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legacy-04.Dockerfile
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FROM rocker/rstudio:4.0.5
WORKDIR /workspace
# Prefixes for RSPM URLs to use in install.packages() repos argument
ENV RSPM_SOURCE=https://packagemanager.posit.co/cran \
RSPM=https://packagemanager.posit.co/all/__linux__/focal \
LANG=en_GB.UTF-8
# Install system requirements in system-packages.txt: libgit2-dev, liblz4-dev, pandoc
# In original container the versions are
# libgit2-dev (0.26.0+dfsg.1-1)
# liblz4-dev (0.0~r131-2ubuntu)
# pandoc (1.19.2.4~dfsg-1b)
# brms requires: libglpk40 libxml2 libv8dev
# rgdal requires: libgdal-dev
# sf requires: libudunits2-dev
# magick requires: libmagick++-dev
# And change locale from en_US.UTF-8 to C.UTF-8
RUN apt-get update && \
apt-get install -y --no-install-recommends \
libgdal-dev \
libgit2-dev \
libglpk40 \
liblz4-dev \
libmagick++-dev \
libudunits2-dev \
libv8-dev \
libxml2 \
pandoc && \
apt-get autoremove -y && \
apt-get autoclean -y; \
/usr/sbin/locale-gen --lang "${LANG}" && \
/usr/sbin/update-locale --reset LANG="${LANG}"
# Installing Linux binary packages from the public RStudio Package Manager (RSPM) repository
# URLs for repos were obtained by selecting the relevant date on the calendar on
# https://packagemanager.rstudio.com/client/#/repos/1/overview
# Uninstall additional and packages at wrong versions from r-ver and add them at correct versions
RUN R -e "remove.packages(c('littler', \
'docopt')); \
remove.packages(c('boot', \
'class', \
'cluster', \
'codetools', \
'foreign', \
'KernSmooth', \
'Matrix', \
'nnet'), \
lib = '/usr/local/lib/R/library'); \
install.packages(c('boot', \
'class', \
'cluster', \
'codetools', \
'foreign', \
'KernSmooth', \
'Matrix', \
'nnet'), \
repos = '${RSPM}/2020-05-26+DBtWw7pO')"
# 2020-08-20: Install packages listed in Dockerfile
# Apart from
# - renv which is not in container
# - mgcv of which a slightly later version is required
RUN R -q -e "install.packages(c( \
'knitr', \
'DBI', \
'GGally', \
'Hmisc', \
'NHPoisson', \
'Rcpp', \
'survival', \
'binom', \
'brms', \
'cowplot', \
'data.table', \
'deSolve', \
'doParallel', \
'dplyr', \
'dtplyr', \
'foreach', \
'furrr', \
'ggdist', \
'here', \
'janitor', \
'lme4', \
'lubridate', \
'magrittr', \
'maptools', \
'matrixStats', \
'mice', \
'mvtnorm', \
'naniar', \
'nlme', \
'parallel', \
'plotrix', \
'relsurv', \
'rgdal', \
'rgeos', \
'sandwich', \
'sf', \
'stats', \
'stringr', \
'tictoc', \
'tidyverse', \
'zoo' \
), \
repos = '${RSPM}/2020-08-20+MTozMTIsMjoyODc7RUIwRDc1MDI')"
# 2020-08-31: mgcv
RUN R -q -e "install.packages('mgcv', \
repos = '${RSPM}/2020-08-31+MTozMTYsMjoyODc7N0Q0MzBBRTI')"
# 2020-09-03: pacman
RUN R -q -e "install.packages('pacman', \
repos = '${RSPM}/2020-09-03+MTozMTksMjoyODc7RTQ1OEMyMUQ')"
# 2020-11-25: caret
RUN R -q -e "install.packages('caret', \
