[Bioc-devel] BiocUpgrades updates to devel instead of stable

Related to this, running 'biocLite("BiocUpgrade")' with an bioc-3.0 triggers an
upgrade to bioc-3.1 which is non-existing.

Best wishes
Julian


On 22.04.2014 14:38, Julian Gehring wrote:

Hi,

Alejandro and I digged deeper into this:

The bug I described before as caused by 'BiocInstaller:::.onLoad' which
sets 'BiocInstaller:::IS_UPGRADEABLE' to TRUE for every bioc release
with an even minor (e.g. 2.12, 2.14).  Within the load function,

   (BIOC_VERSION$minor %% 2L) == 0L

checks against the minor of the bioc number, which looks
non-informative.  Rather, checking if the minor of the 'BiocInstaller'
package is even or odd could be more useful here

   (packageVersion("BiocInstaller")$minor %% 2L) == 0L

which is TRUE for stable and FALSE for devel.

Best wishes
Julian


On 17.04.2014 18:50, Steve Lianoglou wrote:

HI,

On Thu, Apr 17, 2014 at 7:09 AM, Julian Gehring
<julian.gehring at embl.de> wrote:

Hi,

When I run

   source("http://bioconductor.org/biocLite.R")
   biocLite("BiocUpgrade")

on a stable R-3.1.0 with bioc 2.14 already installed, bioc wants to
upgrade to bioc 3.0 (devel):

   Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for help
   Upgrade all packages to Bioconductor version 3.0? [y/n]

Is this intentional?  The documentation on the website and ?BiocUpgrade
suggests that it upgrades to the latest bioc 'release'.

Is this some potential weirdness with ?BiocInstaller::useDevel maybe?

-steve