RMarkdown: preserve source code formatting in code cell - r

Question

My Rmarkdown source looks like (screenshot from RStudio):
(notice the empty lines)
When I press CTRL+Shift+k I got view as expected (with empty lines). However, if I run the chunk (evaluate) and then compile (CTRL+Shift+k), I get:
(no empty lines)
Is there any way how to preserve the empty lines in the source code? (I checked knitr options: strip.white=FALSE, tidy=TRUE, tidy.opts=list(blank=TRUE) but no joy.)
I'm using RStudio 1.0.153
Other info:
sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)
Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rvest_0.3.2 xml2_1.1.1 dplyr_0.7.1 purrr_0.2.2.2
[5] readr_1.1.1 tidyr_0.6.3 tibble_1.3.3 ggplot2_2.2.1
[9] tidyverse_1.1.1
loaded via a namespace (and not attached):
[1] pbdZMQ_0.2-6 reshape2_1.4.2 haven_1.1.0 lattice_0.20-35
[5] colorspace_1.3-2 htmltools_0.3.6 yaml_2.1.14 base64enc_0.1-3
[9] XML_3.98-1.9 rlang_0.1.1 foreign_0.8-69 glue_1.1.1
[13] selectr_0.3-1 readxl_1.0.0 modelr_0.1.0 semver_0.2.0
[17] bindrcpp_0.2 bindr_0.1 plyr_1.8.4 stringr_1.2.0
[21] cellranger_1.1.0 munsell_0.4.3 binman_0.1.0 gtable_0.2.0
[25] caTools_1.17.1 psych_1.7.5 evaluate_0.10.1 knitr_1.16
[29] forcats_0.2.0 wdman_0.2.2 curl_2.7 parallel_3.4.1
[33] broom_0.4.2 Rcpp_0.12.11 openssl_0.9.6 backports_1.1.0
[37] scales_0.4.1 formatR_1.5 RSelenium_1.7.1 jsonlite_1.5
[41] mnormt_1.5-5 hms_0.3 digest_0.6.12 stringi_1.1.5
[45] grid_3.4.1 rprojroot_1.2 tools_3.4.1 bitops_1.0-6
[49] magrittr_1.5 lazyeval_0.2.0 pkgconfig_2.0.1 lubridate_1.6.0
[53] httr_1.2.1 assertthat_0.2.0 rmarkdown_1.6 R6_2.2.2
[57] nlme_3.1-131 compiler_3.4.1

Answer 1

As far as I can see, you can't do that with an HTML notebook. If you don't need all the special notebook features, you can ask for an html_document instead of an html_notebook and formatting will be preserved. If you do need the notebook features, you probably need to make a feature request on the rmarkdown development page https://github.com/rstudio/rmarkdown to add this.