I’m now seeing the same "semi-transparency" error on my Mac builds for Cardinal. My vignettes have used transparency for years now and this has never been an issue before (on merida1 or otherwise).
I can reproduce the error locally with an X11() device, but not with quartz(), png(), png(), etc. (Note that my Cardinal 2.5.9 builds are currently failing due to an unrelated issue that I’ve since fixed, but the build system hasn’t gotten to 2.5.11 yet.) ~~~ Kylie Ariel Bemis (she/her) Khoury College of Computer Sciences Northeastern University kuwisdelu.github.io<https://kuwisdelu.github.io> On Apr 23, 2020, at 11:28 PM, Hervé Pagès <hpa...@fredhutch.org<mailto:hpa...@fredhutch.org>> wrote: Ok so I'm changing my mind about this. I suspect that the error is actually related to the warning. The error comes from the magick package (a wrapper around the ImageMagick software) and it indicates a failure to crop an empty image. It can easily be reproduced with: ## Generate an empty image. png("myplot.png", bg="transparent") plot.new() dev.off() ## Try to crop it. magick::image_trim(magick::image_read("myplot.png")) # Error in magick_image_trim(image, fuzz) : # R: GeometryDoesNotContainImage `/Users/biocbuild/myplot.png' @ # warning/attribute.c/GetImageBoundingBox/247 So I suspect that what happens is that the images generated on Mac by the code in the vignette are empty (because of the semi-transparency problem on Mac) which would explain why later knitr fails to crop them (it uses magick::image_trim() for that). I don't exactly understand why we wouldn't have seen the problem on merida1 though (same version of knitr (1.28) and magick (2.3) on both machines) but it seems that chimeraviz has changed significantly between BioC 3.10 and 3.11. Did you start using semi-transparency recently in your plots? Best, H. On 4/23/20 19:42, Hervé Pagès wrote: 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: plot.new() 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... H. 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 <stianlags...@gmail.com<mailto:stianlags...@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://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__bioconductor.org_checkResults_3.11_bioc-2DLATEST_chimeraviz_machv2-2Dbuildsrc.html%26d%3DDwIFaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DQ1W5ctHOQ2Hjw49pX7VAGBn7-u5l3mAqH1rt9tFNnZM%26s%3DA7jGEFF5ehz2Hsxmlr_vGmPSX3Xy2SwZErgyi1mPIuw%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7C0fefe5ade3994ca1943e08d7e7ff9084%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637232957151727562&sdata=jz%2FO8NrKC2VZTuK4Z%2F7Fo19ExLg9d1C4LpzbZddhcQ8%3D&reserved=0 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 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org<mailto:hpa...@fredhutch.org> Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel&data=02%7C01%7Ck.bemis%40northeastern.edu%7C0fefe5ade3994ca1943e08d7e7ff9084%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637232957151727562&sdata=%2BSIWViTvvcbrxJdXzw0IobmTldrBgK4DNLz%2F%2B2QJb%2FI%3D&reserved=0 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
