On Wed, Oct 9, 2019 at 6:55 AM Andrzej Oleś wrote:
> Hi Vince,
>
> I briefly communicated with Martin regarding this issue a few days ago.
> The ImageMagick convert tool called by BiocStyle through a knitr figure
> cropping hook can certainly be improved, as pointed out by Yihui in the in
> the G
Hi Vince,
I briefly communicated with Martin regarding this issue a few days ago. The
ImageMagick convert tool called by BiocStyle through a knitr figure
cropping hook can certainly be improved, as pointed out by Yihui in the in
the GitHub issue linked by Christian. This is something I will look i
Just wondering whether this has been followed up. I am still seeing build
errors for
windows related to this.
On Tue, Sep 17, 2019 at 10:20 AM Christian Mertes wrote:
> I just came across this issue on rmarkdown which links the same problem to
> BiocStyle.
> The post is from Nov 2017.
>
> https
I just came across this issue on rmarkdown which links the same problem
to BiocStyle.
The post is from Nov 2017.
https://github.com/rstudio/rmarkdown/issues/1207
Maybe this helps to understand the underlying problem?
It was suggested to check this in BiocStyle:
Have you reported to the authors
New to me too. But it seems that knitr suggests magick, which itself has
SystemRequirements: ImageMagick++: ImageMagick-c++-devel (rpm) or
libmagick++-dev (deb)
Don't know when this knitr dep on magick was introduced tough... Bummer!
H.
On 9/11/19 06:13, Kasper Daniel Hansen wrote:
> Yeah,
Yeah, does this imply that the render operation uses (or tries to use)
ImageMagick? That's news to me, but I am not following this closely.
On Wed, Sep 11, 2019 at 5:21 AM Pages, Herve wrote:
> On 9/11/19 00:50, Vincent Carey wrote:
> > I seem to be running into a similar problem with BiocOncoTK
On 9/11/19 00:50, Vincent Carey wrote:
> I seem to be running into a similar problem with BiocOncoTK on windows
>
> The build report for tokay1 shows:
>
> Loading required package: ontologyIndex
> Invalid Parameter - /figure-html
> Warning in shell(paste(c(cmd, args), collapse = " ")) :
>'con
I seem to be running into a similar problem with BiocOncoTK on windows
The build report for tokay1 shows:
Loading required package: ontologyIndex
Invalid Parameter - /figure-html
Warning in shell(paste(c(cmd, args), collapse = " ")) :
'convert "BiocOncoTK_files/figure-html/lkgbm-1.png" -trim
"B
Thanks a lot for the info! So from my understanding we dont use any
trimming or editing function from ImageMagick directly. I think this is
rather knitr based since we just include png files in the vignette.
I guess it was an hickup since now the error is gone over night.
Best regards,
Christian
You don't declare any systems requirements for ImageMagick (doing so will
probably not solve your problem, but you really should).
Alternatively you could look into using the tools provided by the magick
package, which wraps ImageMagick.
But it looks like you're editing PNG files for your vignett
Dear BioC team,
I just noticed that our package is failing on the bioconductor build
system during the build of the vignette on Windows and on MacOS platforms.
>From the error I would guess its a problem with the installation of the
ImageMagick package. Please correct me if Im wrong.
It goes thr
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