atusy/atusyverse

atusy's universe of R environment

atusyverse's Issues

Dockerfile: `sudo -u user` より `USER user` すべし

USER の切り替えは最小限にすべし．
sudo は機能豊富なので控えるべし．
ソースはどこだっけ……．

atusyverse/docker/Dockerfile

Line 23 in 35d65f3

&& sudo -u rstudio Rscript -e "tinytex::install_tinytex()" \

は

USER rstudio
RUN Rscript -e "tinytex::install_tinytex()"
USER root

にする

Dockerfile: ユーザーとして hugo をインストールしておかないと update できない

Dockerfile を以下に直す

USER rstudio
RUN Rscript -e "blogdown::install_hugo()"

従来は

atusyverse/docker/Dockerfile

Lines 42 to 44 in 35d65f3

	&& echo "options(blogdown.hugo.dir = system.file(package = 'blogdown'))" >> \
	/usr/local/lib/R/etc/Rprofile.site \
	&& Rscript -e "blogdown::install_hugo()" \

で blogdown::update_hugo() すると以下のエラーが出ていた

The latest Hugo version is 0.54.0
trying URL 'https://github.com/gohugoio/hugo/releases/download/v0.54.0/hugo_0.54.0_Linux-64bit.tar.gz'
Content type 'application/octet-stream' length 7767211 bytes (7.4 MB)
==================================================
downloaded 7.4 MB

Hugo has been installed to /home/rstudio/bin
Warning message:
In file.copy(exec, destdir, overwrite = TRUE) :
  problem copying ./hugo to /usr/local/lib/R/site-library/blogdown/hugo: Permission denied

rocker/r-ver は MRAN の snapshot を使うらしい

https://github.com/rocker-org/rocker-versioned/blob/17a5005a6b09e527c86869c035126303b7574d28/r-ver/3.5.2/Dockerfile#L112

install_hugo installs hugo into /root/bin not in ~/bin

Dockerfile: use installGithub.r instead of remotes::install_github

tinytex::install_tinytex(force = TRUE) seems to be required

Otherwise, error occurs due to permission error

copy /opt/TinyTeX/tlpkg/texlive.tlpdb.tmp to /opt/TinyTeX/tlpkg/texlive.tlpdb failed: Operation not permitted at /opt/TinyTeX/tlpkg/TeXLive/TLPDB.pm line 630.
tlmgr path add

On a first trial, I used reinstall_tinytex resulting following error messages, but seems working.

sh: 1: path: not found
install: target 'zapfding' is not a directory
sh: 1: conf: not found
TinyTeX installed to /home/rstudio/.TinyTeX
Error in root_dir(normalizePath(path), "..", "..", "..") : 
  /home/rstudio/.TinyTeX does not seem to be the root directory of TeX Live (no "bin/" dir under it)
In addition: Warning messages:
1: In system2(bin, c("path", "add")) : error in running command
2: In system2(bin, c("conf", "auxtrees", "add", r_texmf_path())) :
  error in running command
You may have to restart your system after installing TinyTeX to make sure ~/bin appears in your PATH variable (https://github.com/yihui/tinytex/issues/16).