Re: [Rd] Writing R documentation
Suzette Blanchard wrote:
Greetings,
I used latex type code in my Rd files.
The pdf version using
R CMD Rd2dvi --output=PKtools.pdf --pdf --title="PKtools" PKtools man
came out quite nice.
However, my current HTML version does not tex the latex so there is
latex code in the files and looks bad.
Sorry, I don't understand "HTML version does not tex the latex"?
example problem code:
AIC$_c$
or
\begin{itemize}
\item NLME:
\begin{itemize}
\item population level: identify(MM\$mm\$fitted[,1], MM\$pkdata\$conc)
\item individual level: identify(MM\$mm\$fitted[,2], MM\$pkdata\$conc)
\end{itemize}
\item NONMEM:
\begin{itemize}
\item population level: identify(NM\$pred\$PRED, NM\$pred\$CONC)
\item individual level: identify(NM\$pred\$IPRE, NM\$pred\$CONC)
\end{itemize}
\item WinBUGS:
\begin{itemize}
\item population level: identify(WB\$pred\$ppred, WB\$pred\$conc)
\item individual level: identify(WB\$pred\$ipred, WB\$pred\$conc)
\end{itemize}
Is there a way to fix this?
.Rd is not .tex.
Please read the manual "Writing R Extensions". You cannot use
mathematical environments that way. There are \eqn{} environments, if
you really need it.
Uwe Ligges
I tried Rdconv using --type=HTML but that did not work.
>
Any help you can send would be appreciated.
Thank you,
Suzette
=
Suzette Blanchard, Ph.D.
UCSD-PPRU
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Re: [Rd] trouble building r-devel
[EMAIL PROTECTED] wrote: Thanks Seth (and Duncan)-- the murdoch-sutherland page seems to fix everything. The slimmed-down INSTALL file in R-devel src gnuwin32 doesn't refer to the page-- it might be good to add a reference. Mark, I disagree. This "slimmed-down" file points you to the thorough Chapter "Installing R under Windows" in the "`R Installation and Administration' manual in the doc/manual directory". Quite at the top of Section "Building from source" there is the Subsection "Getting the tools". I think we do NOT want to point people to Duncan's page at first, or they would not read the more comprehensive manual any more. Uwe Mark Mark Bravington CSIRO Mathematical & Information Sciences Marine Laboratory Castray Esplanade Hobart 7001 TAS ph (+61) 3 6232 5118 fax (+61) 3 6232 5012 mob (+61) 438 315 623 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Seth Falcon Sent: Tuesday, 22 March 2005 3:32 PM To: r-devel@stat.math.ethz.ch Subject: Re: [Rd] trouble building r-devel <[EMAIL PROTECTED]> writes: cp unicode/iconv.dll ../../modules/ cp: cannot stat `unicode/iconv.dll': No such file or directory make[2]: *** [rmodules] Error 1 make[1]: *** [rbuild] Error 2 make: *** [all] Error 2 See the section Unicode support here: http://www.murdoch-sutherland.com/Rtools/ Basically, you just need to download and then copy the iconv.dll to the right spot and you should be on your way. + seth __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] can R_do_slot_assign change slot type
Hi,
It seems that R_do_slot_assign can change the type of an S4 class slot.
For example I have a class
setClass("ostream", representation(id = "integer", keepOpen =
"logical"))
and inside a C-function I was able to assign a RAW vector to the id
slot. Is this intentional? I remember reading somewhere that the slot
type is guaranteed by R. Maybe this doesn't extend to C code?
Now, in the above example I actually don't know the eventual type of the
'id' slot, it will be set up in some C code that intializes the class
instance. What is the right way to define the representation in such a
case?
