Thomas Petzoldt <[EMAIL PROTECTED]> writes:
> Hello,
>
> apologies if I missed something well known. I'm just revising an own
> package and wonder if it is still common to use "generating
> functions" which have the same name as the corresponding S4 class as
> suggested by Chambers, 2001. "Classes
Thomas Petzoldt <[EMAIL PROTECTED]> writes:
> One odd thing I found was that initialize does obviously not allow to
> incorporate additional named parameters which are not slots.
?! Does for me:
setClass("FOO", representation(x="numeric"))
[1] "FOO"
setMethod("initiali
Stephen Pope <[EMAIL PROTECTED]> writes:
> With:
>
> R version 2.4.1 Patched (2007-01-22 r40548)
>
> "rep" is missing from methods:::.BasicFunsList, causing
> methods:::genericForPrimitive("rep") to fail, which in turn causes
> setMethod("rep", ...) to fail. (setGeneric("rep") of course fails as
Thomas Petzoldt <[EMAIL PROTECTED]> writes:
> Your example works but one can not arbitrarily mix slots, other named
> arguments and the default callNextMethod(). The documentation states:
>
> "... Data to include in the new object. Named arguments correspond
> to slots in the class definition."
A
Jörg Beyer <[EMAIL PROTECTED]> writes:
> Hello all,
>
> I'd like to report a problem related to S4 classes.
>
> Platform:
> Mac G4/400 PCI (PPC-architecture)
> Mac OS 10.4.8
> R 2.4.1 for Mac OS X (CRAN binary, 2006-12-19) w/ R.app 1.18
I see the same thing using a fairly recent R-devel:
> se
cstrato <[EMAIL PROTECTED]> writes:
> Thank you for your fast answer.
> Sorrowly, I don´t know how to use a debugger on MacOS X, I am using
> old-style print commands.
You should be able to use gdb on OS X (works for me, YMMV). So you
could try:
R -d gdb
run
# source a script
"Gabor Grothendieck" <[EMAIL PROTECTED]> writes:
> You can use
>
> if(require(myPackage)) { ... }
Probably you will want:
if (suppressWarnings(require("somePkg"))) { ... }
This way, you won't get a lot of noise when somePkg isn't installed.
Running the examples at least some of the time seem
Robin Hankin <[EMAIL PROTECTED]> writes:
> Hello everyone
>
> Suppose I have an S3 class "dog" and a function plot.dog() which
> looks like this:
>
> plot.dog <- function(x,show.uncertainty, ...){
>
>if (show.uncertainty){
>and superimpose the results on the simple plot>
>
Herve Pages <[EMAIL PROTECTED]> writes:
> So apparently here extracting with dat[i, ] is 300 times faster than
> extracting with dat[key, ] !
>
>> system.time(for (i in 1:100) dat["1", ])
>user system elapsed
> 12.680 0.396 13.075
>
>> system.time(for (i in 1:100) dat[1, ])
>user syst
d so that R's output doesn't confuse
itself and gcc when doing R CMD INSTALL, seems like it should be
possible.
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cribing what isn't valid about the
object. Don't call warning() or print().
Also, you don't need those ';'
And finally, you are operating on a _copy_ in the validity method
(just like everywhere else) and so this
> if (substr(strg, nchar(strg), nchar(strg))
g, TRUE)); nprotect++;
+ thisClass = R_data_class(arg, TRUE);
UNPROTECT(1); /* for arg */
+ PROTECT(thisClass); nprotect++;
}
SET_VECTOR_ELT(classes, i, thisClass);
lwidth += strlen(STRING_VALUE(thisClass)) + 1;
--
Seth Falcon | Computational Bio
call <- sys.call(-4)
dcall <- deparse(call)[1]
prefix <- paste("Error in", dcall, ": ")
--
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standardGeneric("frob2")
})
setMethod("frob1", "integer",
function(x) vector(mode="integer", length=x))
setMethod("frob2", "integer",
function(x) vector(mode="integer", length=x))
###
onality defined in baseClass, analogously to C++ methods.
> If this is possible, does there exist an example?
The S4 object system is generic function based. Methods are not
contained inside classes.
You can define a generic 'myfunction' and then define methods for
BaseClass and
generic that are applicable and orders them so that the most
specific method comes first. When you call callNextMethod, you enter
the next most specific method.
+ seth
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Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
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___
> code at the R prompt via ':::' which I find just handy.
If you switched to _className, then there would be no S3 confusion.
There are performance implications in doing things this way, but I
agree it is convenient.
Cheers,
+ seth
--
Seth Falcon | Computational
Peter Dalgaard <[EMAIL PROTECTED]> writes:
> I have just committed my variation of Seth's patch, so please check the
> current r-devel too.
