Re: [Rd] Active bindings in attached environments
On Thu, Nov 5, 2009 at 9:53 AM, Jeffrey Horner jeffrey.hor...@gmail.com 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 marc_schwartz at 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] 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) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[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] .GlobalEnve 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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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 jeffrey.hor...@gmail.com 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] .GlobalEnve 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) __ 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] 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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Marine Laboratory
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TAS
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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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Department of Statistics andFax: 319-335-3017
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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