Thanks,
Vadim
[[alternative HTML version deleted]]
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RE: [Rd] trouble building r-devel
Thanks Seth (and Duncan)-- the murdoch-sutherland page seems to fix everything. The slimmed-down INSTALL file in R-devel src gnuwin32 doesn't refer to the page-- it might be good to add a reference. Mark Mark Bravington CSIRO Mathematical & Information Sciences Marine Laboratory Castray Esplanade Hobart 7001 TAS ph (+61) 3 6232 5118 fax (+61) 3 6232 5012 mob (+61) 438 315 623 > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Seth Falcon > Sent: Tuesday, 22 March 2005 3:32 PM > To: r-devel@stat.math.ethz.ch > Subject: Re: [Rd] trouble building r-devel > > <[EMAIL PROTECTED]> writes: > > cp unicode/iconv.dll ../../modules/ > > cp: cannot stat `unicode/iconv.dll': No such file or directory > > make[2]: *** [rmodules] Error 1 > > make[1]: *** [rbuild] Error 2 > > make: *** [all] Error 2 > > See the section Unicode support here: > http://www.murdoch-sutherland.com/Rtools/ > > Basically, you just need to download and then copy the > iconv.dll to the right spot and you should be on your way. > > + seth > > __ > R-devel@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] trouble building r-devel
<[EMAIL PROTECTED]> writes: > cp unicode/iconv.dll ../../modules/ > cp: cannot stat `unicode/iconv.dll': No such file or directory > make[2]: *** [rmodules] Error 1 > make[1]: *** [rbuild] Error 2 > make: *** [all] Error 2 See the section Unicode support here: http://www.murdoch-sutherland.com/Rtools/ Basically, you just need to download and then copy the iconv.dll to the right spot and you should be on your way. + seth __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
RE: [Rd] trouble building r-devel
[Mark Bravington]> >I haven't been able to build yesterday's R-devel (or, as a test, > >R-devel_2005-03-11) on Windows XP. The error message I'm > getting is to > >do with 'arithmetic.c', as shown below. [Duncan Murdoch]> My guess would be that you are using bad headers, or perhaps > an out of date compiler. I just recompiled today's > arithmetic.c with no error, using > > $ gcc --version > gcc.exe (GCC) 3.4.2 (mingw-special) > Copyright (C) 2004 Free Software Foundation, Inc. Thanks (but please read on ..!) (i) My original problem occurred with gcc version 3.2. I downloaded MinGW-3.1.0-1.exe (as named in the Windows INSTALL file) and this gave me gcc version 3.2.3 *BUT* this gave me exactly the same problem. (ii) I then downloaded MinGW-3.2.0-rc-3.exe (giving me gcc 3.4.2) and this did get me past arithmetic.c. [So presumably my headers are OK.] But this isn't yet a full release of gcc, is it?-- so if this particular gcc version is required, perhaps some mention is needed in the Windows INSTALL and in the release notes. (iii) In any case, there was still a crash later on with 3.4.2. This looks unrelated but I am equally at a loss: windres -i dllversion.rc -o dllversion.o gcc --shared -s -o vfonts.dll vfonts.def g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o dllversion.o -L../../gnuw in32 -lR mkdir -p ../../../modules cp vfonts.dll ../../../modules/vfonts.dll cp unicode/iconv.dll ../../modules/ cp: cannot stat `unicode/iconv.dll': No such file or directory make[2]: *** [rmodules] Error 1 make[1]: *** [rbuild] Error 2 make: *** [all] Error 2 Mark > -Original Message- > From: Duncan Murdoch [mailto:[EMAIL PROTECTED] > Sent: Tuesday, 22 March 2005 11:27 AM > To: Bravington, Mark (CMIS, Hobart) > Cc: r-devel@stat.math.ethz.ch > Subject: Re: [Rd] trouble building r-devel > > On Tue, 22 Mar 2005 10:09:30 +1100, <[EMAIL PROTECTED]> wrote : > > >I haven't been able to build yesterday's R-devel (or, as a test, > >R-devel_2005-03-11) on Windows XP. The error message I'm > getting is to > >do with 'arithmetic.c', as shown below. > > > >Current R-patched seems to build fine, and I've built > previous R-devels > >from source fairly often in the past-- though I have no > understanding > >whatsoever of what's going on. FWIW the only changes I made > to MkRules > >are (i) WINHELP=NO and (ii) TCL_HOME=C:/R/Tcl, which are the > same ones > >I always make. > > > >Any help appreciated! > > > >Mark > > > >C:\R\R-devel\src\gnuwin32> make > ><< some OK bits of output, to help show where the problem is>> ... > >making vfonts.d from vfonts.c > >gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H > >-DR_DLL_BUILD -c CConverters.c -o CConverters.o gcc -O2 -Wall > >-pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H > -DR_DLL_BUILD -c > >CommandLineArgs.c -o CommandLineArg s.o gcc -O2 -Wall -pedantic > >-DLEA_MALLOC -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -c > Rdynload.c > >-o Rdynload.o gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include > >-DHAVE_CONFIG_H -DR_DLL_BUILD -c Renviron.c -o Renviron.o gcc -O2 > >-Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H > -DR_DLL_BUILD > >-c RNG.c -o RNG.o gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include > >-DHAVE_CONFIG_H -DR_DLL_BUILD -c apply.c -o apply.o gcc -O2 -Wall > >-pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H > -DR_DLL_BUILD -c > >arithmetic.c -o arithmetic.o > >arithmetic.c: In function `do_math1': > >arithmetic.c:887: `acosh' undeclared (first use in this function) > >arithmetic.c:887: (Each undeclared identifier is reported only once > >arithmetic.c:887: for each function it appears in.) > >arithmetic.c:888: `asinh' undeclared (first use in this function) > >arithmetic.c:889: `atanh' undeclared (first use in this function) > >make[4]: *** [arithmetic.o] Error 1 > >make[3]: *** [rlibs] Error 2 > >make[2]: *** [../../bin/R.dll] Error 2 > >make[1]: *** [rbuild] Error 2 > >make: *** [all] Error 2 > > My guess would be that you are using bad headers, or perhaps > an out of date compiler. I just recompiled today's > arithmetic.c with no error, using > > $ gcc --version > gcc.exe (GCC) 3.4.2 (mingw-special) > Copyright (C) 2004 Free Software Foundation, Inc. > > Duncan Murdoch > > __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] NaN and linear algebra
On 21/03/2005, at 10:09 PM, David Firth wrote: I am sorry that I wasn't clear. All that I meant was that *this* problem can result in different behaviour in "ordinary" statistical applications. For example, if the objective function in a call to optim() involves calling one of these linear algebra routines, the result may be NaN (on systems other than Mac OS X) --- which optim will typically handle sensibly --- or something else (an error, or perhaps some consequence of getting 0 for the determinant) under Mac OS X . Probably this was obvious to you. Apologies if I misled you into thinking that there was some other problem I knew about. Best regards, David At 11:57 AM + 3/16/05, David Firth wrote: I don't know whether this is a bug, or a problem with the way I built R 2.0.1 (under Mac OS 10.3 on a G5), or something else. Can anyone else confirm (or otherwise) that this happens in their R 2.0.1 on Mac OS X? d<-matrix(NaN,3,3) d [,1] [,2] [,3] [1,] NaN NaN NaN [2,] NaN NaN NaN [3,] NaN NaN NaN solve(d) Error in solve.default(d) : Lapack routine dgesv: system is exactly singular chol(d) Error in chol(d) : the leading minor of order 1 is not positive definite det(d) [1] 0 Doing the same thing on a Windows setup gave a different (and more useful, I think) result As I see it, the MacOS X behaviour is not IEEE-754 compliant. I had a quick look at the IEEE web site and it seems quite clear that NaNs should not cause errors, but propagate through calculations to be tested at some appropriate (not too frequent) point. It seems to me the most useful response is to file a bug on Apple's bug reporter complete with simple test case etc. It might also help to bitch about it on Apple's scitech or hpc mail lists, which get monitored by Apple people. It certainly is not up to R developers to fix it. Bill Northcott __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] trouble building r-devel
On Tue, 22 Mar 2005 10:09:30 +1100, <[EMAIL PROTECTED]> wrote : >I haven't been able to build yesterday's R-devel (or, as a test, >R-devel_2005-03-11) on Windows XP. The error message I'm getting is to >do with 'arithmetic.c', as shown below. > >Current R-patched seems to build fine, and I've built previous R-devels >from source fairly often in the past-- though I have no understanding >whatsoever of what's going on. FWIW the only changes I made to MkRules >are (i) WINHELP=NO and (ii) TCL_HOME=C:/R/Tcl, which are the same ones I >always make. > >Any help appreciated! > >Mark > >C:\R\R-devel\src\gnuwin32> make ><< some OK bits of output, to help show where the problem is>> >... >making vfonts.d from vfonts.c >gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H >-DR_DLL_BUILD -c CConverters.c -o CConverters.o >gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H >-DR_DLL_BUILD -c CommandLineArgs.c -o CommandLineArg >s.o >gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H >-DR_DLL_BUILD -c Rdynload.c -o Rdynload.o >gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H >-DR_DLL_BUILD -c Renviron.c -o Renviron.o >gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H >-DR_DLL_BUILD -c RNG.c -o RNG.o >gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H >-DR_DLL_BUILD -c apply.c -o apply.o >gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H >-DR_DLL_BUILD -c arithmetic.c -o arithmetic.o >arithmetic.c: In function `do_math1': >arithmetic.c:887: `acosh' undeclared (first use in this function) >arithmetic.c:887: (Each undeclared identifier is reported only once >arithmetic.c:887: for each function it appears in.) >arithmetic.c:888: `asinh' undeclared (first use in this function) >arithmetic.c:889: `atanh' undeclared (first use in this function) >make[4]: *** [arithmetic.o] Error 1 >make[3]: *** [rlibs] Error 2 >make[2]: *** [../../bin/R.dll] Error 2 >make[1]: *** [rbuild] Error 2 >make: *** [all] Error 2 My guess would be that you are using bad headers, or perhaps an out of date compiler. I just recompiled today's arithmetic.c with no error, using $ gcc --version gcc.exe (GCC) 3.4.2 (mingw-special) Copyright (C) 2004 Free Software Foundation, Inc. Duncan Murdoch __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] pch=NA (PR#7737)
I'd like to suggest changes to three help pages, regarding the use of
pch=NA to suppress plotting symbols. See below.
