Displaying 20 results from an estimated 4000 matches similar to: "warning creating an as.array method in a package"
2010 Nov 30
1
warning creating an as.array method in a package
[Env: R 2.11.1, Win Xp, using Eclipse/StatET]
In a package I'm working on, I want to create as.matrix() and as.array()
methods for a particular kind of
object (log odds ratios). These are returned in a loddsratio object as
the $coefficients component,
a vector, but really reflect an underlying (R-1)x(C-1)xstrata array,
whose attributes are contained in other
components.
I define coef,
2010 Dec 16
1
defining a formula method for a weighted lm()
In the vcdExtra package on R-Forge, I have functions and generic methods
for calculating log odds ratios
for R x C x strata tables. I'd like to define methods for fitting
weighted lm()s to the resulting loddsratio objects,
but I'm having problems figuring out how to do this generally.
# install.packages("vcdExtra", repos="http://R-Forge.R-Project.org")
2013 Mar 13
1
S4 generic not exported correctly / incorrect dispatch?
In this post
https://stat.ethz.ch/pipermail/bioc-devel/2013-March/004152.html
a package author reports that S4 dispatch fails. I can reproduce this with a
PkgA (attached; 'intervals' is a relatively light-weight CRAN package) that has
DESCRIPTION with
Depends: intervals
Imports: graphics
NAMESPACE:
importFrom(graphics, "plot")
export("plot")
2013 Sep 12
6
declaring package dependencies
I received the following email note re: the vcdExtra package
> A vcd update has shown that packages TIMP and vcdExtra are not
> declaring their dependence on colorspace/MASS: see
>
> http://cran.r-project.org/web/checks/check_results_vcdExtra.html
But, I can't see what to do to avoid this, nor understand what has
changed in R devel.
Sure enough, CRAN now reports errors in
2010 Feb 14
1
How S3method() is implemented and called? And when to use it?
R-exts.pdf discribes S3method a little bit. But I want to understand
more on how it is called, implemented and when to use it.
I don't find it in an R session. But I see S3method() in some NAMESPACE files.
> S3method
Error: object 'S3method' not found
> ?S3method
No documentation for 'S3method' in specified packages and libraries:
you could try '??S3method'
I
2009 May 27
1
"Error: package/namespace load failed"
I am writing my first R package, and I have been getting the following series of errors when I run R CMD check:
* checking S3 generic/method consistency ... WARNING
Error: package/namespace load failed for 'REEMtree'
Call sequence:
2: stop(gettextf("package/namespace load failed for '%s'", libraryPkgName(package)),
call. = FALSE, domain = NA)
1: library(package,
2013 Aug 22
1
Confusion about Depends:, Imports:, Enhances:, import(), inportFrom()
In checking my vcdExtra package, the following NOTE newly appeared
(R-Forge, using R version 3.0.1 Patched (2013-08-20 r63635))
Package in Depends field not imported from: ?gnm?
These packages needs to imported from for the case when
this namespace is loaded but not attached.
In the DESCRIPTION file, I have
Depends: R (>= 2.10), vcd, gnm (>= 1.0.3)
In NAMESPACE:
# we are a vcd
2015 Jul 07
3
List S3 methods and defining packages
Hi,
from the man page ?methods, I expected to be able to build pairs
(class,package) for a given S3 method, e.g., print, using
attr(methods(print), 'info').
However all the methods, except the ones defined in base or S4
methods, get the 'from' value "registered S3method for print", instead
of the actual package name (see below for the first rows).
Is this normal
2004 Oct 17
2
Errors while compiling packages with namespace?
Hello,
I try to set up namespaces for packages. It is fine for several of them,
except one whose compilation fails (under Windows XP & R 2.0.0):
---------- Making package svViews ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
Error in parse(file, n, text, prompt) : syntax error on line 21
Execution halted
make[2]: *** [nmspace] Error 1
make[1]: ***
2013 Apr 19
2
NAMESPACE and imports
I am cleaning up the rms package to not export functions not to be called
directly by users. rms uses generic functions defined in other packages.
For example there is a latex method in the Hmisc package, and rms has a
latex method for objects of class "anova.rms" so there are anova.rms and
latex.anova.rms functions in rms. I use:
2006 Sep 01
1
as.environment(NULL)
Hi
In NEWS, it says
R CMD check now tests that the package can be loaded, and that
the package and namespace (if there is one) can each be loaded
in startup code (before the standard packages are loaded).