Thanks, Peter. And I agree that your variation is cleaner.
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Res
\r. In general, any status output of calculation should be
optional since they can get in the way of things like Sweave, etc.
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http://bioconductor.org
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this to be useful, you need to have package code that
checks if(OPTIONS$debug) and does something different.
+ seth
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http://bioconductor.org
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> storage.mode(x) <- "integer"
tracemem[0x1fa6df8 -> 0x1fa6d60]:
tracemem[0x1fa6d60 -> 0x1fa6808]: as.integer.default as.integer eval eval
storage.mode<-
tracemem[0x1fa6808 -> 0x2c26b18]: as.integer.default as.integer eval eval
storage.mode<-
trac
3
[6,] 612 18 24
class(vv)
[1] "matrix"
typeof(vv)
[1] "list"
vv[1, 1]
[[1]]
[1] 1
vv[1, ]
[[1]]
[1] 1
[[2]]
[1] 7
[[3]]
[1] 13
[[4]]
[1] 19
+ seth
--
Seth Falco
guaranteed structure and so you can't avoid
[[1]] since [1] will return a list and it can contain *anything*.
What could be useful is the notion of a vector of S4 objects. There
you could ensure they are all the same type.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson
"hadley wickham" <[EMAIL PROTECTED]> writes:
> That's rather a contrived example. In practice, you would create a
> list containing the same type of objects. eg:
Yes, great. But when you have code that is expecting a matrix
argument, you can't know what you are going to get. I suspect there
is
Hi,
Package authors can specify the minimum required version of a
dependency using:
Depends: somePackage (>= 1.2.3)
Is there a way to demand a minimum version when importing a
dependency? Version specifiers in the Imports field are currently
ignored AFAICT.
+ seth
--
Seth Fal
A further improvement to apropos() would be to sort the output.
Currently, the output of apropos is in the order found on the search
list and this will rarely be useful to the user.
All that is needed is a sort(x) at the end of the function.
+ seth
--
Seth Falcon | Computational Biology | Fred
ion which attempts to unload the name space and S4
methods if TRUE. It will fail if the name space is in use by another
package.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org
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Prof Brian Ripley <[EMAIL PROTECTED]> writes:
> Seems sensible, but 2.5.0 is in feature freeze and it is possible that
> someone has relied on this.
>
> I've added this (and a \value section to the help file) for R-devel.
Excellent. Thank you.
+ seth
--
Seth Falcon
} else {
+if(canCache) { # make into method definition
+ asMethod <- .asCoerceMethod(asMethod, sig, FALSE)
+}
}
## cache in the coerce function's environment
if(canCache && !is.null(asMethod)) {
at hand.
+ seth
## 8<--8<---
setClass("Foo", representation(name="character"), contains="matrix")
f <- new("Foo", name="Sam", matrix())
f
m <- as(f, "matrix")
m
print(m)
install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,
I don't have this problem when using a recent R-devel. And I'm
guessing that Matrix works with the release, but haven't had time to
check this.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson
L, panel = "panel.dotplot", ...)
> {
> ocall <- ccall <- match.call()
> ccall$data <- data
> ccall$panel <- panel
> ccall[[1]] <- as.name("bwplot")
> evalenv <- new.env(parent = parent.frame())
> assign(&qu
nd determine whether it
errored out or not and set action based on that.
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packages("Biobase", repos=rep, installWithVers=TRUE)
I would also be curious to understand your motivation for wanting
installWithVers. BioC packages are developed for a particular R
release and in general I would not expect BioC packages developed
older R's to work with
Update:
Seth Falcon <[EMAIL PROTECTED]> writes:
> And for me it does.
Almost. With a clean package library, I end up with an error
installing matchprobes because library.dynam can't find a shared
library called matchprobes_1.8.0. Since other packages that have
native code are i
quot;, pkgname, lib)
Thanks! I've fixed this for the release and devel versions of
matchprobes.
> (That's not an uncommon mistake, BTW: EBarrays, puma and twilight of
> BioC seem to share it.)
Indeed. I will contact the maintainers of those packages.
+ seth
--
Seth Falcon |
)
[1] "package:AnnotationDbi" "package:base"
The package code I'm working with imports the package that defines the
mget method (and this package does exportMethods(mget)), yet the
problem seems to be that the mget generic is not found -- but I find
(ename == "") {
cat(" first five entires\n")
print(ls(etmp)[1:5])
}
etmp <- parent.env(etmp)
}
}
One thing to note: One might expect each import to be in the chain of
parent environments. Instead all impo
ackage that only sets methods on generic "foo", an
exportMethods("foo") directive does not re-export the "foo"
generic. I find it confusing that exportMethods sometimes
exports the generic and sometimes not. The generic can be
re-exported using ex
to package developers
to dynamically register routines. Just as R can load packages to make
new routines available, I don't see why an R package should not be
able to provide an analogous plugin mechanism of its own.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer
name))
[1] "$"
## But it doesn't work. Why?
f$bo
NULL
f$al
NULL
## Here is a hackish workaround.
setMethod("$", "Foo", function(x, name)
eval(substitute([EMAIL PROTECTED], list(FOO=name))))
[1] "$"
f$
;- "bob"
>> `$`(f, nm)
> NULL
Thanks, this is the piece I was missing.
+ seth
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ng to do
(and your subject line is confusing, this isn't a best practice
question IMO, but a how do I use R objects in C question).
Perhaps the above hints will get you going. I would recommend reading
over the relevant sections of the Writing R Extensions manual and the
R internals manual.
+
enu <- paste("Vignettes", pkgName, sep="/")
winMenuAdd(pkgMenu)
for (i in vigs) {
item <- sub(".pdf", "", basename(i))
winMenuAddItem(pkgMenu, item, paste("shell.exec(\"",
as.charac
ng at a time, I guess.
If there is some agreement about vignettes being automatically added
and that this only happens when a package is attached, then I can look
into modifying the existing function to handle this.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Cente
Simon Urbanek <[EMAIL PROTECTED]> writes:
> On May 15, 2007, at 1:57 PM, Prof Brian Ripley wrote:
>
>> On Mon, 14 May 2007, Seth Falcon wrote:
>>
>>> Duncan Murdoch <[EMAIL PROTECTED]> writes:
>>>> I'm interested in making vignettes more
s a hook such that
a GUI can add the vignette info for attached packages. Comments from
others in this thread suggest that there is a desire that this be an
opt-in feature for package authors [I don't really understand this
desire as it seems to me it should be a feature/decision of the GUI]
and aga
signature. However, by adding an
argument, we are able to move more slowly towards a non-partially
matching [[ (eventually, the default could be exact=TRUE, but that is
a discussion for another day).
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research
l matching is
desirable because it saves typing during interactive sessions now has
a lot less weight. The recent integration of the completion code
gives less typing and complete names.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.o
lace under inst/).
You might also look at the vsn package in Bioconductor which uses a
Makefile to avoid R CMD check from building its vignette because it is
too time consuming...
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Resea
ure="flesh",
function(flesh, skeleton=attr(flesh, "skeleton")
standardGeneric("foo")))
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Hi again,
Robert has committed the proposed patch to R-devel. So [[ now has an
'exact' argument and the behavior is as described:
Seth Falcon <[EMAIL PROTECTED]> writes:
>1. [[ gains an 'exact' argument with default value NA
>
>2. Behavior of &
Andrew Clausen <[EMAIL PROTECTED]> writes:
> Hi Seth,
>
> On Mon, May 21, 2007 at 05:15:10PM -0700, Seth Falcon wrote:
>> I will also add that the notion of a default argument on a generic
>> function seems a bit odd to me. If an argument is available for
>> disp
)
Ncells 5837253 311.86910418 369.1 6193578 330.8
Vcells 16831859 128.5 45712717 348.8 39456690 301.1
Best Wishes,
+ seth
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methods for a generic documented elsewhere.
+ seth
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"TSdoc") <- value ; x })
>
> setGeneric("TSdoc",
>def= function(x) standardGeneric("TSdoc"),
>useAsDefault= function(x) attr(x, "TSdoc"))
Aside:
It seems odd to me to define such defaults. How do you know x is
going to have a TSd
lected when no R object refers to them. This would allow
> for example
>
> readLines(gzfile("foo.gz"))
I think this would be a nice improvement as it matches what many
people already assume happens as well as matches what some other
languages do (in particular, Python).
+
e when
coding R and it would be nice to make it work for connections.
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>
> http://wiki.r-project.org/rwiki/doku.php?id=developers:r_connections_api
I wanted to voice a "me too" for wanting to see an interface added for
working with connections from C in package code. There are a number
of places where this would be useful and provide cleaner solution
vailable to them -- I just had a question from someone who wanted to
know how to make a plot that appeared in a vignette, for example.
+ seth
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http://bioconductor.org
ude/Rinternals.h
Best Wishes,
+ seth
PS: Nice to see you again :-)
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CHARSXP, it does not work.
>
> So, how could I get the actual values in the column names?
