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

Bemis, Kylie k@bem|@ @end|ng |rom northe@@tern@edu
Fri Apr 24 07:57:33 CEST 2020 

Worked for me without errors or warnings:

kuwisdelu using 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 using 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, Hervé Pagès <hpages using fredhutch.org<mailto:hpages using 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:

https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.11%2Fbioc-LATEST%2Fchimeraviz%2Fmachv2-buildsrc.html&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427&sdata=s9fJRfwSMO0UkPEwdmrW7mZhEM%2FgCOYtQm3HO12DknA%3D&reserved=0

Get the source with

 git clone https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.bioconductor.org%2Fpackages%2Fchimeraviz&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427&sdata=cTfgpg28qU2zPXAZn2DZs7k8TQKk290wYyj2vjD6Khw%3D&reserved=0

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, Hervé Pagès <hpages using fredhutch.org <mailto:hpages using 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 <https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__kuwisdelu.github.io%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DCO4n__SJ6oQxnPyEFpNoDuHw2Pa0aC_CznlpINGGORQ%26s%3DNl-SFGWHUlZqtDsccYwD2EHptbV_1lbboQkoGIwfeKI%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427&sdata=wWHZczFLad0imdTwrpSBsiqqdYyTX09n0MNXkpdpFVo%3D&reserved=0> <https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__kuwisdelu.github.io%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DiIfSQOsSomvKm_1GHwSPKYxnfvicYz3rNyk04PTXhxU%26s%3DitZMZz7G1z4hEn_h6m-WLnSXgIbD-41KOovzdseVHT4%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427&sdata=zcOG%2BEG%2Bk16OXD2SN6pCGrZrQX8Rpwpx07gqYuBGPBE%3D&reserved=0 <https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Furldefense.proofpoint.com-252Fv2-252Furl-253Fu-253Dhttps-2D3A-5F-5Fkuwisdelu.github.io-2526d-253DDwMGaQ-2526c-253DeRAMFD45gAfqt84VtBcfhQ-2526r-253DBK7q3XeAvimeWdGbWY-5FwJYbW0WYiZvSXAJJKaaPhzWA-2526m-253DiIfSQOsSomvKm-5F1GHwSPKYxnfvicYz3rNyk04PTXhxU-2526s-253DitZMZz7G1z4hEn-5Fh6m-2DWLnSXgIbD-2D41KOovzdseVHT4-2526e-253D-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257C557e92d7107a41f63ec208d7e8098af2-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233000008658074-26amp-3Bsdata-3D9TmRy1lpNBJjGLZcqPqJY-252BMP32z2kgbsmTdvSn4RUk8-253D-26amp-3Breserved-3D0%26d%3DDwMGaQ%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DCO4n__SJ6oQxnPyEFpNoDuHw2Pa0aC_CznlpINGGORQ%26s%3DhNiYK5Qxom3Q8JMAgB15vH_K86oAT1s-ZFy1NFMtBcw%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132949421&sdata=F9edg0Pf5jT9RZGC8B%2FIxJvV4DpW8Ztv3ZUDkw06tcs%3D&reserved=0>>
On Apr 23, 2020, at 11:28 PM, Hervé Pagès <hpages using fredhutch.org <mailto:hpages using fredhutch.org> <mailto:hpages using 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 <stianlagstad using gmail.com <mailto:stianlagstad using gmail.com> <mailto: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://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%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132949421&sdata=%2BST%2B9JRGaOFHqb2h49INMs6j%2FmHm0PRG9q7OF5uQoa4%3D&reserved=0 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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:hpages using fredhutch.org <mailto:hpages using fredhutch.org> <mailto:hpages using fredhutch.org>
Phone:  (206) 667-5791
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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: hpages using fredhutch.org <mailto:hpages using fredhutch.org>
Phone:  (206) 667-5791
Fax:    (206) 667-1319

--
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 using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319


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