[Rd] R.exe crashes on R v2.12.0dev (Windows Vista)
Using the latest developers version of R [2.12.0 Under development (unstable) (2010-05-21 r52061)], R.exe crashes: %ProgramFiles%/R/R-2.12.0dev/bin/i386/R.exe with Windows reporting: Problem signature: Problem Event Name: APPCRASH Application Name: R.exe Application Version: 2.120.52061.0 Application Timestamp:4bf638bd Fault Module Name:R.exe Fault Module Version: 2.120.52061.0 Fault Module Timestamp: 4bf638bd Exception Code: c005 Exception Offset: 1d94 OS Version: 6.0.6002.2.2.0.256.6 Locale ID:1033 Additional Information 1: 1c1d Additional Information 2: e064c795479179a5f08d19e37de8915e Additional Information 3: 50ea Additional Information 4: 02a385f4f3dc3301c3a9d270f946 same occurs when calling: %ProgramFiles%/R/R-2.12.0dev/bin/R.exe However, C:\Users\hb\braju.com.R\R.matlab,R-forge%ProgramFiles%/R/R-2.12.0dev/bin/i386/Rterm.exe -e sessionInfo() R version 2.12.0 Under development (unstable) (2010-05-21 r52061) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i386-pc-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. sessionInfo() R version 2.12.0 Under development (unstable) (2010-05-21 r52061) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] exmaple problems
I do not know if this has been reported already (I searched the headers of the recent messages to r-devel) It seems that 'example' in R 2.11.0 has a problem when the help file does not contain any example. This is what happens on R 2.11.0 on Windows XP. library(tools) example(Rdiff) Error in file(con, r) : cannot open the connection In addition: Warning message: In file(con, r) : cannot open file 'C:\DOCUME~1\neuwirth\LOCALS~1\Temp\RtmpmknOJe\Rex678418be': No such file or directory The error does not occur when there is an example marked #Not Run: The problem does not appear in R 2.10.1 library(tools) example(Rdiff) Warning message: In example(Rdiff) : 'Rdiff' has a help file but no examples -- Erich Neuwirth, University of Vienna Faculty of Computer Science Center for Computer Science Didactics and Learning Research Visit our SunSITE at http://sunsite.univie.ac.at Phone: +43-1-4277-39902 Fax: +43-1-4277-39459 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] dyn.load() strange behavior
- Does bar really dyn.load its shared library on load?
- Have you told package foo (in the DESCRIPTION) it is LinkingTo: bar ?
Uwe Ligges
On 21.05.2010 22:35, Dominick Samperi wrote:
Hello,
I am observing the following strange behavior when I try to
load a shared library using dyn.load() under Linux...
The library foo.so refers to a symbol in another package bar
(with shared library bar.so), I get:
dyn.load('foo.so') # error message because I forgot to load bar
library(bar) # so I fix it
dyn.load('foo.so') # works this time and everything is fine
But, if restart my R session and do it right the second
time there is a surprise:
library(bar)
dyn.load('foo.so') # fails
library(bar) # just to be sure?
dyn.load('foo.so) # fails again
dyn.load('/usr/local/lib64/library/bar/lib/libbar.so') # just to be really
sure?
dyn.load('foo.so')
In other words, it is possible to load foo.so, but only
after a failed attempt. If I remember to load the required
package bar I cannot load the depenent library foo.so.
Any ideas?
Thanks,
Dominick
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Re: [Rd] dyn.load() strange behavior
Thanks for taking the time to look at this Uwe. Turns out the
problem was caused by the fact that foo.so was built with
incorrect linker options (not pointing to bar.so), so there were
undefined symbols. Why it worked at all is a puzzle.
2010/5/22 Uwe Ligges lig...@statistik.tu-dortmund.de
- Does bar really dyn.load its shared library on load?
- Have you told package foo (in the DESCRIPTION) it is LinkingTo: bar ?
Uwe Ligges
On 21.05.2010 22:35, Dominick Samperi wrote:
Hello,
I am observing the following strange behavior when I try to
load a shared library using dyn.load() under Linux...
