[Rd] strange interaction between rasterImage and Grid graphics
Dear all, This may be specific to Mac, I haven't had a chance to test another platform. Consider this, plot(1,1,t=n) rasterImage(matrix(1),1,1,1,1) library(grid) grid.rect(gp=gpar(fill=grey)) The grid.rect covers the full device window as expected. However, when I resize the window ever so slightly (interactive device) the rectGrob is suddenly clipped to the previous plot window. I cannot understand this behavior, and it doesn't happen if one removes the rasterImage() call, so I suspect something iffy is going on with the display list or something. The only device I've tried is quartz(), x11() crashed with rasterImage, *** caught segfault *** address 0x28, cause 'memory not mapped' Traceback: 1: rasterImage(matrix(1), 1, 1, 1, 1) sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] scoping goes wrong when some functions are used within others.
Dear,
I'm following the r tag on stackoverflow.com, and couldn't but notice
there are quite some questions popping up that deal with scoping in
relation to custom functions. I grinded my teeth on it already, and I
have absolutely no clue what goes wrong. The general pattern is as
follows :
ff - function(x){
y - some_value
some_function(y)
}
ff(x)
Error in eval(expr, envir, enclos) : object 'y' not found
I tried to report this as a bug earlier, but got the message I used
the wrong channel. I also don't know how to formalize it into a bug
report on the report site. That's why I bring it to your attention
this way, and want to ask you whether this is by design and we're all
doing something wrong, whether these are problems within certain
packages/situations, ...
I solve these problems now by adding an environment to my global
environment, and delete it after the function finished running. But
this can't be the correct way.
The problem is described here :
http://stackoverflow.com/questions/3840769/scoping-and-functions-in-r-2-11-1-whats-going-wrong
Links to different reports, all having that same pattern but with
different functions :
http://stackoverflow.com/questions/3742415/r-statistical-scoping-error-using-transformby-part-of-the-doby-package
http://stackoverflow.com/questions/3768417/how-to-use-acast-reshape2-within-a-function-in-r
http://stackoverflow.com/questions/3661500/why-cant-i-pass-a-dataset-to-a-function
http://stackoverflow.com/questions/3574858/values-not-being-copied-to-the-next-local-environment
http://stackoverflow.com/questions/2646402/using-functions-and-environments
--
Joris Meys
Statistical consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
tel : +32 9 264 59 87
joris.m...@ugent.be
---
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Re: [Rd] scoping goes wrong when some functions are used within others.
Joris Meys wrote:
Dear,
I'm following the r tag on stackoverflow.com, and couldn't but notice
there are quite some questions popping up that deal with scoping in
relation to custom functions. I grinded my teeth on it already, and I
have absolutely no clue what goes wrong. The general pattern is as
follows :
ff - function(x){
y - some_value
some_function(y)
}
ff(x)
Error in eval(expr, envir, enclos) : object 'y' not found
I get:
Error in ff(x) : object 'some_value' not found
which is entirely consistent, since it has not been bound to a value.
I tried to report this as a bug earlier, but got the message I used
the wrong channel. I also don't know how to formalize it into a bug
report on the report site. That's why I bring it to your attention
this way, and want to ask you whether this is by design and we're all
doing something wrong, whether these are problems within certain
packages/situations, ...
I solve these problems now by adding an environment to my global
environment, and delete it after the function finished running. But
this can't be the correct way.
The problem is described here :
http://stackoverflow.com/questions/3840769/scoping-and-functions-in-r-2-11-1-whats-going-wrong
Links to different reports, all having that same pattern but with
different functions :
http://stackoverflow.com/questions/3742415/r-statistical-scoping-error-using-transformby-part-of-the-doby-package
http://stackoverflow.com/questions/3768417/how-to-use-acast-reshape2-within-a-function-in-r
http://stackoverflow.com/questions/3661500/why-cant-i-pass-a-dataset-to-a-function
http://stackoverflow.com/questions/3574858/values-not-being-copied-to-the-next-local-environment
http://stackoverflow.com/questions/2646402/using-functions-and-environments
__
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Re: [Rd] scoping goes wrong when some functions are used within others.
