[Bioc-devel] incomplete vignette on macosx

Hervé Pagès hpages at fredhutch.org
Thu Oct 27 03:34:54 CEST 2016

Hi Renan,

I'm not familiar with Rhtml vignettes and I couldn't get to the
bottom of this but it seems to me that the calls to dev.new()
in your plotting functions somehow get in the way and confuse
the knit engine. If I remove them the problem goes away i.e. the
images get generated and embedded in the HTML vignette.

All these calls to dev.new() are placed inside if statements like this:

       dev.new(width=8, height=2*n)

so make sure that the if condition evaluates to FALSE during vignette
generation (names(dev.cur()) should be "null device" in the context of
vignette generation).

I have to admit that I don't understand why we would see this problem
only on our Mac builders morelia and oaxaca. Is the knit engine using
Pandoc for processing Rhtml documents? Could the problem be related
to different versions of Pandoc on the different build machines?
For the record, we have version on morelia, malbec1, malbec2,
version on oaxaca, and version 1.17.2 on tokay1 and tokay2.
Not sure that's so helpful, sorry.

Hoping that someone could provide some insight on this...


On 10/25/2016 08:52 AM, Renan Valieris wrote:
> Hello,
> I noticed the vignette of the macosx build of my package[1] is incomplete,
> the generated images were not included in the html. The windows,
> linux and the online vignette was generated properly.
> I built the package locally on my macosx without any errors and the
> vignette
> is generated properly so I am not sure what is the problem,
> the build reports don't have any warnings or errors either.
> Does anyone have any idea of what the problem could be ?
> thanks.
> 1. https://www.bioconductor.org/packages/release/bioc/html/signeR.html
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
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