[Bioc-devel] Using BiocInstaller with R 3.4.0 beta

Gordon K Smyth smyth at wehi.edu.au
Tue Apr 11 10:25:35 CEST 2017

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?


> 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

[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/BiocInstaller_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
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,

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