[Rd] tilde expansion with install.packages
I've noticed recently that 'update.packages' and 'install.packages' seem to not
do tilde expansion anymore, i.e. when I run
update.packages("~/R-local/lib")
on R-alpha (r41043) I get the message
/home/rpeng/install/R-alpha/lib64/R/bin/INSTALL: line 304: cd: ~/R-local/lib: No
such file or directory
and the package is subsequently installed in the current working directory.
The attached patch solves the problem for me.
-roger
--
Roger D. Peng | http://www.biostat.jhsph.edu/~rpeng/
Index: src/scripts/INSTALL.in
===
--- src/scripts/INSTALL.in (revision 41043)
+++ src/scripts/INSTALL.in (working copy)
@@ -294,6 +294,7 @@
shift
done
+lib=`tilde_expand "${lib}"`
if test -z "${lib}"; then
lib=`echo "cat('~~~', .libPaths()[1], sep = '')" | \
R_DEFAULT_PACKAGES=NULL "${R_EXE}" --no-save --slave | \
@@ -332,7 +333,6 @@
exit 1
fi
-lib=`tilde_expand "${lib}"`
if (test -d "${lib}" && test -w "${lib}") || \
${MKDIR_P} "${lib}" 2> /dev/null; then
lib=`cd "${lib}" && ${GETWD}`
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Re: [Rd] 'R CMD check' fails when suggested package is not available
On Wed, 2007-04-04 at 17:05 -0700, Herve Pages wrote:
> Hi there,
>
> I was wondering why I get the following error message:
>
> * checking package dependencies ... ERROR
> Packages required but not available:
> Rmpi
>
> when I run 'R CMD check' on a package that _suggests_ Rmpi?
> Why isn't it OK to not have all the suggested packages installed?
>
Hi there too,
This has been discussed before:
http://tolstoy.newcastle.edu.au/R/devel/05/09/2326.html
Then the Core decided to maintain the Mafia style suggestion ("that you
can't refuse"), but later seems to have introduced a new field
"enhances" which to me looks like a suggestion in the meaning of the
word I know: a suggestion that you can refuse.
I think that the R-ext description is somewhat confusing and misleading
for fields "Requires", "Suggests", "Enhances". The R extension manual
"suggests" different situations where the author of the manual thinks
that other people would like to use these fields. However, the manual
does not clearly say what are the practical and real consequences of
selecting a certain entry. It seems that "Requires" means that a package
is always required, "Suggests" means that the package is required in
check (with a threat of error), but only suggested for normal use, and
"Enhances" means that the package only is suggested. It does not matter
whether the package really "enhances" anything, but this is the meaning
of the word in behaviouristic sense.
cheers, jari oksanen
> Maybe one of the 3 following behaviours would be more appropriate:
>
> a) Having the error saying something like:
>
> Package suggested but not available:
> Rmpi
>
> b) Make this a warning instead of an error.
>
> c) Don't do anything at all for suggested packages.
>
> This issue showed up today while I was checking a new Bioconductor package:
> the package suggests Rmpi but the vignette and the examples don't use it. If
> I remove
> Rmpi from the Suggests field then 'R CMD check' runs all the examples and
> re-create
> the vignette with no problem. Most users will not have Rmpi on their machine
> neither
> will they be interested in getting into the trouble of installing it.
> The package I was checking suggests Rmpi only because it contains 1 function
> that tries
> to use it if it's installed but will work perfectly fine otherwise.
> In this case it seems reasonable to have Rmpi in the Suggests field but this
> will
> make 'R CMD check' to fail which is problematic in the context of automated
> builds :-/
> If 'R CMD check' can't be a little bit more relaxed about this, then I guess
> we will
> need to remove Rmpi from the Suggests field, but then 'R CMD check' will
> complain that:
>
> * checking for unstated dependencies in R code ... WARNING
> 'library' or 'require' calls not declared from:
> Rmpi
--
"Object-oriented programming is an exceptionally bad idea that could
only have been invented in California." -- Edsger Dijkstra
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Re: [Rd] tilde expansion with install.packages
Looks right, and now committed, thanks.
