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

[Julian Gehring]

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
>