[Bioc-devel] CRAN package with Bioconductor dependencies
On 03/02/2015 03:22 PM, Ryan C. Thompson wrote:
I thought CRAN packages weren't allowed to depend on Bioconductor packages for exactly this reason.
CRAN packages can and do depend on Bioconductor packages.
The different versioning schemes use by CRAN and by Bioconductor can lead to
confusion, and can end in tears.
My advice is to use, and tell your users to use, biocLite() for everything
(including, in devel, github, e.g., biocLite("mtmorgan/biocdb"), which delegates
to devtools).
Martin
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?
Laurent
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793