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

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

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Center for Cancer Research
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https://seandavi.github.io/
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