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.dun...@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@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