Arni
R 2.0.1 on WinXP
===
help(bxp)
===
The argument outpch=" " needs to be replaced with outpch=NA in two places.
I actually wrote this part of the documentation myself at one point, but
have now realized that pch=NA and pch=" " are not the same:
x <- split(rlnorm(26e4), letters)
## NA generates small file
postscript("na.ps");boxplot(x,outpch=NA); dev.off()
## Space generates large file
postscript("space.ps"); boxplot(x,outpch=" "); dev.off()
===
help(par)
help(points)
===
Please specify that pch=NA can be used to suppress plotting symbols.
I'm aware of type="n", but pch=NA can be a useful feature inside functions
and should be documented somewhere. Other negative-sounding values
(-1,0,NULL,""," ") generate different results, and only pch=NA does the
job properly.
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[Rd] Writing R documentation
Greetings,
I used latex type code in my Rd files.
The pdf version using
R CMD Rd2dvi --output=PKtools.pdf --pdf --title="PKtools" PKtools man
came out quite nice.
However, my current HTML version does not tex the latex so there is
latex code in the files and looks bad.
example problem code:
AIC$_c$
or
\begin{itemize}
\item NLME:
\begin{itemize}
\item population level: identify(MM\$mm\$fitted[,1], MM\$pkdata\$conc)
\item individual level: identify(MM\$mm\$fitted[,2], MM\$pkdata\$conc)
\end{itemize}
\item NONMEM:
\begin{itemize}
\item population level: identify(NM\$pred\$PRED, NM\$pred\$CONC)
\item individual level: identify(NM\$pred\$IPRE, NM\$pred\$CONC)
\end{itemize}
\item WinBUGS:
\begin{itemize}
\item population level: identify(WB\$pred\$ppred, WB\$pred\$conc)
\item individual level: identify(WB\$pred\$ipred, WB\$pred\$conc)
\end{itemize}
Is there a way to fix this?
I tried Rdconv using --type=HTML but that did not work.
Any help you can send would be appreciated.
Thank you,
Suzette
=
Suzette Blanchard, Ph.D.
