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

[James W. MacDonald]

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/
> 13597696049eda5858b755ca2777486f5b88f588
> ).
>
> 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

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