[R-pkg-devel] Warning: rBind is deprecated-- but I don't call it

[Thierry Onkelinx]

Dear Bill,

The best way to fix your problem is IMHO to have it fixed in lme4. I've
cc'ed Ben Bolker (lme4 maintainer) to inform him of this problem.

Best regards,


ir. Thierry Onkelinx
Statisticus / Statistician

Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkelinx at inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

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2018-03-21 21:12 GMT+01:00 William Revelle <lists at revelle.net>:

> Thanks. I had suspected another package, but couldn’t figure out how to
> show that.
>
> debug(Matrix::rBind)  shows that the problem is in lme4
> #with
>  debug(Matrix::rBind)
>
> x.df <- structure(list(values = c(9, 6, 8, 7, 10, 6, 2, 1, 4, 1, 5, 2,
> 5, 3, 6, 2, 6, 4, 8, 2, 8, 6, 9, 7), items = structure(c(1L,
> 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L,
> 3L, 4L, 4L, 4L, 4L, 4L, 4L), class = "factor", .Label = c("J1",
> "J2", "J3", "J4")), id = structure(c(1L, 2L, 3L, 4L, 5L, 6L,
> 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L,
> 5L, 6L), .Label = c("S1", "S2", "S3", "S4", "S5", "S6"), class =
> "factor")), row.names = c(NA,
> -24L), class = "data.frame")
>
> mod.lmer <- lme4::lmer(values ~ 1 + (1 | id) + +(1 | items),
>     data = x.df, na.action = na.omit)
>
> #it calls rBind and then throws the warning which win.builder then calls
> and error.
>
> Now, I will work on how to get around this (not use lmer?)  but at least
> now I know the problem.
>
> Bill
>
>
>
>
> > On Mar 21, 2018, at 2:04 PM, Joris Meys <jorismeys at gmail.com> wrote:
> >
> > I suspect it is used in a function from another package then. The
> devtools function run_examples() allows you to run the examples separately
> so you can find the culprit easier. Function check_failures() extracts info
> from the check logs. Could be helpful too.
> >
> > Cheers
> > Joris
> >
> > On Wed, 21 Mar 2018, 19:49 Alexandre Courtiol, <
> alexandre.courtiol at gmail.com> wrote:
> > Hi William,
> > Perhaps you use rBind indirectly...
> > I don't know the best way to check that, but I would try to set a
> > debug(rBind) before running some of your code in an interactive session.
> > If any function uses rBind, you should notice as it will launch the
> > debugger.
> > Better ideas are welcome.
> > ++
> >
> > Alex
> >
> > On 21 March 2018 at 19:36, William Revelle <lists at revelle.net> wrote:
> >
> > > Dear friends,
> > >
> > > When testing my latest version of psych on win.builder, I keep getting
> the
> > > following Warning:
> > >
> > > * checking installed files from 'inst/doc' ... OK
> > > * checking files in 'vignettes' ... OK
> > > * checking examples ...
> > > ** running examples for arch 'i386' ... [32s] WARNING
> > > Found the following significant warnings:
> > >
> > >   Warning: 'rBind' is deprecated.
> > > Deprecated functions may be defunct as soon as of the next release of
> > > R.
> > > See ?Deprecated.
> > > ** running examples for arch 'x64' ... [39s] WARNING
> > > Found the following significant warnings:
> > >
> > >   Warning: 'rBind' is deprecated.
> > > Deprecated functions may be defunct as soon as of the next release of
> > > R.
> > > See ?Deprecated.
> > > * checking for unstated dependencies in vignettes ... OK
> > >
> > > I know that rBind is deprecated, but I don’t call it.
> > >
> > >
> > > I have searched my code and as far as I can tell, I do not use rBind
> (nor
> > > cBind).   Nor do any of my examples.
> > >
> > > Any help would be appreciated.
> > >
> > > Thanks.
> > >
> > > Bill
> > >
> > >
> > > William Revelle            personality-project.org/revelle.html
> > > Professor                                 personality-project.org
> > > Department of Psychology www.wcas.northwestern.edu/psych/
> > > Northwestern University    www.northwestern.edu/
> > > Use R for psychology         personality-project.org/r
> > > It is 2   minutes to midnight   www.thebulletin.org
> > >
> > > ______________________________________________
> > > R-package-devel at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> > >
> >
> >
> >
> > --
> > Alexandre Courtiol
> >
> > http://sites.google.com/site/alexandrecourtiol/home
> >
> > *"Science is the belief in the ignorance of experts"*, R. Feynman
> >
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-package-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
> William Revelle            personality-project.org/revelle.html
> Professor                                 personality-project.org
> Department of Psychology www.wcas.northwestern.edu/psych/
> Northwestern University    www.northwestern.edu/
> Use R for psychology         personality-project.org/r
> It is 2 1/2  minutes to midnight   www.thebulletin.org
>
> ______________________________________________
> R-package-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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