Re: [Rd] Active bindings in attached environments
On Thu, Nov 5, 2009 at 9:53 AM, Jeffrey Horner wrote:
>
> Hi,
>
> Is this expected behavior for active bindings in attached
> environments, or is this a bug:
>
> > e <- new.env()
> > makeActiveBinding('x',function() 'foo',e)
> > ls(e)
> [1] "x"
> > attach(e)
> > search()
> [1] ".GlobalEnv" "e" "package:graphics"
> [4] "package:grDevices" "package:datasets" "package:utils"
> [7] "package:methods" "Autoloads" "package:base"
> > x
> function() 'foo'
>
> Should this print 'foo' ? The following works as I would expect:
>
> > with(e,x)
> [1] "foo"
>
> but this doesn't:
>
> > f <- function() x
> > f()
> function() 'foo'
>
> However, changing the environment of f does:
>
> > environment(f) <- e
> > f()
> [1] "foo"
Actually, it is my understanding of attach() which is the bug. The
attach documentation clearly states that a copy of the object is
attached, not the object itself.
Thanks,
Jeff
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[Rd] Typos in ?pdf (was Re: Problem with pdf graphics device)
Marc Schwartz me.com> writes:
>
[snip]
> See ?pdf and read through the "Note" section.
>
While I was reading this I noticed two minor typos
in pdf.Rd.
These patches are against the latest SVN devel version.
*** pdf.Rd.orig 2009-11-05 14:37:44.0 -0500
--- pdf.Rd 2009-11-05 14:38:24.0 -0500
***
*** 199,205
problem is much more likely to be in your viewer than in \R. Try
another viewer if possible. Symptoms for which the viewer has been at
fault are apparent grids on image plots (turn off graphics
! anti-aliasing in your viewer if you) and missing or incorrect glyphs
in text (viewers silently doing font substitution).
Unfortunately the default viewers on most Linux and Mac OS X systems
--- 199,205
problem is much more likely to be in your viewer than in \R. Try
another viewer if possible. Symptoms for which the viewer has been at
fault are apparent grids on image plots (turn off graphics
! anti-aliasing in your viewer if you can) and missing or incorrect glyphs
in text (viewers silently doing font substitution).
Unfortunately the default viewers on most Linux and Mac OS X systems
***
*** 224,230
On some systems the default plotting character \code{pch = 1} is
displayed in some PDF viewers incorrectly as a \code{"q"}
character. (These seem to be viewers based on the \samp{poppler} PDF
! rendering library). This may be due to incorrect or incomplete mapping
of font names to those used by the system. Adding the following lines
to \file{~/.fonts.conf} or \file{/etc/fonts/local.conf} may circumvent
this problem.
--- 224,230
On some systems the default plotting character \code{pch = 1} is
displayed in some PDF viewers incorrectly as a \code{"q"}
character. (These seem to be viewers based on the \samp{poppler} PDF
! rendering library.) This may be due to incorrect or incomplete mapping
of font names to those used by the system. Adding the following lines
to \file{~/.fonts.conf} or \file{/etc/fonts/local.conf} may circumvent
this problem.
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[Rd] A fix that for 'bquote' that may work (PR#14031)
This is a fix for 'bquote' that may work.
function (expr, where =3D parent.frame())=20
{
unquote <- function(e) {
if (length(e) <=3D 1 || !is.language(e))=20
e
else if (e[[1]] =3D=3D as.name("."))=20
eval(e[[2]], where)
else as.call(lapply(e, unquote))
}
unquote(substitute(expr))
}
=0A=0A=0A Get your preferred Email name!=0ANow you can @ymail.com and =
@rocketmail.com. =0Ahttp://mail.promotions.yahoo.com/newdomains/aa/
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[Rd] Error when adding package RMySQL (PR#14044)
Full_Name: Kåre Jonsson
Version: 2.10
OS: WinXP
Submission from: (NULL) (85.225.178.169)
I made a brand new installation of R 2.10 in two machines and got the same
problem.
Machine 1 is Win XP on metal installation
machine 2 is virtual in VMWare running a hacky OS named Tiny XP in which any
Microsoft windows XP siftware always successfully is installed.
Operation 1. Add package RMySQL from Swedish CRAN.
Operation 2. library(RMySQL)
You can see the textual dump below. I need help to understand what is wrong.
