Many thanks, Vince! I will fix the printf and markdown errors.
With release date now not far off, I propose (Bioc policymakers please weigh in
if this is inadequate) to
- remove web browser communication from vignette, examples and unit tests
- evaluate stubs and/or "mocks" for possible use in a future release
- run full web browser tests on my own, separate from the bioc build
Any objections to this approach?
- Paul
> On Apr 9, 2018, at 7:15 PM, Vincent Carey <st...@channing.harvard.edu> wrote:
>
> Thanks Paul. Package works. Browser visualizations look really nice.
>
> I tried to run your unit tests and they
> use a function called "printf". Setting printf = sprintf allowed the tests
> to all run to completion.
>
> The following vignette chunk is problematic ... maybe you meant eval=FALSE,
> echo=TRUE to show what the
> user needs to do?
>
> ```{r createLoad, echo=TRUE, echo=FALSE, results='hide'}
> igv <- IGV()
> setBrowserWindowTitle(igv, "MEF2C")
> setGenome(igv, "hg19")
> ```
>
> It does seem to me that you would need to avoid running
> the browser in tests and vignette and examples. Using
> if (interactive()) can help with vignette and examples.
> The unit testing of such a package should I think focus
> on verifying that the essential data manipulations succeed,
> without requiring browser communication. But others in the
> group will have more authoritative remarks on this.
>
> I don't know whether the methods sketched in
>
> https://stackoverflow.com/questions/15509231/unit-testing-node-js-and-websockets-socket-io
>
> could be used in this task, to go beyond checking the basic
> R manipulations.
>
>
>> On Mon, Apr 9, 2018 at 8:15 PM, Paul Shannon <pshan...@systemsbiology.org>
>> wrote:
>> Hi Vince,
>>
>> My dumb mistake, sorry. Now fixed, version 0.99.9,
>> https://github.com/paul-shannon/IGV
>>
>> I’m looking forward to hearing your suggestions.
>>
>> - Paul
>>
>>
>>
>> > On Apr 9, 2018, at 4:49 PM, Vincent Carey <st...@channing.harvard.edu>
>> > wrote:
>> >
>> > Hi Paul -- I am trying to build your vignette but it has
>> >
>> > load("~/s/work/priceLab/AD/tbl.gwas.level_1.RData")
>> >
>> > I think it should be possible to get your package through
>> > check, but I would like to get the vignette built and
>> > check out the tests before commenting further.
>> >
>> >
>> > On Mon, Apr 9, 2018 at 1:52 PM, Paul Shannon
>> > <paul.thurmond.shan...@gmail.com> wrote:
>> > > "Once your package builds and checks without errors or (avoidable)
>> > > warnings, a Bioconductor team member will provide a technical review of
>> > > your package. Other Bioconductor developers and users with domain
>> > > expertise are encouraged to provide additional community commentary.
>> > > Reviewers will add comments to the issue you created.”
>> >
>> > I don’t believe my submission, IGV, quite fits the mold. As best I can
>> > tell, no web browser can be summoned on any of the architectures by IGV
>> > during build or check. So the package build always times out. And so,
>> > according to the guideline quoted above, it will never be reviewed!
>> >
>> > IGV is a BrowserViz version >=2 subclass; BrowserViz was recently uprev’d
>> > in devel. Like RCyjs, IGV's raison d’être is the provision of R access to
>> > interactive graphics in your web browser, in this case to Jim Robinson’s
>> > igv.js.
>> >
>> > My analysis may be incorrect. Can this matter receive a little attention,
>> > despite the bioc submission guideline quoted above, in hopes that the
>> > package can move forward?
>> >
>> > Thank you,
>> >
>> > - Paul
>> > _______________________________________________
>> > Bioc-devel@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
>
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