[Bioc-devel] new package IGV needs web browsers on the build machines to pass build & check

[Paul Shannon]

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 <stvjc at 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.shannon at 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
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