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

2021-03-31 Thread Stian Lågstad 
Thank you very much, Hervé!

On Wed, Mar 31, 2021 at 8:25 AM Hervé Pagès 
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 Lågstad wrote:
> > Thank you very much for the help so far!
> >
> > On Fri, Apr 24, 2020 at 8:08 AM Hervé Pagès  > > 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@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  > 
> >  >> >>
> 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.htmldata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427sdata=s9fJRfwSMO0UkPEwdmrW7mZhEM%2FgCOYtQm3HO12DknA%3Dreserved=0
> > <
>

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

2021-03-31 Thread Hervé Pagès 

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 Lågstad wrote:

Thank you very much for the help so far!

On Fri, Apr 24, 2020 at 8:08 AM Hervé Pagès > 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@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 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.htmldata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427sdata=s9fJRfwSMO0UkPEwdmrW7mZhEM%2FgCOYtQm3HO12DknA%3Dreserved=0



 >>

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

2020-04-24 Thread Stian Lågstad 
Thank you very much for the help so far!

On Fri, Apr 24, 2020 at 8:08 AM Hervé Pagès  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@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  >> > 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.htmldata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427sdata=s9fJRfwSMO0UkPEwdmrW7mZhEM%2FgCOYtQm3HO12DknA%3Dreserved=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=DwMGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=ChvNTQebsUvVKYAGSEtFgFNOcwgSzxXYjQ69oO9oBM0=Rkoe-LwrUsVZyqv9zyv00KH__7fWXhf-n8-ZTmYFdP4=
> >
> >>
> >> Get the source with
> >>
> >>  git clone
> >>
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.bioconductor.org%2Fpackages%2Fchimeravizdata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427sdata=cTfgpg28qU2zPXAZn2DZs7k8TQKk290wYyj2vjD6Khw%3Dreserved=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   > wrote:
> 
>  Hi Kylie,
> 
>  I get the warnings on merida1 for Cardinal too e.g. when I run the
>  code in the

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

2020-04-24 Thread Hervé Pagès 
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 > 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.htmldata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427sdata=s9fJRfwSMO0UkPEwdmrW7mZhEM%2FgCOYtQm3HO12DknA%3Dreserved=0 



Get the source with

 git clone 
https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.bioconductor.org%2Fpackages%2Fchimeravizdata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427sdata=cTfgpg28qU2zPXAZn2DZs7k8TQKk290wYyj2vjD6Khw%3Dreserved=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 > 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

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

2020-04-23 Thread Bemis, Kylie 
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 
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.htmldata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427sdata=s9fJRfwSMO0UkPEwdmrW7mZhEM%2FgCOYtQm3HO12DknA%3Dreserved=0

Get the source with

 git clone 
https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.bioconductor.org%2Fpackages%2Fchimeravizdata=02%7C01%7Ck.bemis%40northeastern.edu%7Ca50b7fbb03654f8b503208d7e811f4b5%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637233036132939427sdata=cTfgpg28qU2zPXAZn2DZs7k8TQKk290wYyj2vjD6Khw%3Dreserved=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 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

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

2020-04-23 Thread Hervé Pagès 

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://bioconductor.org/checkResults/3.11/bioc-LATEST/chimeraviz/machv2-buildsrc.html

Get the source with

  git clone https://git.bioconductor.org/packages/chimeraviz

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 > 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 
 
>
On Apr 23, 2020, at 11:28 PM, Hervé

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

2020-04-23 Thread Bemis, Kylie 
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 
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 

On Apr 23, 2020, at 11:28 PM, Hervé Pagès 
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

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

2020-04-23 Thread Hervé Pagès 

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 












On Apr 23, 2020, at 11:28 PM, Hervé Pagès > 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 = "#FF80")
I think that the 4th byte (80) in the color specification 
("#FF80") 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 
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),

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

2020-04-23 Thread Bemis, Kylie 
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










On Apr 23, 2020, at 11:28 PM, Hervé Pagès 
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 = "#FF80")
I think that the 4th byte (80) in the color specification ("#FF80") 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 
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%3Ddata=02%7C01%7Ck.bemis%40northeastern.edu%7C0fefe5ade3994ca1943e08d7e7ff9084%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637232957151727562sdata=jz%2FO8NrKC2VZTuK4Z%2F7Fo19ExLg9d1C4LpzbZddhcQ8%3Dreserved=0

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
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list

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

2020-04-23 Thread Hervé Pagès 
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 = 
"#FF80")


I think that the 4th byte (80) in the color specification ("#FF80") 
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 
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://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.11_bioc-2DLATEST_chimeraviz_machv2-2Dbuildsrc.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Q1W5ctHOQ2Hjw49pX7VAGBn7-u5l3mAqH1rt9tFNnZM=A7jGEFF5ehz2Hsxmlr_vGmPSX3Xy2SwZErgyi1mPIuw= 



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
Phone:  (206) 667-5791
Fax:(206) 667-1319

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

2020-04-23 Thread Hervé Pagès 

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 = "#FF80")

I think that the 4th byte (80) in the color specification ("#FF80") 
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 
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://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_3.11_bioc-2DLATEST_chimeraviz_machv2-2Dbuildsrc.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=Q1W5ctHOQ2Hjw49pX7VAGBn7-u5l3mAqH1rt9tFNnZM=A7jGEFF5ehz2Hsxmlr_vGmPSX3Xy2SwZErgyi1mPIuw=

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
Phone:  (206) 667-5791
Fax:(206) 667-1319

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

2020-04-22 Thread Stian Lågstad 
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 
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:
> http://bioconductor.org/checkResults/3.11/bioc-LATEST/chimeraviz/machv2-buildsrc.html
>
> If anyone has seen something like this before then I'd appreciate some
> help. Thank you!
>
> --
> Stian Lågstad
> +47 41 80 80 25
>


-- 
Stian Lågstad
+47 41 80 80 25

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