repos = '${RSPM}/2020-11-25+MTozNzQsMjozNzA7NEFFRTA4MEU')"
# 2020-12-03: odbc, SCCS
RUN R -q -e "install.packages(c( \
'odbc', \
'SCCS' \
), \
repos = '${RSPM}/2020-12-14+MToyNTI3MzcsMjoxNzc2OTI7NEExNUIxQUU')"
# Installing packages additionally listed in packages.txt
# - As much as possible trying to follow the order they were installed in the commit history
# 2021-01-20: patchwork, svglite, skimr, gt
RUN R -q -e "install.packages(c( \
'patchwork', \
'svglite', \
'skimr', \
'gt' \
), \
repos = '${RSPM}/2021-01-20+MTo5MDgzNjAsMjo3ODQzNDk7RTRBRDQ2M0Y')"
# 2021-01-27: flexsurv
RUN R -q -e "install.packages('flexsurv', \
repos = '${RSPM}/2021-01-27+MToxMDMzMzc0LDI6Nzg0MzQ5Ozg2QzlGMzYw')"
# 2021-02-10: survminer, pch, fontquiver
RUN R -q -e "install.packages(c( \
'survminer', \
'pch', \
'fontquiver' \
), \
repos = '${RSPM}/2021-02-10+Y3JhbiwyOjc4NDM0OTsyMjZCRjQ3QQ')"
# 2021-02-16: detectseparation, parglm
RUN R -q -e "install.packages(c( \
'detectseparation', \
'parglm' \
), \
repos = '${RSPM}/2021-02-16+Y3JhbiwyOjc4NDM0OTs3MTk1MTkyMg')"
# 2021-02-18: interactions, fastDummies, splines2
RUN R -q -e "install.packages(c( \
'interactions', \
'fastDummies', \
'splines2' \
), \
repos = '${RSPM}/2021-02-18+MToxNDI2MzI2LDI6Nzg0MzQ5OzM4MDhDMkI2')"
# 2021-03-02: gtsummary, modelsummary, mnlogit
RUN R -q -e "install.packages(c( \
'gtsummary', \
'modelsummary', \
'mnlogit' \
), \
repos = '${RSPM}/2021-03-02+MToxNjQwNjc3LDI6Nzg0MzQ5OzJGOTI4NjFC')"
# 2021-03-16: Gmisc
RUN R -q -e "install.packages('Gmisc', \
repos = '${RSPM}/2021-03-16+MToxNzk3OTgwLDI6MTc1MDc1MjtBQzkxREVDNA')"
# 2021-04-12: coxme
RUN R -q -e "install.packages('coxme', \
repos = '${RSPM}/2021-04-12+MToyMzA1MDg2LDI6MTc1MDc1MjsyN0Q1QzMyRA')"
# 2021-05-04: estimatr
RUN R -q -e "install.packages('estimatr', \
repos = '${RSPM}/2021-05-04+MToyNzE2MzY1LDI6MTc1MDc1Mjs2QzhGQkNCQQ')"
# 2021-05-13: feather, cpp11, arrow
RUN R -q -e "install.packages(c( \
'feather', \
'cpp11', \
'arrow' \
), \
repos = '${RSPM}/2021-05-13+MToyODg2NTAzLDI6Mjg0NzY4OTtBNDBFNzg2Qg')"
# 2021-06-18: detectseparation, brglm2, MatchIt, egg
RUN R -q -e "install.packages(c( \
'detectseparation', \
'brglm2', \
'MatchIt', \
'egg' \
), \
repos = '${RSPM}/2021-06-21+MTozNjU2OTE4LDI6MzMxODAzMTtBNDFFNDI3Ng')"
# 2021-09-08: optparse
RUN R -q -e "install.packages('optparse', \
repos = '${RSPM}/2021-09-09+MTo1MDA2MDA0LDI6NDUyNjIxNTtEMzU5RjQ1Nw')"
# 2021-09-09: caTools, gets
RUN R -q -e "install.packages(c( \
'caTools', \
'gets' \
), \
repos = '${RSPM}/2021-09-09+MTo1MDA2MDA0LDI6NDUyNjIxNTtEMzU5RjQ1Nw')"
# 2021-10-25: ggalluvial
RUN R -q -e "install.packages('ggalluvial', \
repos = '${RSPM}/2021-10-26+MTo1ODY5NzUwLDI6NDUyNjIxNTtCOTkwOUY5OQ')"
# 2022-01-11: ggvenn
RUN R -q -e "install.packages('ggvenn', \
repos = '${RSPM}/2022-01-11+MTo3NTI2MDgxLDI6NDUyNjIxNTs0MDBDOEM3QQ')"
# 2022-01-12: rms
RUN R -q -e "install.packages('rms', \
