[Bioc-devel] Need help figuring out GeometryDoesNotContainImage-error on machv2-build for chimeraviz
Thank you very much, Herv?! On Wed, Mar 31, 2021 at 8:25 AM Herv? Pag?s <hpages.on.github at gmail.com> wrote:
Hi Stian, I know I know, this thread is almost 1 year old. I had s sticker hanging around to remind me about this, and, today, I spent the entire afternoon looking into this, found the problem, and implemented a fix. Long story short: On our Mac builders, the png() device was using the "Xlib" type by default. Problem is that png(type="Xlib") does not support semi-transparency (and this seems to be the case on all Mac and Linux systems). I changed this to use the "cairo" type by default (this is the default on Linux). With this change, I was finally able to run 'R CMD build chimeraviz' successfully on the machine. I also found out that this problem was also breaking the srnadiff package. We won't see the effect of that change on today's build report, but hopefully we will on tomorrow's report. Cheers, H. On 4/23/20 11:33 PM, Stian L?gstad wrote:
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
<mailto: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>
>> <mailto: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:
>>
>>
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
<
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>>
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<
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>>
>> 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
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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>
>>>> <mailto: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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>>>>>
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>>>>>
<
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>>>>>
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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 <mailto: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 <mailto: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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<
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>>>>>>>>>
<
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>>>>>>>>>
<
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>>>>>>>>>
<
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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:E-mail%3Ahpages at fredhutch.org> <mailto:hpages at fredhutch.org
<mailto: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 <mailto:Bioc-devel at r-project.org>>
>>>>>> <mailto:Bioc-devel at r-project.org
<mailto:Bioc-devel at 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%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132949421&sdata=Bdf8dvgaOBLd7EvbwojiUrB1cuLxzLq4FoIqWHj6aKA%3D&reserved=0
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>>>>>>
<
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>>>>>>
<
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>>>>>>
<
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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>
<mailto: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 <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 <mailto:hpages at fredhutch.org>
Phone: (206) 667-5791
Fax: (206) 667-1319
--
Stian L?gstad
+47 41 80 80 25
-- Herv? Pag?s Bioconductor Core Team hpages.on.github at gmail.com
Stian L?gstad +47 41 80 80 25 [[alternative HTML version deleted]]