Thank you all for your answers. Laurent
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 >> 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(). > > Martin > >> >> Laurent >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> -- Laurent Gatto http://cpu.sysbiol.cam.ac.uk/ _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
