[Bioc-devel] Minimal update of relevant packages only

Luo Weijun luo_weijun at yahoo.com
Wed Nov 13 22:29:13 CET 2013

I noticed that under R 3.0, I frequently get prompt to update other packages after package installation like:
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.x.
Old packages: (long list of packages) … 
Update all/some/none? [a/s/n]:

I am reluctant to update all my bioc packages. It takes a long time to download/update all outdated ones in a Linux machine. And I just did this a little time ago. And packages update frequently, I don’t want to keep updating for unessential/irrelavant changes (to me).
Here is a question, is there a way to mark or check the essential updates (stopper/conflict fixes) so that the update of one package will automatically trigger only NECESSARY UPDATES of its dependencies? I understand we can now update bioc package using 'biocLite()' now based on http://www.bioconductor.org/install/#update-bioconductor-package. Another related question, I think it would be nice if we can update specific package and its dependencies like:
biocLite("pathview", dependencies=T)
I tried it, it doesn’t work as I expected. Dependencies (depends/imports) for pathview, including Rgraphviz, graph, org.Hs.eg.db, etc are not updated this way, even though they are outdated based on the “Update all/some/none” list. A few other dependencies get updated this way indeed, including 'AnnotationDbi', 'KEGGREST', 'org.Mm.eg.db'. A little curious, why dependencies are treated differently.
Adding these features would make BioC users/developers life much easiers. Just my 2 cents.

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