[R-pkg-devel] NOTE regarding dependencies in R code: Missing or unexported object
Rune Haubo
rune.haubo at gmail.com
Sat Apr 21 16:27:43 CEST 2018
I don't think 'summary' is actually exported by lmerTest (version >= 3.0-0):
library(lmerTest)
fm <- lmer(Informed.liking ~ Gender + Information * Product + (1 | Consumer) +
(1 | Consumer:Product), data=ham)
lmerTest::summary(fm) # gives: Error: 'summary' is not an exported
object from 'namespace:lmerTest'
On the other hand
summary(fm)
works just fine. lmerTest defines the S3 method 'summary' for
'lmerModLmerTest' objects, so if you change sx <-
lmerTest::summary(x) to sx <- summary(x) you should be fine assuming
that x is of class 'lmerModLmerTest'.
For more details see
https://stat.ethz.ch/pipermail/r-sig-mixed-models/2018q1/026596.html
and perhaps https://github.com/runehaubo/lmerTestR/blob/master/pkg_notes/new_lmerTest.pdf
(which you were also pointed to previously).
Best regards
Rune
On 20 April 2018 at 21:53, David Hervás via R-package-devel
<r-package-devel at r-project.org> wrote:
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> ---------- Forwarded message ----------
> From: "David Hervás" <ddhervas at yahoo.es>
> To: "r-package-devel at r-project.org" <r-package-devel at r-project.org>
> Cc:
> Bcc:
> Date: Fri, 20 Apr 2018 19:53:50 +0000 (UTC)
> Subject: NOTE regarding dependencies in R code: Missing or unexported object
> 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"
This seems to be from an older version of lmerTest.
>
>
> 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.
Have you checked that you are using a recent version of lmerTest with
3.4.4 and 3.5 RC? I think that might explain the diff.
> What should I do to fix this?
> [[alternative HTML version deleted]]
>
>
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