[R] spurious locking of packages

[Jan Galkowski]

I have been having a problem installing binary packages on Windows, since 3.6.x hit the streets.


I am using the
> 
> INSTALL_opts = c('--no-lock')
> 
option, but it occurs nevertheless. My habit is to install an update of R (latest, 3.6.2), then run update.packages(.):

> 
> trying URL 'https://cran.cnr.berkeley.edu/bin/windows/contrib/3.6/zoib_1.5.4.zip'
> Content type 'application/zip' length 350788 bytes (342 KB)
> downloaded 342 KB
> 
> package ‘elasticnet’ successfully unpacked and MD5 sums checked
> package ‘ellipse’ successfully unpacked and MD5 sums checked
> package ‘elliptic’ successfully unpacked and MD5 sums checked
> package ‘EMCluster’ successfully unpacked and MD5 sums checked
> package ‘EMD’ successfully unpacked and MD5 sums checked
> Warning: cannot remove prior installation of package ‘EMD’
> Warning in file.copy(savedcopy, lib, recursive = TRUE) :
>  problem copying C:\Program Files\R\R-2.13.1\library\00LOCK\EMD\libs\x64\EMD.dll to C:\Program Files\R\R-2.13.1\library\EMD\libs\x64\EMD.dll: Permission denied
> Warning: restored ‘EMD’
> package ‘emdbook’ successfully unpacked and MD5 sums checked
> package ‘emdist’ successfully unpacked and MD5 sums checked
> package ‘emmeans’ successfully unpacked and MD5 sums checked
> package ‘emoa’ successfully unpacked and MD5 sums checked
> Error in unpackPkgZip(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib, libs_only, :
>  ERROR: failed to lock directory ‘C:\Program Files\R\R-2.13.1\library’ for modifying
> Try removing ‘C:\Program Files\R\R-2.13.1\library/00LOCK’
> >
> 


Note the above is preceded by a long list of packages which are, in each case, re-loaded from whatever repo at a mirror being used.

I have found the p_unlock() from package pacman useful. After assigning global variable P to the results of available.packages(), I repeatedly do:
> 
> > p_unlock()
> The following 00LOCK has been deleted:
> C:/Program Files/R/R-2.13.1/library/00LOCK
> > match(c("emoa"), P)
> [1] 13
> > P<- P[13:length(P)]
> > update.packages(method=NULL, ask=FALSE, checkBuilt=TRUE, type="win.binary", instPkgs=P,
> + dependencies=c("Imports", "Depends", "Suggests"), INSTALL_opts=c("--no-lock"))
> 

where *emoa* is a stand-in for whatever package faulted during the load. (I also have no idea why *EMD* is locked in the above.)

My *sessionInfo()* is:

> > sessionInfo()
> R version 3.6.2 (2019-12-12)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 7 x64 (build 7601) Service Pack 1
> 
> Matrix products: default
> 
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C 
> [5] LC_TIME=English_United States.1252 
> 
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base 
> 
> loaded via a namespace (and not attached):
> [1] compiler_3.6.2
> >
> 

Eventually, I get to the end of P and call it done.

Anyone have a suggestion for an easier workaround?

 - Jan Galkowski


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