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

[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

[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

[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] Cannot reproduce a regionReport 1.21.7 error on the Bioc 3.11 Linux builder

[Leonardo Collado Torres]

Hi Bioc-devel again,


I believe that I have found the source of my regionReport problem and
a workaround. We'll know tomorrow if it goes through the Bioc builds
but it works at
https://github.com/leekgroup/regionReport/actions/runs/86364716.

The problem is related to
https://github.com/ropensci/magick/issues/171 and similar issues. The
workaround is to use `crop = NULL` on R Markdown code chunks to
disable the default image cropping behavior by
BiocStyle::html_document, and thus avoid cache issues from magick (R)
and ImageMagick (not R).

Both the Bioc-devel Linux machine and GitHub Actions using
Bioconductor devel run into a problem where there's not enough
resources in the cache for cropping the images produced by
regionReport::derfinderReport(). Either (a) the Bioc-devel Windows and
macOS machines don't have magick installed (so no cropping gets
attempted), (b) use a compiled version of magick that ships with the
right version of ImageMagick, or (c) they have more resources than the
bioc Linux build machine and the bioc devel docker running on GHA
Linux

In any case, disabling cropping circumvents this issue.


Here's the full investigative report.




## A new lead

I recently stumbled upon [1] and re-reading it now I see that they
link to [2] which mentions that BiocStyle crops by default and that
this can be turned off using `crop = NULL`.

regionReport uses BiocStyle::html_document both for its vignettes as
well as the reports it makes by default. Actually at [3], which was
built using the Bioconductor devel docker & GitHub Actions (GHA), I
see tons of messages that are similar to:

## The magick package is required to crop
"basicExploration_files/figure-html/pvals-1.png" but not available.

For reference, [4] is how that example from
regionReport::derfinderReport() looks built using GHA. I copied the
log of messages to a gist at [5]. From [6] I found [7] where Mike
Smith explains to Aaron Lun the default behavior of BiocStyle and
again suggests to use `crop = NULL` just like Yihui Xie mentioned
earlier at [2]. I see at [8] that Kevin Rue-Albrecht also ran into a
`crop = NULL` problem in iSEE.


So I have a good lead now!


## Adding magick to Suggests

We can see clearly that magick is not available on my GitHub Actions
run using the Biocondutor devel docker: regionReport 1.21.7 doesn't
mention magick on it's DESCRIPTION so it's never installed on GHA.
However, magick is likely installed on the Bioconductor 3.11 Linux
build machine and thus it is used for cropping. At [9] I bumped
regionReport to 1.21.8 after adding magick to suggests. Actually, this
is what Yihui Xie recommends BiocStyle could/should do in [2]. That
crashed and burned on GHA Linux with Bioc-docker at [10], thus
reproducing the Linux build machine error.

Quitting from lines 224-229 (basicExploration.Rmd)
35Error: processing vignette 'regionReport.Rmd' failed with diagnostics:
36R: cache resources exhausted
`/tmp/RtmpfaoqUE/Rbuild74c3a6bf655/regionReport/vignettes/report/html/basicExploration_files/figure-html/plotRegions-17.png'
@ error/cache.c/OpenPixelCache/4083

Actually, this error message is more informative than the one from the
Bioc Linux builder as it gives the actual image name where it all
burned down.


## Moving problematic code from the vignette to an example

At [11] I moved the problematic code to an example instead of the
vignette. On GHA, it failed again at [12] predictably on another image
than in [10]. Also predictably, R CMD build worked this time, but R
CMD check failed. However, now the I get the full logs that help me
see the details much better and link it to code [13] (so if that was
the bug source, I would know where to look).

Quitting from lines 399-400 (basicExploration.Rmd)
355Error in magick_image_trim(image, fuzz) :
356 R: cache resources exhausted
`/__w/regionReport/regionReport/check/regionReport.Rcheck/derfinderReport-example/basicExploration/basicExploration_files/figure-html/genomeOverview3-1.png'
@ error/cache.c/OpenPixelCache/4083
357Calls: derfinderReport ...  -> assert_image ->
 -> magick_image_trim
358Execution halted


## Using crop = NULL

At [14] I dropped magick from the DESCRIPTION and added crop = NULL to
the template Rmd files in regionReport. On GHA the Linux build ran
well [15] and the resulting example report [overwrote 4] looks well =)


## Other OS?

What about the other OS? Well, I guess that they have some extra
resources than the Linux one. For example, locally on my macOS laptop
regionReport 1.2.8 did build [16] with magick being available.

