[R-pkg-devel] NOTE regarding dependencies in R code: Missing or unexported object

Sat, Apr 21, 2018 7:44 AM

On 20/04/2018 3:53 PM, David Herv?s via R-package-devel wrote:

Hi,
I have sent my package "clickR" to CRAN and was asked to fix the following NOTE:
* checking dependencies in R code ... NOTE
Missing or unexported object: 'lmerTest::summary'
I'm not sure what's going on, here is the Imports section of my DESCRIPTION file:
Imports: beeswarm, boot, lme4, lmerTest, methods, ReporteRs, xtable



Here are the first lines of the function causing this NOTE:
report.merModLmerTest<-function(x, file=NULL, type="word", digits=3, digitspvals=3,? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? font=ifelse(Sys.info()["sysname"] == "Windows", "Arial",? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? "Helvetica")[[1]], pointsize=11, info=TRUE, ...){? sx <- lmerTest::summary(x)? cor <- as.data.frame(lme4::VarCorr(x))? ...

And here is the output from?getNamespaceExports("lmerTest")?where "summary" is listed at position [23]

  [1] "lmer"? ? ? ? ? ? ? ? ? ?"lsmeansLT"? ? ? ? ? ? ? ".__T__is.infinite:base"?[4] ".__T__as.integer:base"? ".__T__as.numeric:base"? ".__T__%*%:base"? ? ? ???[7] ".__T__dim:base"? ? ? ? ?".__T__summary:base"? ? ?".__T__$<-:base"? ? ? ??[10] ".__T__^:base"? ? ? ? ? ?".__T__sum:base"? ? ? ? ?".__T__rep:base"? ? ? ??[13] ".__T__*:base"? ? ? ? ? ?".__T__[<-:base"? ? ? ? ?".__T__as.logical:base"?[16] ".__T__dimnames:base"? ? ".__T__%/%:base"? ? ? ? ?".__T__prod:base"? ? ? ?[19] ".__T__[[<-:base"? ? ? ? ".__T__/:base"? ? ? ? ? ?"step"? ? ? ? ? ? ? ? ??[22] "calcSatterth"? ? ? ? ? ?"summary"? ? ? ? ? ? ? ? ".__T__anova:stats"? ? ?[25] ".__T__is.finite:base"? ?".__T__anyNA:base"? ? ? ?".__T__!:base"? ? ? ? ??[28] ".__T__all:base"? ? ? ? ?".__T__+:base"? ? ? ? ? ?".__T__any:base"? ? ? ??[31] ".__T__dim<-:base"? ? ? ?".__T__-:base"? ? ? ? ? ?".__T__[:base"? ? ? ? ??[34] "anova"? ? ? ? ? ? ? ? ? "difflsmeans"? ? ? ? ? ? "lsmeans"? ? ? ? ? ? ? ?[37] "rand"? ? ? ? ? ? ? ? ? ?".__C__merModLmerTest"? ?".__T__length:base"? ? ?[40] ".__T__is.na:base"? ? ? ?".__T__dimnames<-:base"? ".__T__&:base"? ? ? ? ??[43] ".__T__%%:base"? ? ? ? ? ".__T__$:base"


I have tried to reproduce this problem in my computer with different versions of R (3.4.4, 3.5 RC and R-devel) and only get the NOTE when performing the check with R-devel.
What should I do to fix this?

getNamespaceExports() is described on its help page as an internal 
function, not intended for users.  If you want to see the exports of a 
package, look at its NAMESPACE file.  For example,

file.show(system.file("NAMESPACE", package="lmerTest"))

which lists these lines as exports:

export(as_lmerModLmerTest)
export(calcSatterth)
export(contest)
export(contest1D)
export(contestMD)
export(difflsmeans)
export(get_model)
export(lmer)
export(ls_means)
export(lsmeansLT)
export(ranova)
export(show_tests)
export(step)

The summary() function isn't listed there, as Rune demonstrated.

Duncan Murdoch