[Bioc-devel] CRAN package with Bioconductor dependencies
Ryan C. Thompson
rct at thompsonclan.org
Tue Mar 3 00:22:07 CET 2015
I thought CRAN packages weren't allowed to depend on Bioconductor
packages for exactly this reason.
On 03/02/2015 03:18 PM, Laurent Gatto wrote:
> 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
> 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
> 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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