Alternatively, the other Bioc-devel build machines (Windows, macOS)
might not have magick installed, hence no cropping was attempted and
no errors would have been detected, like in GHA's Linux regionReport
1.2.7 build.


I replied to Thomas Lumley about the lead idea at [17] before doing
all these tests.



Best,
Leo

[1] https://github.com/yihui/knitr/issues/1785#issuecomment-574723631
[2] 

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

[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

[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

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

[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

[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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[Bioc-devel] Cannot reproduce a regionReport 1.21.7 error on the Bioc 3.11 Linux builder

[Leonardo Collado Torres]

Hi Bioc-devel,

I'm having trouble with my regionReport package on the Bioc-devel
(3.11) Linux builds. Two weeks ago, using the Bioconductor devel
docker I was able to reproduce an error that was solved by ggbio
bumping their version number to 1.35.2 as described in [1]. I've tried
my best to reproduce the error shown at [2] which is:

Quitting from lines 224-229 (basicExploration.Rmd)
Error: processing vignette 'regionReport.Rmd' failed with diagnostics:
R: unable to get registry ID `cache:hosts' @
error/registry.c/GetImageRegistry/202

Recently [3], I bumped the regionReport version to 1.21.7 where I
explicitly asked for ggbio 1.35.2 to be available. I suspected that
the Linux builder still had version ggbio 1.35.1 installed. But that
did not resolve the issue as the current build report is for
regionReport version 1.21.7 and there's no error about ggbio 1.21.7
not being available. Hm... the required versions for the dependencies
does get checked at R CMD build (or even install), right?

At [4] you can see that regionReport 1.21.7 can be successfully
checked against Bioconductor devel's docker. This uses GitHub actions
that has 7 GB of RAM available [5]. The memory resources (7GB vs 2.5
GB? [6]), disk space (14 GB vs ?) and some system dependencies are the
only differences I can think of (installed through [7], none seem to
me to be related from what I see at [8]) besides the Linux builder
differences vs the Bioconductor devel docker (dunno what they are).

If you have any suggestions, please let me know.

Best,
Leo

[1] https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016538.html
[2] 
https://master.bioconductor.org/checkResults/3.11/bioc-LATEST/regionReport/malbec2-buildsrc.html
[3] 
https://github.com/leekgroup/regionReport/commit/5e7d956f71011f8551f2431f5af0e212d04be9f1
[4] 
https://github.com/leekgroup/regionReport/runs/604161822?check_suite_focus=true#step:8:98
[5] 
https://help.github.com/en/actions/reference/virtual-environments-for-github-hosted-runners#supported-runners-and-hardware-resources
[6] 
https://github.com/Bioconductor/Contributions/issues/1389#issuecomment-605024369
2.5 GB is used for the 32-bit windows Single Package Builder.
[7] 
https://github.com/leekgroup/regionReport/runs/604161822?check_suite_focus=true#step:6:2
[8] 
https://github.com/leekgroup/regionReport/runs/604161822?check_suite_focus=true#step:6:167

Leonardo Collado Torres, Ph. D., Research Scientist
Lieber Institute for Brain Development
855 N Wolfe St, Suite 300
Baltimore, MD 21205
http://lcolladotor.github.io

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Re: [Bioc-devel] ChemmineOB build failing on windows

[Hervé Pagès]

On 4/23/20 12:52, Hervé Pagès wrote:

On 4/23/20 12:45, Hervé Pagès wrote:

On 4/23/20 10:45, Kevin Horan wrote:

Bioc,

The build of ChemmineOB is failing on windows, which is also causing 
3 other packages to fail (ChemmineR, eiR, and fmcsR). I was able to 
build the package on my own windows machine (Windows Server 2012 R2 
Standard) without any error. I used R devel. The content of this 
package has not been changed since October 2018.


Right but the toolchain used for R 4.0.0 on Windows now is Rtool40 
which is a huge upgrade from the previous one. Could this be related 
to the compilation failure?


It also occurs to me that we might need to recompile Open Babel with the 
new toolchain on tokay2. Could that be the problem?