Kind regards,
Kåre Jonsson
> utils:::menuInstallPkgs()
--- Please select a CRAN mirror for use in this session ---
also installing the dependency DBI
trying URL
'http://ftp.sunet.se/pub/lang/CRAN/bin/windows/contrib/2.10/DBI_0.2-4.zip'
Content type 'application/zip' length 375508 bytes (366 Kb)
opened URL
downloaded 366 Kb
trying URL
'http://ftp.sunet.se/pub/lang/CRAN/bin/windows/contrib/2.10/RMySQL_0.7-4.zip'
Content type 'application/zip' length 284408 bytes (277 Kb)
opened URL
downloaded 277 Kb
package 'DBI' successfully unpacked and MD5 sums checked
package 'RMySQL' successfully unpacked and MD5 sums checked
The downloaded packages are in
C:\Documents and Settings\Administrator\Local
Settings\Temp\Rtmpjqc0Bc\downloaded_packages
> library(RMySQL)
Loading required package: DBI
Error in utils::readRegistry("SOFTWARE\\MySQL AB", hive = "HLM", maxdepth = 2) :
Registry key 'SOFTWARE\MySQL AB' not found
Error : .onLoad failed in 'loadNamespace' for 'RMySQL'
Error: package/namespace load failed for 'RMySQL'
> MySQL()
Error: could not find function "MySQL"
> con <- dbConnect(dbDriver("MySQL"), dbname = "mysql")
Error in do.call(as.character(drvName), list(...)) :
could not find function "MySQL"
Error in is(object, Cl) :
error in evaluating the argument 'drv' in selecting a method for function
'dbConnect'
> version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 10.0
year 2009
month 10
day26
svn rev50208
language R
version.string R version 2.10.0 (2009-10-26)
>
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[Rd] Active bindings in attached environments
Hi,
I was wondering if this is expected behavior for active bindings in
attached environments, or if this is a bug:
> e <- new.env()
> makeActiveBinding('x',function() 'foo',e)
> ls(e)
[1] "x"
> attach(e)
> search()
[1] ".GlobalEnv""e" "package:graphics"
[4] "package:grDevices" "package:datasets" "package:utils"
[7] "package:methods" "Autoloads" "package:base"
> x
function() 'foo' # Should this print 'foo' ?
This works as I would expect:
> with(e,x)
[1] "foo"
but this doesn't:
> f <- function() x
> f()
function() 'foo'
However, changing the environment of f does:
> environment(f) <- e
> f()
[1] "foo"
Jeff
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[Rd] Typo in R Help INSTALL {utils} (PR#14045)
Full_Name: Neil Tiffin
Version: R version 2.10.0 (2009-10-26)
OS: [R.app GUI 1.30 (5511) i386-apple-darwin9.8.0]
Submission from: (NULL) (99.68.31.116)
In the help section 'INSTALL {utils}' half way down the page the line
Use R CMD INSTALL help for concise usage information, including all the
available options
should have two '-' in front of help. Therefor it should read
Use R CMD INSTALL -help for concise usage information, including all the
available options
At least when I copied and pasted the line it did not work until I added the
second '-'.
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Re: [Rd] Active bindings in attached environments
An explanation of this would be nice in ?makeActiveBinding, e.g.,
NOTE:
When an environment is attach()'ed to the search path, any active
bindings in it are not preserved as active bindings. This happens
because attach() actually adds a new environment to the search path, and
copies objects into it. Thus, active bindings are evaluated and their
values copied into the attached environment.
(Is this explanation correct?)
-- Tony Plate
(PS: Thunderbird wants to spell-correct "makeActiveBinding" to
"vindictivenesses", which seems an amusingly appropriate allusion to the
nature of this "gotcha" :-)
Jeffrey Horner wrote:
On Thu, Nov 5, 2009 at 9:53 AM, Jeffrey Horner wrote:
Hi,
Is this expected behavior for active bindings in attached
environments, or is this a bug:
e <- new.env()
makeActiveBinding('x',function() 'foo',e)
ls(e)
[1] "x"
attach(e)
search()
[1] ".GlobalEnv""e" "package:graphics"
[4] "package:grDevices" "package:datasets" "package:utils"
[7] "package:methods" "Autoloads" "package:base"
x
function() 'foo'
Should this print 'foo' ? The following works as I would expect:
with(e,x)
[1] "foo"
but this doesn't:
f <- function() x
f()
function() 'foo'
However, changing the environment of f does:
environment(f) <- e
f()
[1] "foo"
Actually, it is my understanding of attach() which is the bug. The
attach documentation clearly states that a copy of the object is
attached, not the object itself.
