Re: [Rd] R package Matrix failing to build with R-devel on Ubuntu AMD64
MWK == Mark W Kimpel [EMAIL PROTECTED] on Tue, 29 Jan 2008 23:14:30 -0500 writes: MWK Switched back to R-devel tonight after using R-2.6.1 for awhile and when MWK I updated my devel packages Matrix installation failed. Not critical for MWK me but thought I should report it. I am using Ubuntu Gusty AMD64 OS. MWK Tail of install output and sessionInfo follows. Mark MWK Loading required package: methods MWK Loading required package: lattice MWK Attaching package: 'Matrix' MWK The following object(s) are masked from package:stats : MWK xtabs MWK Error in new(dgCMatrix) : MWK trying to generate an object from a virtual class (dgCMatrix) MWK Calls: Anonymous ... eval.parent - eval - eval - eval - eval - MWK new - .Call MWK Execution halted MWK ERROR: installing package indices failed MWK ** Removing '/home/mkimpel/R_HOME/site-library/Matrix' MWK ** Restoring previous '/home/mkimpel/R_HOME/site-library/Matrix' MWK The downloaded packages are in MWK /tmp/RtmpJviXfF/downloaded_packages MWK Warning message: MWK In install.packages(Matrix) : MWK installation of package 'Matrix' had non-zero exit status sessionInfo() MWK R version 2.7.0 Under development (unstable) (2008-01-29 r44238) MWK x86_64-unknown-linux-gnu Thank you, Mark, for the report. Indeed --- to my own very big astonishment --- I *can* reproduce the problem. In the above messages, it's pretty funny that dgCMatrix is said to be a virtual class (which it is clearly not from the Matrix source). The daily CRAN package checks don't show the problem yet, but the checks' R version is R 2.7.0 Under development (unstable) (2008-01-27 r44199) which is a bit older, than the one you used (and even older than the one I used . r44258) I'm pretty sure I know around where the problem appeared.. More on this later. Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Documentation of the dev.copy2eps function. (PR#10656)
Thanks for replying. On Jan 30, 2008 2:28 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Tue, 29 Jan 2008, [EMAIL PROTECTED] wrote: The documentation of the dev.copy2eps() function should mention the file option which set the output file name Current R says ...: Arguments to the 'device' function above. For 'dev.print', this includes 'which' and by default any 'postscript' arguments. In my humble opinion, in the sentence Arguments to the 'device' function above, it is not clear to what the 'device' function above refers because 'device' is an argument in the text above this sentence. Therefore, I think it's difficult to understand which are the possible arguments for the copy2eps function. For 'dev.copy2eps', 'width' and 'height' are taken from the current device unless otherwise specified. If just one of 'width' and 'height' is specified, the other is adjusted to preserve the aspect ratio of the device being copied. The default file name is 'Rplot.eps'. I'm not sure why 'file' is more important than any other argument mentioned in ..., but we do say what the default is (because it is different). Can you tell us what more we 'should' say in your opinion, and why? I mentioned the 'file' argument because it was the one which I was looking for while reading the doc. Maybe all arguments valid for the postscript device are allowed for the copy2eps function but it is still not clear to me. Best regards, Clément. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] [rfc] Package to access the internal zlib library.
And Duncan Temple Lang writes: This deals with various compression schemes and does things in memory. Hopefully there isn't much overlap and the two might be complementary. Rcompression provides what's necessary for R.matlab's readMat. I'll switch to using it instead. What would it take to move Rcompression into CRAN? Jason __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] The standalone Rmath library and VC++ 2003
Yes, I used Rtools to compile the standalone Rmath library. However,
C:\Rtools\MinGW\lib\libm.a does not contain log1p;
C:\Rtools\MinGW\lib\libmingwex.a does. Once I replaced libm.a with
libmingwex.a, the application linked successfully and the following test
program was successful:
#include iostream
#define MATHLIB_STANDALONE
#include Rmath.h
int main()
{
double d = dbeta(0.5, 2.0, 3.0, 1);
double q = qbeta(0.5, 2.0, 3.0, 1, 0);
double p = pbeta(0.5, 2.0, 3.0, 1, 0);
double r = rbeta(0.5, 2.0);
std::cout dbeta = d \n;
std::cout qbeta = q \n;
std::cout pbeta = p \n;
std::cout rbeta = r \n;
}
dbeta = 0.405465
qbeta = 0.385728
pbeta = 0.6875
rbeta = 0.422286
Press any key to continue
Thanks
Oran
-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
Sent: Wednesday, January 30, 2008 1:06 PM
To: Oran Johnson
Cc: r-devel@r-project.org
Subject: Re: [Rd] The standalone Rmath library and VC++ 2003
On Tue, 29 Jan 2008, Oran Johnson wrote:
Linking my VC++ application with the standalone Rmath library yields
the
following;
Looks like you compiled the standalone Rmath library with MinGW. You
can't expect to mix-and-match compilers and link together a static
library
built under another compiler.