FWIW the RProtoBufLib/cytolib maintainers had to do this for the 
protobuf and they made the updated binaries available here: 
http://rglab.github.io/binaries/


It seems to be pretty typical with C++ code that the binaries tend to 
break with major updates of the compiler (generally because of changes 
to how the compiler mangles method names).


H.



H.



Best,
H.



Can someone please look into it? Thanks. The build link is 
https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ChemmineOB_tokay2-2Dbuildsrc.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=wmRn4CjxRi7ewvrtWLIyKM2Tockd3ZOaWfhhytkrbCM=hoMGH754DpRKnA8RGcuSStVub2IwW2BGrG6lvBK4io4= 



Kevin

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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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Re: [Bioc-devel] ChemmineOB build failing on windows

[Kevin Horan]

Hervé,

    It could be. The test I did today was on a clean windows machine, 
so I did build open babel from scratch with Rtools40. I don't have an 
openbabel built with the old version to check. The INSTALL file of 
ChemmineOB provides detail instructions for building OpenBabel on windows.


Kevin

On 4/23/20 12:52 PM, Hervé Pagès wrote:

On 4/23/20 12:45, Hervé Pagès wrote:

On 4/23/20 10:45, Kevin Horan wrote:

Bioc,

The build of ChemmineOB is failing on windows, which is also causing 
3 other packages to fail (ChemmineR, eiR, and fmcsR). I was able to 
build the package on my own windows machine (Windows Server 2012 R2 
Standard) without any error. I used R devel. The content of this 
package has not been changed since October 2018.


Right but the toolchain used for R 4.0.0 on Windows now is Rtool40 
which is a huge upgrade from the previous one. Could this be related 
to the compilation failure?


It also occurs to me that we might need to recompile Open Babel with 
the new toolchain on tokay2. Could that be the problem?


H.



Best,
H.



Can someone please look into it? Thanks. The build link is 
https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ChemmineOB_tokay2-2Dbuildsrc.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=wmRn4CjxRi7ewvrtWLIyKM2Tockd3ZOaWfhhytkrbCM=hoMGH754DpRKnA8RGcuSStVub2IwW2BGrG6lvBK4io4= 



Kevin

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Re: [Bioc-devel] ChemmineOB build failing on windows

[Hervé Pagès]

On 4/23/20 13:18, Kevin Horan wrote:

Hervé,

     It could be. The test I did today was on a clean windows machine, 
so I did build open babel from scratch with Rtools40. I don't have an 
openbabel built with the old version to check. The INSTALL file of 
ChemmineOB provides detail instructions for building OpenBabel on windows.


We'll try this. That is unfortunate as it requires more time than we can 
realistically spend on the builders to satisfy the needs of 1800+ 
software packages. It would be really appreciated if in the future you 
could provide Open Babel binaries that we can just unzip on the Windows 
builders.


Thanks,
H.



Kevin

On 4/23/20 12:52 PM, Hervé Pagès wrote:

On 4/23/20 12:45, Hervé Pagès wrote:

On 4/23/20 10:45, Kevin Horan wrote:

Bioc,

The build of ChemmineOB is failing on windows, which is also causing 
3 other packages to fail (ChemmineR, eiR, and fmcsR). I was able to 
build the package on my own windows machine (Windows Server 2012 R2 
Standard) without any error. I used R devel. The content of this 
package has not been changed since October 2018.


Right but the toolchain used for R 4.0.0 on Windows now is Rtool40 
which is a huge upgrade from the previous one. Could this be related 
to the compilation failure?


It also occurs to me that we might need to recompile Open Babel with 
the new toolchain on tokay2. Could that be the problem?


H.



Best,
H.



Can someone please look into it? Thanks. The build link is 
https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ChemmineOB_tokay2-2Dbuildsrc.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=wmRn4CjxRi7ewvrtWLIyKM2Tockd3ZOaWfhhytkrbCM=hoMGH754DpRKnA8RGcuSStVub2IwW2BGrG6lvBK4io4= 



Kevin

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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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Re: [Bioc-devel] ChemmineOB build failing on windows

[Hervé Pagès]

On 4/23/20 10:45, Kevin Horan wrote:

Bioc,

The build of ChemmineOB is failing on windows, which is also causing 3 
other packages to fail (ChemmineR, eiR, and fmcsR). I was able to build 
the package on my own windows machine (Windows Server 2012 R2 Standard) 
without any error. I used R devel. The content of this package has not 
been changed since October 2018.