On Wed, 4 Apr 2007, Roger D. Peng wrote:
> I've noticed recently that 'update.packages' and 'install.packages' seem to
> not do tilde expansion anymore, i.e. when I run
>
> update.packages("~/R-local/lib")
>
> on R-alpha (r41043) I get the message
>
> /home/rpeng/install/R-alpha/lib64/R/bin/INSTALL: line 304: cd:
> ~/R-local/lib: No such file or directory
>
> and the package is subsequently installed in the current working directory.
>
> The attached patch solves the problem for me.
>
> -roger
>
--
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
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[Rd] issue with pdf(paper="a4") in 2.5.0 alpha
In the latest windows binary (2007-04-03 r41023) pdf() with an argument
paper="a4" gives an error, this was still ok in (2007-03-18 r40854)
Jan Oosting
> pdf("test.pdf",paper="a4")
Error in pdf("test.pdf", paper = "a4") : invalid paper type 'a4' (pdf)
> sessionInfo()
R version 2.5.0 alpha (2007-04-03 r41023)
i386-pc-mingw32
locale:
LC_COLLATE=Dutch_Netherlands.1252;LC_CTYPE=Dutch_Netherlands.1252;LC_MONETARY=Dutch_Netherlands.1252;LC_NUMERIC=C;LC_TIME=Dutch_Netherlands.1252
attached base packages:
[1] "stats" "graphics" "grDevices" "utils" "datasets" "methods"
[7] "base"
>
[[alternative HTML version deleted]]
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[Rd] StructTS
I apologize in advance if I picked the wrong list to post this to. I have made an effort to find the answers to these questions on CRAN, but if they are there, I couldn't find them, and I was going to email the developer of StructTS directly but could not find who that is. I have 2 interrelated questions about StructTS 1. Where can I obtain the source code for StructTS if I wanted to produce a similar function with an extended capability? 2. Would the person who developed StructTS have any interest in adding the ability to include an AR term and/or a stochastic cycle? Thanks in advance, -Roy M. ** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center 1352 Lighthouse Avenue Pacific Grove, CA 93950-2097 e-mail: [EMAIL PROTECTED] (Note new e-mail address) voice: (831)-648-9029 fax: (831)-648-8440 www: http://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] is.loaded() and dyn.load()
Dear all,
I am puzzled at the behaviour of is.loaded() when a dyn.load() call to a a
FORTRAN shared library is included in a file to be sourced.
A reproducible example is the following:
1. the attached fortran subroutine try_it.f90 performs a summation of the
elements of a REAL*8 vector
compile with
gfortran try_it.f90 -shared -s -otry_it.dll
2. create a file to be sourced (see the attached try_it.R) containing the
following commands:
BEGIN try_it.R
dyn.load("try_it.dll");
try.it <- function(X){
N <- length(X);
S <- .Fortran("try_it_",as.double(X),as.integer(N),S=as.double(0))$S
return(S)
}
END try_it.R
3. Switch to R
source("try_it.R")
try.it(1:10)
Error in .Fortran("try_it_", as.double(X), as.integer(N), S = as.double(0))
:
Fortran symbol name "try_it_" not in load table
is.loaded("try_it_")
[1] TRUE
try.it(1:10)
[1] 55
it looks like is.loaded() triggers the loading, inserting
is.loaded("try_it_")in
the file try_it.R does the trick but
is this behaviour expected?
Thank you,
Regards
Simone
R.version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 4.1
year 2006
month 12
day18
svn rev40228
language R
version.string R version 2.4.1 (2006-12-18)
--
__
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
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Re: [Rd] is.loaded() and dyn.load()
Did you read the comments under ?.Fortran about this? What you are doing
is quite explicitly said not to be supported.
gfortran is not a supported Fortran compiler for R for Windows 2.4.1.