Thanks,
Jeff
--
http://biostat.mc.vanderbilt.edu/JeffreyHorner
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Re: [Rd] Error when adding package RMySQL (PR#14044)
k...@modlab.se wrote:
> Full_Name: Kåre Jonsson
> Version: 2.10
> OS: WinXP
> Submission from: (NULL) (85.225.178.169)
>
>
> I made a brand new installation of R 2.10 in two machines and got the same
> problem.
>
> Machine 1 is Win XP on metal installation
> machine 2 is virtual in VMWare running a hacky OS named Tiny XP in which any
> Microsoft windows XP siftware always successfully is installed.
>
> Operation 1. Add package RMySQL from Swedish CRAN.
> Operation 2. library(RMySQL)
>
> You can see the textual dump below. I need help to understand what is wrong.
>
> Kind regards,
> Kåre Jonsson
>
>
>> utils:::menuInstallPkgs()
> --- Please select a CRAN mirror for use in this session ---
> also installing the dependency DBI
>
> trying URL
> 'http://ftp.sunet.se/pub/lang/CRAN/bin/windows/contrib/2.10/DBI_0.2-4.zip'
> Content type 'application/zip' length 375508 bytes (366 Kb)
> opened URL
> downloaded 366 Kb
>
> trying URL
> 'http://ftp.sunet.se/pub/lang/CRAN/bin/windows/contrib/2.10/RMySQL_0.7-4.zip'
> Content type 'application/zip' length 284408 bytes (277 Kb)
> opened URL
> downloaded 277 Kb
>
> package 'DBI' successfully unpacked and MD5 sums checked
> package 'RMySQL' successfully unpacked and MD5 sums checked
>
> The downloaded packages are in
> C:\Documents and Settings\Administrator\Local
> Settings\Temp\Rtmpjqc0Bc\downloaded_packages
>> library(RMySQL)
> Loading required package: DBI
> Error in utils::readRegistry("SOFTWARE\\MySQL AB", hive = "HLM", maxdepth =
> 2) :
>
> Registry key 'SOFTWARE\MySQL AB' not found
So you probably forgot to install MySQL?
Why do you think this is a bug in the base R distribution?
Note that bugs of contributed packages (if they are really bugs) should
be reported to the corresponding package maintainer rather than to the R
bug tracking system.
Best,
Uwe Ligges
> Error : .onLoad failed in 'loadNamespace' for 'RMySQL'
> Error: package/namespace load failed for 'RMySQL'
>> MySQL()
> Error: could not find function "MySQL"
>> con <- dbConnect(dbDriver("MySQL"), dbname = "mysql")
> Error in do.call(as.character(drvName), list(...)) :
> could not find function "MySQL"
> Error in is(object, Cl) :
> error in evaluating the argument 'drv' in selecting a method for function
> 'dbConnect'
>> version
>_
> platform i386-pc-mingw32
> arch i386
> os mingw32
> system i386, mingw32
> status
> major 2
> minor 10.0
> year 2009
> month 10
> day26
> svn rev50208
> language R
> version.string R version 2.10.0 (2009-10-26)
>
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Re: [Rd] Typo in R Help INSTALL {utils} (PR#14045)
The source file reads
Use \command{R CMD INSTALL --help} for concise usage information,
so I see no 'typo'.
The issue is apparently in the rendering of -- as - in \command. I
am presuming you are viewing HTML in the Mac GUI, but can you please
confirm exactly what you are looking at.
On Thu, 5 Nov 2009, ne...@neiltiffin.com wrote:
Full_Name: Neil Tiffin
Version: R version 2.10.0 (2009-10-26)
OS: [R.app GUI 1.30 (5511) i386-apple-darwin9.8.0]
Submission from: (NULL) (99.68.31.116)
In the help section 'INSTALL {utils}' half way down the page the line
Use R CMD INSTALL ?help for concise usage information, including all the
available options
should have two '-' in front of help. Therefor it should read
Use R CMD INSTALL ?-help for concise usage information, including all the
available options
I suspect from the ? I see (twice) in your message that you are
seeing an endash and not a single hyphen. That's what HTML help on
Linux is showing as for me.
