Re: [Rd] S4 Inheritance of environments
On 24/04/2010 1:15 PM, Christopher Brown wrote: I looked through the documentation and the mailing lists and could not find an answer to this. My apologies if it has already been answered. If it has, a pointer to the relevant discussion would be greatly appreciated. Environments are unusual in that they are reference objects: if e is an environment, and you assign f - e, then f refers to the same object as e does. This is unusual in R, where most objects are copied on assignment (logically, not always physically). It means that attributes on environments behave strangely: if you put an attribute on e and remove the same attribute from f, it is gone from e too. We've discussed removing the possibility of putting attributes on environments (just as you can't put attributes on NULL), but haven't done so yet. What you should do if you want to use an environment in the way you're using it is to put it in a container. For S4, that could mean using an environment as a slot, or inheriting from an object like list(e), rather than directly from e. Duncan Murdoch Creating S4 classes containing environments exhibits unexpected behavior/features. These have a different in two ways: 1) slotName for the data: .xData instead of .Data and do not respond to the 2) Response to the is.* function seems to indicate that the object does not know of its inheritance. ( Notably, the inherits function works as expected. ) Here is a working illustration: # LIST setClass( 'inheritList', contains='list') [1] inheritList inList - new( 'inheritList' ) class( inList ) [1] inheritList attr(,package) [1] .GlobalEnv is.list( inList ) # TRUE [1] TRUE slotNames(inList) # .Data [1] .Data inherits(inList, 'list' ) # TRUE [1] TRUE # ENVIRONMENT setClass( 'inheritEnv', contains='environment' ) Defining type environment as a superclass via class .environment [1] inheritEnv inEnv - new( 'inheritEnv' ) class(inEnv) [1] inheritEnv attr(,package) [1] .GlobalEnv is.environment(inEnv) # FALSE [1] FALSE slotNames(inEnv) # .xData [1] .xData inherits(inEnv, 'environment' ) # TRUE [1] TRUE My questions is whether this behavior is a bug? By design? A work around? Etc.? Thanks kindly for your reply, Chris the Open Data Group http://www.opendatagroup.com http://blog.opendatagroup.com __ 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] S4 Inheritance of environments
On Sun, Apr 25, 2010 at 1:09 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 24/04/2010 1:15 PM, Christopher Brown wrote: I looked through the documentation and the mailing lists and could not find an answer to this. My apologies if it has already been answered. If it has, a pointer to the relevant discussion would be greatly appreciated. Environments are unusual in that they are reference objects: if e is an environment, and you assign f - e, then f refers to the same object as e does. This is unusual in R, where most objects are copied on assignment (logically, not always physically). It means that attributes on environments behave strangely: if you put an attribute on e and remove the same attribute from f, it is gone from e too. We've discussed removing the possibility of putting attributes on environments (just as you can't put attributes on NULL), but haven't done so yet. What you should do if you want to use an environment in the way you're using it is to put it in a container. For S4, that could mean using an environment as a slot, or inheriting from an object like list(e), rather than directly from e. I can confirm these reported issues. FYI, what Duncan is suggesting is exactly the design behind the Object class (encapsulates an environment) in the R.oo package. The difference is that it is working with S3. It's been working flawlessly for 9 years. Others have had idea to do the same but with S4, but I'm not sure if that ever took of. /Henrik (R.oo author) Duncan Murdoch Creating S4 classes containing environments exhibits unexpected behavior/features. These have a different in two ways: 1) slotName for the data: .xData instead of .Data and do not respond to the 2) Response to the is.