The library foo.so refers to a symbol in another package bar
(with shared library bar.so), I get:
dyn.load('foo.so') # error message because I forgot to load bar
library(bar) # so I fix it
dyn.load('foo.so') # works this time and everything is fine
But, if restart my R session and do it right the second
time there is a surprise:
library(bar)
dyn.load('foo.so') # fails
library(bar) # just to be sure?
dyn.load('foo.so) # fails again
dyn.load('/usr/local/lib64/library/bar/lib/libbar.so') # just to be really
sure?
dyn.load('foo.so')
In other words, it is possible to load foo.so, but only
after a failed attempt. If I remember to load the required
package bar I cannot load the depenent library foo.so.
Any ideas?
Thanks,
Dominick
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Re: [Rd] S4 method defined but not used
Hi Thibaut --
On 05/21/2010 08:34 AM, Jombart, Thibaut wrote:
Dear R developers,
I am having a slightly weird issue with a S4 method defined in my package
adegenet 1.2-4, with R 2.11.0. As far as I know, the problem is new, and the
code implementing the method has not changed for more than a year and worked
well so far.
The problem is the following. I define, in the package, a method [ for the
S4 class 'genind'. The method's definition is:
setMethod([, signature(x=genind, i=ANY, j=ANY, drop=ANY),
function(x, i, j, ..., loc=NULL, treatOther=TRUE, drop=FALSE) {
... ## code of the function
})
When sourcing the code directly from R, this method is found and used
normally. However, when loading the package, the method does not seem to be
found any longer by the dispatcher. For instance, here is an error I get:
### R code
library(adegenet)
data(nancycats) # nancycat is a S4 object with class 'genind'
class(nancycats)
[1] genind
attr(,package)
[1] adegenet
nancycats[1]
Error in nancycats[1] : object of type 'S4' is not subsettable # [ IS NOT
USED HERE
### end R code
For what it's worth, I can't reproduce this problem, and in a new R
session after library(adegenet) I have
sessionInfo()
R version 2.11.0 Patched (2010-05-01 r51886)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] adegenet_1.2-4 MASS_7.3-5
which has a different set of attached / loaded packages -- maybe you are
picking up something from .RData or .Rprofile, and you need to start R
with --vanilla?
Martin
And still, the method is defined in the environment:
### R code
showMethods([, class=genind)
Function: [ (package base)
x=genind
findMethods([, classes=genind)$genind
Method Definition:
function (x, i, j, ..., drop = FALSE)
{
.local - function (x, i, j, ..., loc = NULL, treatOther = TRUE,
drop = FALSE)
{
if (missing(i))
i - TRUE
if (missing(j))
j - TRUE
pop - NULL
... # rest of the code of the function
### end R code
findMethods and showMethods find the method. However, getMethod doesn't:
### R code
getMethod([,genind)
Error in getMethod([, genind) :
No method found for function [ and signature genind
### end R code
Now, if I just try the same thing after sourcing the code of the method
manually, everything works fine. showMethods then reads:
### R code
showMethods([, classes=genind)
Function: [ (package base)
x=genind
x=genind, i=ANY, j=ANY, drop=ANY
x=genind, i=numeric, j=missing, drop=missing
(inherited from: x=genind, i=ANY, j=ANY, drop=ANY)
### end R code
My R version/session is:
### R code
R.version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status
major 2
minor 11.0
year 2010
month 04
day22
svn rev51801
language R
version.string R version 2.11.0 (2010-04-22)
sessionInfo()
R version 2.11.0 (2010-04-22)
i686-pc-linux-gnu
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] adegenet_1.2-4 MASS_7.3-5
loaded via a namespace (and not attached):
[1] graph_1.26.0 phylobase_0.5 tcltk_2.11.0 tools_2.11.0
### end R code
R was compiled from the sources. All packages are up-to-date (as of the 21
May 2010). My system is a Ubuntu 10.04 (32 bits), with kernel
2.6.31-20-generic. I could not reproduce the problem using R 2.11.0 on
Windows Vista, or on Debian testing (R 2.11.0 compiled from the sources). The
package adegenet does not have a namespace. The error arises whether using a
field 'Collate' in DESCRIPTION, or not. I checked that the source file is
indeed sourced when loading the package: it is. The method [ is not defined
by any other
