[Bioc-devel] Vignette update after change in git mirror repo

[Maia Smith]

Thanks for your feedback James. I'm not sure why this error is appearing,
because the latest svn commit *changed* that error, and shouldn't be
looking for "frac" any longer - here is the code copied from the
bioconductor mirror -

stop("Perturbations data frame must have the following column names: ",
          "\"pert_name\", \"prev_tp\"")



On Fri, Apr 21, 2017 at 1:53 PM, James W. MacDonald <jmacdon at uw.edu> wrote:

> The update won't get built if there is an error during check:
>
> Quitting from lines 42-54 (timescape_vignette.Rmd)
> Error: processing vignette 'timescape_vignette.Rmd' failed with
> diagnostics:
> Perturbations data frame must have the following column names:
> "pert_name", "prev_tp", "frac"
> Execution halted
>
> You can either check the build page (which you should be doing, since
> packages that fail check won't be part of the release on MONDAY):
> http://bioconductor.org/checkResults/devel/bioc-LATEST/ or (better yet),
> you should build and check locally before you check in your changes.
>
> On Fri, Apr 21, 2017 at 4:41 PM, Maia Smith <mas29 at sfu.ca> wrote:
>
>> I believe I did (see diff in DESCRIPTION file in the commit -
>> https://github.com/Bioconductor-mirror/timescape/commit/1359
>> 7696049eda5858b755ca2777486f5b88f588
>> ).
>>
>> Maia
>>
>>
>>
>> On Fri, Apr 21, 2017 at 10:53 AM, Sean Davis <seandavi at gmail.com> wrote:
>>
>> > Be sure that you bumped the version number to trigger a build.
>> >
>> > Sean
>> >
>> >
>> > On Fri, Apr 21, 2017 at 1:18 PM, Maia Smith <mas29 at sfu.ca> wrote:
>> >
>> >> Hi Sean,
>> >>
>> >> Thanks for your response, perhaps I was unclear. I used "Scenario 1:
>> Use
>> >> Git Locally, No GitHub Repository" in the how-to page, and committed
>> to svn
>> >> (I think!). The changes are reflected in the bioconductor mirror (
>> >> https://github.com/Bioconductor-mirror/timescape) but not in the
>> >> vignette (https://bioconductor.org/packages/devel/bioc/vignettes/time
>> >> scape/inst/doc/timescape_vignette.html). Perhaps I made an error
>> >> somewhere?
>> >>
>> >> Best,
>> >> Maia
>> >>
>> >> On Thu, Apr 20, 2017 at 1:24 PM, Sean Davis <seandavi at gmail.com>
>> wrote:
>> >>
>> >>> Hi, Maia.
>> >>>
>> >>> The git mirror is not used for building packages.  Instead, you will
>> >>> need to commit to svn for changes to show up on Bioconductor.  See
>> here for
>> >>> details of working with git and svn together.
>> >>>
>> >>> https://www.bioconductor.org/developers/how-to/git-mirrors/
>> >>>
>> >>> If I misunderstood what you are saying, could you clarify a bit?
>> >>>
>> >>> Sean
>> >>>
>> >>>
>> >>> On Thu, Apr 20, 2017 at 3:35 PM Maia Smith <mas29 at sfu.ca> wrote:
>> >>>
>> >>>> How long does it take for the html vignette to update after a change
>> in
>> >>>> the
>> >>>> git mirror has taken place? I changed my code in the git mirror a few
>> >>>> days
>> >>>> ago, and the html vignette hasn't incorporated these changes yet.
>> >>>>
>> >>>> Thanks in advance for your help.
>> >>>>
>> >>>> Maia
>> >>>>
>> >>>>         [[alternative HTML version deleted]]
>> >>>>
>> >>>> _______________________________________________
>> >>>> Bioc-devel at r-project.org mailing list
>> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >>>>
>> >>>
>> >>
>> >
>> >
>> > --
>> > Sean Davis, MD, PhD
>> > Center for Cancer Research
>> > National Cancer Institute
>> > National Institutes of Health
>> > Bethesda, MD 20892
>> > https://seandavi.github.io/
>> > https://twitter.com/seandavis12
>> >
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>

	[[alternative HTML version deleted]]