It behaves differently from the supported g77.
The behaviour is adapted to the compiler used when configure is used, and
on Windows that is what the maintainers used, not you are using. If you
follow the advice not to use underscores in names you are much less likely
to confuse yourself and produce portable code.
On Thu, 5 Apr 2007, Simone Giannerini wrote:
> Dear all,
>
> I am puzzled at the behaviour of is.loaded() when a dyn.load() call to a a
> FORTRAN shared library is included in a file to be sourced.
> A reproducible example is the following:
>
> 1. the attached fortran subroutine try_it.f90 performs a summation of the
> elements of a REAL*8 vector
> compile with
>
> gfortran try_it.f90 -shared -s -otry_it.dll
>
> 2. create a file to be sourced (see the attached try_it.R) containing the
> following commands:
>
> BEGIN try_it.R
> dyn.load("try_it.dll");
>
>
> try.it <- function(X){
> N <- length(X);
> S <- .Fortran("try_it_",as.double(X),as.integer(N),S=as.double(0))$S
> return(S)
> }
> END try_it.R
>
>
> 3. Switch to R
>
>> source("try_it.R")
>> try.it(1:10)
> Error in .Fortran("try_it_", as.double(X), as.integer(N), S = as.double(0))
> :
> Fortran symbol name "try_it_" not in load table
>> is.loaded("try_it_")
> [1] TRUE
>> try.it(1:10)
> [1] 55
>>
> it looks like is.loaded() triggers the loading, inserting
> is.loaded("try_it_")in
> the file try_it.R does the trick but
> is this behaviour expected?
>
> Thank you,
>
> Regards
>
> Simone
>
>> R.version
> _
> platform i386-pc-mingw32
> arch i386
> os mingw32
> system i386, mingw32
> status
> major 2
> minor 4.1
> year 2006
> month 12
> day18
> svn rev40228
> language R
> version.string R version 2.4.1 (2006-12-18)
>
--
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
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[Rd] Implementation of pretty
Hi, I'm trying to track down any references for the implementation of pretty (or grid.pretty) in R. Is it original work? Thanks, Hadley __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Implementation of pretty
> "hadley" == hadley wickham <[EMAIL PROTECTED]>
> on Thu, 5 Apr 2007 10:43:41 -0500 writes:
hadley> Hi, I'm trying to track down any references for the
hadley> implementation of pretty (or grid.pretty) in R. Is
hadley> it original work?
Much of it is. The original version, say R version 0.01, may
have been based on some reference, but we have added quite a few extra tweaks,
where in my case I sat down with a piece of paper, considered
and transformed some inequalities and also did computer
experiments additionally.
I've even started to make more coherent notes eventually, but
not electronically, and hence no tech.report / publication / ...
{ Did you really want to know this :-) }
Regards,
Martin
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[Rd] some SPSS 15 files wont open in R 2.4.0
Trying to open some SPSS .sav files (saved with SPSS 15) gives the following:
read.spss('/data/big/unzipped_ukda/seh3767/3767SPSS_570D6A086C9A1B0636F13255F25A58C1/prgrp95.sav')
Error in
read.spss("/data/big/unzipped_ukda/seh3767/3767SPSS_570D6A086C9A1B0636F13255F25A58C1/prgrp95.sav"):
error reading system-file header
In addition: Warning message:
/data/big/unzipped_ukda/seh3767/3767SPSS_570D6A086C9A1B0636F13255F25A58C1/prgrp95.sav:
File-indicated character representation code (Unknown) is not ASCII
Some are fine in R, some are not.
The file opens in SPSS, and googling the error message gives
this mail about PSPP
http://www.nabble.com/problem-loading-SPSS-15.0-save-files-t2726500.html
which includes a diff for the PSPP code which opens R files
and throws that exact error message back.
R documentation says that it uses some code based on PSPP,
I can't see it in the R distribution?. Does anyone with more
clue than I know whether the above is likely to fix it, and
where I should be looking for the code to change?