* function seems to indicate that the object does not know of its inheritance. ( Notably, the inherits function works as expected. ) Here is a working illustration: # LIST setClass( 'inheritList', contains='list') [1] inheritList inList - new( 'inheritList' ) class( inList ) [1] inheritList attr(,package) [1] .GlobalEnv is.list( inList ) # TRUE [1] TRUE slotNames(inList) # .Data [1] .Data inherits(inList, 'list' ) # TRUE [1] TRUE # ENVIRONMENT setClass( 'inheritEnv', contains='environment' ) Defining type environment as a superclass via class .environment [1] inheritEnv inEnv - new( 'inheritEnv' ) class(inEnv) [1] inheritEnv attr(,package) [1] .GlobalEnv is.environment(inEnv) # FALSE [1] FALSE slotNames(inEnv) # .xData [1] .xData inherits(inEnv, 'environment' ) # TRUE [1] TRUE My questions is whether this behavior is a bug? By design? A work around? Etc.? Thanks kindly for your reply, Chris the Open Data Group http://www.opendatagroup.com http://blog.opendatagroup.com __ 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Miktex does not work with R CMD check
Dear DevelopeRs,
the issue I am stuck with (I am on Windows, R-2.11): My Miktex (version
2.8) does not work with R CMD check, although Miktex on its own can
pdflatex the tex-file in the Rcheck directory. (This issue has been
going on for a while, and now, after having updated to R-2.11, I finally
want to get it fixed.) Although I have found several similar posts, none
of the answers appears to solve my problem, which seems to be
path-related. In case it is relevant: in the past, I did have issues
with paths to my documents because these contain a German Umlaut on my
computer, which is why I moved all R packages to the directory c:/rtests.
I would appreciate any help on this issue. The relevant portion of R CMD
check and the content of Rdlatex.log are included below.
Best regards,
Ulrike
The end of the R CMD check output looks like this:
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
* checking PDF version of manual without index ... ERROR
LaTeX error when running command:
Rcmd.exe Rd2dvi --batch --no-preview --pdf
--build-dir=C:/WINDOWS/Temp/Rd2dvi611638299 --no-clean --no-index -o
DoE.base-manual.pdf /dev/null 21 C:/rtests/DoE.base.Rcheck/DoE.base
Re-running with no redirection of stdout/stderr.
The file Rdlatex.log contains the following text:
Hmm ... looks like a package
latex.exe: A required file system path could not be retrieved.
latex.exe: Data: 28
Creating pdf output from LaTeX ...
pdflatex.exe: A required file system path could not be retrieved.
pdflatex.exe: Data: 28
Error in running pdflatex command ('pdflatex')
You may want to clean up by 'rm -rf C:/WINDOWS/Temp/Rd2dvi611638299'
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Question of R CMD check
Hi all,
I find the problem.See below.
Today, i installed the newest R-VERSION2.11.0 for checking. Different
error occurred. I checked the log and found 'Hmisc' package caused this. At
present, binary package was not provided. After i installed an old version
of 'Hmisc' package, it works very well.
I think there should be no problem for R. It may be caused by
the dependent package 'Hmisc' that has no newest binary package in the
CRAN. Sorry about this.
2010/4/23 rusers.sh rusers...@gmail.com
Hi Duncan,
Enclosed is the example package and the checking results. No rm() or
remove() in the example. Before this re-installation of R and other tools
(e.g. Rtools), there are no errors for package checking.
Thanks.
2010/4/23 Duncan Murdoch murdoch.dun...@gmail.com
On 23/04/2010 1:19 PM, rusers.sh wrote:
Hi Duncan,
Thanks for reminding me. See below for the error information from *.Rout
file
It seems that 'pkgname' was not found. I am not sure whether there is
some
problem with my functions or it is a little bug.
Thanks a lot.
###
assign(ptime, proc.time(), pos = CheckExEnv)
## at least one package changes these via ps.options(), so do this
## before loading the package.
## Use postscript as incomplete files may be viewable, unlike PDF.
## Choose a size that is close to on-screen devices, fix paper
grDevices::ps.options(width = 7, height = 7, paper = a4, reset = TRUE)
grDevices::postscript(paste(pkgname, -Ex.ps, sep=))
Error in paste(pkgname, -Ex.ps, sep = ) : object 'pkgname' not found
Calls: Anonymous - checkIntFormat - gsub - paste
Execution halted
The very first line of stam-Ex.R should be
pkgname - stam
Is it? If not, I'd like to see the package; could you send me a copy? If
it is, then something in one of your examples is messing with it. Do you
have any calls to rm() or remove() in your examples?
