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
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---
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Institut für Statistik Tel: (+49 89) 2180 3165
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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.
-
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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.
>
> __
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[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
[Rd] using zlib in a package: problems in windows
Dear All, I am having trouble getting an R package to build and install correctly under Windows. In this package, which builds and checks OK under Linux, I use zlib (among other functions, gzprintf). As mentioned by Prof. Ripley a while back, the file "CHANGES" under src/gnuwin32 says explains that to, to use zlib, one has to set $(ZLIB_LIBS) in PKG_LIBS. I have a Makefile.win with just that. I have also downloaded the Windows toolset (Rtools.exe) which I have used to successfully build R-patched. However, I still cannot get the package to compile. >From the log, it seems that in fact the build is trying to use zlib, but the gzprintf symbol is not found. However, gzprintf is in the zlib.h header. 00install.out follows below. What am I doing wrong? Thanks, R. P.D. I am using Windows 2000 (under vmware). -- Making package RJaCGH ** WARNING: this package has a configure script It probably needs manual configuration ** adding build stamp to DESCRIPTION installing NAMESPACE file and metadata making DLL ... making nnhl.d from nnhl.c gcc -std=gnu99 -Ic:/R/R-patc~1/include -O3 -Wall -c nnhl.c -o nnhl.o windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I c:/R/R-patc~1/include -i RJaCGH_res.rc -o RJaCGH_res.o gcc -std=gnu99 -shared -s -o RJaCGH.dll RJaCGH.def nnhl.o RJaCGH_res.o -Lc:/R/R-patc~1/bin -lRzlib -lR nnhl.o:nnhl.c:(.text+0x138f): undefined reference to `gzprintf' nnhl.o:nnhl.c:(.text+0x13ae): undefined reference to `gzprintf' nnhl.o:nnhl.c:(.text+0x13d2): undefined reference to `gzprintf' nnhl.o:nnhl.c:(.text+0x13f6): undefined reference to `gzprintf' nnhl.o:nnhl.c:(.text+0x1415): undefined reference to `gzprintf' nnhl.o:nnhl.c:(.text+0x1451): more undefined references to `gzprintf' follow collect2: ld returned 1 exit status make[3]: *** [RJaCGH.dll] Error 1 make[2]: *** [srcDynlib] Error 2 make[1]: *** [all] Error 2 make: *** [pkg-RJaCGH] Error 2 *** Installation of RJaCGH failed *** -- Ramon Diaz-Uriarte Statistical Computing Team Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] using zlib in a package: problems in windows
gzprintf is not in Rzlib.dll. It has been commented out in the R build. So you will need to use you own copy of zlib. On Tue, 20 May 2008, Ramon Diaz-Uriarte wrote: Dear All, I am having trouble getting an R package to build and install correctly under Windows. In this package, which builds and checks OK under Linux, I use zlib (among other functions, gzprintf). As mentioned by Prof. Ripley a while back, the file "CHANGES" under src/gnuwin32 says explains that to, to use zlib, one has to set $(ZLIB_LIBS) in PKG_LIBS. I have a Makefile.win with just that. I have also downloaded the Windows toolset (Rtools.exe) which I have used to successfully build R-patched. However, I still cannot get the package to compile. From the log, it seems that in fact the build is trying to use zlib, but the gzprintf symbol is not found. However, gzprintf is in the zlib.h header. 00install.out follows below. What am I doing wrong? Thanks, R. P.D. I am using Windows 2000 (under vmware). -- Making package RJaCGH ** WARNING: this package has a configure script It probably needs manual configuration ** adding build stamp to DESCRIPTION installing NAMESPACE file and metadata making DLL ... making nnhl.d from nnhl.c gcc -std=gnu99 -Ic:/R/R-patc~1/include -O3 -Wall -c nnhl.c -o nnhl.o windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I c:/R/R-patc~1/include -i RJaCGH_res.rc -o RJaCGH_res.o gcc -std=gnu99 -shared -s -o RJaCGH.dll RJaCGH.def nnhl.o RJaCGH_res.o -Lc:/R/R-patc~1/bin -lRzlib -lR nnhl.o:nnhl.c:(.text+0x138f): undefined reference to `gzprintf' nnhl.o:nnhl.c:(.text+0x13ae): undefined reference to `gzprintf' nnhl.o:nnhl.c:(.text+0x13d2): undefined reference to `gzprintf' nnhl.o:nnhl.c:(.text+0x13f6): undefined reference to `gzprintf' nnhl.o:nnhl.c:(.text+0x1415): undefined reference to `gzprintf' nnhl.o:nnhl.c:(.text+0x1451): more undefined references to `gzprintf' follow collect2: ld returned 1 exit status make[3]: *** [RJaCGH.dll] Error 1 make[2]: *** [srcDynlib] Error 2 make[1]: *** [all] Error 2 make: *** [pkg-RJaCGH] Error 2 *** Installation of RJaCGH failed *** -- Ramon Diaz-Uriarte Statistical Computing Team Structural Biology and Biocomputing Programme Spanish National Cancer Centre (CNIO) http://ligarto.org/rdiaz __ 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
