Re: [Rd] bug, feature of mistery?
Giuseppe Ragusa <[EMAIL PROTECTED]> writes: > I have two machines a linux_amd64_x86 (gentoo_amd64) and a > linux_x86. You might want to try running valgrind on your code on the 32bit machine. This may turn up a silent coding error that is manifesting on the 64bit platform. I think there is a new R CMD check option to do valgrind. + seth __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Feature request: report the url if 404 error occurs
Currently, the connection code does not include the URL in the warning message when a 404 response is received: myUrl = "http://www.r-project.org/ABadPage.html"; con = url(myUrl) readLines(con) Error in readLines(con) : cannot open the connection In addition: Warning message: cannot open: HTTP status was '404 Not Found' Would it be possible (and desirable) to include the URL in the warning message? Here's an example: Error in readLines(con) : cannot open the connection In addition: Warning message: cannot open 'http://www.r-project.org/ABadPage.html': HTTP status was '404 Not Found' + seth __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Objects in R
Duncan Murdoch <[EMAIL PROTECTED]> writes: > What S4 is missing is "encapsulation". Wikipedia's article on > object-oriented programming gives a good definition: > > "Encapsulation - Ensures that users of an object cannot change the > internal state of the object in unexpected ways; only the object's own > internal methods are allowed to access its state. Each object exposes an > interface that specifies how other objects may interact with it." > > Neither of these properties holds in S4. I don't like the definition of encapsulation in the Wikipedia. If nothing else, I think the second part about objects exposing an interface specifying how to interact with them should come first --- and S4 provides that. In my experience, the ability to create "obvious" interfaces to classes is the important part of encapsulation. Python's object system, for example, does not (easily) provide protections against abuse, but other than some initial misgivings, I've not missed it. + seth __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Overloading methods in R
"Ali -" <[EMAIL PROTECTED]> writes: > On the other hand, I caouldn't find a decent OO package which is > based on S4 AND comes with the official release of R. The OO system that comes with R and is based on S4 *is* S4. The challenge is that it is a different way of doing OO as compared to Java. But for most uses, it works just fine once you get used to "spelling" things differently. + seth __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] S4 methods semantics questions
John Chambers <[EMAIL PROTECTED]> writes:
> Well, the intent is that defaults are indeed taken from the method, if
> there is a default there, otherwise from the generic. It looks as if
> there is a bug in the case that the generic has NO default for that
> argument (unless, of course, it's a subtle feature, but not that I can
> think of at the moment).
>
> Your example works as intended if there is a default expression for y
> in the generic:
>
> R> setGeneric("foo",function(x,y=stop("Need y")) standardGeneric("foo"))
> [1] "foo"
> R> setMethod("foo","numeric",function(x,y=2) x+y)
> [1] "foo"
> R> foo(1)
> [1] 3
FWIW, I've encountered the same error that the OP described. I
certainly don't know if it is a bug, but I can say that I expected it
to work based on the documentation of setMethod.
I ended up with a different workaround: if you don't need to do
dispatching on the default arguments, you can set
setGeneric("foo", function(x, ...) standardGeneric("foo"))
and then methods with defaults defined in their function do the
expected thing.
Best,
+ seth
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Re: [Rd] trouble building r-devel
<[EMAIL PROTECTED]> writes: > cp unicode/iconv.dll ../../modules/ > cp: cannot stat `unicode/iconv.dll': No such file or directory > make[2]: *** [rmodules] Error 1 > make[1]: *** [rbuild] Error 2 > make: *** [all] Error 2 See the section Unicode support here: http://www.murdoch-sutherland.com/Rtools/ Basically, you just need to download and then copy the iconv.dll to the right spot and you should be on your way. + seth __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Buglet in install.packages warning message
I've been experimenting with install.packages and it's new ability to
track down dependencies from a list of repositories and encountered
this:
install.packages(c("foo", "bar"), repos="http://cran.r-project.org";,
dependencies=c("Depends", "Suggests"))
dependencies 'foo' are not availabledependencies 'bar' are not available
With the following change (see below) I get what I suspect is the
intended warning message:
dependencies 'foo', 'bar' are not available
+ seth
Index: packages2.R
===
--- packages2.R (revision 33678)
+++ packages2.R (working copy)
@@ -125,7 +125,7 @@
cat(sprintf(ngettext(sum(miss),
"dependency %s is not available",
"dependencies %s are not available"),
-paste(sQuote(p1[miss]), sep=", ")), "\n\n", sep ="")
+paste(sQuote(p1[miss]), collapse=", ")), "\n\n", sep ="")
flush.console()
}
p1 <- p1[!miss]
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Re: [Rd] Trouble debugging with gdb, R on Windows
Paul Roebuck <[EMAIL PROTECTED]> writes: > Not a Windows developer so this may be off but did you try > loading the shared library prior to setting your breakpoint? > > (gdb) break WinMain > (gdb) run > (gdb) info share Yes, in the transcript of gdb included in my post I did the first two lines of the above. Just tried the 'info share' and I see R.dll is loaded, but I still get the same error when trying to set another breakpoint. Thanks, + seth __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Trouble debugging with gdb, R on Windows