Right but the toolchain used for R 4.0.0 on Windows now is Rtool40 which 
is a huge upgrade from the previous one. Could this be related to the 
compilation failure?


Best,
H.



Can someone please look into it? Thanks. The build link is 
https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ChemmineOB_tokay2-2Dbuildsrc.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=wmRn4CjxRi7ewvrtWLIyKM2Tockd3ZOaWfhhytkrbCM=hoMGH754DpRKnA8RGcuSStVub2IwW2BGrG6lvBK4io4= 



Kevin

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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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Re: [Bioc-devel] ChemmineOB build failing on windows

[Hervé Pagès]

On 4/23/20 12:45, Hervé Pagès wrote:

On 4/23/20 10:45, Kevin Horan wrote:

Bioc,

The build of ChemmineOB is failing on windows, which is also causing 3 
other packages to fail (ChemmineR, eiR, and fmcsR). I was able to 
build the package on my own windows machine (Windows Server 2012 R2 
Standard) without any error. I used R devel. The content of this 
package has not been changed since October 2018.


Right but the toolchain used for R 4.0.0 on Windows now is Rtool40 which 
is a huge upgrade from the previous one. Could this be related to the 
compilation failure?


It also occurs to me that we might need to recompile Open Babel with the 
new toolchain on tokay2. Could that be the problem?


H.



Best,
H.



Can someone please look into it? Thanks. The build link is 
https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_ChemmineOB_tokay2-2Dbuildsrc.html=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=wmRn4CjxRi7ewvrtWLIyKM2Tockd3ZOaWfhhytkrbCM=hoMGH754DpRKnA8RGcuSStVub2IwW2BGrG6lvBK4io4= 



Kevin

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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] current openbabel version on tokay2

[Hervé Pagès]

Hi Kevin,

The only thing I found that gives an indication of what version we have 
on tokay2 is this line at the top of the README.md file in the Open 
Babel src folder (c:\openbabel\src\i386\):


  Open Babel README version 2.4.0

Best,
H.


On 4/23/20 09:01, Kevin Horan wrote:


I have a build error on my ChemmineOB package on windows, Tokay2. So 
that I can try to reproduce the error locally, could you let me know 
what version of OpenBabel is on that machine? My assumption would be 
that it is 2.4.1. It's not an R package, so it's not listed on your 
website. Thanks.


Kevin Horan

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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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Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Charles Warden]

Hi H,

Thank you for the additional information.

I have pushed the git updates using tempdir() instead of getwd().  It sounds 
like that will probably fix the problem, and I will check tomorrow.

Best Wishes,
Charles

-Original Message-
From: Hervé Pagès  
Sent: Thursday, April 23, 2020 12:23 PM
To: Charles Warden ; Shepherd, Lori 
; 'bioc-devel@r-project.org' 

Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Attention: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.]

--
Hi Charles,

On 4/23/20 10:19, Charles Warden wrote:

> My guess was that creating the temporary file in the working directory 
> instead of another folder might help.

FWIW here are 2 important reasons for writing temporary stuff to
tempdir() instead of the current working directory:

1. tempdir() is the only place that is guaranteed to be writable on every 
system. Yes the user home is very likely to be writable too but there is 
actually no guarantee and some systems have unconventional setups where it's 
not.

2. Whatever you put in tempdir() will automatically be removed at the end of 
the R session. Even though there are ways to achieve this with the temporary 
stuff you write in the user home, it's not automatic and hard to get right.

Cheers,
H.

--
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] Windows Development Build Error Message for COHCAP

[Hervé Pagès]

Hi Charles,

On 4/23/20 10:19, Charles Warden wrote:


My guess was that creating the temporary file in the working directory instead 
of another folder might help.


FWIW here are 2 important reasons for writing temporary stuff to 
tempdir() instead of the current working directory:


1. tempdir() is the only place that is guaranteed to be writable on 
every system. Yes the user home is very likely to be writable too but 
there is actually no guarantee and some systems have unconventional 
setups where it's not.