Alternatively, has anyone got any ideas on opening these files?
Thanks
Sam
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Re: [Rd] Problem with S4 inheritance: unexpected re-initialization?
Dear Herve
Thank you once again for taking your time, I appreciate it very much.
I followed your advice and kept only the minimum code, which I believe
is necessary. I have even removed SubClassA, so the inheritance tree is:
BaseClass <- SubClassB <- SubSubClassB1
<- SubClassB <- SubSubClassB2
The source code is shown below and the examples are:
> subsubB1 <- new("SubSubClassB1", filename="MyFileNameB1",
nameB="MyNameB")
> subsubB2 <- new("SubSubClassB2", filename="MyFileNameB2",
nameB="MyNameB")
Although SubSubClassB1 and SubSubClassB2 differ only slightly, the results
for "subsubB1" are correct, while "subsubB2" gives a wrong result, see:
> subsubB2 <- new("SubSubClassB2", filename="MyFileNameB2",
nameB="MyNameB")
> subsubB2
An object of class "SubSubClassB2"
Slot "nameB2":
[1] "MyNameB"
Slot "nameB":
[1] ""
Slot "filename":
[1] "MyFileNameB2"
Only, when adding "nameB2="MyNameB2", I get the correct result, see:
> subsubB2 <- new("SubSubClassB2", filename="MyFileNameB2",
nameB="MyNameB",nameB2="MyNameB2")
> subsubB2
An object of class "SubSubClassB2"
Slot "nameB2":
[1] "MyNameB2"
Slot "nameB":
[1] "MyNameB"
Slot "filename":
[1] "MyFileNameB2"
It is not clear to me why omitting "nameB2" results in the wrong assignemt
of the value for "nameB" to "nameB2"?
When running both examples, the sequence of initialization and validation
method is also completely different.
For "SubSubClassB1" I get the correct and expected sequence of events:
> subsubB1 <- new("SubSubClassB1", filename="MyFileNameB1",
nameB="MyNameB")
--initialize:SubSubClassB1
--initialize:SubClassB
--initialize:BaseClass
--setValidity:BaseClass
--setValidity:SubClassB
--setValidity:SubSubClassB1
In contrast, for "SubSubClassB2" I get the following sequence of events:
> subsubB2 <- new("SubSubClassB2", filename="MyFileNameB2",
nameB="MyNameB")
--initialize:SubSubClassB2
--initialize:SubClassB
--initialize:BaseClass
--setValidity:BaseClass
--initialize:SubClassB
--initialize:BaseClass
--setValidity:BaseClass
--setValidity:SubClassB
--setValidity:SubClassB
--initialize:SubClassB
--initialize:BaseClass
--setValidity:BaseClass
--setValidity:SubClassB
--setValidity:SubSubClassB2
Furthermore, the slot "filename" is first initialized correctly to
"filename=MyFileNameB2", but then it is twice initialized incorrectly
to "filename=ERROR_FileName", indicating that it may not have been
initialized at all. I do not understand this behavior, why is this so?
I really hope that this time the code below is acceptable to you.
Thank you for your help.
Best regards
Christian
# - - - - - - - - - - - - - - - - BEGIN - - - - - - - - - - - - - - - -
- - - -
setClass("BaseClass",
representation(filename = "character", "VIRTUAL"),
prototype(filename = "DefaultFileName")
)
setClass("SubClassB",
representation(nameB = "character"),
contains=c("BaseClass"),
prototype(nameB = "NameB")
)
setClass("SubSubClassB1",
contains=c("SubClassB")
)
setClass("SubSubClassB2",
representation(nameB2 = "character"),
contains=c("SubClassB"),
prototype(nameB2 = "NameB2")
)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
setMethod("initialize", "BaseClass",
function(.Object, filename="", ...) {
cat("--initialize:BaseClass--\n")
cat("BaseClass:init:class(.Object) = ", class(.Object), "\n", sep="")
if (filename == "" || nchar(filename) == 0) filename <-
"ERROR_FileName"
cat("BaseClass:init:filename = ", filename, "\n", sep="")
.Object <- callNextMethod(.Object, filename=filename, ...)