It is possible that this will work if you try linking to Rmath.dll:
WIndows' DLLs are fairly portable (although parameter passing
conventions
do differ, and we know 'double complex' is not portable). I assume you
know how to make a VC++ import library from a DLL, which you would need
to
do.
If you compiled standalone Rmath under VC++, you would not have got a .a
but a lib, at least by default. You are welcome to try that: it has
been
done in the past but is not something we support (nor even would want to
answer questions about).
-- Build started: Project: Complex plugin, Configuration: Debug
Win32 --
Linking...
Creating library .\../Debug/complex_plugin.lib and object
.\../Debug/complex_plugin.exp
libRmath.a(mlutils.o) : warning LNK4217: locally defined symbol __iob
imported in function _REprintf
libRmath.a(dbeta.o) : error LNK2019: unresolved external symbol _log1p
referenced in function _dbeta
libRmath.a(qbeta.o) : error LNK2019: unresolved external symbol _log1p
referenced in function _qbeta
libRmath.a(lbeta.o) : error LNK2019: unresolved external symbol _log1p
referenced in function _lbeta
libRmath.a(toms708.o) : error LNK2001: unresolved external symbol
_log1p
libRmath.a(qbeta.o) : error LNK2019: unresolved external symbol _expm1
referenced in function _qbeta
libRmath.a(mlutils.o) : error LNK2019: unresolved external symbol
___fpclassify referenced in function _R_pow
../Debug/complex_plugin.dll : fatal error LNK1120: 3 unresolved
externals
Build log was saved at file://c:\starting point\Debug\BuildLog.htm
Complex plugin - 7 error(s), 1 warning(s)
-- Done --
Build: 0 succeeded, 1 failed, 0 skipped
At first glance, it looks like C:\Rtools\MinGW\lib\libm.a is missing.
After adding it to my project properties, the results are the same. It
looks like VC++ is OK with GNU libraries because it appears to accept
libRmath which was built on the same machine using Rtools. Also it
does
not appear to be a configuration issue, because it's only found
'C:\Rtools\MinGW\lib' and VC+ is complaining about not finding it.
Any ideas?
Oran
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Re: [Rd] [rfc] Package to access the internal zlib library.
And Brian Ripley writes: The *only* safe thing to do is to include your own copy of zlib, and compile it into the package (optionally linking instead to the system copy if it exists). Fair enough, and likely necessary on AIX with XCOFF's restrictions. The Rcompression package mentioned by Duncan Lang has most of what I need, so I should help with Rcompression instead. Please note that Uwe Ligges provides a Windows testing service: see 'Writing R Extensions' and the R-admin manual. You don't need to ask others to do this for you. Great! Thank you and Uwe Ligges! I completely missed the Services section. Jason __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] X11 device distortion (PR#10666)
Full_Name: Thomas Zumbrunn Version: 2.6.1 OS: GNU/Linux (openSuse 10.3 2.6.22.13-0.3-default) Submission from: (NULL) (131.152.125.199) With my particular X11 settings, the width to height ratio of the x11 device is distorted, with the width being half that of the height. This results in wrongly proportioned plots, wrongly positioned text etc. Other devices are not affected. I already asked about his on the mailing list (https://stat.ethz.ch/pipermail/r-help/2007-December/147891.html) but no one seemed to have an answer. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] logical operator and addition (PR#10665)