For package "onion", I think I have followed all of
sections 1.6.1 - 1.6.6 of R-exts, and it passes R CMD check for
R-2.3.1.
However, using R version 2.4.0 Under
2019 May 14
2
[R-pkg-devel] Three-argument S3method declaration does not seem to affect dispatching from inside the package.
CCing r-devel.
On Tue, 14 May 2019 at 02:11, Pavel Krivitsky <pavel at uow.edu.au> wrote:
>
> Dear All,
>
> I've run into this while updating a package with unfortunately named
> legacy functions. It seems like something that might be worth changing
> in R, and I want to get a sense of whether this is a problem before
> submitting a report to the Bugzilla.
>
>
2012 Oct 22
4
Help with applying a function to all possible 2x2 submatrices
Hi all,
I'm working with a large data set (on the order of 300X300) and trying to
apply a function which compares the elements of all possible 2x2
submatrices. There are rc(r-1)(c-1) such submatrices, so obviously the naive
method of looping through the rows and columns is computationally unfeasible
for my data set:
for(i in 1:(nrow(data)-1)) {
for(j in (i+1):nrow(data)) {
for (m
2013 Apr 24
1
Problem with S3 method dispatch and NAMESPACE
I have updated the rms package to extensively use NAMESPACE. I cannot get
certain S3 methods to dispatch. For example I have in NAMESPACE
S3method(anova, rms)
S3method(latex, anova.rms)
anova.rms produces an object of class "anova.rms" and there is a
latex.anova.rms function in rms. But when I do latex(anova(fit)) I get an
invocation of latex.default.
I have tried using
2007 Nov 05
2
namespace crash on S3method("as.ff",function)
Dear all,
I have defined a generic as.ff(x, ...) and a method as.ff.function(x, ...) which converts a standard R function x into a chunked version operating on large ff objects. Everything works fine, but when registering
S3method("as.ff",function)
in NAMESPACE, the installation fails with some kind of parsing error:
adding build stamp to DESCRIPTION
installing NAMESPACE file
2019 May 14
2
[R-pkg-devel] Three-argument S3method declaration does not seem to affect dispatching from inside the package.
On Tue, 14 May 2019 at 12:31, Pavel Krivitsky <pavel at uow.edu.au> wrote:
>
> > Note that disabling name-based dispatch implies two things: 1) the
> > inability to override your method by defining gen.formula in the
> > global environment, and 2) another package can break yours (i.e.,
> > internal calls to gen()) by registering an S3 method for gen() after
>
2010 Sep 01
1
S3 method for package listed in suggest/enhance
Hi all,
The profr package provides a method for displaying its output with
ggplot: ggplot.print. You don't need this ggplot2 to use profr, so
ggplot2 is listed under enhances in the DESCRIPTION file.
If I have just S3method(ggplot, profr) in my NAMESPACE, then I get:
** testing if installed package can be loaded
Error : object 'ggplot' not found whilst loading namespace
2015 May 04
1
Define replacement functions
No. I fixed that, the NAMESPACE file now contains:
S3method("[[<-", mylist)
S3method("$<-", mylist)
It still does not work. I also created a print method (print.mylist) which did work out of the box, regardless of being in the NAMESPACE file or not. Could it be somehow in here (also in my NAMESPACE file):
exportPattern("^[[:alpha:]]+")
Or could it be that
2023 Apr 28
1
Should '@" now be listed in tools:::.get_internal_S3_generics() ?
I was building a package that uses the new generic @ and kept having errors with ?roxygen2? documentation. ?roxygen2? generated NAMESPACE added `@.newclass` as a newly exported function, not as a S3method.
At first I thought this must be a bug in roxygen2 and they lag behind the new developments in R. But after some investigation I found that ?roxygen2? is using tools:::.get_internal_S3_generis()
2012 Feb 13
1
Overwrite S3 methond from base package
Dear all,
I am developing a package, which bundles my most frequently used
functions. One of those is a modified version of droplevels from the
base package (basically, it preserves any contrast function which was
used to create the factor, contrast matrices are not kept, for they
could be wrong if a level is dropped).
In my NAMESPACE file I've the following directives, which should export