At least when I copied and pasted the line it did not work until I added the
second '-'.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
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] parse_Rd and/or lazyload problem
On Thu, 5 Nov 2009, mark.braving...@csiro.au wrote:
Great-- thanks for the info.
For now, hopefully I can get the behaviour I want by sticking a .Call(
'R_lazyLoadDBflush'...) [as per 'detach'] before calling 'lazyLoad'. Seems to
work on my examples, but please let me know if you don't think it'll work
generally-- if not, I could presumably create the files under different names
and then change them.
Is there merit in making 'makeLazyLoadDB' public, just as 'lazyLoad' already
is? It's useful.
The internals of the lazy load mechanism are intended to be private.
This is now emphasized in the lazyLoad help page. This is under
active development, and we need the freedom to be able to change these
internals as needed. They may change without notice, so using them
directly in user code or packages is not a good idea and is strongly
discouraged.
luke
Mark
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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
l...@stat.uiowa.edu wrote:
Here is a more stripped down variant generates and error on OS X for
me:
mkEg <- function(tm) list(scrunge = as.POSIXct(tm))
extract <- function(db) {
e<- new.env()
lazyLoad(db, e)
as.list( e)
}
eg <- mkEg("2009-11-04 12:49:53")
eg1 <- mkEg("2009-11-04 12:49:28")
tools:::makeLazyLoadDB( eg, '/tmp/ll')
extract('/tmp/ll') # force; OK
tools:::makeLazyLoadDB( eg1, '/tmp/ll')
extract('/tmp/ll')
Changing the second set of /tmp/ll makes the symptom go away.
I believe this comes down to unintended use of the lazyload mechanism
-- in particular it is not intended that a database be rewritten
after it has been loaded. There is a chaching mechanism for improved
performance on slow file systems, and I believe what is happening is
that the new indices are being used to look in the old chached data.
There might be some merit in having lazyLoad call R_lazyLoadDBflush.
luke
On Tue, 3 Nov 2009, Seth Falcon wrote:
Hi,
On 11/3/09 6:51 PM, mark.braving...@csiro.au wrote:
file.copy( 'd:/temp/Rdiff.Rd', 'd:/temp/scrunge.Rd') # Rdiff.Rd
from 'tools' package source
eglist<- list( scrunge=parse_Rd( 'd:/temp/scrunge.Rd'))
tools:::makeLazyLoadDB( eglist, 'd:/temp/ll')
e<- new.env()
lazyLoad( 'd:/temp/ll', e)
as.list( e) # force; OK
eglist1<- list( scrunge=parse_Rd( 'd:/temp/Rdiff.Rd'))
tools:::makeLazyLoadDB( eglist1, 'd:/temp/ll')
e<- new.env()
lazyLoad( 'd:/temp/ll', e)
as.list( e) # Splat
It doesn't make any difference which file I process first; the error
comes the second time round.
If I adjust this example in terms of paths and run on OS X, I get the
following error on the second run:
as.list(e) # Splat
Error in as.list.environment(e) : internal error -3 in R_decompress1
I haven't looked further yet.
+ seth
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Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics andFax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: l...@stat.uiowa.edu
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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[Rd] bug in heatmap?
Using R 2.10 on WinXP heatmap(mymap, Rowv=NA, Colv=NA) with mymap values of 0 1 2 3 4 0 NaN 0.0 0.00621118 0.000 NaN 10 0.0 0.01041667 0.125 NaN 20 0.004705882 0.02105263 0.333 NaN 30 0.004081633 0.0222 0.500 0 40 0.0 0.01923077 0.167 NaN 60 0.0 0. 0.000 NaN 10 0 0.002840909 0. 0.000 NaN 20 0 0.002159827 0. NaN NaN 40 NaN 0.009433962 0. NaN NaN (the first row and column are labels, not data) produces a plot in which all of the row labelled 6 (all 0's and NaN) is white. This is the same color showing for the NaN values. In contrast, all other 0 values appear as dark red. Have I missed some subtlety, or is this a bug? Ross Boylan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
