On 11/13/2013 01:29 PM, Luo Weijun wrote:
I noticed that under R 3.0, I frequently get prompt to update other packages
after package installation like:
invoking biocLite with biocLite(suppressUpdates=TRUE) gives you a quieter
version.
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download/update all outdated ones in a Linux machine.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)
There is no way to distinguish between trivial and non-trivial changes.
> 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way, even though they are outdated based on the “Update all/some/none” list.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.
biocLite("pathview", dependencies=TRUE) uses install.packages(), and
'dependencies=TRUE' checks that the dependecies are installed, not that they are
current. The R-devel mailing list would be the place to argue for a different
behavior (of install.packages).
I don't think that there is a simple invocation of old.packages / etc that would
behave the way you'd like. Maybe something along the lines of
biocUpdatePackages <-
function(pkgs, lib, dependencies = NA, ...)
{
if (is.logical(dependencies) && is.na(dependencies))
dependencies <- if (!missing(lib) && length(lib) > 1L)
FALSE
else c("Depends", "Imports", "LinkingTo")
avail <- available.packages(contriburl=contrib.url(biocinstallRepos()))
deps <- avail[pkgs, depends, drop=FALSE]
deps <- unique(unlist(apply(deps, 1, utils:::.clean_up_dependencies)))
deps <- deps[deps %in% rownames(avail)]
update.packages(oldPkgs=deps, repos=biocinstallRepos(), ...)
}
Then biocUpdatePackages("pathview") (perhaps with ask=FALSE to just do it).
Martin
Adding these features would make BioC users/developers life much easiers. Just
my 2 cents.
Weijun
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