How about:
SEXP colnums;
int *ivals;
PROTECT(colnums = coerceVector(cl, INTSXP));
ivals = INTEGER(colnums);
Here you convert the STRSXP cl into an INTSXP. If you want the actual
int
silenced.
[Note 1: I don't have any ideas at the moment for how this could
work.]
[Note 2: Despite the false-positives, I've already caught a handful of
bugs by reading over these NOTEs and think they provide a lot of value
to the check process]
+ seth
--
Seth Falcon | Computational Bio
nt contains environments. The lazy loading db is
important at runtime when users may only need to access one or two of
the environments. We generate the lazy-loading dbs by hand so that
users installing from source do not have to repeat the process
themselves. Since the environments are lar
/MakePkg -s
lazyload
endif
- @$(MAKE) --no-print-directory -f $(RHOME)/src/gnuwin32/MakePkg -s
$(DPKG)/demo $(DPKG)/exec $(DPKG)/inst $(DATA)
ifeq ($(strip $(LAZYDATA)),true)
@$(MAKE) --no-print-directory -f $(RHOME)/src/gnuwin32/MakePkg -s
lazydata
endif
--
Seth Falcon
tter to have outdated documents than crippled documents.
I'm not trying to argue that the function shouldn't change, but if it
is so annoying, you can also resolve this problem by defining your own
step function and calling it (forgetting about withC
Seth Falcon <[EMAIL PROTECTED]> writes:
> On Windows, package files in the inst/ subdir are installed after the
> lazyload creation. This differs from Linux where inst/ is installed
> _before_ lazyload creation.
>
> Since packages may need data in inst, I think the order o
ake sense so making it work seems like a good idea. I'll
agree that it working might encourage someone to try formals<-(), but
the fact that it cannot do anything but error seems like a strange
reason not to make formals() work.
+ seth
--
Seth Falcon | Computational Biology | Fred Hut
uot;
> > setAs("TSconnection", "DBIConnection", def = function(from) [EMAIL
> PROTECTED])
I think things work as you expect up until this pint.
> > setIs("TSconnection", "DBIConnection", coerce = function(x)
> > [EMAIL PROTECTED])
I'
omplicate your desire to use X11(), but
perhaps with Xvfb run from the screen session things will work. Do
all of the graphics devices require access to X11()? I thought you
could use pdf() for example, without X11() but I'm not certain.
+ seth
--
Seth Falcon | Computational Biology |
userprimary.net/software/dict_0.0.4.tar.gz
Windows binary:
R-2.5.x: http://userprimary.net/software/dict_0.0.4.zip
+ seth
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is what we see with an environment:
> e = new.env(hash=T, size=2^14)
> for (k in keys2) e[[k]] = k
> summary(env.profile(e)$counts)
Min. 1st Qu.Median Mean 3rd Qu. Max.
0.0.0.0.79350. 2700.
--
Se
t it might actually be useful to
people. It's main use may turn out to be for investigating hash
functions behavior and for a test tool it may be sufficient as-is.
+ seth
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gate other hashing functions
since computing the next prime and doing so for resizes will take
longer than not having to do it and it will add complexity to the
code.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http:
reateSession(attributes);
> void* temp = session;
It isn't clear from your example, are you sure that temp is valid at
this point?
> SEXP out = R_MakeExternalPtr(temp, R_NilValue, R_NilValue);
I was expecting to see:
SEXP out = R_MakeExternalPtr((void *)sesPtr, R_NilValue,
i;
SEXP cvect;
PROTECT(cvect = allocVector(STRSXP, numStrings));
for (i = 0; i < numStrings; i++) {
SET_STRING_ELT(cvect, i, mkChar(yourStrings[i]));
}
UNPROTECT(cvect);
return cvect;
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer
eck can not be executed. The error message is:
Instead of require(pkgname), simply list pkgname in the Depends field
of your package's DESCRIPTION file. See the Writing R Extensions
manual for details.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
Bi
ly, then it will be much easier to
simply edit the source for pkg, reinstall and test. If you find and
fix a bug, most package maintainers will be quite happy to integrate
your fix.
+ seth
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you from getting things done, or
just a concern that there is a leak that needs fixing? It is worth
noting that the internal handling of character vectors has changed in
R-devel and so IMO testing there would make sense before persuing this
further, I suspect your results will be di
ding up with multiple copies of
the object on the R side during some of your operations. I would
recommend recompiling with --enable-memory-profiling and using
tracemem() to see if you can identify places where copies of your
large object are occurring. You can also take a look at
Rprof(memory.
narrow it down, gctorture may help or running the examples
under valgrind.
