[Rd] [Fwd: buglet (?) in de.restore()]
I'm resending this after a decent interval of 20 days -- any opinions? Should I file it as a bug report? Is it my mistake? cheers Ben Bolker Original Message Subject:buglet (?) in de.restore() Date: Tue, 21 Aug 2007 13:29:33 -0400 From: Ben Bolker <[EMAIL PROTECTED]> To: r-devel@r-project.org If one calls data.entry() with a matrix: A = matrix(0,2,2) data.entry(A) everything works fine except that it triggers a warning: Warning message: the condition has length > 1 and only the first element will be used in: if (dim(x) == dim(args[[i]])) rn <- dimnames(args[[i]])[[1]] else rn <- NULL This is triggered by the following lines in de.restore() [in src/library/utils/R/de.R]: > if( dim(x) == dim(args[[i]]) ) > rn <- dimnames(args[[i]])[[1]] > else rn <- NULL It would seem to make sense to replace the condition with if (nrow(x) == nrow(args[[i]])) (de.restore() is only called if an element of the list passed to data.entry has more than one column) On a side note, I'm curious why > > A = matrix(0,2,2) > > is.vector(A) > [1] FALSE > > is(A,"vector") > [1] TRUE ... -- sessionInfo() R version 2.5.1 (2007-06-27) i486-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [Fwd: buglet (?) in de.restore()]
On 9/10/2007 8:47 AM, Ben Bolker wrote: > I'm resending this after a decent interval of 20 days -- any > opinions? Should I file it as a bug report? Is it my mistake? I think a bug report is in order. > > cheers > Ben Bolker > > > Original Message > Subject: buglet (?) in de.restore() > Date: Tue, 21 Aug 2007 13:29:33 -0400 > From: Ben Bolker <[EMAIL PROTECTED]> > To: r-devel@r-project.org > > > > If one calls data.entry() with a matrix: > > A = matrix(0,2,2) > data.entry(A) > > everything works fine except that it triggers a warning: > > Warning message: > the condition has length > 1 and only the first element will be used in: > if (dim(x) == dim(args[[i]])) rn <- dimnames(args[[i]])[[1]] else rn > <- NULL > > This is triggered by the following lines in de.restore() [in > src/library/utils/R/de.R]: >> if( dim(x) == dim(args[[i]]) ) >> rn <- dimnames(args[[i]])[[1]] >> else rn <- NULL > It would seem to make sense to replace the condition with > > if (nrow(x) == nrow(args[[i]])) > > (de.restore() is only called if an element of the list passed to > data.entry > has more than one column) > > On a side note, I'm curious why > >> > A = matrix(0,2,2) >> > is.vector(A) >> [1] FALSE >> > is(A,"vector") >> [1] TRUE The glib answer for the first result is that it's because it's documented that way. I guess it's so that you can distinguish simple vectors from matrices or other more complex objects. As to the second, you're testing whether A inherits from the class "vector", i.e. indexing works on it. Most things in R inherit from class vector, so that comes out TRUE. (Things that don't: NULL, environments, some other special stuff.) Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [Fwd: buglet (?) in de.restore()]
Ben Bolker wrote: > I'm resending this after a decent interval of 20 days -- any > opinions? Should I file it as a bug report? Is it my mistake? > It just slipped through the cracks, I suppose. I think it looks like a buglet -- the [[1]] in dimnames(args[[i]])[[1]] doesn't make sense unless dim(args[[i]]) is nonscalar. The suggested fix should be neutral since nrow(x)==dim(x)[1] by definition. I've fixed it now, but in principle it is the kind of material that bug reports are made of. -p > cheers > Ben Bolker > > > Original Message > Subject: buglet (?) in de.restore() > Date: Tue, 21 Aug 2007 13:29:33 -0400 > From: Ben Bolker <[EMAIL PROTECTED]> > To: r-devel@r-project.org > > > > If one calls data.entry() with a matrix: > > A = matrix(0,2,2) > data.entry(A) > > everything works fine except that it triggers a warning: > > Warning message: > the condition has length > 1 and only the first element will be used in: > if (dim(x) == dim(args[[i]])) rn <- dimnames(args[[i]])[[1]] else rn > <- NULL > > This is triggered by the following lines in de.restore() [in > src/library/utils/R/de.R]: > >> if( dim(x) == dim(args[[i]]) ) >> rn <- dimnames(args[[i]])[[1]] >> else rn <- NULL >> > It would seem to make sense to replace the condition with > > if (nrow(x) == nrow(args[[i]])) > > (de.restore() is only called if an element of the list passed to > data.entry > has more than one column) > > On a side note, I'm curious why > > >>> A = matrix(0,2,2) >>> is.vector(A) >>> >> [1] FALSE >> >>> is(A,"vector") >>> >> [1] TRUE >> > ... > > -- > sessionInfo() > R version 2.5.1 (2007-06-27) > i486-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" > [7] "base" > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] partial correlation function for multivariate time series
Dear all, I found the following behaviour with pacf() in the multivariate case, set.seed(10) x <- rnorm(1000,sd=1) y <- rnorm(1000,sd=1) pacf(ts(cbind(x,y)),plot=FALSE,lag.max=10) Partial autocorrelations of series 'cbind(x, y)', by lag , , x x y 0.047 ( 1)0.000 ( -1) 0.011 ( 2)0.000 ( -2) 0.005 ( 3)0.000 ( -3) 0.013 ( 4)0.000 ( -4) 0.050 ( 5)0.000 ( -5) 0.034 ( 6)0.000 ( -6) 0.026 ( 7)0.000 ( -7) -0.029 ( 8)0.000 ( -8) -0.010 ( 9)0.000 ( -9) -0.013 ( 10)0.000 (-10) , , y x y 374.052 ( 1) -0.045 ( 1) 66.717 ( 2) -0.024 ( 2) -535.810 ( 3) -0.031 ( 3) 120.802 ( 4) -0.020 ( 4) 142.824 ( 5)0.004 ( 5) -211.711 ( 6) -0.010 ( 6) 201.856 ( 7)0.058 ( 7) 286.079 ( 8) -0.035 ( 8) -134.057 ( 9)0.032 ( 9) -18.200 ( 10)0.019 ( 10) Since there are multiple ways of defining the pacf for multivariate time series (see e.g. G.C. Reinsel, Elements of multivariate time series analysis, II edition, Springer, section 3.3) and given that in ?pacf there is no reference to articles or books regarding its computation I do not know whether this behaviour is expected or it is a bug instead. In the first case could you provide a reference for it? In the second case I might file a bug report. Thank you for the great work you are doing for the scientific community. kind regards, Simone Giannerini WINDOWS platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 5.1 year 2007 month 06 day27 svn rev42083 language R version.string R version 2.5.1 (2007-06-27) LINUX > R.Version() $platform [1] "x86_64-unknown-linux-gnu" $arch [1] "x86_64" $os [1] "linux-gnu" $system [1] "x86_64, linux-gnu" $status [1] "" $major [1] "2" $minor [1] "5.1" $year [1] "2007" $month [1] "06" $day [1] "27" $`svn rev` [1] "42083" $language [1] "R" $version.string [1] "R version 2.5.1 (2007-06-27)" -- __ Simone Giannerini Dipartimento di Scienze Statistiche "Paolo Fortunati" Universita' di Bologna Via delle belle arti 41 - 40126 Bologna, ITALY Tel: +39 051 2098262 Fax: +39 051 232153 __ [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Snow on Windows Cluster
Thanks for the note.
Could you give me more info on the "small failures on stopping cluster"?
I don't currently have a windows system I can test this on so I can't
fold it into the snow release yet. But hopefully I can in the next
month or so. I may get back in touch at that point.
