.8
Series News and not found anything that I recognized as either a fix
or an indication this is intended behavior. (Doesn't mean it isn't
there, of course...)
By way of background, I sometimes use the class AsIs for the reason
described in?AsIs, i.e.,
Protecting an object by enclosing it in 'I()' in a call to
'data.frame' inhibits the conversion of character vectors to
factors...
and that's what led to this discovery.
Thanks
-Don
--
--
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Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
925-423-1062
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[Rd] Error in building library - R CMD build mypkg.
- Forwarded by Ajay DAS/US/BMNA01 on 05/19/2008 03:11 PM - Ajay DAS To: [EMAIL PROTECTED] 05/19/2008 01:00 cc: PM Subject: Error in building library - R CMD build mypkg. Hi, I am getting an error when I am trying to build a library in R for windows . I am using R 2.7.0 in windows. I am following the instructions listed in the R Help for package creation. require(stats) ## two functions and two data sets : f - function(x,y) x+y g - function(x,y) x-y d - data.frame(a=1, b=2) e - rnorm(1000) package.skeleton(list=c(f,g,d,e), name=mypkg) Then in the command prompt I executed the following command: R CMD build mypkg I am getting the following error : * checking for file 'mypkg/DESCRIPTION' ... OK * preparing 'mypkg': * checking DESCRIPTION meta-information ... ERROR During startup - Warning messages: 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : ' there is no package called 'NULL in options(defaultPackages) was not found What is it that I am not doing right ? Thanks, Ajay. - AVIS : Ce courrier et ses pieces jointes sont destines a leur seul destinataire et peuvent contenir des informations confidentielles appartenant a bioMerieux. Si vous n'etes pas destinataire, vous etes informe que toute lecture, divulgation, ou reproduction de ce message et des pieces jointes est strictement interdite. Si vous avez recu ce message par erreur merci d'en prevenir l'expediteur et de le detruire, ainsi que ses pieces jointes. NOTICE: This message and attachments are intended only for the use of their addressee and may contain confidential information belonging to bioMerieux. If you are not the intended recipient, you are hereby notified that any reading, dissemination, distribution, or copying of this message, or any attachment, is strictly prohibited. If you have received this message in error, please notify the original sender immediately and delete this message, along with any attachments. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error in building library - R CMD build mypkg.
What does your DESCRIPTION file look like? Have you edited it to specify the required information? Read the Writing R Extensions manual. On Mon, May 19, 2008 at 4:11 PM, Ajay DAS [EMAIL PROTECTED] wrote: - Forwarded by Ajay DAS/US/BMNA01 on 05/19/2008 03:11 PM - Ajay DAS To: [EMAIL PROTECTED] 05/19/2008 01:00 cc: PM Subject: Error in building library - R CMD build mypkg. Hi, I am getting an error when I am trying to build a library in R for windows . I am using R 2.7.0 in windows. I am following the instructions listed in the R Help for package creation. require(stats) ## two functions and two data sets : f - function(x,y) x+y g - function(x,y) x-y d - data.frame(a=1, b=2) e - rnorm(1000) package.skeleton(list=c(f,g,d,e), name=mypkg) Then in the command prompt I executed the following command: R CMD build mypkg I am getting the following error : * checking for file 'mypkg/DESCRIPTION' ... OK * preparing 'mypkg': * checking DESCRIPTION meta-information ... ERROR During startup - Warning messages: 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : ' there is no package called 'NULL in options(defaultPackages) was not found What is it that I am not doing right ? Thanks, Ajay. - AVIS : Ce courrier et ses pieces jointes sont destines a leur seul destinataire et peuvent contenir des informations confidentielles appartenant a bioMerieux. Si vous n'etes pas destinataire, vous etes informe que toute lecture, divulgation, ou reproduction de ce message et des pieces jointes est strictement interdite. Si vous avez recu ce message par erreur merci d'en prevenir l'expediteur et de le detruire, ainsi que ses pieces jointes. NOTICE: This message and attachments are intended only for the use of their addressee and may contain confidential information belonging to bioMerieux. If you are not the intended recipient, you are hereby notified that any reading, dissemination, distribution, or copying of this message, or any attachment, is strictly prohibited. If you have received this message in error, please notify the original sender immediately and delete this message, along with any attachments. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] schoolmath (PR#11488)
Full_Name: Will Gray Version: 2.7.0 OS: GNU/Linux (Debian) Submission from: (NULL) (160.129.18.69) The schoolmath package has several inaccuracies in it. Here is just a sample of some ways to get prime numbers between 1,000,000 and 1,000,100. Each method returns a different set and each result contains non-primes. data(primlist) (a - primlist[primlist 100 primlist 1000100]) (b - is.prim(a)) which(!b) (c - primes(100,1000100)) (d - is.prim(c)) which(!d) Even the example for the function 'primes' gives some bad results. example(primes) - x (y - is.prim(x$value)) which(!y) I've tried contacting the maintainer(s) to let them know, but have not received a reply. In the meantime, I suggest this package be removed from CRAN. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
