[Bioc-devel] Tracking Current release (http://www.bioconductor.org/packages/current redirect to http://www.bioconductor.org/packages/2.14)

Don Armstrong don at donarmstrong.com
Thu May 8 20:27:13 CEST 2014

On Wed, 07 May 2014, Martin Morgan wrote:
> http://bioconductor.org/packages/release goes to the current release
> 'biocViews', with packages under release/ being the current release
> versions. http://bioconductor.org/bioc-version is probably what you'll
> end up using (though I believe it's hand curated),

Cool; http://bioconductor.org/bioc-version is good enough for my
purposes; thanks.

> Of course this is a valid concern and we can work toward a more secure
> approach.

I figure just using SSL is probably good enough; there are better
methods, but SSL is easy and fast.
> Perhaps I could take the opportunity to ask a naive question about
> debian binary distributions of R. [...] In particular, are they
> unversioned, /usr/lib/R/library etc, as opposed to say
> /usr/lib/R-3.1/library ?

They're unversioned.

> I'm asking because a number of users seem to show up with say R-3.1
> reporting a mix of R-3.1 and R-3.0.2 packages, usually to ill effect;
> this is not necessarily likely for user-installed packages, because
> the system directories won't be writeable and R will prompt with a
> versioned directory ~/R/x86_64-unknown-linux-gnu-library/3.1 as the
> location to install libraries.

All Debian R packages currently require at least the version of R that
they were built against to be installed. However, there is currently a
problem where you can have a package installed which was built against
an old version of R which is incompatible with a newer R version. [For
example, as happened when R 3.0 released.]

The latter problem needs to be fixed; unfortunately, it blocks on
available time to coordinate the fix and get it deployed everywhere in

In general, though, if someone is running versions of packages specific
to the Debian release they are running, they should be OK.

Don Armstrong                      http://www.donarmstrong.com

The major difference between a thing that might go wrong and a thing
that cannot possibly go wrong is that when a thing that cannot
possibly go wrong goes wrong it usually turns out to be impossible to
get at or repair.
 -- Douglas Adams  _Mostly Harmless_

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