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

[Martin Morgan]

On 04/22/2014 05:55 AM, Julian Gehring wrote:
> Related to this, running 'biocLite("BiocUpgrade")' with an bioc-3.0 triggers an
> upgrade to bioc-3.1 which is non-existing.

This will be addressed, sorry for not responding sooner. Martin

>
> 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
>>>
>>
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>
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