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

[Dan Tenenbaum]

----- Original Message -----
> From: "Don Armstrong" <don at donarmstrong.com>
> To: bioc-devel at r-project.org
> Sent: Thursday, May 8, 2014 11:27:13 AM
> Subject: Re: [Bioc-devel] Tracking Current release (http://www.bioconductor.org/packages/current redirect to
> http://www.bioconductor.org/packages/2.14)
> 
> 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.

It would be great if there was a package built-in to R that supported HTTPS downloads.
download.file() does not. This would avoid the chicken and egg problem of needing to download RCurl
(plus the curl system dependencies) in order to securely download other packages.

Dan


>  
> > 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
> Debian.
> 
> 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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