Dear Martin, dear package developers,
I had a very similar case three days ago in one of our packages. Our aim
was to provide an S3 method matplot.deSolve and an alternative and more
specific non-S3 function matplot.1D because the .1D follows the naming
scheme of other related functions.
The
This is a topic ' apparent S3 methods note in R CMD check '
from R-package-devel
https://stat.ethz.ch/pipermail/r-package-devel/2015q2/000126.html
which is relevant to here because some of us have been thinking
about extending R because of the issue.
John Fox, maintainer of the 'effects'
On 12/06/2015 7:16 AM, Kurt Hornik wrote:
Duncan Murdoch writes:
On 12/06/2015 4:12 AM, Martin Maechler wrote:
This is a topic ' apparent S3 methods note in R CMD check '
from R-package-devel
https://stat.ethz.ch/pipermail/r-package-devel/2015q2/000126.html
which is relevant to here
On 12/06/2015 6:41 AM, John Fox wrote:
And my non-cross-posted cross-posting:
Dear Martin,
Thank you for addressing this issue. Introducing a nonS3method() directive in
NAMESPACE seems a reasonable solution. It could replace export() for
functions with .s in their names.
I think these
And my non-cross-posted cross-posting:
Dear Martin,
Thank you for addressing this issue. Introducing a nonS3method() directive in
NAMESPACE seems a reasonable solution. It could replace export() for functions
with .s in their names.
Best,
John
On Fri, 12 Jun 2015 10:12:07 +0200
Martin
On 12/06/2015 4:12 AM, Martin Maechler wrote:
This is a topic ' apparent S3 methods note in R CMD check '
from R-package-devel
https://stat.ethz.ch/pipermail/r-package-devel/2015q2/000126.html
which is relevant to here because some of us have been thinking
about extending R because
Duncan Murdoch writes:
On 12/06/2015 4:12 AM, Martin Maechler wrote:
This is a topic ' apparent S3 methods note in R CMD check '
from R-package-devel
https://stat.ethz.ch/pipermail/r-package-devel/2015q2/000126.html
which is relevant to here because some of us have been thinking
about
Duncan Murdoch writes:
On 12/06/2015 7:16 AM, Kurt Hornik wrote:
Duncan Murdoch writes:
On 12/06/2015 4:12 AM, Martin Maechler wrote:
This is a topic ' apparent S3 methods note in R CMD check '
from R-package-devel
https://stat.ethz.ch/pipermail/r-package-devel/2015q2/000126.html
On Jun 12, 2015, at 1:24 AM, Mick Jordan mick.jor...@oracle.com wrote:
Is the mechanism by which packages are tested on CRAN described
anywhere? Is it by any chance written in R? The FastR
https://bitbucket.org/allr/fastr/wiki/Home team is interested in
running a virtual CRAN where we
In addition to what has been said already, you should check C code for
-pedantic compiler warnings (in particular GNU extensions) and verify
that the package builds with parallel make (e.g. MAKE=make -j8).
On Fri, Jun 12, 2015 at 7:24 AM, Mick Jordan mick.jor...@oracle.com wrote:
Is the
Dear list members,
Use of platform-specific code to open new plot devices (e.g., `quartz`,
`x11`) is discouraged in favour of using `dev.new`; however, this does not
work in RStudio. A purported solution introduced in R 3.1.1 was to call
`dev.new(noRStudioGD = TRUE)`, which works on Windows, but
Analogously to how S4 methods are declared in the code, cf.
methods::setMethod(), I'd find it more natural to also declare S3
methods in the code and note in the NAMESPACE. For example:
# S3 method summary() for class 'aov':
summary.aov - function(x, ...) {
# something
}
S3class(summary.aov)
Some (unofficial) tips.
Some of the hardware and software they use is listed here:
http://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-debian-clang
You can get the current R-release and R-oldrel versions from here:
http://rversions.r-pkg.org/r-release
Awesome!
Here's the code in case others want to add the shields to their github
readme files. https://gist.github.com/lcolladotor/de2e0b67fbf33518b922
derfinder example (software package)
https://github.com/lcolladotor/derfinder
derfinderData example (experiment data package)
- Original Message -
From: Leonardo Collado Torres lcoll...@jhu.edu
To: Dan Tenenbaum dtene...@fredhutch.org
Cc: bioc-devel@r-project.org
Sent: Friday, June 12, 2015 11:43:09 AM
Subject: Re: [Bioc-devel] Use and Usability metrics / shields
Awesome!
Here's the code in case
Ahh, I missed the 2 versions on the platforms shield. I am using
both build shields. I'll make some edits then.
On Fri, Jun 12, 2015 at 2:49 PM, Dan Tenenbaum dtene...@fredhutch.org wrote:
- Original Message -
From: Leonardo Collado Torres lcoll...@jhu.edu
To: Dan Tenenbaum
Actually, between this and other things coming from 'R CMD check' these
days,
I disagree that this is reasonable at all - it's a hack at best that only
fixes
this particular issue. Better would be to introduce lint-like directives
that
turn off certain R CMD check notes/warnings at different
If Martin's proposal for declaring non-S3 methods in NAMESPACE is
feasible, it would be very helpful. The packages we support have
multiple examples of unfortunately named functions non-S3 functions, so
creating a route for migrating them into compliance would be great.
best,
-skye
On
To me, it seems like there's actually two problems here:
1) Preventing all() from dispatching to all.effects() for objects of
class effects
2) Eliminating the NOTE in R CMD check
My impression is that 1) actually causes few problems, particularly
since people are mostly now aware of the problem
Hadley Wickham h.wick...@gmail.com
on Fri, 12 Jun 2015 09:53:20 -0500 writes:
To me, it seems like there's actually two problems here:
1) Preventing all() from dispatching to all.effects() for objects of
class effects
2) Eliminating the NOTE in R CMD check
Sure. ...
On 12/06/2015 10:53 AM, Hadley Wickham wrote:
To me, it seems like there's actually two problems here:
1) Preventing all() from dispatching to all.effects() for objects of
class effects
2) Eliminating the NOTE in R CMD check
My impression is that 1) actually causes few problems,
The notes available off the devloper page
https://developer.r-project.org/ describe some of the rationale for
the S3 method search design. One thing that has changed since then is
that all packages now have name spaces. We could change the search
algorithm to skip attached package exports (and
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