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
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