Duncan Murdoch
2010/4/23 Duncan Murdoch murdoch.dun...@gmail.com
On 21/04/2010 9:48 PM, rusers.sh wrote:
Hi all,
Today, i just installed the newest R version 2.10.1 and other
necessary
tools for building R package under windows,e.g. Rtools, perl. All are
the
newest version.
After the correct configuration under windows (configuration should be
correct), i use it to re-check my old package. I found the following
prolem
when checking EXAMPLEs in each function, which did not exist before
this
re-installation.
* checking examples ... ERROR
Running examples in 'stam-Ex.R' failed.
I used \dontrun{} % enddontrun in all the examples of my functions
that
should be no problem, i think. I checked my package before and did not
find
errors. I also browsed the checking results in 'stam-Ex.R'. It listed
all
the example codes in that file, something like this,
cleanEx(); nameEx(stcdt)
### * stcdt
flush(stderr()); flush(stdout())
###example codes
I did not met this problem before. Any ideas on solving this?
Thanks a lot.
You need to show us the end of the stam-Ex.Rout file. It will contain
the
error message.
Duncan Murdoch
--
-
Jane Chang
Queen's
--
-
Jane Chang
Queen's
[[alternative HTML version deleted]]
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] problem with Rcmdr Plugins
Dear R Development People: I have written a couple of plugins for Rcmdr and they do not seem to work with R-2.11.0. Here is the output: library(RcmdrPlugin.epack) Loading required package: Rcmdr Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: car --- Please select a CRAN mirror for use in this session --- Rcmdr Version 1.5-4 Attaching package: 'Rcmdr' The following object(s) are masked from 'package:tcltk': tclvalue Loading required package: rgl Loading required package: TeachingDemos Loading required package: tseries Loading required package: quadprog Loading required package: zoo 'tseries' version: 0.10-22 'tseries' is a package for time series analysis and computational finance. See 'library(help=tseries)' for details. Loading required package: abind Loading required package: MASS Error : package 'rgl' is required by 'RcmdrPlugin.epack' so will not be detached Error in library(RcmdrPlugin.epack) : .First.lib failed for 'RcmdrPlugin.epack' This is on a Windows XP. I'm downloading the Rcmdr requirements on a Linux machine as we speak. Have you run into this please? Thanks, Erin Erin M. Hodgess, PhD Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: hodge...@uhd.edu [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] a side note to the Rcmdr issue
Hi again. On Windows, when I try to use the install packages from the menu, there is no Rcmdr and no RcmdrPlugins to be seen. thanks, Erin Erin M. Hodgess, PhD Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: hodge...@uhd.edu [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] a side note to the Rcmdr issue
Dear Erin, Unlike in previous version of R for Windows, the package list is alphabetized with uppercase letters preceding lowercase letters. Thus look under uppercase R and then lowercase c. Regards, John John Fox Senator William McMaster Professor of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada web: socserv.mcmaster.ca/jfox -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Hodgess, Erin Sent: April-25-10 2:56 PM To: r-devel@r-project.org Subject: [Rd] a side note to the Rcmdr issue Hi again. On Windows, when I try to use the install packages from the menu, there is no Rcmdr and no RcmdrPlugins to be seen. thanks, Erin Erin M. Hodgess, PhD Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: hodge...@uhd.edu [[alternative HTML version deleted]] __ 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] problem with Rcmdr Plugins