On 01/10/2010 12:00 PM, Joris Meys wrote:
Dear,
I'm following the r tag on stackoverflow.com, and couldn't but notice
there are quite some questions popping up that deal with scoping in
relation to custom functions. I grinded my teeth on it already, and I
have absolutely no clue what goes wrong. The general pattern is as
follows :
I think each of the reports is really a separate bug, mostly in the
implementation of some_function. As far as I could see, only the last one
|y- new.env()
with(y, x- 1)
f- function(env,z) {
with(env, x+z)
}
f(y,z=1)
|
involves base R functions, and there I think the problem is with your
reading of the documentation, not with the function. The documentation
may suggest that should work by saying The environment has the caller's
environment as its parent, but there's no way it possibly could.
Environments only have one parent. If you read carefully you'll see that
this is documented correctly in (Note: if ‘data’ is already an
environment then this is used with its existing parent.)
Duncan Murdoch
ff- function(x){
y- some_value
some_function(y)
}
ff(x)
Error in eval(expr, envir, enclos) : object 'y' not found
I tried to report this as a bug earlier, but got the message I used
the wrong channel. I also don't know how to formalize it into a bug
report on the report site. That's why I bring it to your attention
this way, and want to ask you whether this is by design and we're all
doing something wrong, whether these are problems within certain
packages/situations, ...
I solve these problems now by adding an environment to my global
environment, and delete it after the function finished running. But
this can't be the correct way.
The problem is described here :
http://stackoverflow.com/questions/3840769/scoping-and-functions-in-r-2-11-1-whats-going-wrong
Links to different reports, all having that same pattern but with
different functions :
http://stackoverflow.com/questions/3742415/r-statistical-scoping-error-using-transformby-part-of-the-doby-package
http://stackoverflow.com/questions/3768417/how-to-use-acast-reshape2-within-a-function-in-r
http://stackoverflow.com/questions/3661500/why-cant-i-pass-a-dataset-to-a-function
http://stackoverflow.com/questions/3574858/values-not-being-copied-to-the-next-local-environment
http://stackoverflow.com/questions/2646402/using-functions-and-environments
__
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Re: [Rd] scoping goes wrong when some functions are used within others.
One of the complaints in your stackoverlow references
concerned doBy::transformBy and the error message came
from eval(). Using eval() means you are throwing the
usual scoping rules out the window and making up some
new ones. Using a non-core package means you are at
the mercy of its writer.
In transformBy I believe there is an error in the use
of parent.frame() that can be fixed by changing the
current
head(doBy::transformBy)
1 function (formula, data, ...)
2 {
3 transform2 - function(data, ...) {
4 e - eval(substitute(list(...)), data, parent.frame())
5 tags - names(e)
6 inx - match(tags, names(data))
to
head(transformBy)
1 function (formula, data, ...)
2 {
3 PARENT.FRAME - parent.frame()
4 transform2 - function(data, ...) {
5 e - eval(substitute(list(...)), data, PARENT.FRAME)
6 tags - names(e)
transform2's parent.frame will always be transformBy
and we really want to look for variables in the expressions
in the .. list in transformBy's parent frame, not in
transformBy itself.
Using parent.frame() often causes problems because you don't
always know how many frames come between your user's code and
your function's code. (E.g., using methods may insert extra
frames.) In this case I think it was always looking in the
wrong place. The fix doesn't guarentee that it will always
look in the right place, but it should be right more often.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-devel-boun...@r-project.org
[mailto:r-devel-boun...@r-project.org] On Behalf Of Joris Meys
Sent: Friday, October 01, 2010 9:01 AM
To: r-devel@r-project.org
Subject: [Rd] scoping goes wrong when some functions are used
within others.
Dear,
I'm following the r tag on stackoverflow.com, and couldn't but notice
there are quite some questions popping up that deal with scoping in
relation to custom functions. I grinded my teeth on it already, and I
have absolutely no clue what goes wrong. The general pattern is as
follows :
ff - function(x){
y - some_value
some_function(y)
}
ff(x)
Error in eval(expr, envir, enclos) : object 'y' not found
I tried to report this as a bug earlier, but got the message I used
the wrong channel. I also don't know how to formalize it into a bug
report on the report site. That's why I bring it to your attention
this way, and want to ask you whether this is by design and we're all
doing something wrong, whether these are problems within certain
packages/situations, ...
