Re: [R-pkg-devel] Warning: rBind is deprecated

2018-03-22 Thread Martin Maechler 
>From a small thread over at the 'R-package-devel' mailing list,

this now goes to the R-devel mailing list
(CC'ing the original R-package-devel very exceptionally). 

Note that I, as maintainer("Matrix") had introduced rBind() and
cBind() to be used for Matrix package matrices as substitute for
rbind() and cbind() because back then it was not reasonably
possible to provide S4 methods for these.

But for almost three years now, they have been deprecated,
unfortunately *not* with a warning [which was a lapsus of mine].
The help page for these has started, for a long time now, as

| cBind  package:Matrix  R Documentation
| 
| Versions of 'cbind' and 'rbind' recursively built on cbind2/rbind2
| 
| Description:
| 
|  The base functions ‘cbind’ and ‘rbind’ are defined for an
|  arbitrary number of arguments and hence have the first formal
|  argument ‘...’.  For that reason, in the past S4 methods could
|  easily be defined for binding together matrices inheriting from
|  ‘Matrix’.
| 
|  For that reason, ‘cbind2’ and ‘rbind2’ have been provided for
|  binding together _two_ matrices, and we have defined methods for
|  these and the ‘'Matrix'’-matrices.
| 
|  Before R version 3.2.0 (April 2015), we have needed a substitute
|  for _S4-enabled_ versions of ‘cbind’ and ‘rbind’, and provided
|  ‘cBind’ and ‘rBind’ with identical syntax and semantic in order to
|  bind together multiple matrices (‘"matrix"’ or ‘"Matrix"’ and
|  vectors.  With R version 3.2.0 and newer, ‘cBind’ and ‘rBind’ are
|  _deprecated_ and produce a deprecation warning (via
|  ‘.Deprecated’), and your code should start using ‘cbind()’ and
|  ‘rbind()’ instead.

and finally, the next version of Matrix, which will be the
(recommended, hence bundled) Matrix package for R version 3.5.0
will produce warnings -- only once per session -- whenever
cBind() or rBind() are still used. 

This currently is true e.g., for lme4 and also for another
several dozens of CRAN packages, and unknown but probably
non-zero number of bioconductor packages.

There are even two CRAN packages which in their tests turn every
warning into an error and these packages will even fail their 'R
CMD check' in about a month when R 3.5.0 will appear.

Please package authors, do update the source of your packages:

a) replace  cBind() by cbind()  and rBind() by rbind()
b) Ensure that your package depends on at least R 3.2.0,
   i.e. possibly add a
  'Depends: R (>= 3.2.0)'
   to your DESCRIPTION file.

Of course feel free to comment / ask
privately or here {R-devel only} if necessary.

With best regards,

Martin Maechler
ETH Zurich

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

2018-03-21 Thread William Revelle 
Thierry,
Agreed.  I just filed a bug report on the gitHub site.

Bill



> On Mar 21, 2018, at 3:21 PM, Thierry Onkelinx  
> wrote:
> 
> 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.onkel...@inbo.be
> Havenlaan 88 bus 73, 1000 Brussel
> www.inbo.be
> 
> ///
> To call in the statistician after the experiment is done may be no more than 
> asking him to perform a post-mortem examination: he may be able to say what 
> the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does not 
> ensure that a reasonable answer can be extracted from a given body of data. ~ 
> John Tukey
> ///
> 
> 
> 
> 2018-03-21 21:12 GMT+01:00 William Revelle :
> 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  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, 
> >  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  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 Revellepersonality-project.org/revelle.html
> > > Professor personality-project.org
> > > Department of Psychology www.wcas.northwestern.edu/psych/
> > > Northwestern Universitywww.northwestern.edu/
> > > Use R for psychology personality-project.org/r
> > > It is 2   minutes to midnight   www.thebulletin.org
> > >
> > > __
> > > R-package-devel@r-project.org mailing list
> > >

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

2018-03-21 Thread 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.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be

///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///



2018-03-21 21:12 GMT+01:00 William Revelle :

> 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  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.court...@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  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 Revellepersonality-project.org/revelle.html
> > > Professor personality-project.org
> > > Department of Psychology www.wcas.northwestern.edu/psych/
> > > Northwestern Universitywww.northwestern.edu/
> > > Use R for psychology personality-project.org/r
> > > It is 2   minutes to midnight   www.thebulletin.org
> > >
> > > __
> > > R-package-devel@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

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

2018-03-21 Thread William Revelle 
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  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,  
> 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  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 Revellepersonality-project.org/revelle.html
> > Professor personality-project.org
> > Department of Psychology www.wcas.northwestern.edu/psych/
> > Northwestern Universitywww.northwestern.edu/
> > Use R for psychology personality-project.org/r
> > It is 2   minutes to midnight   www.thebulletin.org
> >
> > __
> > R-package-devel@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@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel

William Revellepersonality-project.org/revelle.html
Professor personality-project.org
Department of Psychology www.wcas.northwestern.edu/psych/
Northwestern Universitywww.northwestern.edu/
Use R for psychology personality-project.org/r
It is 2 1/2  minutes to midnight   www.thebulletin.org

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

2018-03-21 Thread Duncan Murdoch 

On 21/03/2018 2:48 PM, Alexandre Courtiol 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.


That's a good idea; setting options(warn=2) (so the warning becomes an 
error) might also be good. To narrow the search, look at the log file 
from the check.  Specifically, if checking package "foo", look at 
foo-Ex.Rout for the output from running all the examples (and which 
should contain the warning at an informative spot), or foo-Ex.R if you 
want all the code that was run to get that output.


Duncan Murdoch


++

Alex

On 21 March 2018 at 19:36, William Revelle  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 Revellepersonality-project.org/revelle.html
Professor personality-project.org
Department of Psychology www.wcas.northwestern.edu/psych/
Northwestern Universitywww.northwestern.edu/
Use R for psychology personality-project.org/r
It is 2   minutes to midnight   www.thebulletin.org

__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel







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