I have had similar notes, but in cases where the dataset was created
internally by a function:
* checking R code for possible problems ... NOTE
vm_diagnostics: no visible binding for global variable 'Median'
vm_diagnostics: no visible binding for global variable 'Index'
vm_diagnostics: no visible binding for global variable 'LL'
vm_diagnostics: no visible binding for global variable 'UL'
and the relevant code is here (the function creates a dataset called
'sigma' and always names the variables Index, Median, LL, UL):
p.sigma <- ggplot(sigma, aes(Index, Median, ymin = LL, ymax = UL)) +
geom_pointrange() +
labs(y = "Median + 95% CI for Sigma") +
theme_classic()
is the appropriate way to remove warnings in this case also to have the
function attach the data it internally created?
On Wed, Aug 27, 2014 at 8:09 PM, peter dalgaard <pda...@gmail.com> wrote:
> The change would seem to be this
>
> \item \command{R CMD check} now by default checks code usage
> directly on the package namespace without loading and attaching
> the package and its suggests and enhances.
>
> and perhaps the remedies could be stated more clearly?
>
> Putting the data objects in the namespace would seem the obvious thing to
> do.
>
> One oddity is that they are sort of in there already:
>
> > Lahman::battingLabels
> variable label
> 1 playerID Player ID code
> 2 yearID Year
> 3 stint Player's stint
> 4 teamID Team
> 5 lgID League
> 6 G Games
> 7 G_batting Games as batter
> 8 AB At Bats
> 9 R Runs
> 10 H Hits
> 11 X2B Doubles
> 12 X3B Triples
> 13 HR Homeruns
> 14 RBI Runs Batted In
> 15 SB Stolen Bases
> 16 CS Caught Stealing
> 17 BB Base on Balls
> 18 SO Strikeouts
> 19 IBB Intentional walks
> 20 HBP Hit by pitch
> 21 SH Sacrifice hits
> 22 SF Sacrifice flies
> 23 GIDP Grounded into double plays
> 24 G_Old Old version of games (deprecated)
>
> But then again, actually not:
>
> > Lahman::Label()
> Error in rbind(battingLabels, pitchingLabels, fieldingLabels) :
> object 'battingLabels' not found
>
> This is documented (:: can access datasets made available by
> lazy-loading), but it sort of suggests that we might want to improve
> consistency in this area.
>
> -pd
>
>
> On 27 Aug 2014, at 11:24 , Martin Maechler <maech...@stat.math.ethz.ch>
> wrote:
>
> >>>>>> Michael Friendly <frien...@yorku.ca>
> >>>>>> on Tue, 26 Aug 2014 17:58:34 -0400 writes:
> >
> >> I'm updating the Lahman package of baseball statistics to the 2013
> >> release. In addition to
> >> the main data sets, the package also contains several convenience
> >> functions that make use
> >> of these data sets. These now trigger the notes below from R CMD check
> >> run with
> >> Win builder, R-devel. How can I avoid these?
> >
> >> * using R Under development (unstable) (2014-08-25 r66471)
> >> * using platform: x86_64-w64-mingw32 (64-bit)
> >> ...
> >> * checking R code for possible problems ... NOTE
> >> Label: no visible binding for global variable 'battingLabels'
> >> Label: no visible binding for global variable 'pitchingLabels'
> >> Label: no visible binding for global variable 'fieldingLabels'
> >> battingStats: no visible binding for global variable 'Batting'
> >> battingStats: no visible global function definition for 'mutate'
> >> playerInfo: no visible binding for global variable 'Master'
> >> teamInfo: no visible binding for global variable 'Teams'
> >
> >> One such function:
> >
> >> ## function for accessing variable labels
> >
> >> Label <- function(var, labels=rbind(battingLabels, pitchingLabels,
> >> fieldingLabels)) {
> >> wanted <- which(labels[,1]==var)
> >> if (length(wanted)) labels[wanted[1],2] else var
> >> }
> >
> > and you are using the data sets you mentioned before,
> > (and the checking has been changed recently here).
> >
> > This is a bit subtle:
> > Your data sets are part of your package (thanks to the default
> > lazyData), but *not* part of the namespace of your package.
> > Now, the reasoning goes as following: if someone uses a function
> > from your package, say Label() above,
> > by
> > Lahman::Label(..)
> > and your package has not been attached to the search path,
> > your user will get an error, as the datasets are not found by
> > Label().
> >
> > If you consider something like Lahman::Label(..)
> > for a bit and the emphasis we put on R functions being the
> > primary entities, you can understand the current, i.e. new,
> > R CMD check warnings.
> >
> > I see the following two options for you:
> >
> > 1) export all these data sets from your NAMESPACE
> > For this (I thinK), you must define them in Lahman/R/ possibly via a
> > Lahman/R/sysdata.rda
> >
> > 2) rewrite your functions such that ensure the data sets are
> > loaded when they are used.
> >
> >
> > "2)" actually works by adding
> > stopifnot(require(Lahman, quietly=TRUE))
> > as first line in Label() and other such functions.
> >
> > It works in the sense that Lahman::Label("yearID") will
> > work even when Lahman is not in the search path,
> > but R-devel CMD check will still give the same NOTE,
> > though you can argue that that note is actally a "false positive".
> >
> > Not sure about another elegant way to make "2)" work, apart from
> > using data() on each of the datasets inside the
> > function. As I haven't tried it, that may *still* give a
> > (false) NOTE..
> >
> > This is a somewhat interesting problem, and I wonder if everyone
> > else has solved it with '1)' rather than a version of '2)'.
> >
> > Martin
> >
> > ______________________________________________
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd....@cbs.dk Priv: pda...@gmail.com
>
> ______________________________________________
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
--
Joshua F. Wiley
Ph.D. Student, UCLA Department of Psychology
http://joshuawiley.com/
Senior Analyst, Elkhart Group Ltd.
http://elkhartgroup.com
Office: 260.673.5518
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