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update docker
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@ThierryO
ThierryO committed Apr 2, 2024
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209 changes: 47 additions & 162 deletions Dockerfile
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FROM rocker/verse
FROM rocker/verse:latest

ARG BUILD_DATE
ARG VCS_REF
Expand All @@ -18,174 +18,59 @@ ENV DEBCONF_NONINTERACTIVE_SEEN true

## Install nano
RUN apt-get update \
&& apt upgrade -y \
&& apt-get install -y --no-install-recommends \
nano

COPY docker/.Rprofile $R_HOME/etc/Rprofile.site

## install assertthat
RUN apt update \
&& apt install -y --no-install-recommends r-cran-assertthat \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("assertthat")'

## install desc
RUN apt update \
&& apt install -y --no-install-recommends r-cran-desc \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("desc")'

## install fs
RUN apt update \
&& apt install -y --no-install-recommends r-cran-fs \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("fs")'

## install jsonlite
RUN apt update \
&& apt install -y --no-install-recommends r-cran-jsonlite \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("jsonlite")'

## install hunspell
RUN apt update \
&& apt install -y --no-install-recommends r-cran-hunspell \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("hunspell")'

## install R6
RUN apt update \
&& apt install -y --no-install-recommends r-cran-r6 \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("R6")'

## install httr
RUN apt update \
&& apt install -y --no-install-recommends r-cran-httr \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("httr")'

## install gert
RUN apt update \
&& apt install -y --no-install-recommends r-cran-gert \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("gert")'

## install knitr
RUN apt update \
&& apt install -y --no-install-recommends r-cran-knitr \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("knitr")'

## install sessioninfo
RUN apt update \
&& apt install -y --no-install-recommends r-cran-sessioninfo \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("sessioninfo")'

## install withr
RUN apt update \
&& apt install -y --no-install-recommends r-cran-withr \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("withr")'

## install yaml
RUN apt update \
&& apt install -y --no-install-recommends r-cran-yaml \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("yaml")'

## install curl
RUN apt update \
&& apt install -y --no-install-recommends r-cran-curl \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("curl")'

## install renv
RUN Rscript --no-save --no-restore -e 'remotes::install_cran("renv")'

## install covr
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
libharfbuzz-dev \
libfribidi-dev \
r-cran-covr \
&& apt-get clean \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("covr")'

## install lintr
RUN Rscript --no-save --no-restore -e 'remotes::install_cran("lintr")'

## install rcmdcheck
RUN apt update \
&& apt install -y --no-install-recommends r-cran-rcmdcheck \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("rcmdcheck")'

## install rmarkdown
RUN apt update \
&& apt install -y --no-install-recommends r-cran-rmarkdown \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("rmarkdown")'

## install roxygen2
RUN apt update \
&& apt install -y --no-install-recommends r-cran-roxygen2 \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("roxygen2")'

## install INLA
RUN Rscript --no-save --no-restore -e 'remotes::install_cran("INLA", type = "source")'

## install bookdown
RUN apt update \
&& apt install -y --no-install-recommends r-cran-bookdown \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("bookdown")'

## install mockery
RUN apt update \
&& apt install -y --no-install-recommends r-cran-mockery \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("mockery")'

## install pdftools
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
libpoppler-cpp-dev \
r-cran-pdftools \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("pdftools")'

## install rstudioapi
RUN apt update \
&& apt install -y --no-install-recommends r-cran-rstudioapi \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("rstudioapi")'

## install codemetar
RUN Rscript --no-save --no-restore -e 'remotes::install_cran("codemetar")'

## install testthat
RUN apt update \
&& apt install -y --no-install-recommends r-cran-testthat \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("testthat")'

## install pkgdown
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
libfontconfig1-dev \
libfreetype6-dev \
libjpeg-dev \
libpng-dev \
libtiff5-dev \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("pkgdown")'

## install sysfonts
RUN Rscript --no-save --no-restore -e 'remotes::install_cran("sysfonts")'

## install showtext
RUN Rscript --no-save --no-restore -e 'remotes::install_cran("showtext")'

## install hexSticker
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
libmagick++-dev \
&& apt-get clean \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("hexSticker")'