repos = '${RSPM}/2022-01-12+MTo3NTQ3NjcwLDI6NDUyNjIxNTsxMjkzRTE5Rg')"
# 2022-01-24: finalfit
RUN R -q -e "install.packages('finalfit', \
repos = '${RSPM}/2022-01-26+MTo3ODU1NDgwLDI6NDUyNjIxNTs3MDQwQTNDNQ')"
# 2022-03-08: pammtools, cmprsk
RUN R -q -e "install.packages(c( \
'pammtools', \
'cmprsk' \
), \
repos = '${RSPM}/2022-03-08+MTo4NzMwODE3LDI6NDUyNjIxNTtBMTU2NEMzNQ')"
# 2022-03-08: magick from source
RUN R -q -e "install.packages('magick', \
repos = '${RSPM_SOURCE}/2022-03-08/')"
# 2022-04-01: VGAM, segmented
RUN R -q -e "install.packages(c( \
'VGAM', \
'segmented' \
), \
repos = '${RSPM}/2022-04-01+MTo5MjUzNjk4LDI6NDUyNjIxNTtCQUE2OUVEQQ')"
# 2022-04-28: Epi, vcd, tsModel
RUN R -q -e "install.packages(c( \
'Epi', \
'vcd', \
'tsModel' \
), \
repos = '${RSPM}/2022-04-28+MTo5ODM5OTQ4LDI6NDUyNjIxNTtBMERDQzYyNA')"
# 2022-05-06: ggh4x, RcppRoll
RUN R -q -e "install.packages(c( \
'ggh4x', \
'RcppRoll' \
), \
repos = '${RSPM}/2022-05-06+MToxMDAxNzE4OSwyOjQ1MjYyMTU7RTE3MTg5QTI')"
# 2022-05-18: bayesm
RUN R -q -e "install.packages('bayesm', \
repos = '${RSPM}/2022-05-18+MToxMDI5MjcxNSwyOjQ1MjYyMTU7OTBDOEJBRTI')"
# 2022-05-23: consort
RUN R -q -e "install.packages('consort', \
repos = '${RSPM}/2022-05-23+MToxMDQwOTg0NiwyOjQ1MjYyMTU7MUM3RDRGMDM')"
# Fix up packages with incorrect versions
# Remove MASS, mgcv, nlme, spatial, survival from /usr/local/lib/R/library
RUN R -q -e "remove.packages(c( \
'MASS', \
'mgcv', \
'nlme', \
'spatial', \
'survival' \
), \
lib = '/usr/local/lib/R/library')"
# Fix backports from 1.2.1 (2020-12-09) to 1.1.9 (2020-08-24)
RUN R -q -e "remove.packages('backports'); \
install.packages('backports', \
repos = '${RSPM}/2020-08-27+MTozMTUsMjoyODc7QzYyODgyRDQ')"
# Fix conquer from 1.0.1 (2020-05-06) to 1.0.2 (2020-08-27)
RUN R -q -e "remove.packages('conquer'); \
install.packages('conquer', \
repos = '${RSPM}/2020-08-31+MTozMTYsMjoyODc7N0Q0MzBBRTI')"
# Fix glue from 1.4.1 (2020-05-13) to 1.4.2 (2020-08-27)
RUN R -q -e "remove.packages('glue'); \
install.packages('glue', \
repos = '${RSPM}/2020-08-31+MTozMTYsMjoyODc7N0Q0MzBBRTI')"
# Fix lmtest from 0.9-38 (2020-09-09) to 0.9-37 (2019-04-30)
RUN R -q -e "remove.packages('lmtest'); \
install.packages('lmtest', \
repos = '${RSPM}/2020-08-31+MTozMTYsMjoyODc7N0Q0MzBBRTI')"
# Fix maptools from 1.0-1 (2020-05-14) to 1.0-2 (2020-08-24)
RUN R -q -e "remove.packages('maptools'); \
install.packages('maptools', \
repos = '${RSPM}/2020-08-31+MTozMTYsMjoyODc7N0Q0MzBBRTI')"
# Install MASS 7.3-52 (2020-08-18)
RUN R -q -e "install.packages('MASS', \
repos = '${RSPM}/2020-09-01+MTozMTcsMjoyODc7QkNBMjZDNQ')"
# Fix naniar from 0.5.2 (2020-06-29) to 0.6.0 (2020-09-02)
RUN R -q -e "remove.packages('naniar'); \
install.packages('naniar', \
repos = '${RSPM}/2020-09-08+MTozMjEsMjoyODc7RkVBRjQyMzM')"
# Install nlme 3.1-149 (2020-08-23)
RUN R -q -e "install.packages('nlme', \
