From c0e9a22d2e01a692baaafa596c1e2323485da28d Mon Sep 17 00:00:00 2001 From: Heather Turner Date: Mon, 19 Feb 2018 21:39:42 +0000 Subject: [PATCH] fix knitr table options to pass check --- cran-comments.md | 19 ++++--------------- vignettes/Overview.Rmd | 5 ++++- 2 files changed, 8 insertions(+), 16 deletions(-) diff --git a/cran-comments.md b/cran-comments.md index eb61a61..ae4f4e7 100644 --- a/cran-comments.md +++ b/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. diff --git a/vignettes/Overview.Rmd b/vignettes/Overview.Rmd index 1100dea..651a7e1 100644 --- a/vignettes/Overview.Rmd +++ b/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) ```