[Bioc-devel] CRAN package with Bioconductor dependencies

[Laurent Gatto]

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
installation

  http://cran.r-project.org/web/packages/MSeasy/index.html
  Depends: amap, clValid, cluster, fpc, mzR, xcms

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

R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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
	‘/tmp/Rtmp4T40ub/downloaded_packages’
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?

Laurent