The BiocGenerics package was designed to solve this issue within
Bioconductor. It wouldn't be the worst thing in the world to depend on the
simple BiocGenerics package for now, but ideally the base generics would be
defined higher up, perhaps in the methods package itself. Maybe someone
else has a
Perhaps a patch to R such that generics don't clobber each-other's method
tables if the signatures agree? I haven't dug deeply, but simply merging
the method tables seems like it would be safe when there are no conflicts.
That way this type of multiplicity would not be a problem, though it
That might be worth thinking about generally, but it would still be nice to
have the base generics pre-defined, so that people are not copy and pasting
the definitions everywhere, hoping that they stay consistent.
On Wed, Mar 26, 2014 at 6:13 AM, Gabriel Becker gmbec...@ucdavis.eduwrote:
Hi I am the maintainer of oneChannelGUI,
I am very sorry to be in dealy to have a package version without
warnings, but to correct warning I added some stupid errors in the
version 1.29.8. On the 25th night, Seattle time, I fixed them in version
1.29.10 but it seems that this version was not
Dear list
It is possible to store expected output for tests and examples. From the
manual: If tests has a subdirectory Examples containing a file
pkg-Ex.Rout.save, this is compared to the output file for running the
examples when the latter are checked. And, earlier (written in the
context
[cross-posted to R-devel and bioc-devel]
Hi,
I am trying to implement a 'sort' method in one of the CRAN packages I
am maintaining ('apcluster'). I started with using setMethod(sort,
...) in my package, which worked fine. Since many users of my package
are from the bioinformatics field, I
The BiocGenerics package was designed to solve this issue within
Bioconductor. It wouldn't be the worst thing in the world to depend on the
simple BiocGenerics package for now, but ideally the base generics would be
defined higher up, perhaps in the methods package itself. Maybe someone
else has a
Perhaps a patch to R such that generics don't clobber each-other's method
tables if the signatures agree? I haven't dug deeply, but simply merging
the method tables seems like it would be safe when there are no conflicts.
That way this type of multiplicity would not be a problem, though it
That might be worth thinking about generally, but it would still be nice to
have the base generics pre-defined, so that people are not copy and pasting
the definitions everywhere, hoping that they stay consistent.
On Wed, Mar 26, 2014 at 6:13 AM, Gabriel Becker gmbec...@ucdavis.eduwrote:
On 26/03/2014, 9:13 AM, Gabriel Becker wrote:
Perhaps a patch to R such that generics don't clobber each-other's method
tables if the signatures agree? I haven't dug deeply, but simply merging
the method tables seems like it would be safe when there are no conflicts.
That way this type of
First of all, thanks for the very interesting and encouraging replies
that have been posted so far!
Let me quickly add what I have tried up to now:
- setMethod(sort, signature(ExClust), function(x, decreasing=FALSE,
%...%) %...% , sealed=TRUE) without any call to setGeneric(), i.e.
assuming
On Thu, 20 Mar 2014, Dirk Eddelbuettel wrote:
o Roger correctly notes that R scripts and packages are just one issue.
Compilers, libraries and the OS matter. To me, the natural approach these
days would be to think of something based on Docker or Vagrant or (if you
must, VirtualBox). The
Hello,
I’d like to compare two strings internally the way R would, so I need Scollate
which is not part of the authorized R api.
So:
- Can Scollate (and perhaps Seql) be promoted to api ?
- If not what are the alternatives ? Using strcmp or stroll does not seem as
general as Scollate.
I haven't looked at this in detail, but my guess is the following is the
distinction:
A simple call setGeneric(sort) makes a generic of the existing
function _with the existing package_:
setGeneric(sort)
[1] sort
sort
standardGeneric for sort defined from package base
function (x,
On 26 March 2014 at 17:22, Romain François wrote:
| I’d like to compare two strings internally the way R would, so I need
Scollate which is not part of the authorized R api.
|
| So:
| - Can Scollate (and perhaps Seql) be promoted to api ?
| - If not what are the alternatives ? Using strcmp
On Wed, Mar 26, 2014 at 9:50 AM, Dirk Eddelbuettel e...@debian.org wrote:
On 26 March 2014 at 17:22, Romain François wrote:
| I'd like to compare two strings internally the way R would, so I need
Scollate which is not part of the authorized R api.
|
| So:
| - Can Scollate (and perhaps
From: Richard Cotton richiero...@gmail.com
The rep function is very versatile, but that versatility comes at a
cost: it takes a bit of effort to learn (and remember) its syntax.
This is a problem, since rep is one of the first functions many
beginners will come across. Of the three main
Hi,
I agree. I can't think of an easy way to avoid this kind of clashes
between BioC and non-BioC S4 generics, other than by having things
like sort() already defined as an S4 generic in base R.
Note that, just having setMethod(sort, ...) in your package Ulrich,
and not putting a setGeneric()
Le 26 mars 2014 à 18:03, Gabriel Becker gmbec...@ucdavis.edu a écrit :
On Wed, Mar 26, 2014 at 9:50 AM, Dirk Eddelbuettel e...@debian.org wrote:
On 26 March 2014 at 17:22, Romain François wrote:
| Id like to compare two strings internally the way R would, so I need
Scollate which is not
On 26 Mar 2014, at 18:24 , Radford Neal radf...@cs.toronto.edu wrote:
From: Richard Cotton richiero...@gmail.com
The rep function is very versatile, but that versatility comes at a
cost: it takes a bit of effort to learn (and remember) its syntax.
This is a problem, since rep is one of the
On 26/03/2014 22:00, peter dalgaard wrote:
On 26 Mar 2014, at 18:24 , Radford Neal radf...@cs.toronto.edu wrote:
From: Richard Cotton richiero...@gmail.com
The rep function is very versatile, but that versatility comes at a
cost: it takes a bit of effort to learn (and remember) its syntax.
Hi,
On 03/26/2014 10:24 AM, Radford Neal wrote:
From: Richard Cotton richiero...@gmail.com
The rep function is very versatile, but that versatility comes at a
cost: it takes a bit of effort to learn (and remember) its syntax.
This is a problem, since rep is one of the first functions many
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