UCSD-PPRU
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[Rd] trouble building r-devel
I haven't been able to build yesterday's R-devel (or, as a test, R-devel_2005-03-11) on Windows XP. The error message I'm getting is to do with 'arithmetic.c', as shown below. Current R-patched seems to build fine, and I've built previous R-devels from source fairly often in the past-- though I have no understanding whatsoever of what's going on. FWIW the only changes I made to MkRules are (i) WINHELP=NO and (ii) TCL_HOME=C:/R/Tcl, which are the same ones I always make. Any help appreciated! Mark C:\R\R-devel\src\gnuwin32> make << some OK bits of output, to help show where the problem is>> ... making vfonts.d from vfonts.c gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -c CConverters.c -o CConverters.o gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -c CommandLineArgs.c -o CommandLineArg s.o gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -c Rdynload.c -o Rdynload.o gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -c Renviron.c -o Renviron.o gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -c RNG.c -o RNG.o gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -c apply.c -o apply.o gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -c arithmetic.c -o arithmetic.o arithmetic.c: In function `do_math1': arithmetic.c:887: `acosh' undeclared (first use in this function) arithmetic.c:887: (Each undeclared identifier is reported only once arithmetic.c:887: for each function it appears in.) arithmetic.c:888: `asinh' undeclared (first use in this function) arithmetic.c:889: `atanh' undeclared (first use in this function) make[4]: *** [arithmetic.o] Error 1 make[3]: *** [rlibs] Error 2 make[2]: *** [../../bin/R.dll] Error 2 make[1]: *** [rbuild] Error 2 make: *** [all] Error 2 Mark Bravington CSIRO Mathematical & Information Sciences Marine Laboratory Castray Esplanade Hobart 7001 TAS ph (+61) 3 6232 5118 fax (+61) 3 6232 5012 mob (+61) 438 315 623 __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compiling "R Embedded" examples
Mauron Laurent (KETR 31) wrote: > Hi, > > I haven't made any progress regarding compiling the "R embedding" example ( > http://tolstoy.newcastle.edu.au/R/devel/05/03/0143.htm ) and I am running out > of ideas. > > I would be very grateful if someone could give me some reference or pointers > where to look. In other words, how would you attack the problem if you were > in the same situation? I would install a different version of gcc (e.g. gcc-3.3.3) as that works on one of the Solaris machines I use. SunOS 5.8 Generic_117000-05 sun4u sparc SUNW,Ultra-5_10 On that machine, all works fine. > > Thanks for your help, > > Laurent > > __ > R-devel@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Duncan Temple Lang[EMAIL PROTECTED] Department of Statistics work: (530) 752-4782 371 Kerr Hall fax: (530) 752-7099 One Shields Ave. University of California at Davis Davis, CA 95616, USA __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
RE: [Rd] Compiling "R Embedded" examples
Hi, I haven't made any progress regarding compiling the "R embedding" example ( http://tolstoy.newcastle.edu.au/R/devel/05/03/0143.htm ) and I am running out of ideas. I would be very grateful if someone could give me some reference or pointers where to look. In other words, how would you attack the problem if you were in the same situation? Thanks for your help, Laurent __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] loadings generic?
Martin Maechler wrote:
"PaulG" == Paul Gilbert <[EMAIL PROTECTED]>
on Sun, 20 Mar 2005 10:37:29 -0500 writes:
PaulG> Can loadings in stats be made generic?
It becomes a (S4) generic automagically when you define an S4 method
for it. ;-)
{yes, I know this isn't the answer you wanted to hear;
but really, maybe it's worth considering to use S4 classes and
methods ?}
Yes, sometime.
For S3, it's a bit uglier, but I think you could still do -- in your
package --
if(!exists("loadings.default", mode="function")) {
loadings.default <- loadings
loadings <- function(x, ...) UseMethod("loadings")
}
loadings. <- function(x, ...) {
.
}
and S3-export these.
I am doing this, but expect others will want to do it too. I think it
gets a bit messy when multiple packages need to define the same generic.
At least, it seems to me it would make more sense for the generic to be
defined in one place that everyone uses.
Paul
Martin
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Re: [Rd] loadings generic?
> "PaulG" == Paul Gilbert <[EMAIL PROTECTED]>
> on Sun, 20 Mar 2005 10:37:29 -0500 writes:
PaulG> Can loadings in stats be made generic?
It becomes a (S4) generic automagically when you define an S4 method
for it. ;-)
{yes, I know this isn't the answer you wanted to hear;
but really, maybe it's worth considering to use S4 classes and
methods ?}
For S3, it's a bit uglier, but I think you could still do -- in your
package --
if(!exists("loadings.default", mode="function")) {
loadings.default <- loadings
loadings <- function(x, ...) UseMethod("loadings")
}
loadings. <- function(x, ...) {
.
}
and S3-export these.
