[Bioc-devel] CRAN package with Bioconductor dependencies

Laurent Gatto lg390 at cam.ac.uk
Tue Mar 3 00:18:58 CET 2015

Dear all,

I had never realised that CRAN packages that depended on Bioc packages
could actually not be installed with install.packages without setting a
repo or using BiocInstaller::bioLite. Here is an example using a fresh R

  Depends: amap, clValid, cluster, fpc, mzR, xcms

$ docker run --rm -ti rocker/r-base R

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> install.packages("MSeasy")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Warning: dependencies ‘mzR’, ‘xcms’ are not available
also installing the dependencies ‘modeltools’, ‘DEoptimR’, ‘mclust’, ‘flexmix’, ‘prabclus’, ‘diptest’, ‘mvtnorm’, ‘robustbase’, ‘kernlab’, ‘trimcluster’, ‘amap’, ‘clValid’, ‘fpc’


ERROR: dependencies ‘mzR’, ‘xcms’ are not available for package ‘MSeasy’
* removing ‘/usr/local/lib/R/site-library/MSeasy’

The downloaded source packages are in
Warning message:
In install.packages("MSeasy") :
  installation of package ‘MSeasy’ had non-zero exit status

This does sound really counter-intuitive. Am I missing anything?


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