[Bioc-devel] Need help figuring out GeometryDoesNotContainImage-error on machv2-build for chimeraviz
Thank you very much for the help so far!
On Fri, Apr 24, 2020 at 8:08 AM Herv? Pag?s <hpages at fredhutch.org> wrote:
OK, thanks testing that. This suggests that the problem is on our side... sigh! I will need to dig deeper into this. Best, H. On 4/23/20 22:57, Bemis, Kylie wrote:
Worked for me without errors or warnings: kuwisdelu at Eva-02-Dash Projects % R CMD build chimeraviz * checking for file ?chimeraviz/DESCRIPTION? ... OK * preparing ?chimeraviz?: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Removed empty directory ?chimeraviz/docker? * building ?chimeraviz_1.13.8.tar.gz? kuwisdelu at Eva-02-Dash Projects % R CMD INSTALL chimeraviz_1.13.8.tar.gz * installing to library ?/Users/kuwisdelu/Library/R/4.0/library? * installing *source* package ?chimeraviz? ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (chimeraviz) Under:
sessionInfo()
R version 4.0.0 RC (2020-04-18 r78249) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.3 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.0.0 tools_4.0.0 The vignette looks okay as far as I can tell. -Kylie
On Apr 24, 2020, at 1:40 AM, Herv? Pag?s <hpages at fredhutch.org <mailto:hpages at fredhutch.org>> wrote: Interesting indeed. Thanks for checking this. Even though I'm not sure what conclusion to draw from all this. Since you are on a Mac, can I ask you another big favor? Do you think you could run 'R CMD build' on chimeraviz and see if you can reproduce the error we see on the build report here:
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Get the source with git clone
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Thanks, H. On 4/23/20 21:55, Bemis, Kylie wrote:
That?s interesting. I did:
BiocManager::install("Cardinal", type="mac.binary.el-capitan?)
browseVignettes("Cardinal")
from R 3.6.3, and the figures using transparency in the vignettes look fine to me. When I use X11() to reproduce the warning locally, the transparent colors get truncated, so that the higher-alpha colors appear opaque and the lower-alpha colors don?t appear at all. However, in the merida1 vignette, the figures appear as I?d normally get form quartz() or pdf() locally, which don?t produce warnings for me on macOS 10.15.3. -Kylie
On Apr 24, 2020, at 12:39 AM, Herv? Pag?s <hpages at fredhutch.org <mailto:hpages at fredhutch.org>> wrote: Hi Kylie, I get the warnings on merida1 for Cardinal too e.g. when I run the code in the Cardinal-2-stats vignette: merida1:vignettes biocbuild$ pwd /Users/biocbuild/bbs-3.10-bioc/meat/Cardinal/vignettes merida1:vignettes biocbuild$ R CMD Stangle Cardinal-2-stats.Rmd Output file: Cardinal-2-stats.R merida1:vignettes biocbuild$ R ...
> source("Cardinal-2-stats.R", echo=TRUE)
... There were 14 warnings (use warnings() to see them)
> warnings()
Warning messages: 1: In rect(left, top, r, b, angle = angle, density = density, ...
:
semi-transparency is not supported on this device: reported only once per page 2: In rect(left, top, r, b, angle = angle, density = density, ...
:
semi-transparency is not supported on this device: reported
only once per page
...
The thing is that 'R CMD build' does not display warnings, unless
there is an error. Maybe that's why you've never seen them until now
because of the error you have on machv2 (and other platforms).
It's be interesting to know if the plots included in the vignette
are actually OK. Have you checked them? You can do this by
installing the Mac binary for Cardinal in BioC 3.10 with:
BiocManager::install("Cardinal", type="mac.el-capitan.binary")
(make sure you do this in R 3.6). This will install the vignette
generated on merida1. Then open the vignette via
browseVignettes("Cardinal") and check the plots. Do they look ok
despite the "semi-transparency" problem?
Thanks,
H.
On 4/23/20 20:39, Bemis, Kylie wrote:
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 <
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On Apr 23, 2020, at 11:28 PM, Herv? Pag?s <hpages at fredhutch.org
<mailto:hpages at fredhutch.org> <mailto:hpages at 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, Herv? Pag?s 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 L?gstad 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 L?gstad <stianlagstad at gmail.com <mailto:stianlagstad at gmail.com> <mailto:stianlagstad at 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:
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If anyone has seen something like this before then I'd appreciate some help. Thank you! -- Stian L?gstad +47 41 80 80 25
-- Herv? Pag?s 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 <mailto:hpages at fredhutch.org> <mailto:hpages at fredhutch.org> Phone: (206) 667-5791 Fax: (206) 667-1319
_______________________________________________ Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> <mailto:Bioc-devel at r-project.org>mailing list
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-- Herv? Pag?s 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 <mailto:hpages at fredhutch.org> Phone: (206) 667-5791 Fax: (206) 667-1319
-- Herv? Pag?s 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
-- Herv? Pag?s 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
Stian L?gstad +47 41 80 80 25 [[alternative HTML version deleted]]