Martin
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[Rd] PR#6904
Problem #6904 seems to have been fixed (thanks) between 1.9.0 and 2.0.1 and can be moved from Add-ons to Add-ons-fixed. Jonathan Swinton __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] initial Hessian in optim's BFGS
Dear all, I'd like to ask if it would be a good idea to add an extra argument to 'optim' (with default value NULL) to give a initial Hessian for the BFGS algorithm. This could be handy in some cases where this initial approximation is available and thus it isn't required 'optim' to compute it again. Thanks for any comments, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/16/336899 Fax: +32/16/337015 Web: http://www.med.kuleuven.ac.be/biostat/ http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Re: [R-SIG-Mac] NaN and linear algebra
I am sorry that I wasn't clear. All that I meant was that *this* problem can result in different behaviour in "ordinary" statistical applications. For example, if the objective function in a call to optim() involves calling one of these linear algebra routines, the result may be NaN (on systems other than Mac OS X) --- which optim will typically handle sensibly --- or something else (an error, or perhaps some consequence of getting 0 for the determinant) under Mac OS X . Probably this was obvious to you. Apologies if I misled you into thinking that there was some other problem I knew about. Best regards, David On 20 Mar, 2005, at 15:08, stefano iacus wrote: No, blas/veclib is tested, so aprt this extreme case you should report some other more commonly used cases in which something fails on OS X. This will help us to work it out. As said, I'll try some tests without using veclib and let you know. I've fowarded this mail to r-devel, which seems to be the right place, so for future msg on the subject please use r-devel. stefano On 19/mar/05, at 17:44, David Firth wrote: Dear Don, Bill and Stefano Many thanks for your helpful replies on this. I do think this is pretty serious: the example I gave is an extreme one, but in real problems (e.g., calls to optim()) this sort of thing can and does result in different behaviour on the Mac than on other systems. And that has to be a Bad Thing. I'm unsure whether it is better to press Apple to improve vecLib, or to test R with an alternative BLAS (and if successful, recommend using that BLAS in place of vecLib). Or both. Unfortunately I don't know enough about these routines and the relevant standards to pursue either route myself. Best regards, David At 11:57 AM + 3/16/05, David Firth wrote: I don't know whether this is a bug, or a problem with the way I built R 2.0.1 (under Mac OS 10.3 on a G5), or something else. Can anyone else confirm (or otherwise) that this happens in their R 2.0.1 on Mac OS X? > d<-matrix(NaN,3,3) d [,1] [,2] [,3] [1,] NaN NaN NaN [2,] NaN NaN NaN [3,] NaN NaN NaN solve(d) Error in solve.default(d) : Lapack routine dgesv: system is exactly singular chol(d) Error in chol(d) : the leading minor of order 1 is not positive definite det(d) [1] 0 Doing the same thing on a Windows setup gave a different (and more useful, I think) result d<-matrix(NaN,3,3) d [,1] [,2] [,3] [1,] NaN NaN NaN [2,] NaN NaN NaN [3,] NaN NaN NaN solve(d) [,1] [,2] [,3] [1,] NaN NaN NaN [2,] NaN NaN NaN [3,] NaN NaN NaN chol(d) [,1] [,2] [,3] [1,] NaN NaN NaN [2,]0 NaN NaN [3,]00 NaN det(d) [1] NaN Any thoughts? David Professor David Firth Dept of Statistics University of Warwick Coventry CV4 7AL United Kingdom Voice: +44 (0)247 657 2581 Fax: +44 (0)247 652 4532 Web: http://www.warwick.ac.uk/go/dfirth ___ R-SIG-Mac mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- -- Don MacQueen Environmental Protection Department Lawrence Livermore National Laboratory Livermore, CA, USA -- ___ R-SIG-Mac mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-sig-mac __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Buglet in install.packages warning message
> "Seth" == Seth Falcon <[EMAIL PROTECTED]>
> on Sun, 20 Mar 2005 18:34:13 -0800 writes:
Seth> I've been experimenting with install.packages and it's
Seth> new ability to track down dependencies from a list of
Seth> repositories and encountered this:
Seth> install.packages(c("foo", "bar"),
Seth> repos="http://cran.r-project.org";,
Seth> dependencies=c("Depends", "Suggests"))
Seth> dependencies 'foo' are not availabledependencies 'bar'
Seth> are not available
Seth> With the following change (see below) I get what I
Seth> suspect is the intended warning message:
Seth>dependencies 'foo', 'bar' are not available
Indeed.
Thank you Seth! - I've committed your change
to be in '` R-alpha of 2005-03-22 ''
Apropos: Please, all users of R-2.1.0 (alpha) {aka "R-devel"}:
``keep your eyes open'' for not quite correctly
formatted error messages, or even other problems in
error and warning messages.
The large amount of work that was put in (mostly by Prof Brian
Ripley) rationalizing these messages in order to make them
more consistent (for translation, e.g.!) may have lead to a few
typos that are unavoidable when changing those thousand of
lines of code efficiently.
Martin
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