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at R CMD check
doesn't recurse really isn't a problem. You can have a driver script
at the top-level that runs as many of the tests in subdirs as you
want. And this is really a good thing since as you mentioned later in
your response, some tests take a long time to run and prob
quot;yes"
can write
"yes"
## start new R session
for (i in 1:75) file("foo")
gc()
warnings()[1:3]
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 149603 4.0 35 9.4 35 9.4
Vcells 101924 0.8 786432 6.0 486908 3.8
There w
he_size=64000 and synchronous=0 and that this was determined by a
handful of experiments on typical annotation dbs.
Columns with few levels may not benefit from an index. See this
thread:
http://thread.gmane.org/gmane.comp.db.sqlite.general/23683/focus=23693
But your column with many levels sho
l probably already wrote it) but what you get from
> getInstallOrder() should suit your needs here.
makeDepGraph returns a graphNEL instance and Rgraphviz knows how to
plot those. The entire graph will likely not produce a particularly
compelling visualization. But you can subs
= {
> close(con)
> })
This doesn't address isOpen, but why do you have the call to close
inside the tryCatch block? Isn't the idea that finally will always be
run and so you can be reasonably sure that close gets called once?
If your real
gexpr("", "abc", fixed=TRUE)
[[1]]
[1] 1 2 3
attr(,"match.length")
[1] 0 0 0
> gregexpr("", "abc", perl=TRUE)
[[1]]
[1] 1 2 3
attr(,"match.length")
[1] 0 0 0
+ seth
--
Seth Falcon | [EMAI
Hi again,
> Herve wrote:
> > gregexpr("", "abc", fixed=TRUE)
>
>*** caught segfault ***
> address 0x1c09000, cause 'memory not mapped'
This should be fixed in latest svn. Thanks for the report.
+ seth
--
Seth Falcon | [EMAI
ckageName(package, version);
> }
> pattern <- sprintf("package:%s", package);
> (pattern %in% s);
> }
This only tests whether or not the given package is attached to the
search path. You also (I think) want to search loaded namespaces.
Bu
majority of
R's internal string processing functions use standard C semantics
and truncated at first nul there has always been some room for
"interesting" behavior. The change in R-2.7 was an attempt to start
resolving these inconsistencies. Since then the core team has agr
of namespaces, looking
> in the search list seems a bad idea in principle.
I agree that using the dynamic lookup when the static lookup is
available is bad programming practice. However, given the flexibility
of the current tools, it seems not unreasonable to expect that
picking up a method via the se
> in
> RSQLite/src/RS-DBI.h
I will see about making such a change. I suspect the correct fix is
one that tweaks configure to determine where things are based on the
current system (the current code is correct for gcc I believe).
Anyhow, thanks for the report. I will try to have an up
Hi all,
A new version of RSQLite has been uploaded to CRAN and should be
available soon. This update contains a minor change to the C code
that should improve compatibility on various unix OS.
+ seth
--
Seth Falcon | http://userprimary.net/user
ovided by pkgA, then you can use the LinkingTo
field in the DESCRIPTION file as described in Writing R Extensions
in the "Registering native routines" section.
+ seth
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is-a
integer. The fact that the as() method dispatch doesn't match that of
SQLiteConnection should really be that surprising.
I don't see how this could be the responsibility of the author of the
class you've subclassed.
I would also quest
A couple more comments...
* On 2008-09-15 at 10:07 -0700 Seth Falcon wrote:
> > The example is with RSQLite but the same thing happens with
> > RMySQL, and other DBI packages.
The use of as() within the various DBI packages should be
re-evaluated. I suspect some of that code was amo
* On 2008-09-17 at 19:25 -0700 Seth Falcon wrote:
> In the latest R-devel code (svn r46542), this behaves differently (and
> works as you were hoping). I get:
>
> library("RSQLite")
> setClass("SQLConPlus", contains=c("SQLiteConnection","
Continuing to talk to myself here...
* On 2008-09-17 at 21:06 -0700 Seth Falcon wrote:
> *argh* I'm certain this was working for me and yet when I try to
> reproduce in a new R shell it errors out.
This looks like an infelicity in the methods caching.
To make it work:
libra
intf (call=0x10cb470, op=0x1018924, args=, env=0x10a40b0) at
../../../../R-devel-all/src/main/sprintf.c:179
#5 0x003fe1af in do_internal (call=0x10cb4a8, op=0x100fc38, args=0x10a40e8,
env=0x10a40b0) at ../../../../R-devel-all/src/main/names.c:1140
+ seth
--
Seth Falcon | http://us
ifferent run paths
resulted in different allocation patterns, one of which triggered the
bug.
+ seth
--
Seth Falcon | http://userprimary.net/user/
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