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

[Maia Smith]

I suppose it's a circular problem - the biocLite code can't be updated
until the vignette works, and the vignette doesn't work because the
biocLite code is not updated and the vignette depends on the updated code,
etc.

On Fri, Apr 21, 2017 at 3:20 PM, Maia Smith <mas29 at sfu.ca> wrote:

> 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
>>
>
>

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