In case someone is wondering: The patch has also been applied in release.
Any packages currently failing with the error
Error: processing vignette 'x.Rmd' failed with diagnostics:
unused arguments (self_contained, lib_dir, output_dir)
Execution halted
should recover with BiocStyle v.2.2.1
Dear all,
the compatibility issue with rmarkdown 1.2 have been resolved in
https://github.com/Bioconductor-mirror/BiocStyle/commit/307ad19
Guangchuang, thank you for the heads up on the problem. Even though I was
aware of the incompatibility with rmarkdown release candidate, I couldn't
address it
I found the issue was filed by yihui half month ago on github,
https://github.com/Bioconductor/BiocStyle/issues/18, and the solution is
quite intuitive by removing those un-supported paramters (self_contained,
lib_dir, output_dir). Hope it will be fixed soon.
On Wed, Nov 23, 2016 at 2:25 PM, Leon
Guangchuang, you can see at
https://github.com/Bioconductor/BiocStyle/issues/19 (the main github
repo for this package) that this issue is already been reported and
will be addressed asap by BiocStyle's maintainer.
On Tue, Nov 22, 2016 at 9:46 PM, Yu, Guangchuang wrote:
>
> Dear all,
>
> I recomp
Dear all,
I recompile my package and it throw the following error when building
vignettes:
unused arguments (self_contained, lib_dir, output_dir)
I search ?opts_knit, and couldn't find these parameters.
In ?opts_knit, I find *self.contained* instead of *self_contained*.
I remove the dependenc