2. Whatever you put in tempdir() will automatically be removed at the 
end of the R session. Even though there are ways to achieve this with 
the temporary stuff you write in the user home, it's not automatic and 
hard to get right.


Cheers,
H.

--
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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[Bioc-devel] ChemmineOB build failing on windows

[Kevin Horan]

Bioc,

The build of ChemmineOB is failing on windows, which is also causing 3 
other packages to fail (ChemmineR, eiR, and fmcsR). I was able to build 
the package on my own windows machine (Windows Server 2012 R2 Standard) 
without any error. I used R devel. The content of this package has not 
been changed since October 2018.


Can someone please look into it? Thanks. The build link is 
https://bioconductor.org/checkResults/devel/bioc-LATEST/ChemmineOB/tokay2-buildsrc.html



Kevin

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Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Shepherd, Lori]

In your vignette you also use   `getwd()`  to define your output directory.  
Please change this to use a temporary directory  `tempdir()`


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Shepherd, Lori 

Sent: Thursday, April 23, 2020 8:00 AM
To: Charles Warden ; 'bioc-devel@r-project.org' 

Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Thank you for your inquiry

R 4.0.0 can be downloaed from the following page. This patched page exists a 
few weeks out from the official R release for the patched version of R windows:


https://secure-web.cisco.com/1rVmbsYV5l6Byh8Yxia7uE_vjkELNEv9x-phlPOD4JZps4zzXWvkm5y5iT6tN_xdLE5OKhw5aFcayOxFdH1TZaOdeZSnP4jNV20TSyigyof9gxL32zvj2VKmeAycLaq__vn63nmNQcrcNfrV307jWUNM0QeREQq8TO7cM1fYdIpG1-OKb47JpH7YMFZqJyWENSteiqzz76lEINnJxX5SIY6_YknZtLWp8xRWkVjlTNKiT72Y6eAPRrCvC9FN1_Gqz4logMBLltKQBvUBbE7JY99_EtVCHLQqhmnbGg4dVxKOD75bWlau_K7grnxO6NCbAOjFnVUHVM-IEkSQruW_KPA/https%3A%2F%2Fcran.r-project.org%2Fbin%2Fwindows%2Fbase%2Frpatched.html


2.  Landing pages can have different versions of the file for different 
platforms when a package will build cleanly for one platform but not another.  
We only propagate and make available successfully built packages.


3.  You can wait a day or two if you like but realize the 3.11 release is fast 
approaching.  If this stay ERROR and it is not fixed by monday you will have to 
push fixes to both a release 3.11 and the new devel branch (master branch 
prepping for 3.12 in fall).


4.  I'll try and log on our windows builder later today to see if I can track 
down any additional information for you to help debug.  If I find anything I 
will contact you about it.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Charles Warden 

Sent: Wednesday, April 22, 2020 12:00 PM
To: 'bioc-devel@r-project.org' 
Subject: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi,

I noticed that I received a few error messages in the Windows build for COHCAP:

http://secure-web.cisco.com/14soK-lir-qt5k3KJCJKxxSPwdESxh91c_rkfAkfpDOqOUvXzM0n9MzRO_j5W5YsMzlMpHKj8hD4qgXS8qgJycZANUXuMoVlTuxKCDTotDQku3EGNvVwLIWjyC4ZeIDnSRnFJE4KnTbacOABfRotIDmjhuZqWJmXADjmoBsUTEpAhwIEMAHLe-De7YiQGt-OJNvo_Op4ArktJnzOfxhWMOUG0kZvelbmwKwV_MmvFVJpgOljB5EAcUHLuOLpvN1dlH5gsWhslkm1FvMX9gmvNJ2y0T3onSd5pHZ2FbwM8-8sgSPEbuxXjtT1WQUYyFdqUIBNQY7Xv8iEdEBt1q7qVTw/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FCOHCAP%2Ftokay2-buildsrc.html

I changed the default settings to avoid an earlier error message (again, just 
on Windows), but I am currently getting an error message that I am having some 
trouble reproducing.

Can you help me with either of the following questions?