## install devtools
RUN apt update \
&& apt install -y --no-install-recommends r-cran-devtools \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("devtools")'

## install zen4R
RUN apt update \
&& apt install -y --no-install-recommends libsecret-1-dev \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("zen4R")'

## install microbenchmark
RUN Rscript --no-save --no-restore -e 'remotes::install_cran("microbenchmark")'
&& apt install -y --no-install-recommends \
gdal-bin libgdal-dev libproj-dev libudunits2-dev r-cran-class \
r-cran-classint r-cran-cli r-cran-dbi r-cran-e1071 r-cran-fansi \
r-cran-units r-cran-dplyr r-cran-generics r-cran-glue \
r-cran-kernsmooth r-cran-lattice r-cran-lifecycle r-cran-magrittr \
r-cran-matrix r-cran-pillar r-cran-pkgconfig r-cran-proxy \
r-cran-r6 r-cran-rcpp r-cran-rlang r-cran-s2 r-cran-sf r-cran-sp \
r-cran-tibble r-cran-tidyselect r-cran-utf8 r-cran-vctrs r-cran-withr \
r-cran-wk \
&& Rscript --no-save --no-restore -e 'update.packages(ask = FALSE)' \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("fmesher")' \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("INLA", type = "source")'

## install sn
RUN apt update \
&& apt install -y --no-install-recommends \
r-cran-matrixmodels r-cran-mnormt r-cran-numderiv r-cran-quantreg \
r-cran-sn r-cran-sparsem \
&& Rscript --no-save --no-restore -e 'update.packages(ask = FALSE)' \
&& Rscript --no-save --no-restore -e 'remotes::install_cran("sn")'

## install checklist dependencies
RUN apt update \
&& apt install -y --no-install-recommends \
r-cran-askpass r-cran-assertthat r-cran-backports r-cran-base64enc \
r-cran-brew r-cran-brio r-cran-cachem r-cran-callr r-cran-clipr \
r-cran-commonmark r-cran-crayon r-cran-credentials r-cran-crul r-cran-curl \
r-cran-desc r-cran-devtools r-cran-diffobj r-cran-digest r-cran-downlit \
r-cran-ellipsis r-cran-evaluate r-cran-fastmap r-cran-fs r-cran-gert \
r-cran-gh r-cran-gitcreds r-cran-highr r-cran-htmltools r-cran-htmlwidgets \
r-cran-httpcode r-cran-httpuv r-cran-httr r-cran-hunspell r-cran-ini \
r-cran-jsonlite r-cran-jquerylib r-cran-knitr r-cran-later r-cran-lazyeval \
r-cran-memoise r-cran-mime r-cran-miniui r-cran-openssl r-cran-pingr \
r-cran-pkgbuild r-cran-pkgload r-cran-praise r-cran-prettyunits \
r-cran-processx r-cran-promises r-cran-ps r-cran-purrr r-cran-ragg \
r-cran-rappdirs r-cran-rcmdcheck r-cran-rematch2 r-cran-rex \
r-cran-rmarkdown r-cran-roxygen2 r-cran-remotes r-cran-rprojroot \
r-cran-rstudioapi r-cran-rversions r-cran-sass r-cran-sessioninfo \
r-cran-shiny r-cran-sourcetools r-cran-stringi r-cran-stringr r-cran-sys \
r-cran-systemfonts r-cran-testthat r-cran-textshaping r-cran-tinytex \
r-cran-triebeard r-cran-urltools r-cran-usethis r-cran-waldo \
r-cran-whisker r-cran-xfun r-cran-xml2 r-cran-xopen r-cran-xtable \
r-cran-yaml r-cran-zip \
&& Rscript --no-save --no-restore -e 'update.packages(ask = FALSE)' \
&& Rscript --no-save --no-restore -e 'remotes::install_cran(c("bslib", "codemeta", "codemetar", "cyclocompt", "fontawesome", "httr2", "lintr", "pkgdown", "profvis", "renv", "urlchecker", "xmlparsedata"))'

## install checklist
COPY . /checklist/
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