I solve these problems now by adding an environment to my global
environment, and delete it after the function finished running. But
this can't be the correct way.
The problem is described here :
http://stackoverflow.com/questions/3840769/scoping-and-functio
ns-in-r-2-11-1-whats-going-wrong
Links to different reports, all having that same pattern but with
different functions :
http://stackoverflow.com/questions/3742415/r-statistical-scopi
ng-error-using-transformby-part-of-the-doby-package
http://stackoverflow.com/questions/3768417/how-to-use-acast-re
shape2-within-a-function-in-r
http://stackoverflow.com/questions/3661500/why-cant-i-pass-a-d
ataset-to-a-function
http://stackoverflow.com/questions/3574858/values-not-being-co
pied-to-the-next-local-environment
http://stackoverflow.com/questions/2646402/using-functions-and
-environments
--
Joris Meys
Statistical consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
tel : +32 9 264 59 87
joris.m...@ugent.be
---
Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php
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Re: [Rd] scoping goes wrong when some functions are used within others.
Thank you for all your answers, this really helped me out. I've been
digging into scoping rules in R and although I'm going to need quite
some more studying to fully grasp it, I do see where the errors come
from.
Thanks again.
@Erik : I know that some_value was not declared. I just gave some
pseudo-code to illustrate the general pattern of the errors, to
indicate why I thought they were linked. Sorry if I wasn't clear
enough on that one.
Cheers
Joris
On Fri, Oct 1, 2010 at 7:21 PM, Erik Iverson er...@ccbr.umn.edu wrote:
Joris Meys wrote:
Dear,
I'm following the r tag on stackoverflow.com, and couldn't but notice
there are quite some questions popping up that deal with scoping in
relation to custom functions. I grinded my teeth on it already, and I
have absolutely no clue what goes wrong. The general pattern is as
follows :
ff - function(x){
y - some_value
some_function(y)
}
ff(x)
Error in eval(expr, envir, enclos) : object 'y' not found
I get:
Error in ff(x) : object 'some_value' not found
which is entirely consistent, since it has not been bound to a value.
I tried to report this as a bug earlier, but got the message I used
the wrong channel. I also don't know how to formalize it into a bug
report on the report site. That's why I bring it to your attention
this way, and want to ask you whether this is by design and we're all
doing something wrong, whether these are problems within certain
packages/situations, ...
I solve these problems now by adding an environment to my global
environment, and delete it after the function finished running. But
this can't be the correct way.
The problem is described here :
http://stackoverflow.com/questions/3840769/scoping-and-functions-in-r-2-11-1-whats-going-wrong
Links to different reports, all having that same pattern but with
different functions :
http://stackoverflow.com/questions/3742415/r-statistical-scoping-error-using-transformby-part-of-the-doby-package
http://stackoverflow.com/questions/3768417/how-to-use-acast-reshape2-within-a-function-in-r
http://stackoverflow.com/questions/3661500/why-cant-i-pass-a-dataset-to-a-function
http://stackoverflow.com/questions/3574858/values-not-being-copied-to-the-next-local-environment
http://stackoverflow.com/questions/2646402/using-functions-and-environments
--
Joris Meys
Statistical consultant
Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control
tel : +32 9 264 59 87
joris.m...@ugent.be
---
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[Rd] Will PrintWarnings remain non static?
Hi, The C function PrintWarnings is currently not in the C API, but it is declared non static in the svn trunk as of revision 53110 . As this is the only function that creates the last.warning object used by the R function warnings(), I think it would be useful for programs that embed R to be able to call it. So, will it remain non static, that is callable although it's not declared in the public C API? Thanks, Jeff __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] cleanup_pkg() in tools:::.build_packages() is broken
Hi, The cleanup_pkg() function defined the big tools:::.build_packages() function in tools/R/build.R is currently broken. When Makefiles are used cleanup_pkg() doesn't clean anything because of the way system2() is called. For example, the call to Ssystem() on line 304 (Ssystem is a silent version of system2) is basically trying to do this: system2(paste(Sys.getenv(MAKE, make), makefiles, clean)) sh: make -f '/home/hpages/R-2.12/etc//Makeconf' -f Makefile clean: not found But it seems that with this new system2(), the arguments to the system command need to be passed separately thru the 'args' argument. Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
