Update:
After upgrading to Linux 18.3, I now have pandoc 2.3.1 installed on my laptop. Compilation from R using bookdown::render_book('index.Rmd', "bookdown::gitbook", encoding='UTF-8' results in the correct html encoding (ie, user's guide).
Session info on laptop:
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 18.3
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
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
loaded via a namespace (and not attached):
[1] compiler_3.4.4 backports_1.1.1 magrittr_1.5 bookdown_0.7
[5] rprojroot_1.2 htmltools_0.3.6 tools_3.4.4 rstudioapi_0.7
[9] yaml_2.1.14 Rcpp_0.12.18 stringi_1.1.5 rmarkdown_1.7
[13] knitr_1.20 stringr_1.2.0 digest_0.6.12 xfun_0.3
[17] evaluate_0.10.1
Session info on production server:
R version 3.4.3 (2017-11-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.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
loaded via a namespace (and not attached):
[1] compiler_3.4.3 backports_1.1.2 magrittr_1.5 bookdown_0.7
[5] rprojroot_1.3-2 htmltools_0.3.6 tools_3.4.3 rstudioapi_0.7
[9] yaml_2.1.18 Rcpp_0.12.16 stringi_1.1.7 rmarkdown_1.9
[13] knitr_1.20 stringr_1.3.0 digest_0.6.15 xfun_0.3
[17] evaluate_0.10.1