[Bioc-devel] Need help figuring out GeometryDoesNotContainImage-error on machv2-build for chimeraviz

Hervé Pagès hp@ge@ @end|ng |rom |redhutch@org
Fri Apr 24 04:42:43 CEST 2020

Hi Stian,

I went on machv2 and gave this a shot. I can reproduce the 
GeometryDoesNotContainImage error in an interactive session. I don't 
have an answer yet but I was curious about the "semi-transparency is not 
supported on this device" warning and was wondering if it could somehow 
be related with the error.

It turns out that the warning is actually easy to reproduce on a Mac 
with something like this:

   lines(c(0.1, 0.22), c(0.5, 0.44), type = "l", lwd = 1, col = "#FF000080")

I think that the 4th byte (80) in the color specification ("#FF000080") 
is the level of transparency.

I can get this warning on machv2 **and** merida1. Some googling 
indicates that this is a pretty common warning on Mac. Since we don't 
get the vignette error on merida1 I think it's unlikely that the warning 
is related to the error.

I'll keep investigating the GeometryDoesNotContainImage error...


On 4/22/20 01:59, Stian Lågstad wrote:
> I'm still unable to reproduce this error on my end. If anyone with a mac
> could try building locally I would be very grateful. Thanks.
> On Sat, Apr 18, 2020 at 4:06 PM Stian Lågstad <stianlagstad using gmail.com>
> wrote:
>> Hi,
>> I'm haven't been able to figure out this error for the latest machv2 build
>> for chimeraviz:
>> ```
>> Warning in doTryCatch(return(expr), name, parentenv, handler) :
>>    semi-transparency is not supported on this device: reported only once
>> per page
>> Quitting from lines 108-126 (chimeraviz-vignette.Rmd)
>> Error: processing vignette 'chimeraviz-vignette.Rmd' failed with
>> diagnostics:
>> R: GeometryDoesNotContainImage
>> `/private/tmp/RtmpdBrrvk/Rbuild9ed5154894cc/chimeraviz/vignettes/chimeraviz-vignette_files/figure-html/unnamed-chunk-7-1.png'
>> @ warning/attribute.c/GetImageBoundingBox/247
>> --- failed re-building ‘chimeraviz-vignette.Rmd’
>> ```
>> The build in question:
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.11_bioc-2DLATEST_chimeraviz_machv2-2Dbuildsrc.html&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Q1W5ctHOQ2Hjw49pX7VAGBn7-u5l3mAqH1rt9tFNnZM&s=A7jGEFF5ehz2Hsxmlr_vGmPSX3Xy2SwZErgyi1mPIuw&e=
>> If anyone has seen something like this before then I'd appreciate some
>> help. Thank you!
>> --
>> Stian Lågstad
>> +47 41 80 80 25

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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