[Bioc-devel] CRAN package with Bioconductor dependencies
lg390 at cam.ac.uk
Tue Mar 3 00:18:58 CET 2015
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
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.
You are welcome to redistribute it under certain conditions.
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.
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
In install.packages("MSeasy") :
installation of package ‘MSeasy’ had non-zero exit status
This does sound really counter-intuitive. Am I missing anything?
More information about the Bioc-devel