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@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@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 <hpa...@fredhutch.org
<mailto:hpa...@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
<https://urldefense.proofpoint.com/v2/url?u=https-3A__nam05.safelinks.protection.outlook.com_-3Furl-3Dhttps-253A-252F-252Fbioconductor.org-252FcheckResults-252F3.11-252Fbioc-2DLATEST-252Fchimeraviz-252Fmachv2-2Dbuildsrc.html-26amp-3Bdata-3D02-257C01-257Ck.bemis-2540northeastern.edu-257Ca50b7fbb03654f8b503208d7e811f4b5-257Ca8eec281aaa34daeac9b9a398b9215e7-257C0-257C0-257C637233036132939427-26amp-3Bsdata-3Ds9fJRfwSMO0UkPEwdmrW7mZhEM-252FgCOYtQm3HO12DknA-253D-26amp-3Breserved-3D0&d=DwMGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ChvNTQebsUvVKYAGSEtFgFNOcwgSzxXYjQ69oO9oBM0&s=Rkoe-LwrUsVZyqv9zyv00KH__7fWXhf-n8-ZTmYFdP4&e=>
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 <hpa...@fredhutch.org
<mailto:hpa...@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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<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 <hpa...@fredhutch.org
<mailto: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>
<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%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:hpa...@fredhutch.org <mailto: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>
<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%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132949421&sdata=Bdf8dvgaOBLd7EvbwojiUrB1cuLxzLq4FoIqWHj6aKA%3D&reserved=0
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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 <mailto:hpa...@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: hpa...@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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel