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 withou
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 ‘chimeravi
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
* c
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:
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,
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/m
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 fi
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.
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 im
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
Hi,
I went to google again and maybe
https://github.com/phw/peek/issues/112#issuecomment-296690302 is the
answer? It would require someone with access to the Linux builder to
check this particular ImageMagick config XML file.
I had linked to this thread earlier
https://stat.ethz.ch/pipermail/bioc
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 repro
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
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 f
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.
Kev
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.
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
Standar
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
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
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(
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
b
Hi Lori,
Thank you very much.
Yes - I understand that there is an upcoming deadline.
If I install the version of R for Windows that you provided and I install
Rtools from the following link
(https://cran.r-project.org/bin/windows/Rtools/), then I can still successfully
install the devel versi
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,
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.
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 th
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