[EMAIL PROTECTED] <- filename
.Object
}
)
setValidity("BaseClass",
function(object) {
cat("--setValidity:BaseClass--\n")
cat("BaseClass:val:class(.Object) = ", class(object), "\n", sep="")
msg <- NULL
if (!(is.character([EMAIL PROTECTED])))
msg <- cat("missing filename\n")
cat("BaseClass:val:filename = ",[EMAIL PROTECTED], "\n", sep="")
if (is.null(msg)) TRUE else msg
}
)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
setMethod("initialize", "SubClassB",
function(.Object, nameB="", ...) {
cat("--initialize:SubClassB--\n")
cat("SubClassB:init:class(.Object) = ", class(.Object), "\n", sep="")
.Object <- callNextMethod(.Object, nameB=nameB, ...)
[EMAIL PROTECTED] = nameB
.Object
}
)
setValidity("SubClassB",
function(object) {
cat("--setValidity:SubClassB--\n")
cat("SubClassB:val:class(object) = ", class(object), "\n", sep="")
msg <- NULL
if (!(is.character([EMAIL PROTECTED]) && length([EMAIL PROTECTED]) > 0))
msg <- cat("missing nameB\n")
cat("SubClassB:val:nameB = ",[EMAIL PROTECTED], "\n", sep="")
if (is.null(msg)) TRUE else msg
}
)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Re: [Rd] some SPSS 15 files wont open in R 2.4.0
On Thu, 5 Apr 2007, Sam Smith wrote:
>
> Trying to open some SPSS .sav files (saved with SPSS 15) gives the following:
>
>
> read.spss('/data/big/unzipped_ukda/seh3767/3767SPSS_570D6A086C9A1B0636F13255F25A58C1/prgrp95.sav')
> Error in
> read.spss("/data/big/unzipped_ukda/seh3767/3767SPSS_570D6A086C9A1B0636F13255F25A58C1/prgrp95.sav"):
> error reading system-file header
> In addition: Warning message:
>
> /data/big/unzipped_ukda/seh3767/3767SPSS_570D6A086C9A1B0636F13255F25A58C1/prgrp95.sav:
> File-indicated character representation code (Unknown) is not ASCII
>
> Some are fine in R, some are not.
This is not 'in R', it is in contributed (recommended) package 'foreign',
so it is that's version that is relevant here. (We do ask for
sessionInfo() in the R posting guide for good reason.)
> The file opens in SPSS, and googling the error message gives
> this mail about PSPP
>
> http://www.nabble.com/problem-loading-SPSS-15.0-save-files-t2726500.html
> which includes a diff for the PSPP code which opens R files
> and throws that exact error message back.
'R files'? Surely, 'SPSS 15 files'!
That just removes a test. If Ben Pfaff thinks it is no longer needed, I
suppose we could just remove it, but what happens if SPSS has Latin-1 or
UTF-8 data? I think we should give a warning if not an error.
> R documentation says that it uses some code based on PSPP,
> I can't see it in the R distribution?.
Look in the tarball for foreign (in src/library/Recommended).
> Does anyone with more
> clue than I know whether the above is likely to fix it, and
> where I should be looking for the code to change?
>
> Alternatively, has anyone got any ideas on opening these files?
Use SPSS and re-save in an open format?
--
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
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Re: [Rd] Implementation of pretty
On 4/5/07, Martin Maechler <[EMAIL PROTECTED]> wrote:
> > "hadley" == hadley wickham <[EMAIL PROTECTED]>
> > on Thu, 5 Apr 2007 10:43:41 -0500 writes:
>
> hadley> Hi, I'm trying to track down any references for the
> hadley> implementation of pretty (or grid.pretty) in R. Is
> hadley> it original work?
