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
<https://urldefense.proofpoint.com/v2/url?u=https-3A__kuwisdelu.github.io&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iIfSQOsSomvKm_1GHwSPKYxnfvicYz3rNyk04PTXhxU&s=itZMZz7G1z4hEn_h6m-WLnSXgIbD-41KOovzdseVHT4&e=>
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
<https://urldefense.proofpoint.com/v2/url?u=https-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttp-2D3A-5F-5Fbioconductor.org-5FcheckResults-5F3.11-5Fbioc-2D2DLATEST-5Fchimeraviz-5Fmachv2-2D2Dbuildsrc.html-2526d-253DDwIFaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253DQ1W5ctHOQ2Hjw49pX7VAGBn7-2Du5l3mAqH1rt9tFNnZM-2526s-253DA7jGEFF5ehz2Hsxmlr-5FvGmPSX3Xy2SwZErgyi1mPIuw-2526e-253D-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257C0fefe5ade3994ca1943e08d7e7ff9084-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637232957151727562-26amp-3Bsdata-3Djz-252FO8NrKC2VZTuK4Z-252F7Fo19ExLg9d1C4LpzbZddhcQ8-253D-26amp-3Breserved-3D0&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=iIfSQOsSomvKm_1GHwSPKYxnfvicYz3rNyk04PTXhxU&s=P62BYr_gq2eIDAUWhWL4PX7IoRmhTn06cUUU4o6QdPE&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
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
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--
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
Phone: (206) 667-5791
Fax: (206) 667-1319
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