[EMAIL PROTECTED] wrote: Full_Name: Nicolas Simonis Version: 2.6.1 OS: windows Submission from: (NULL) (155.52.10.223) Very funny bug : 0.60.6 [1] FALSE 0.60.4+0.2 [1] TRUE I don't see a bug here, I see failure to read FAQ 7.31. The value 0.6 is less than 0.4+0.2, when the operation is done in floating point approximations. None of those three numbers is exactly representable. (0.4+0.2) - 0.6 [1] 1.110223e-16 Duncan Murdoch control : 0.70.7 [1] FALSE 0.70.4+0.3 [1] FALSE With R 2.6.1 windows. it's not doing it with R 2.3.1 linux... __ 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] logical operator and addition (PR#10665)
Full_Name: Nicolas Simonis Version: 2.6.1 OS: windows Submission from: (NULL) (155.52.10.223) Very funny bug : 0.60.6 [1] FALSE 0.60.4+0.2 [1] TRUE control : 0.70.7 [1] FALSE 0.70.4+0.3 [1] FALSE With R 2.6.1 windows. it's not doing it with R 2.3.1 linux... __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] logical operator and addition (PR#10665)
This seems another instance of FAQ Q7.31 0.6 - (0.4 + 0.2) [1] -1.110223e-16 On Wed, 30 Jan 2008, [EMAIL PROTECTED] wrote: Full_Name: Nicolas Simonis Version: 2.6.1 OS: windows Submission from: (NULL) (155.52.10.223) Very funny bug : (rather a very common FAQ, when asked as a question) 0.60.6 [1] FALSE 0.60.4+0.2 [1] TRUE control : 0.70.7 [1] FALSE 0.70.4+0.3 [1] FALSE With R 2.6.1 windows. it's not doing it with R 2.3.1 linux... It depends on the compiler and optimization settings: it is doing it on 2.3.1 Linux for me (and 2.6.2 RC). __ 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] X11 device distortion (PR#10666)
On Thu, 31 Jan 2008, [EMAIL PROTECTED] wrote: Full_Name: Thomas Zumbrunn Version: 2.6.1 OS: GNU/Linux (openSuse 10.3 2.6.22.13-0.3-default) Submission from: (NULL) (131.152.125.199) With my particular X11 settings, the width to height ratio of the x11 device is distorted, with the width being half that of the height. This results in wrongly proportioned plots, wrongly positioned text etc. So your X11 settings are wrong: R is just using what X11 tells it. The most likely setting is DisplaySize in xorg.conf, which controls how inches are mapped to pixels. Other devices are not affected. I already asked about his on the mailing list (https://stat.ethz.ch/pipermail/r-help/2007-December/147891.html) but no one seemed to have an answer. __ 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] S4: setGeneric() and setMethod() with changed argument order
Dear R devel team
Using S4 classes in R I found a possible source of mistakes
caused by an inattentive user.
If one uses another order of the arguments for a function in the
setGeneric() as in the setMethod() call, one can get undesired
side effects without any warning.
Would it be desirable to include a warning for such cases? Thank
you for a statement.
R code:
## set generic function test1 with 3 arguments
setGeneric(test1, function(object, printit = TRUE, name = tmp)
standardGeneric(test1))
## Set method for test1 and class numeric, but change the order od the 2nd
## and 3rd arguments - No warning, everything works well?
setMethod(test1, signature(object = numeric),
function(object, name = tmp, printit = TRUE) {
match.call()
})
