[Bioc-devel] incomplete vignette on macosx

[Renan Valieris]

Hi Hervé,

>names(dev.cur()) should be "null device" in the context of vignette
generation

really ? this is intriguing because on the machine I tested it is "png"
instead.
perhaps this is the problem ? I'm going to try to set knitr device as png:

opts_chunk$set(dev = 'png')

on the devel build to see if the problem goes away.

thank you very much.


On Wed, Oct 26, 2016 at 11:34 PM, Hervé Pagès <hpages at fredhutch.org> wrote:

> 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:
>
>   if(!grepl("pdf|postscript|cairo_|png|tiff|jpeg|bmp",
>       names(dev.cur()),perl=TRUE)){
>       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 1.16.0.2 on morelia, malbec1, malbec2,
> version 1.17.0.2 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...
>
> Cheers,
> H.
>
>
>
> 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
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>

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