[Bioc-devel] svn and package version numbers

[Dan Tenenbaum]

On Thu, Jul 4, 2013 at 7:00 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> So this thread is good for my follow up question.
>
> I am setting up a Windows box to test/fix bumphunter (newest version 1.1.7)
> which has been broken (R CMD check) for a while, especially on Windows.
>
> This page (bottom)
>   http://bioconductor.org/packages/2.13/bioc/html/bumphunter.html
> suggests that the latest binary version for Windows is 1.1.0 which is also
> probably the last time it build and checked properly.  So this all reflects
> my expectations of not being able to get a binary version newer than 1.1.0
>
> However, when I install R-3.0.1 under windows, source biocLite and do
> useDevel(TRUE) (getting BiocInstaller version 1.11.3) and then do
>   biocLite("bumphunter")
> I get version 1.1.7. Why?  I am asking for binary versions and nor source.
>

The website wasn't being updated due to an unrelated issue. Fixed now.
Dan


> Best,
> Kasper
>
>
> On Sun, Jun 30, 2013 at 8:55 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>>
>>
>> On Sunday, June 30, 2013, Kasper Daniel Hansen
>> <kasperdanielhansen at gmail.com> wrote:
>> > Doesn't this mean that the issue Wolfgang discusses only arises when
>> > people install from subversion?
>>
>> Yes.
>>
>> Dan
>>
>>
>> > Kasper
>> >
>> > On Sun, Jun 30, 2013 at 6:56 PM, Martin Morgan <mtmorgan at fhcrc.org>
>> > wrote:
>> >>
>> >> On 06/30/2013 03:32 PM, Dan Tenenbaum wrote:
>> >>>
>> >>> On Jun 30, 2013 12:43 PM, "Kasper Daniel Hansen" <
>> >>> kasperdanielhansen at gmail.com> wrote:
>> >>>>
>> >>>> Also, as far as I understand, the package does not get build using
>> >>>> the new
>> >>>> commit, if it has already been build with that version number before.
>> >>>
>> >>> The package is built but not propagated to the web/repository. This
>> >>> "feature" allows developers to check that their changes get built by
>> >>> the
>> >>
>> >> It's more a safety measure -- if the developer FORGETS to bump, then at
>> >> least we are not distributing two implementations under the same version
>> >> number.
>> >>
>> >> As Wolfgang says, version numbers are free so no need to hold back on
>> >> their use.
>> >>
>> >> Martin
>> >>
>> >>> build system, but yes, once you're satisfied that things work, you
>> >>> should
>> >>> bump the version number to propagate the package and avoid the
>> >>> confusion
>> >>> Wolfgang describes.
>> >>>
>> >>> Dan
>> >>>
>> >>>
>> >>>>
>> >>>> Best,
>> >>>> Kasper
>> >>>>
>> >>>>
>> >>>> On Sun, Jun 30, 2013 at 3:12 AM, Wolfgang Huber <whuber at embl.de>
>> >>>> wrote:
>> >>>>
>> >>>>> Hi All,
>> >>>>>
>> >>>>> just a reminder that it is good practice to bump up the package
>> >>>>> version
>> >>>>> when you commit a change to a package's source, even if you consider
>> >>>>> it
>> >>>>> 'trivial'. Version numbers are free, while the confusion ensuing
>> >>>>> from
>> >>>
>> >>> there
>> >>>>>
>> >>>>> being different versions of the software with ostensibly the same
>> >>>
>> >>> version
>> >>>>>
>> >>>>> can waste a great deal of someone's time.
>> >>>>>
>> >>>>> Dan / Bioc-Core team: would it be good to mention this somewhere on
>> >>>>> http://bioconductor.org/developers/source-control ?
>> >>>>>
>> >>>>> Best wishes
>> >>>>>          Wolfgang
>> >>>>> _______________________________________________
>> >>>>> Bioc-devel at r-project.org mailing list
>> >>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>>>>
>> >>>>
>> >>>>          [[alternative HTML version deleted]]
>> >>>>
>> >>>> _______________________________________________
>> >>>> Bioc-devel at r-project.org mailing list
>> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>>
>> >>>         [[alternative HTML version deleted]]
>> >>>
>> >>> _______________________________________________
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>> >>>
>> >>
>> >>
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