## .local is generated with the order from setGeneric(), but is called
## afterwards with the wrong order from setMethod() which can cause an error
## (if you are lucky) or strange results.
selectMethod(test1, signature = signature(object = numeric))
Method Definition:
function (object, printit = TRUE, name = tmp)
{
.local - function (object, name = tmp, printit = TRUE)
{
match.call()
}
.local(object, printit, name)
}
Signatures:
object
target numeric
defined numeric
## Shows that for the argument name printit is used. For the argument
## printit name is used
test1(pi)
.local(object = object, name = printit, printit = name)
Best regards,
Christoph Buser
--
Christoph Buser [EMAIL PROTECTED]
Seminar fuer Statistik, LEO C13
ETH Zurich 8092 Zurich SWITZERLAND
phone: x-41-44-632-4673 fax: 632-1228
http://stat.ethz.ch/~buser/
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Re: [Rd] segfault in gregexpr()
Hi again, Herve wrote: gregexpr(, abc, fixed=TRUE) *** caught segfault *** address 0x1c09000, cause 'memory not mapped' This should be fixed in latest svn. Thanks for the report. + seth -- Seth Falcon | [EMAIL PROTECTED] | blog: http://userprimary.net/user/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] X11 device distortion (PR#10666)
My first thought was that you must be using Xinerama or TwinView - and you did mention Xinerama in your r-help message but not in your bug report - this detail is important. That said, I don't know enough about X11 to say anything - well, maybe I do, but you'll have to show your xorg.conf , and possibly the result of xdpyinfo for anybody to help you. I think your Xinerama setup is broken. for the time being, you could probably run the X11 device through Xnest to get around this. [EMAIL PROTECTED] wrote: Full_Name: Thomas Zumbrunn Version: 2.6.1 OS: GNU/Linux (openSuse 10.3 2.6.22.13-0.3-default) Submission from: (NULL) (131.152.125.199) With my particular X11 settings, the width to height ratio of the x11 device is distorted, with the width being half that of the height. This results in wrongly proportioned plots, wrongly positioned text etc. Other devices are not affected. I already asked about his on the mailing list (https://stat.ethz.ch/pipermail/r-help/2007-December/147891.html) but no one seemed to have an answer. __ 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] Problem with R.2.6.1 and JRI - All worked file wih R2.5.1
Hello Members,
I have posted this message at R-HELP listserv, so my apology for
double posting, but members of R_HELP seem not to know/care about the
problem.
I wonder if someone also having a problem with JRI using new R 2.6.1.
To illustrate the problem, there is a simple Java driver problem
below. The program runs just fine on the other computer with R 2.5.1,
but does not run with R 2.6.1. It gives me no error messages either.
Needles to say, I have jri.dll at the classpath. Also, I have
downloaded the rJava package from R program (packages install
packages rJava), so version must be correct.
Any suggestions are highly appreciated,
Thanks,
Vlad
import org.rosuda.JRI.Rengine;
public class Driver {
public static void main(String[] args){
try {
String[] arg = {};
Rengine re = new Rengine(arg, false, null);
if (!Rengine.versionCheck()) {
Rengine.getVersion();
System.err.println(** Version mismatch);
System.exit(1);
}
if (!re.waitForR()) {
System.out.println(** Cannot load R);
System.exit(1);
}
double d = re.eval(3+5).asDouble();
System.out.print(D = + d);
} catch (RuntimeException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}
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Re: [Rd] X11 device distortion (PR#10666)
Just to follow up, largely in synch with the two replies already, it sounds like there is a good chance that your two displays (the physical panels or monitors) are either of two different sizes and/or have two different resolutions. Somewhat more likely is the latter. In either case, it is likely that the dpi (dots per inch) setting that is being picked up by the X server is incorrect or biased by one display over the other. Hence, when you open the display device on the screen, the size and aspect ratio of the device is wrong. For example, on my system, I have an internal 15 inch laptop lcd panel of 1600x1200 with a dpi of 133. I have an external 20 inch lcd panel which has the same resolution but at 100 dpi. I happen to use TwinView with an nVidia card, but have to tweak the xorg.conf settings to get the displays to look reasonably similar. I actually hard code the 100 dpi setting rather than allowing the server to get the information from the monitors. My xdpyinfo is: $ xdpyinfo | grep dimensions dimensions:3200x1200 pixels (813x305 millimeters) $ xdpyinfo | grep resolution resolution:100x100 dots per inch Note that using TwinView, my two displays effectively show as one. I would suggest that you post to a SUSE or generic Linux forum or perhaps to a graphics card vendor forum specific to your card for detailed guidance. HTH, Marc Schwartz Hin-Tak Leung wrote: My first thought was that you must be using Xinerama or TwinView - and you did mention Xinerama in your r-help message but not in your bug report - this detail is important. That said, I don't know enough about X11 to say anything - well, maybe I do, but you'll have to show your xorg.conf , and possibly the result of xdpyinfo for anybody to help you. I think your Xinerama setup is broken. for the time being, you could probably run the X11 device through Xnest to get around this. [EMAIL PROTECTED] wrote: Full_Name: Thomas Zumbrunn Version: 2.6.1 OS: GNU/Linux (openSuse 10.3 2.6.22.13-0.3-default) Submission from: (NULL) (131.152.125.199) With my particular X11 settings, the width to height ratio of the x11 device is distorted, with the width being half that of the height. This results in wrongly proportioned plots, wrongly positioned text etc. Other devices are not affected. I already asked about his on the mailing list (https://stat.ethz.ch/pipermail/r-help/2007-December/147891.html) but no one seemed to have an answer. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Pb with lapply()
Hi,
If needed, lapply() tries to convert its first argument into a list
before it starts doing something with it:
lapply
function (X, FUN, ...)
