[Bioc-devel] Using BiocInstaller with R 3.4.0 beta

[Gordon K Smyth]

The problem appears to be with installed.packages(). If I start a fresh R 3.4.0beta session, then I can run installed.packages() once with correct results, but running it a second time gives the error message:

> installed.packages()
Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  : 
  missing value where TRUE/FALSE needed


> -----Original Message-----
> From: Gordon K Smyth
> Sent: Tuesday, 11 April 2017 6:26 PM
> To: bioc-devel at r-project.org
> Subject: Using BiocInstaller with R 3.4.0 beta
> 
> I thought I would test out R 3.4.0 beta (for Windows) but now I can't use the
> BiocInstaller package. Attempts to use biocLite() or biocValid() lead to an error
> message as shown below.
> 
> What have I overlooked?
> 
> Thanks
> Gordon
> 
> > sessionInfo()
> R version 3.4.0 beta (2017-04-08 r72499)
> 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_Australia.1252  LC_CTYPE=English_Australia.1252
> LC_MONETARY=English_Australia.1252
> [4] LC_NUMERIC=C                       LC_TIME=English_Australia.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> loaded via a namespace (and not attached):
> [1] compiler_3.4.0
> > remove.packages("BiocInstaller")
> Removing package from 'C:/lib/R/R-3.4.0beta/library'
> (as 'lib' is unspecified)
> Error in find.package(pkgs, lib) :
>   there is no package called 'BiocInstaller'
> > source("https://bioconductor.org/biocLite.R")
> trying URL
> 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/BiocInst
> aller_1.25.3.zip'
> Content type 'application/zip' length 127489 bytes (124 KB)
> downloaded 124 KB
> 
> package 'BiocInstaller' successfully unpacked and MD5 sums checked
> 
> The downloaded binary packages are in
> 
> C:\Users\smyth\AppData\Local\Temp\RtmpOUhCbB\downloaded_packages
> Bioconductor version 3.5 (BiocInstaller 1.25.3), ?biocLite for help
> > BiocInstaller::biocValid()
> Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) &&  :
>   missing value where TRUE/FALSE needed
> 
> 
> ---------------------------------------------
> Professor Gordon K Smyth,
> Head, Bioinformatics Division,
> Walter and Eliza Hall Institute of Medical Research,
> http://www.statsci.org/smyth