  1.  I apologize for the simple question, but where can I download the Windows 
executable for R-4.0.0?  I was able to reproduce and fix an earlier issue with 
R-devel (on Linux), but I was not certain how to get the error message for 
Windows.  I have tried to reproduce the error using the devtools installation 
from the GitHub code 
(https://secure-web.cisco.com/1CMIdB2_FCZaFouyijL6DJBleIv1z6kjb0vJp48UqtfezzRyresTr07xJ9yP83U_HqxDPiTYbIIG_3bYDlfcvr9QH832g8VnWkkNG5dK1P2qxQbm9OWI_b3EERjUTwhY2H8cb6Lsko1ITsutzNvWoL_Dp_fvzUxN0nDwb6eghpCrMMy6ndFekSqrQdkZO0IhVKxvMXODM3MkIZRsiEaomyhKOn6lUKila6pgUgDSfQ9PypaW7BcQcWhGb9U-f8TL9fvtbUqBaB83MoDiXfJKsO_UoJLrlyh8sR6wJ5tNHkt3e-7uUwzz6H360PSI3rxp1a5gXTxLcMp9ymSQR6UF1CQ/https%3A%2F%2Fgithub.com%2Fcwarden45%2FCOHCAP),
 but that can be installed successfully (with Windows R-3.6.3).
  2.  The .zip file for the Windows version on the devel page is different 
(http://secure-web.cisco.com/1L5TyDrJci1NAZMGxCrXIKm2wn3kgWC_9LSEIs73dOegI5BFj7AhvLaYz0i17qdT2pElt5CByZhFvxEMQ2Uunp62vwJ4s_-0G-gi1gOdMQ9Z_rf-1WN7sEym8bdEQgX4sO0SE8JaTNDZUG-zwsHvCZJP6ZYlq4valW3HrFbWU8PbZ5_9r-zCQUNwVxenocEirsb8kzp5kABBj0hI9c9EvH1C2o0oAQ0O9sIKULrkHAmQqjUg3cS8axxnfC_GUNGY2Be1EHLD0Na98zDHgOce95-bK82bGVtTnR5g2ynyW9qcQqeG0SD0_LuQo3YEkSPh3gptJfBs-_myNtkqDePCZCg/http%3A%2F%2Fbioconductor.org%2Fpackages%2F3.11%2Fbioc%2Fhtml%2FCOHCAP.html),
 where I see cohcap_1.33.1.zip for Windows.  I think I saw the first error 
message in 1.33.1, and I made an intermediate change before changing the 
defaults to avoid the error message.  However, the strange thing was that I 
thought I saw an "OK" status while I was waiting for the 1.33.3 version to 
appear in the build reports (which I thought was for COHCAP 1.33.2).  Do all of 
the packages get re-built, regardless of whether an update is uploaded?
 *   I am wondering if there is a chance that I might be able to wait a day 
or two and see if I can get 

[Bioc-devel] current openbabel version on tokay2

[Kevin Horan]

I have a build error on my ChemmineOB package on windows, Tokay2. So 
that I can try to reproduce the error locally, could you let me know 
what version of OpenBabel is on that machine? My assumption would be 
that it is 2.4.1. It's not an R package, so it's not listed on your 
website. Thanks.


Kevin Horan

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Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

[Shepherd, Lori]

Thank you for your inquiry

R 4.0.0 can be downloaed from the following page. This patched page exists a 
few weeks out from the official R release for the patched version of R windows:


https://cran.r-project.org/bin/windows/base/rpatched.html


2.  Landing pages can have different versions of the file for different 
platforms when a package will build cleanly for one platform but not another.  
We only propagate and make available successfully built packages.


3.  You can wait a day or two if you like but realize the 3.11 release is fast 
approaching.  If this stay ERROR and it is not fixed by monday you will have to 
push fixes to both a release 3.11 and the new devel branch (master branch 
prepping for 3.12 in fall).


4.  I'll try and log on our windows builder later today to see if I can track 
down any additional information for you to help debug.  If I find anything I 
will contact you about it.