{
FUN - match.fun(FUN)
if (!is.vector(X) || is.object(X))
X - as.list(X)
.Internal(lapply(X, FUN))
}
But in practice, things don't always seem to work as suggested by
this code (at least to the eyes of a naive user).
I have defined an as.list method for my S4 class A:
setClass(A, representation(data=list))
[1] A
setMethod(as.list, A, function(x, ...) [EMAIL PROTECTED])
Creating a new generic function for as.list in .GlobalEnv
[1] as.list
Testing it:
a - new(A, data=list(8, 2:0))
as.list(a)
[[1]]
[1] 8
[[2]]
[1] 2 1 0
OK.
But lapply() doesn't work on 'a':
lapply(a, typeof)
Error in as.vector(x, list) : cannot type 'S4' coerce to vector
I still have to do the 'as.list(a)' part myself for things to work:
lapply(as.list(a), typeof)
[[1]]
[1] double
[[2]]
[1] integer
Seems like using force() inside lapply() would solve the problem:
lapply2 - function(X, FUN, ...)
{
FUN - match.fun(FUN)
if (!is.vector(X) || is.object(X))
X - force(as.list(X))
.Internal(lapply(X, FUN))
}
It works now:
lapply2(a, typeof)
[[1]]
[1] double
[[2]]
[1] integer
Cheers,
H.
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Re: [Rd] Pb with lapply()
The problem of promises not being evaluated in
lists has been discussed before.
I think its fixed in the development version of R. See
r44139 on Jan 24, 2008 in http://developer.r-project.org/R.svnlog.2007
On Jan 31, 2008 1:26 PM, [EMAIL PROTECTED] wrote:
Hi,
If needed, lapply() tries to convert its first argument into a list
before it starts doing something with it:
lapply
function (X, FUN, ...)
{
FUN - match.fun(FUN)
if (!is.vector(X) || is.object(X))
X - as.list(X)
.Internal(lapply(X, FUN))
}
But in practice, things don't always seem to work as suggested by
this code (at least to the eyes of a naive user).
I have defined an as.list method for my S4 class A:
setClass(A, representation(data=list))
[1] A
setMethod(as.list, A, function(x, ...) [EMAIL PROTECTED])
Creating a new generic function for as.list in .GlobalEnv
[1] as.list
Testing it:
a - new(A, data=list(8, 2:0))
as.list(a)
[[1]]
[1] 8
[[2]]
[1] 2 1 0
OK.
But lapply() doesn't work on 'a':
lapply(a, typeof)
Error in as.vector(x, list) : cannot type 'S4' coerce to vector
I still have to do the 'as.list(a)' part myself for things to work:
lapply(as.list(a), typeof)
[[1]]
[1] double
[[2]]
[1] integer
Seems like using force() inside lapply() would solve the problem:
lapply2 - function(X, FUN, ...)
{
FUN - match.fun(FUN)
if (!is.vector(X) || is.object(X))
X - force(as.list(X))
.Internal(lapply(X, FUN))
}
It works now:
lapply2(a, typeof)
[[1]]
[1] double
[[2]]
[1] integer
Cheers,
H.
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Re: [Rd] Pb with lapply()
Hi Gabor, Quoting Gabor Grothendieck [EMAIL PROTECTED]: The problem of promises not being evaluated in lists has been discussed before. I think its fixed in the development version of R. See r44139 on Jan 24, 2008 in http://developer.r-project.org/R.svnlog.2007 I'm using R-devel r44238 and the problem is still here. Cheers, H. sessionInfo() R version 2.7.0 Under development (unstable) (2008-01-29 r44238) x86_64-unknown-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 base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Problem with R.2.6.1 and JRI - All worked file wih R2.5.1
Vladimir,
your example works without problems in R 2.6.1:
C:\Program Files\R\R-2.6.1\library\rJava\jrijavac -cp JRI.jar
Driver.java
C:\Program Files\R\R-2.6.1\library\rJava\jriset PATH=C:\Program Files
\R\R-2.6.1\bin;%PATH%
C:\Program Files\R\R-2.6.1\library\rJava\jrijava -cp JRI.jar;. Driver
D = 8.0
I suspect that you have some setting mismatch left over from your
previous R version.