repos = '${RSPM}/2020-09-08+MTozMjEsMjoyODc7RkVBRjQyMzM')"
# Fix processx from 3.4.3 (2020-07-05) to 3.4.4 (2020-09-03)
RUN R -q -e "remove.packages('processx'); \
install.packages('processx', \
repos = '${RSPM}/2020-09-08+MTozMjEsMjoyODc7RkVBRjQyMzM')"
# Fix RcppArmadillo from 0.9.900.2.0 (2020-07-17) to 0.9.900.3.0 (2020-09-04)
RUN R -q -e "remove.packages('RcppArmadillo'); \
install.packages('RcppArmadillo', \
repos = '${RSPM}/2020-09-08+MTozMjEsMjoyODc7RkVBRjQyMzM')"
# Fix tidyr from 1.1.1 (2020-07-31) to 1.1.2 (2020-08-27)
RUN R -q -e "remove.packages('tidyr'); \
install.packages('tidyr', \
repos = '${RSPM}/2020-09-08+MTozMjEsMjoyODc7RkVBRjQyMzM')"
# Fix vctrs from 0.3.2 (2020-07-15) to 0.3.4 (2020-08-29)
RUN R -q -e "remove.packages('vctrs'); \
install.packages('vctrs', \
repos = '${RSPM}/2020-09-08+MTozMjEsMjoyODc7RkVBRjQyMzM')"
# Fix XML from 3.99-0.5 (2020-07-23) to 3.99-0.6 (2021-03-16)
RUN R -q -e "remove.packages('XML'); \
install.packages('XML', \
repos = '${RSPM}/2021-03-18+MToxODM1NDIxLDI6MTc1MDc1MjsxNUVERDRFRg')"
# Fix zip from 2.1.0 (2020-08-10) to 2.1.1 (2020-08-27)
RUN R -q -e "remove.packages('zip'); \
install.packages('zip', \
repos = '${RSPM}/2020-09-08+MTozMjEsMjoyODc7RkVBRjQyMzM')"
# 2022-06-13: survey
RUN R -q -e "install.packages('survey', \
repos = '${RSPM}/2022-06-10+MToxMDgyMzY1MSwyOjQ1MjYyMTU7OUEyQzE2QUI')"
# 2022-06-17: incidence
RUN R -q -e "install.packages('incidence', \
repos = '${RSPM}/2022-06-16+MToxMDk3NDM4NSwyOjQ1MjYyMTU7NEZENUU2Qzg')"
# 2022-07-11: predtools
RUN R -q -e "install.packages('predtools', \
repos = '${RSPM}/2022-07-08+MToxMTQ3NTUzNSwyOjQ1MjYyMTU7MzU1RTIxRUM')"
# 2022-07-29: pseudo
RUN R -q -e "install.packages('pseudo', \
repos = '${RSPM}/2022-07-28+MToxMTkzNDQ0MSwyOjQ1MjYyMTU7OUU2MDBBQUY')"
# 2022-09-08: cobalt, WeightIt; one of which updates backports
RUN R -q -e "install.packages(c('cobalt', 'WeightIt'), \
repos = '${RSPM}/2022-09-08+MToxMjg5Njc3MCwyOjQ1MjYyMTU7M0IxRTMxMDU')"
# 2022-10-11: glmnet with dependency shape,
# R.utils with dependency R.oo
# metafor with dependencies mathjaxr, metadat, pbapply,
RUN R -q -e "install.packages(c('glmnet', 'R.utils', 'metafor'), \
repos = '${RSPM}/2022-10-07+MToxMzU2ODg1OSwyOjQ1MjYyMTU7ODZGRDlENjM')"
# 2022-10-12: lcmm
RUN R -q -e "install.packages('lcmm', \
repos = '${RSPM}/2022-10-12+MToxMzY4NDA2NiwyOjQ1MjYyMTU7MkU3MkU1NzA')"
# 2022-10-13: dtwclust version 5.5.10
RUN R -q -e "install.packages('dtwclust', \
repos = '${RSPM}/2022-09-23+MToxMzI0NjI1NSwyOjQ1MjYyMTU7ODhFRDhERjA')"
# 2022-11-02: randomForest version 4.6-14
RUN R -q -e "install.packages('randomForest', \
repos = '${RSPM}/2022-02-01+MTo3OTc5MjY2LDI6NDUyNjIxNTtCQUJBRUEyOQ')"
# 2022-11-02: randomForestExplainer
RUN R -q -e "install.packages('randomForestExplainer', \
repos = '${RSPM}/2022-11-02+MToxNDE2NDA5NiwyOjQ1MjYyMTU7MkZBOUM5RTk')"
