[Bioc-devel] svn and package version numbers

[Dan Tenenbaum]

On Fri, Jul 5, 2013 at 1:33 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
> My confusion is total.
>
> Suppose a package gets build (no errors) but fails check (error) and gets a
> version bump.  Does the package source then get propagated to the
> web/repository?
>

I'm confused by your question (sorry).
>From the point of view of the build system, build and check errors are
the same. Both will prevent a package from being propagated to the
web/repository.

If a package fails check and then gets a version bump it will not
propagate to the web, because presumably a mere version bump did not
fix the problem that caused the check failure.

Dan


> Best,
> Kasper
>
>
> On Fri, Jul 5, 2013 at 3:29 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> 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]]
>> >> >>>
>> >> >>> _______________________________________________
>> >> >>> Bioc-devel at r-project.org mailing list
>> >> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >> >>>
>> >> >>
>> >> >>
>> >> >> --
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>> >
>
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