>
> Much of it is. The original version, say R version 0.01, may
> have been based on some reference, but we have added quite a few extra tweaks,
> where in my case I sat down with a piece of paper, considered
> and transformed some inequalities and also did computer
> experiments additionally.
> I've even started to make more coherent notes eventually, but
> not electronically, and hence no tech.report / publication / ...
>
> { Did you really want to know this :-) }
Yes - that's great! And if you ever do put you notes in electronic
format I'd love to see them. There's very little written on the
subject of choosing good tick marks.
Hadley
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Re: [Rd] Implementation of pretty
On 4/5/2007 1:41 PM, hadley wickham wrote:
> On 4/5/07, Martin Maechler <[EMAIL PROTECTED]> wrote:
>> > "hadley" == hadley wickham <[EMAIL PROTECTED]>
>> > on Thu, 5 Apr 2007 10:43:41 -0500 writes:
>>
>> hadley> Hi, I'm trying to track down any references for the
>> hadley> implementation of pretty (or grid.pretty) in R. Is
>> hadley> it original work?
>>
>> Much of it is. The original version, say R version 0.01, may
>> have been based on some reference, but we have added quite a few extra
>> tweaks,
>> where in my case I sat down with a piece of paper, considered
>> and transformed some inequalities and also did computer
>> experiments additionally.
>> I've even started to make more coherent notes eventually, but
>> not electronically, and hence no tech.report / publication / ...
>>
>> { Did you really want to know this :-) }
>
> Yes - that's great! And if you ever do put you notes in electronic
> format I'd love to see them. There's very little written on the
> subject of choosing good tick marks.
I wrote a little bit on this in a Chance column:
Murdoch, D.J. (2000). Drawing a scatterplot. {\em Chance} {\bf 13.3},
53--55.
Duncan Murdoch
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Re: [Rd] Problem with S4 inheritance: unexpected re-initialization?
Hi Cristian,
cstrato wrote:
[...]
> Although SubSubClassB1 and SubSubClassB2 differ only slightly, the results
> for "subsubB1" are correct, while "subsubB2" gives a wrong result, see:
>> subsubB2 <- new("SubSubClassB2", filename="MyFileNameB2",
> nameB="MyNameB")
>> subsubB2
> An object of class "SubSubClassB2"
> Slot "nameB2":
> [1] "MyNameB"
>
> Slot "nameB":
> [1] ""
>
> Slot "filename":
> [1] "MyFileNameB2"
I think that the problem has to do with the way you use callNextMethod() in your
"initialize" method for SubSubClassB2:
setMethod("initialize", "SubSubClassB2",
function(.Object, nameB2="MyNameB2", ...) {
cat("--initialize:SubSubClassB2--\n")
cat("SubSubClassB2:init:class(.Object) = ", class(.Object), "\n", sep="")
if (nameB2 == "") nameB2 <- "DefaultNameB2";
cat("SubSubClassB2:init:nameB2 = ", nameB2, "\n", sep="")
.Object <- callNextMethod(.Object, nameB2=nameB2, ...)
[EMAIL PROTECTED] <- nameB2
.Object
}
)
As a side note: I don't understand why you want to define a default value for
the 'nameB2' argument since you have defined a prototype for the SubSubClassB2
class (with a different default value for the 'nameB2' slot).
Try this instead:
setMethod("initialize", "SubSubClassB2",
function(.Object, ...) {
cat("--initialize:SubSubClassB2--\n")
cat("SubSubClassB2:init:class(.Object) = ", class(.Object), "\n", sep="")
.Object <- callNextMethod()
if ([EMAIL PROTECTED] == "") [EMAIL PROTECTED] <- "DefaultNameB2"
.Object
}
)
It gives you what you want:
> new("SubSubClassB2", filename="MyFileNameB2", nameB="MyNameB")
--initialize:SubSubClassB2--
SubSubClassB2:init:class(.Object) = SubSubClassB2
--initialize:SubClassB--
SubClassB:init:class(.Object) = SubSubClassB2
--initialize:BaseClass--
BaseClass:init:class(.Object) = SubSubClassB2
BaseClass:init:filename = MyFileNameB2
An object of class "SubSubClassB2"
Slot "nameB2":
[1] "NameB2"
Slot "nameB":
[1] "MyNameB"
Slot "filename":
[1] "MyFileNameB2"
[...]