I'm trying to follow the example in the R for Windows FAQ on running gdb and am getting stuck because gdb tells me "Cannot access memory at address ...". Here's what my gdb session looks like (This one from a cygwin shell, but same results from plain Windows CMD shell): $ cd R-devel/src/gnuwin32 $ gdb ../../bin/Rgui.exe GNU gdb 5.2.1 Copyright 2002 Free Software Foundation, Inc. GDB is free software, covered by the GNU General Public License, and you are welcome to change it and/or distribute copies of it under certain conditions. Type "show copying" to see the conditions. There is absolutely no warranty for GDB. Type "show warranty" for details. This GDB was configured as "i686-pc-mingw32"... (gdb) break WinMain Breakpoint 1 at 0x401296: file ../graphapp/graphappmain.c, line 59. (gdb) run Starting program: y:\falcon\src\R-devel\src\gnuwin32/../../bin/Rgui.exe Breakpoint 1, WinMain (Instance=0x40, PrevInstance=0x0, CmdLine=0x261f26 "", CmdShow=10) at ../graphapp/graphappmain.c:59 59 startgraphapp(Instance, PrevInstance, CmdShow); (gdb) break R_ReadConsole Cannot access memory at address 0x23e17 (gdb) info symbol 0x23e17 R_ReadConsole in section .text (gdb) Any suggestions? Attempting to set other break points (do_BLAH) gives the same result. I compiled with 'make DEBUG=T' per the instructions on Duncan Murdoch's Building R for Windows page. I also tried compiling after modifying the makefiles to remove -02 optimization (see patch below for what I did). Thanks, + seth Index: src/extra/intl/Makefile.win === --- src/extra/intl/Makefile.win (revision 33477) +++ src/extra/intl/Makefile.win (working copy) @@ -18,6 +18,10 @@ endif CFLAGS = -O2 $(DEFS) -I. -I../../include +ifdef DEBUG + CFLAGS = $(DEFS) -I. -I../../include +endif + dcigettext-CFLAGS=-DLOCALEDIR=\"\" SOURCES = \ Index: src/gnuwin32/Makefile === --- src/gnuwin32/Makefile (revision 33477) +++ src/gnuwin32/Makefile (working copy) @@ -33,8 +33,8 @@ ## use FOPTFLAGS where complex*16 is used. FOPTFLAGS=-O2 -Wall ifdef DEBUG - OPTFLAGS+=-g - FOPTFLAGS+=-g + OPTFLAGS=-g -Wall -pedantic + FOPTFLAGS=-g -Wall DLLFLAGS= else DLLFLAGS=-s __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] How to use Rmpi?
Hi Alessandro, "Alessandro Balboni" <[EMAIL PROTECTED]> writes: > I need to rewrite a software in R, that runs on a cluster. If you haven't already, take a look at the snow package on CRAN. It provides an easier to use wrapper around either Rmpi or Rpvm. The included documentation has some examples that should get you going. + seth __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error on Windows installing package to non-default library
On Mar 2, 2005, at 8:54 AM, Prof Brian Ripley wrote: You can't please everyone all the time, and in this case you cannot just make the substitution as 1) some parts of Windows demand \ 2) \ is a trail byte in some Japanese characters. I had a feeling it wouldn't be so simple, but wanted to bring it up in case... Why don't you just ensure that you don't use such paths for .libPaths()? Will do. Thanks, + seth __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Error on Windows installing package to non-default library
Hi all,
I'm seeing an error on Windows when I try to install a package to a
package library path that starts with a digit. I can reproduce the
error as follows using R-devel from Feb 24 on Windows advanced server:
badLib = "c:\\badExample\\2\\foo"
dir.create(badLib, recursive=TRUE)
z = .libPaths()
z = .libPaths(c(badLib, z))
z
[1] "c:\\badExample\\2\\foo" "C:/falcon/sw/rw2010dev/library"
pkg = "c:\\falcon\\abind_1.1-0.zip"
install.packages(pkg, repos=NULL, lib=badLib)
package 'abind' successfully unpacked and MD5 sums checked
updating HTML package descriptions
Error in gsub("^URL: ../../../library", lib0, readLines(cfile)) :
invalid backreference 2 in regular expression
After looking at src/library/utils/R/windows/linkhtml.R, it seems the
error is that the "\\2" part of the path is interpreted by gsub as a
back reference.
Changing "\\" to "/" in the library path fixes this issue:
> okLib = chartr("\\", "/", badLib)
> z = .libPaths(okLib)
> z
[1] "c:/badExample/2/foo""C:/falcon/sw/rw2010dev/library"
> install.packages(pkg, repos=NULL, lib=okLib)
package 'abind' successfully unpacked and MD5 sums checked
updating HTML package descriptions
So adding a call to chartr inside make.search.html would seem to be an
improvement (i.e, it looks good from here, but I haven't tested and
don't know if there are reasons why this would be a bad idea). OTOH,
maybe this should have already happened in the call to .libPaths()?
This came up because on the Windows server I'm using, tempdir()
contains a directory names "2" as part of the path --- and I want to be
able to install package to temporary package libraries for testing
purposes.
+ seth
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Re: [Rd] Regex Crashing R (perl = TRUE) (PR#7564)
A side response... On Jan 25, 2005, at 1:03 PM, [EMAIL PROTECTED] wrote: As a side note, is there a good way of incorporating an uncompiled perl script into an R package to be invoked from a system call? Putting it in the /src directory seems like the obvious place, but I can't convince R to copy over the script uncompiled upon installation. That's what the inst/ directory of a package is for, I believe. Look for details in the Writing R Extensions manual. You might also want to look at system.file() which can help you locate files in an installed package. + seth __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
