From m@ttjdow|e @end|ng |rom gm@||@com  Tue Feb 19 00:26:02 2019
From: m@ttjdow|e @end|ng |rom gm@||@com (Matt Dowle)
Date: Mon, 18 Feb 2019 15:26:02 -0800
Subject: [Rd] Error in rbind(info, getNamespaceInfo(env, "S3methods"))
In-Reply-To: <4bc49f19-5fd4-d515-03eb-28954ac5ee55@gmail.com>
References: <CAOuOy3dRhE47j_W71qDeCc+sKruj2DC0-2AGD1Wyd_t0Bsr8Dg@mail.gmail.com>
 <4bc49f19-5fd4-d515-03eb-28954ac5ee55@gmail.com>
Message-ID: <CAOuOy3eMD3XsRecBpetP1RpBe+oxvepVq1XbX3Zg5VnZ049FsA@mail.gmail.com>

Thanks, Duncan.
I took the approach you suggested and eventually found it was due to
R.matlab (staRdom imports R.matlab).

> require(R.matlab)
Loading required package: R.matlab
Error: package or namespace load failed for ?R.matlab? in rbind(info,
getNamespaceInfo(env, "S3methods")):
 number of columns of matrices must match (see arg 2)
Warning message:
package ?R.matlab? was built under R version 3.6.0
> R.version.string
[1] "R version 3.5.2 (2018-12-20)"

At some point in the past I guess I used R-devel with this library and it
installed R.matlab using R-devel.

Reinstalling R.matlab did the trick and staRdom works fine now.
I checked that none of the other 2,643 packages in this library were built
using R>3.5.2.  It was just R.matlab.

Thanks for your help!
Best, Matt

On Mon, Feb 18, 2019 at 1:28 PM Duncan Murdoch <murdoch.duncan at gmail.com>
wrote:

> On 18/02/2019 4:08 p.m., Matt Dowle wrote:
> > Dear all,
> >
> > I'm experiencing an unusual installation error for one package. Could
> > anyone suggest how I can best investigate this from here please?  I'm
> sorry
> > this isn't very much to go on. Hopefully someone can point me in the
> right
> > direction.
>
> When packages are installed, a hidden environment is created called
> ".__NAMESPACE__.".  It contains a number of objects; it looks as though
> one of yours called "S3methods" is corrupted.  I can't guess whether it
> is one coming from staRdom or one already in your library, but it
> appears yours doesn't have the usual number of columns (which I think is
> 3).
>
> So you could get a list of all packages in your library, and run
>
> sapply(allpackages, function(x)
> ncol(asNamespace(x)$.__NAMESPACE__.$S3methods))
>
> to see which of them don't return 3 as the number of columns.  (This
> will load all of them, so might need to be broken up into batches.)
>
> Duncan Murdoch
>
> >
> > The problem seems to be my library.  It is large (3,418 packages) and I'd
> > like to avoid rebuilding it, if possible.  All packages are up to date
> > according to update.packages().
> >
> > The error is :
> > ** byte-compile and prepare package for lazy loading
> > Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
> >    number of columns of matrices must match (see arg 2)
> > ERROR: lazy loading failed for package ?staRdom?
> > * removing ?/home/mdowle/build/revdeplib/staRdom?
> >
> > This package (staRdom) has had a recent update but CRAN checks page is
> > showing OK, mostly:
> > https://cran.r-project.org/web/checks/check_results_staRdom.html.   The
> two
> > errors there don't seem to be related.
> >
> > The package installs no problem when I don't include my revdeplib.  But
> > when I do include my revdeplib it fails with the error above.
> >
> > I can reproduce as follows :
> >
> > $ export R_LIBS=~/build/revdeplib/
> > $ R
> >> .libPaths()
> > [1] "/home/mdowle/build/revdeplib" "/usr/lib/R/library"
> >> install.packages("staRdom")
> > Installing package into ?/home/mdowle/build/revdeplib?
> > (as ?lib? is unspecified)
> > trying URL 'http://cloud.r-project.org/src/contrib/staRdom_1.0.12.tar.gz
> '
> > Content type 'application/x-gzip' length 2669832 bytes (2.5 MB)
> > ==================================================
> > downloaded 2.5 MB
> > * installing *source* package ?staRdom? ...
> > ** package ?staRdom? successfully unpacked and MD5 sums checked
> > ** R
> > ** data
> > *** moving datasets to lazyload DB
> > ** inst
> > ** byte-compile and prepare package for lazy loading
> > Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
> >    number of columns of matrices must match (see arg 2)
> > ERROR: lazy loading failed for package ?staRdom?
> > * removing ?/home/mdowle/build/revdeplib/staRdom?
> > The downloaded source packages are in
> >          ?/tmp/RtmprvTDCg/downloaded_packages?
> > Warning message:
> > In install.packages("staRdom") :
> >    installation of package ?staRdom? had non-zero exit status
> >>
> >> sessionInfo()
> > R version 3.5.2 (2018-12-20)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > Running under: Ubuntu 18.04.2 LTS
> >
> > Matrix products: default
> > BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
> > LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
> >
> > locale:
> >   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >   LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >   LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> > LC_PAPER=en_US.UTF-8
> >   [8] LC_NAME=C                  LC_ADDRESS=C
>  LC_TELEPHONE=C
> >             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > loaded via a namespace (and not attached):
> > [1] compiler_3.5.2 tools_3.5.2
> >>
> >
> >
> > If I don't include my revdeplib library,  it works fine :
> >
> > $ R
> >> .libPaths()
> > [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
> >   "/usr/lib/R/library"
> >> install.packages("staRdom")
> > Installing package into ?/usr/local/lib/R/site-library?
> > (as ?lib? is unspecified)
> > trying URL 'http://cloud.r-project.org/src/contrib/staRdom_1.0.12.tar.gz
> '
> > Content type 'application/x-gzip' length 2669832 bytes (2.5 MB)
> > ==================================================
> > downloaded 2.5 MB
> >
> > * installing *source* package ?staRdom? ...
> > ** package ?staRdom? successfully unpacked and MD5 sums checked
> > ** R
> > ** data
> > *** moving datasets to lazyload DB
> > ** inst
> > ** byte-compile and prepare package for lazy loading
> > ** help
> > *** installing help indices
> > ** building package indices
> > ** installing vignettes
> > ** testing if installed package can be loaded
> > * DONE (staRdom)
> >
> > The downloaded source packages are in
> >          ?/tmp/RtmpmSiZLa/downloaded_packages?
> >>
> >> sessionInfo()
> > R version 3.5.2 (2018-12-20)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> > Running under: Ubuntu 18.04.2 LTS
> >
> > Matrix products: default
> > BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
> > LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
> >
> > locale:
> >   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >   LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >   LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> > LC_PAPER=en_US.UTF-8
> >   [8] LC_NAME=C                  LC_ADDRESS=C
>  LC_TELEPHONE=C
> >             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > loaded via a namespace (and not attached):
> > [1] compiler_3.5.2 tools_3.5.2
> >>
> >
> > I'm not sure how to debug this because both install.packages() and `R CMD
> > check` start a new instance of R. How do a get debugger() prompt at the
> > point of the error? All I can think of is inserting a browser() in my own
> > compile of R-devel. But that seems a big step. I thought I'd post here
> > first to see if anyone had any suggestions in how to proceed.
> >
> > Thanks in advance,
> > Matt
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
>

	[[alternative HTML version deleted]]



[Rd] Error in rbind(info, getNamespaceInfo(env, "S3methods"))
Matt Dowle