[Bioc-devel] CRAN package with Bioconductor dependencies
lg390 at cam.ac.uk
Tue Mar 3 00:41:39 CET 2015
Thank you all for your answers.
On 2 March 2015 23:27, Martin Morgan wrote:
> 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?
> 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().
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