Dear Erin, I'm not sure why this is a problem with R 2.11.0 and not with earlier versions (I'm sure that someone else will be able to answer), but it is unnecessary for your plug-in package to require rgl, since rgl is already loaded by the Rcmdr package at startup if it is present. The same is true of tseries, abind, and MASS. I hope this helps, John John Fox Senator William McMaster Professor of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada web: socserv.mcmaster.ca/jfox -Original Message- From: r-devel-boun...@r-project.org [mailto:r-devel-boun...@r-project.org] On Behalf Of Hodgess, Erin Sent: April-25-10 2:48 PM To: r-devel@r-project.org Subject: [Rd] problem with Rcmdr Plugins Dear R Development People: I have written a couple of plugins for Rcmdr and they do not seem to work with R-2.11.0. Here is the output: library(RcmdrPlugin.epack) Loading required package: Rcmdr Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: car --- Please select a CRAN mirror for use in this session --- Rcmdr Version 1.5-4 Attaching package: 'Rcmdr' The following object(s) are masked from 'package:tcltk': tclvalue Loading required package: rgl Loading required package: TeachingDemos Loading required package: tseries Loading required package: quadprog Loading required package: zoo 'tseries' version: 0.10-22 'tseries' is a package for time series analysis and computational finance. See 'library(help=tseries)' for details. Loading required package: abind Loading required package: MASS Error : package 'rgl' is required by 'RcmdrPlugin.epack' so will not be detached Error in library(RcmdrPlugin.epack) : .First.lib failed for 'RcmdrPlugin.epack' This is on a Windows XP. I'm downloading the Rcmdr requirements on a Linux machine as we speak. Have you run into this please? Thanks, Erin Erin M. Hodgess, PhD Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: hodge...@uhd.edu [[alternative HTML version deleted]] __ 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] S4 Inheritance of environments
In addition to Duncan Murdoch's explanation, this is discussed in the documentation for Classes (briefly): . Extending a basic type this way allows objects to use old-style code for the corresponding type as well as S4 methods. Any basic type can be used for .Data, but a few types are treated differently because they do not behave like ordinary objects; for example, NULL, environments, and external pointers. Classes extend these types by using a specially named slot, itself inherited from an internally defined S4 class. Inheritance from the nonstandard object type then requires an actual computation, rather than the simple inclusion for other types and classes. The intent is that programmers will not need to take account of the mechanism, but one implication is that you should not explicitly use the type of an S4 object that extends an arbitrary object type. Use is and similar functions instead. ... The code for is.environment() is presumably using the type, whereas inherits() takes account of the indirect mechanism. Generally, you should be able to deal with inheritance from environments in a natural way. John On 4/24/10 10:15 AM, Christopher Brown wrote: I looked through the documentation and the mailing lists and could not find an answer to this. My apologies if it has already been answered. If it has, a pointer to the relevant discussion would be greatly appreciated. Creating S4 classes containing environments exhibits unexpected behavior/features. These have a different in two ways: 1) slotName for the data: .xData instead of .Data and do not respond to the 2) Response to the is.* function seems to indicate that the object does not know of its inheritance. ( Notably, the inherits function works as expected. ) Here is a working illustration: # LIST setClass( 'inheritList', contains='list') [1] inheritList inList- new( 'inheritList' ) class( inList ) [1] inheritList attr(,package) [1] .GlobalEnv is.list( inList ) # TRUE [1] TRUE slotNames(inList) # .Data [1] .Data inherits(inList, 'list' ) # TRUE [1] TRUE # ENVIRONMENT setClass( 'inheritEnv', contains='environment' ) Defining type environment as a superclass via class .environment [1] inheritEnv inEnv- new( 'inheritEnv' ) class(inEnv) [1] inheritEnv attr(,package) [1] .GlobalEnv is.environment(inEnv) # FALSE [1] FALSE slotNames(inEnv) # .xData [1] .xData inherits(inEnv, 'environment' ) # TRUE [1] TRUE My questions is whether this behavior is a bug? By design? A work around? Etc.? Thanks kindly for your reply, Chris the Open Data Group http://www.opendatagroup.com http://blog.opendatagroup.com __ 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
