[Bioc-devel] CRAN package with Bioconductor dependencies

Martin Morgan mtmorgan at fredhutch.org
Tue Mar 3 00:27:15 CET 2015

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
> 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.
> 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.
>> 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?

biocLite("MSeasy") is easy and works.

Otherwise yes, to install a Bioconductor package using install.packages() 
requires that you've selected (via chooseBioCmirror() or options("BioC_mirror")) 
or provided (e.g., install.packages("MSeasy", 
repos=BiocInstaller::biocinstallRepos()) a Bioconductor repository.

Since the mirror choices provided by chooseBioCmirror() are hard-wired, users of 
R3.0.0 + chooseBioCmirror() will get an older version of Biocondcutor than users 
of 3.0.0 + biocLite().


> Laurent
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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