Note that you may want to add System.exit(0) or terminate R, otherwise
your application will be waiting for R to exit.
Cheers,
Simon
On Jan 31, 2008, at 11:37 AM, Vladmir Makarov wrote:
Hello Members,
I have posted this message at R-HELP listserv, so my apology for
double posting, but members of R_HELP seem not to know/care about the
problem.
I wonder if someone also having a problem with JRI using new R 2.6.1.
To illustrate the problem, there is a simple Java driver problem
below. The program runs just fine on the other computer with R 2.5.1,
but does not run with R 2.6.1. It gives me no error messages either.
Needles to say, I have jri.dll at the classpath. Also, I have
downloaded the rJava package from R program (packages install
packages rJava), so version must be correct.
Any suggestions are highly appreciated,
Thanks,
Vlad
import org.rosuda.JRI.Rengine;
public class Driver {
public static void main(String[] args){
try {
String[] arg = {};
Rengine re = new Rengine(arg, false, null);
if (!Rengine.versionCheck()) {
Rengine.getVersion();
System.err.println(** Version mismatch);
System.exit(1);
}
if (!re.waitForR()) {
System.out.println(** Cannot load R);
System.exit(1);
}
double d = re.eval(3+5).asDouble();
System.out.print(D = + d);
} catch (RuntimeException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}
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Re: [Rd] Pb with lapply()
I just checked and the code that previously triggered the promises in lists bug seems to work now so I guess it is a different problem. # code below previously triggered errors but now works # R 2.6.2 (2008-01-26 r44181) on Vista f - function(x) environment() z - as.list(f(7)) dput(z) structure(list(x = 7), .Names = x) z[[1]] == 7 force(z[[1]]) == 7 On Jan 31, 2008 2:33 PM, [EMAIL PROTECTED] wrote: Hi Gabor, Quoting Gabor Grothendieck [EMAIL PROTECTED]: The problem of promises not being evaluated in lists has been discussed before. I think its fixed in the development version of R. See r44139 on Jan 24, 2008 in http://developer.r-project.org/R.svnlog.2007 I'm using R-devel r44238 and the problem is still here. Cheers, H. sessionInfo() R version 2.7.0 Under development (unstable) (2008-01-29 r44238) x86_64-unknown-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 base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Feature request: about lag(), which.min() and cat().
Hello I'm only user of R and have many little knowledge in programming but I permit to send you some whishes/suggestions for R. which.min like which(), which.min() should also include an argument arr.ind. Note that one can have it with which(a==min(a), arr.ind=TRUE) but if there is a reason to build a special function which.min, why not add also this nice argument? lag() If one wants to construct a time series model, it is often useful to have the lags matrix. This is available with embed(ts,k) but the time series class disappears. So it would be nice that the argument k of lag() also admit values of length 1, which would give the same result as embed() but keep the class. In his wish list of 1 January 2008 (point 8), Gabor Grothendieck spoke about a function Lag. Maybe also a function lags otherwise if the idea of length(k)1 is not good? cat() It would be really nice if cat() could also include matrix and lists as values. This would allow big improvements for output written in a file. Thank you for what you make for R, it is a really nice program! __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] X11 device distortion (PR#10666)
On Thursday 31 January 2008, Hin-Tak Leung wrote: My first thought was that you must be using Xinerama or TwinView - and you did mention Xinerama in your r-help message but not in your bug report - this detail is important. Yes, I forgot to mention this. That said, I don't know enough about X11 to say anything - well, maybe I do, but you'll have to show your xorg.conf , and possibly the result of xdpyinfo for anybody to help you. I think your Xinerama setup is broken. Yes, and as Prof. Ripley correctly guessed that the DisplaySize setting was wrong. SaX2, the X11 setup tool of openSUSE, adds up the width values of both Xinerama devices, which results in a wrong DisplaySize width value. I filed a bug at openSUSE and already got a reaction. It seems unclear whether it is correct to add up the values. for the time being, you could probably run the X11 device through Xnest to get around this. Thanks for the advice. Correcting the DisplaySize value helped, and it didn't break the Xinerama setting. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Feature request: about lag(), which.min() and cat().