>
> In contrast, for "SubSubClassB2" I get the following sequence of events:
>> subsubB2 <- new("SubSubClassB2", filename="MyFileNameB2",
> nameB="MyNameB")
> --initialize:SubSubClassB2
> --initialize:SubClassB
> --initialize:BaseClass
> --setValidity:BaseClass
> --initialize:SubClassB
> --initialize:BaseClass
> --setValidity:BaseClass
> --setValidity:SubClassB
> --setValidity:SubClassB
> --initialize:SubClassB
> --initialize:BaseClass
> --setValidity:BaseClass
> --setValidity:SubClassB
> --setValidity:SubSubClassB2
I can reproduce this behaviour with a _much_ simple and shorter code:
setClass("A",
representation(a="character"),
prototype(a="a0")
)
setValidity("A",
function(object) {
cat("--setValidity:A--\n")
tmp <- class(object)
TRUE
}
)
setMethod("initialize", "A",
function(.Object, ...) {
cat("--initialize:A--\n")
callNextMethod()
}
)
setClass("B",
contains="A",
representation(b="character")
)
setValidity("B",
function(object) {
cat("--setValidity:B--\n")
TRUE
}
)
setMethod("initialize", "B",
function(.Object, ...) {
cat("--initialize:B--\n")
callNextMethod()
}
)
Then I get this:
> b <- new("B", b="hello")
--initialize:B--
--initialize:A--
--setValidity:A--
--initialize:A--
--setValidity:B--
Why is initialize:A called twice? I have no idea (bug?) but I agree with you
that
this is unexpected. Note that this line
tmp <- class(object)
in setValidity:A is what triggers the extra call to initialize:A. If you remove
it, things work as expected. Very strange!
Cheers,
H.
> sessionInfo()
R version 2.5.0 alpha (2007-03-30 r40957)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
attached base packages:
[1] "stats" "graphics" "grDevices" "utils" "datasets" "methods"
[7] "base"
>
> Furthermore, the slot "filename" is first initialized correctly to
> "filename=MyFileNameB2", but then it is twice initialized incorrectly
> to "filename=ERROR_FileName", indicating that it may not have been
> initialized at all. I do not understand this behavior, why is this so?
>
> I really hope that this time the code below is acceptable to you.
> Thank you for your help.
> Best regards
> Christian
>
> # - - - - - - - - - - - - - - - - BEGIN - - - - - - - - - - - - - - - -
> - - - -
> setClass("BaseClass",
> representation(filename = "character", "VIRTUAL"),
> prototype(filename = "DefaultFileName")
> )
>
> setClass("SubClassB",
> representation(nameB = "char
[Rd] bquote(function(x,y) T) (PR#9602)
> quote(function(x, y) T) function(x, y) T > bquote(function(x, y) T) function(, y) T > eval(.Last.value) Error in eval(expr, envir, enclos) : invalid formal argument list for "function" > R.version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 4.1 year 2006 month 12 day18 svn rev40228 language R version.string R version 2.4.1 (2006-12-18) -- Felix Andrews / 安福立 PhD candidate, The Fenner School of Environment and Society The Australian National University (Building 48A), ACT 0200 Beijing Bag, Locked Bag 40, Kingston ACT 2604 http://www.neurofractal.org/felix/ voice:+86_1051404394 (in China) mobile:+86_13522529265 (in China) mobile:+61_410400963 (in Australia) xmpp:[EMAIL PROTECTED] 3358 543D AAC6 22C2 D336 80D9 360B 72DD 3E4C F5D8 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