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Charles Warden 

Sent: Wednesday, April 22, 2020 12:00 PM
To: 'bioc-devel@r-project.org' 
Subject: [Bioc-devel] Windows Development Build Error Message for COHCAP

Hi,

I noticed that I received a few error messages in the Windows build for COHCAP:

http://secure-web.cisco.com/14soK-lir-qt5k3KJCJKxxSPwdESxh91c_rkfAkfpDOqOUvXzM0n9MzRO_j5W5YsMzlMpHKj8hD4qgXS8qgJycZANUXuMoVlTuxKCDTotDQku3EGNvVwLIWjyC4ZeIDnSRnFJE4KnTbacOABfRotIDmjhuZqWJmXADjmoBsUTEpAhwIEMAHLe-De7YiQGt-OJNvo_Op4ArktJnzOfxhWMOUG0kZvelbmwKwV_MmvFVJpgOljB5EAcUHLuOLpvN1dlH5gsWhslkm1FvMX9gmvNJ2y0T3onSd5pHZ2FbwM8-8sgSPEbuxXjtT1WQUYyFdqUIBNQY7Xv8iEdEBt1q7qVTw/http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FCOHCAP%2Ftokay2-buildsrc.html

I changed the default settings to avoid an earlier error message (again, just 
on Windows), but I am currently getting an error message that I am having some 
trouble reproducing.

Can you help me with either of the following questions?


  1.  I apologize for the simple question, but where can I download the Windows 
executable for R-4.0.0?  I was able to reproduce and fix an earlier issue with 
R-devel (on Linux), but I was not certain how to get the error message for 
Windows.  I have tried to reproduce the error using the devtools installation 
from the GitHub code 
(https://secure-web.cisco.com/1CMIdB2_FCZaFouyijL6DJBleIv1z6kjb0vJp48UqtfezzRyresTr07xJ9yP83U_HqxDPiTYbIIG_3bYDlfcvr9QH832g8VnWkkNG5dK1P2qxQbm9OWI_b3EERjUTwhY2H8cb6Lsko1ITsutzNvWoL_Dp_fvzUxN0nDwb6eghpCrMMy6ndFekSqrQdkZO0IhVKxvMXODM3MkIZRsiEaomyhKOn6lUKila6pgUgDSfQ9PypaW7BcQcWhGb9U-f8TL9fvtbUqBaB83MoDiXfJKsO_UoJLrlyh8sR6wJ5tNHkt3e-7uUwzz6H360PSI3rxp1a5gXTxLcMp9ymSQR6UF1CQ/https%3A%2F%2Fgithub.com%2Fcwarden45%2FCOHCAP),
 but that can be installed successfully (with Windows R-3.6.3).
  2.  The .zip file for the Windows version on the devel page is different 
(http://secure-web.cisco.com/1L5TyDrJci1NAZMGxCrXIKm2wn3kgWC_9LSEIs73dOegI5BFj7AhvLaYz0i17qdT2pElt5CByZhFvxEMQ2Uunp62vwJ4s_-0G-gi1gOdMQ9Z_rf-1WN7sEym8bdEQgX4sO0SE8JaTNDZUG-zwsHvCZJP6ZYlq4valW3HrFbWU8PbZ5_9r-zCQUNwVxenocEirsb8kzp5kABBj0hI9c9EvH1C2o0oAQ0O9sIKULrkHAmQqjUg3cS8axxnfC_GUNGY2Be1EHLD0Na98zDHgOce95-bK82bGVtTnR5g2ynyW9qcQqeG0SD0_LuQo3YEkSPh3gptJfBs-_myNtkqDePCZCg/http%3A%2F%2Fbioconductor.org%2Fpackages%2F3.11%2Fbioc%2Fhtml%2FCOHCAP.html),
 where I see cohcap_1.33.1.zip for Windows.  I think I saw the first error 
message in 1.33.1, and I made an intermediate change before changing the 
defaults to avoid the error message.  However, the strange thing was that I 
thought I saw an "OK" status while I was waiting for the 1.33.3 version to 
appear in the build reports (which I thought was for COHCAP 1.33.2).  Do all of 
the packages get re-built, regardless of whether an update is uploaded?
 *   I am wondering if there is a chance that I might be able to wait a day 
or two and see if I can get a status of "OK" for all steps on all of the test 
servers.  However, if that is true, then I am a little worried about what 
happens if there is a temporary error in the release version.


Thank you very much!

Sincerely,
Charles
Charles Warden, Bioinformatics Specialist
Integrative Genomics Core
City of Hope National Medical Center
Shamrock Monrovia Building (655 Huntington Dr, Monrovia, CA, 91016)
Room 1086
Internal Ext: 80375 | Direct: 626-218-0375

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