Meanwhile I have been working with a modified shell script that can be
used with mpirun under lam on unix. I've attached the current
version. It may turn out that this approach is a little more
maitainable on the Windows side as well. The way this gets used is
mpirun -np 5 RMPISNOW
to run a master and 4 workers, and then in the master
cl <- getMPIcluster()
instead of using makeCluster or makeMPIcluster. I have not yet found
the MICH2 analog of the LAMRANK environment variable but suspect
something similar does exist.
Best,
luke
On Mon, 3 Sep 2007, Markus Schmidberger wrote:
Hello,
the package snow is not working on a windows cluster with MPICH2 and Rmpi.
There is an error in makeCluster:
launch failed: CreateProcess(/usr/bin/env
"RPROG="C:\Programme\R\R-2.5.1\bin\R" "OUT=/dev/null" "R_LIBS="
C:/Programme/R/R-2.5.1/library/snow/RMPInode.sh) on 'cl1' failed, error 3 -
Das System kann den angegbenen Pfad nicht finden.
I looked into makeMPIcluster. It could not work, mpi.comm.spawn gets the
shell command for unix to start the slaves. A simple solution is to use the
windows-code from mpi.spawn.rslaves, then it looks like this. And is working
on our windows-cluster. (small failures on stopping cluster)
# Fro windows
if (.Platform$OS=="windows"){
workdrive <- unlist(strsplit(getwd(),":"))[1]
tmpdrive <- unlist(strsplit(tempdir(),":"))[1]
worktmp <- as.logical(toupper(workdrive)==toupper(tmpdrive))
tmpdir <- unlist(strsplit(tempdir(),"/Rtmp"))[1]
localhost <- Sys.getenv("COMPUTERNAME")
networkdrive <-.Call("RegQuery",
as.integer(2),paste("NETWORK\\",workdrive,sep=""),
PACKAGE="Rmpi")
remotepath <-networkdrive[which(networkdrive=="RemotePath")+1]
mapdrive=TRUE
mapdrive <- as.logical(mapdrive && !is.null(remotepath))
Rscript=system.file("slaveload.R", package="snow")
arg <- c(Rscript, R.home(), workdrive, getwd(),worktmp, tmpdir,
localhost, mapdrive, remotepath)
#Rscript,R_HOME,WDrive,WDir,WorkTmp,TmpDir,Master,MapDrive,RemotePath
print("super")
count<-mpi.comm.spawn(
slave=system.file("Rslaves.bat", package="Rmpi"),
slavearg=arg,
nslaves=count)
} else{ # for unix
count <- mpi.comm.spawn(slave = "/usr/bin/env",
slavearg = args,
nslaves = count,
intercomm = intercomm)
}
Doing some work, there should be a better and nicer solution with directly
using mpi.spawn.Rslaves.
Best
Markus
--
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics andFax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: [EMAIL PROTECTED]
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu#! /bin/sh
# if definded, prepend R_SNOW_LIB to $_LIBS
if test ! -z "${R_SNOW_LIB}" ; then
R_LIBS=${R_SNOW_LIB}:${R_LIBS}; export R_LIBS
fi
# find the library containing the snow package; should eventually use Rscript
snowdir=`echo 'invisible(cat(tryCatch(dirname(.find.package("snow")), error =
function(e) ""),"\n",sep=""))' | R --slave`
# for now this hijack the R_PROFILE mechanism to start up the R
# sessions and load snow and Rmpi into them
R_PROFILE=${snowdir}/snow/RMPISNOWprofile; export R_PROFILE
if test -z "${LAMRANK}" ; then
echo "not using LAM-MPI; currently only LAM-MPI is supported"
exit 1
else
# use the LAMRANK environment variable set by LAM-MPI's mpirun to
# run R with appropriate arguments for master and workers.
if test "${LAMRANK}" == "0" ; then
exec R $*
else
exec R --slave > /dev/null 2>&1
fi
fi
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[Rd] Test posting
This is a test posting to R-devel used to determine why some postings are dropped. This one avoids mentioning the name of an operating system that may trigger a junk reaction. Please ignore. DS __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
