fix knitr table options to pass check

cran-comments.md

@@ -1,25 +1,14 @@
-## Resubmission
+## Comments
 
-As requested the DESCRIPTION now contains a reference for the Plackett-Luce model.
+This update addresses the warnings caused by not using Suggests 
+conditionally (specifically relying on Biostyle for the vignette).
 
 ## Test environments
 
-(Re-tested with the same results)
-
 * Local
  - Ubuntu 14.04, R 3.4.3
- - Ubuntu 14.04, R Under development (unstable) (2017-12-04 r73829)
+ - Ubuntu 14.04, R Under development (unstable) (2018-02-18 r74270)
  - Windows 8, R 3.4.3
 
 * Via R-hub 
  - Mac OS 10.11 El Capitan, R-release (experimental)
-
-## Comments
-
-On Mac/Ubuntu, R CMD check only returns note that this is a new submission.
-
-On Windows, R CMD check returns the same note in the log, however in the terminal there is the following warning:
-
-   * checking CRAN incoming feasibility ...Warning: running command '"pandoc" "C:\Users\hturner\PlackettLuce.Rcheck\00_pkg_src\PlackettLuce\README.md" -s --email-obfuscation=references --self-contained -o "C:\Users\hturner\AppData\Local\Temp\RtmpyQZw3Z\READMEcf025d05abf.html"' had status 99
-
-The warning seems to be due to pandoc not finding image files in `man/figures`. I could successfully run the pandoc command by either changing directory to "C:\Users\hturner\PlackettLuce.Rcheck\00_pkg_src\PlackettLuce" and calling pandoc on "README.md", or adding `--resource-path "C:\Users\hturner\PlackettLuce.Rcheck\00_pkg_src\PlackettLuce` to the call shown in the warning.

vignettes/Overview.Rmd

@@ -43,7 +43,10 @@ link-citations: true
 ```{r vignette-setup, include = FALSE}
 library(knitr)
 eval_all <- FALSE # evaluate all timings and pltree?
-options(knitr.table.format = opts_knit$get("rmarkdown.pandoc.to"))
+# if render using rmarkdown, use output format to decide table format
+table.format <- opts_knit$get("rmarkdown.pandoc.to")
+if (!identical(table.format, "latex")) table.format <- "html"
+opts_knit$set(knitr.table.format = table.format)
 opts_chunk$set(message = FALSE)
 ```