[Rd] CRAN policies
spencer.graves at prodsyse.com
Thu Mar 29 16:43:02 CEST 2012
On 3/29/2012 7:07 AM, Dirk Eddelbuettel wrote:
> On 29 March 2012 at 07:58, Brian G. Peterson wrote:
> | On Thu, 2012-03-29 at 16:52 +1300, Thomas Lumley wrote:
> |> The 'No visible binding for global variable" is a good example. This
> |> found some bugs in my 'survey' package, which I removed. There is
> |> still one note of this type, which arises when I have to handle two
> |> different versions of the hexbin package with different internal
> |> structures. The note is a false positive because the use is guarded
> |> by an if(), but CMD check can't tell this. So, it's a good idea to
> |> remove all Notes that can be removed without introducing other code
> |> problems, which is nearly all of them, but occasionally there may be a
> |> good reason for code that produces a Note.
> | 'occasionally' seems like an understatement.
> | Here's an example:
> | data(cars)
> | lm(speed ~ dist,cars) #would produce global variables NOTE
> | lm("speed ~ dist",cars) # would not produce the NOTE
Another example using library(ggplot2):
=qplot(time., value, data=X, geom='line',
facets=facets, color=variable, xlim=xlim, ylim=ylim,
xlab='days', ylab='displacement (inches)', ...),
"value" and "variable" are columns of "X". If I knew how to list
this in an "overrides" file, I would do so. My experience is similar to
what others mentioned: 99 percent of the "No visible bindings" messages
I've seen are my coding errors. This one is not. I don't recall for
sure, but I think I checked trying putting "value" and "variable" in
quotes, and it didn't work.
The function that includes this call to "qplot" actually includes
the definition of a global variable "time.", which is NOT used, because
"X" has a column named "time.". The global variable "time." is a
character string, while "X$time." is class POSIXct.
I mention this, because this discussion suddenly told me how to
get rid of this NOTE: Precede this call to qplot with something like
value <- variable <- "NOTE: Define these variables to override
the NOTE impulse in R CMD check'
I haven't tried this with "qplot", but it ignores the global
variable "Time." and uses the "Time." column of "X", so it should work.
I just tried something similar with "lm", and it ignored a global
variable in favor of a column of "X". This is a silly kludge, but it's
simple and does not require a modification to "R CMD check".
> | While the change required to avoid the CRAN NOTE is small, I can't think
> | of a single example or text on using formulas that recommends quoting
> | the formula as a best practice. I'm not sure how users or package
> | authors are supposed to know that they should use a (non standard) way
> | of specifying the formula to avoid wasting their time, and the CRAN
> | volunteers time. I'm certain that there are many other examples, but
> | this one was easy to demonstrate.
> And it's close to my personal favourite of
> with( cars, ... some expression involving dist and / or speed ... )
> which gives the same warning about dist and speed being unknown globals.
> Punishment for good coding style -- gotta love it.
> Now, we all want high-quality packages.
> We all strive to have as few false positives.
> And we all understand that writing a parser if freaking hard.
> One fudge-y way of helping with this may be via an overrides file.
> This is what Debian does to suppress known / tolerated violations of what the
> 'lintian' package checker picks up on. For the R package, I have a fair
> number of these: the file for the r-base-core binary is currently 83 lines
> long and this ends on
> r-base-core: executable-not-elf-or-script usr/lib/R/bin/Rdiff
> r-base-core: image-file-in-usr-lib usr/lib/R/library/graphics/help/figures/mai.png
> r-base-core: image-file-in-usr-lib usr/lib/R/library/graphics/help/figures/oma.png
> r-base-core: image-file-in-usr-lib usr/lib/R/library/graphics/help/figures/pch.png
> r-base-core: executable-not-elf-or-script usr/lib/R/bin/Rd2pdf
> two warnings on files with 755 modes in a non-PATH location (fine, that's how
> R works) and idem with image files below /usr/lib (when the FHS probably
> prefers them below /usr/share/).
> You pipe the output of a lintian run into 'lintian-info' and you get longer
> one or two paragraph descriptions with further pointers on the violations.
> Does this sounds like something worthwhile to add to the R CMD check system ?
> Should we consider to allow overrides to make known good exceptions good away?
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