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 in BiocStyle before rmarkdown 1.2 was released (which happened
only a day ago). Also, please note that the internal changes in rmarkdown
were more complex than only the change of interface to
`rmarkdown:::pandoc_html_highlight_args`, so in order to fix this edits
in multiple places and files were necessary. Regarding the use of `:::`,
I'm currently reviewing the package code in order to avoid it's use if
possible.
Best,
Andrzej
On Wed, Nov 23, 2016 at 8:49 AM, Yu, Guangchuang <gcyu at connect.hku.hk>
wrote:
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, Leonardo Collado Torres <
lcollado at jhu.edu>
wrote:
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 <gcyu at connect.hku.hk>
wrote:
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 dependency of BiocStyle and recompile my package and it
blob/master/R/html_document.R#L66-L70
Now rmarkdown:::pandoc_html_highlight_args (in latest release version
only accepts template and highlight parameters.
This will fail the compilation of many Bioconductor packages. Please
Using ::: is not recommended by Bioconductor and will not passed by
BiocCheck (if I remember it correctly). But I find several packages by
Bioconductor core team use it.
Best wishes,
Guangchuang
--
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Guangchuang Yu, PhD Candidate
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong
Hong Kong SAR, China
www: https://guangchuangyu.github.io
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