# 2023-01-18: ggfortify
RUN R -q -e "install.packages('ggfortify', \
repos = '${RSPM}/2023-01-18+caWj9Yom')"
# 2023-02-09: forestploter
RUN R -q -e "install.packages('forestploter', \
repos = '${RSPM}/2023-02-09+Sbsm30SZ')"
# renv 0.16.0
RUN R -q -e "install.packages('renv', repos = '${RSPM}/2022-09-30+2oOWnlBt')"
# 2023-03-10: PHEindicatormethods
RUN R -q -e "install.packages('PHEindicatormethods', repos = '${RSPM}/2020-06-29+mBrI1rUy')"
# 2023-03-10: rpart.plot
RUN R -q -e "install.packages('rpart.plot', repos = '${RSPM}/2023-03-09+N8dAXCGm')"
# 2023-04-04: fuzzyjoin
RUN R -q -e "install.packages('fuzzyjoin', repos = '${RSPM}/2023-04-04+gySb4cgs')"
# 2023-04-18: emmeans and dependency estimability
RUN R -q -e "install.packages('estimability', repos = '${RSPM}/2022-08-09+aWCdE6gP')"
RUN R -q -e "install.packages('emmeans', repos = '${RSPM}/2022-06-23+A8HJuHif')"
# 2023-04-24 rdrobust
RUN R -q -e "install.packages('rdrobust', repos = '${RSPM}/2023-04-24+Jj8CwMaf')"
# 2023-05-16 twopartm
RUN R -q -e "install.packages('twopartm', repos = '${RSPM}/2023-05-16+VDNBdopv')"
# 2023-05-19 pscl
RUN R -q -e "install.packages('pscl', repos = '${RSPM}/2023-05-19+uqEDUQaz')"
# 2023-06-01 update cli, install fastshap, shapviz
RUN R -q -e "install.packages(c('cli', 'fastshap', 'shapviz'), \
repos = '${RSPM}/2023-06-01+Y3Jx1hNK')"
# 2023-06-16 epitools
RUN R -q -e "install.packages('epitools', repos = '${RSPM}/2023-06-14+j7ezeyBe')"
# 2023-08-22 BayesianTools
RUN R -q -e "install.packages(c('BayesianTools', \
'DHARMa', \
'ape', \
'ellipse', \
'emulator', \
'expm', \
'gap', \
'gap.datasets', \
'gmm', \
'hexbin', \
'IDPmisc', \
'msm', \
'plotly', \
'qgam', \
'tmvtnorm'), repos = '${RSPM}/2023-08-21+PzN22n8L')"
# Fix plotly back to 4.8.0
RUN R -q -e "remove.packages('plotly'); \
install.packages('plotly', repos = '${RSPM}/2019-04-09+vWThhkjm')"
# Fix fastmap to 1.0.1
RUN R -q -e "install.packages('fastmap', repos = '${RSPM}/2019-10-10+EJ_0XuhN')"
# Fix htmltools to 0.5.0 and htmlwidgets to 1.5.1
RUN R -q -e "install.packages(c('htmltools', 'htmlwidgets'), repos = '${RSPM}/2020-06-18+J6zIiIH3')"
# Note I missed some releases here
# 2024-04-02 Add TMB and glmmTMB
RUN R -q -e "install.packages('TMB', repos = '${RSPM_SOURCE}/2023-12-13'); \
install.packages('glmmTMB', repos = '${RSPM_SOURCE}/2021-07-21')"
# ggh4x is now at 0.2.6
RUN R -q -e "install.packages('ggh4x', repos = '${RSPM_SOURCE}/2023-08-31')"
# Deactivate renv because it causes problems on restarts of rstudio-server
RUN R -q -e "renv::deactivate()"
# Write packages-legacy-02.csv and packages-alphabetical-legacy-02.csv in container
RUN R -q -e "ip <- installed.packages()[, c('Package', 'Version')]; \
write.csv(ip, \
row.names = FALSE, \
file = '/packages-legacy-04.csv'); \
write.csv(ip[stringr::str_sort(ip[, 'Package']), ], \
row.names = FALSE, \
file = '/packages-alphabetical-legacy-04.csv')"