On Jan 31, 2008 8:24 AM, Matthieu Stigler [EMAIL PROTECTED] wrote: lag() If one wants to construct a time series model, it is often useful to have the lags matrix. This is available with embed(ts,k) but the time series class disappears. So it would be nice that the argument k of lag() also admit values of length 1, which would give the same result as embed() but keep the class. In his wish list of 1 January 2008 (point 8), Gabor Grothendieck spoke about a function Lag. Maybe also a function lags otherwise if the idea of length(k)1 is not good? It would be nice. Note that lag.zoo in the zoo package does supports this for zoo objects. library(zoo) z - zoo((11:20)^2) lag(z, 1:2) lag1 lag2 1 144 169 2 169 196 3 196 225 4 225 256 5 256 289 6 289 324 7 324 361 8 361 400 9 400 NA # regress z on lag(z, 1:2) using dyn package library(dyn) dyn$lm(z ~ lag(z, 1:2)) Call: lm(formula = dyn(z ~ lag(z, 1:2))) Coefficients: (Intercept) lag(z, 1:2)1 lag(z, 1:2)2 2 2-1 # as a workaround one could convert to zoo and back x - ts((11:20)^2) as.ts(lag(as.zoo(x), 1:2)) Time Series: Start = 1 End = 9 Frequency = 1 lag1 lag2 1 144 169 2 169 196 3 196 225 4 225 256 5 256 289 6 289 324 7 324 361 8 361 400 9 400 NA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] segfault in gregexpr()
Hi Seth, Seth Falcon wrote: Hi again, Herve wrote: gregexpr(, abc, fixed=TRUE) *** caught segfault *** address 0x1c09000, cause 'memory not mapped' This should be fixed in latest svn. Thanks for the report. That's great. Thanks! H. + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] nlme package. Minor change in method print.VarCov (PR#10669)
Hello,
I would like to propose to make a minor change in method print.VarCov
by inserting one line
stdevs - FALSE # Inserted line
as shown later in this email.
By adding this line we would modify the output from
print(corrmtx) as shown in the illustration below. More specifically the
line with redundant information, which reads Standard Deviations: 1 1 1
would be skipped from the output.
Otherwise, to omit line with SDs:1 1 1 from the output we need to use
more cumbersome syntax:
print(corrmtx, corr=TRUE, stdevs=FALSE).
Output from sessionInfo() included at the bottom of this email
Sincerely,
Andrzej Galecki
Illustration
selected.rows - seq(1,308, by=10)
ovary - Ovary[selected.rows,] # selected rows
fm1 - gls(follicles ~ sin(2*pi*Time) + cos(2*pi*Time), ovary,
correlation = corAR1(form = ~ 1 | Mare))
vmtx - getVarCov(fm1) # Covariance matrix
corrmtx - cov2cor(vmtx) # Correlation matrix
print(corrmtx, corr=TRUE)
Marginal correlation matrix
[,1][,2][,3]
[1,] 1.0 0.39172 0.15345
[2,] 0.39172 1.0 0.39172
[3,] 0.15345 0.39172 1.0
Standard Deviations: 1 1 1
print(corrmtx,corr=TRUE,stdevs=FALSE)
Marginal correlation matrix
[,1][,2][,3]
[1,] 1.0 0.39172 0.15345
[2,] 0.39172 1.0 0.39172
[3,] 0.15345 0.39172 1.0
==Part of the Source code with suggested change ===
getS3method(print,VarCov)
function (x, corr = FALSE, stdevs = TRUE, digits = 5, ...)
{
pvc - function(x, type, corr, stdevs, digits) {
cat(c(Random effects, Conditional, Marginal)[match(type,
c(random.effects, conditional, marginal))],
, sep = )
x - as.matrix(x)
class(x) - NULL
attr(x, group.levels) - NULL
if (corr) {
cat(correlation matrix\n)
sds - sqrt(diag(x))
print(signif(t(x/sds)/sds, digits))
stdevs - FALSE # Inserted line
}
else {
cat(variance covariance matrix\n)
print(signif(x, digits))
if (stdevs)
sds - sqrt(diag(x))
}
===
sessionInfo()
R version 2.6.1 (2007-11-26)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] nlme_3.1-86
loaded via a namespace (and not attached):
[1] grid_2.6.1 lattice_0.17-2 tools_2.6.1
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