/
install.R
executable file
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/
install.R
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#!/usr/bin/env r
# Install devtools so we can install versioned packages
install.packages("devtools")
source("/tmp/class-libs.R")
# install ottr, needs to go first issue #3216
# install ottr, 1.4.0, issue #5314
# install ottr, 1.5.0 https://github.com/berkeley-dsep-infra/datahub/issues/5498
devtools::install_version("ottr", version = "1.5.0", repos = "https://cran.r-project.org", upgrade = "never", quiet = FALSE)
# dplyr package + backends
# From https://github.com/rocker-org/rocker-versioned2/blob/b8d23396468c5dc73115cce6c5716424d80ffcb0/scripts/install_tidyverse.sh#L30
dplyr_packages = c(
"dplyr", "1.0.2",
"arrow", "2.0.0",
"dbplyr", "2.0.0",
"DBI", "1.1.0",
"dtplyr", "1.0.1",
"nycflights13", "1.0.2",
"Lahman", "8.0-0",
"RMariaDB", "1.1.0",
"RPostgres", "1.3.0",
"RSQLite", "2.2.1",
"fst", "0.9.4"
)
# From https://github.com/rocker-org/rocker-versioned2/blob/b8d23396468c5dc73115cce6c5716424d80ffcb0/scripts/install_verse.sh#L82
publishing_packages = c(
"tinytex", "0.28",
"blogdown", "0.21",
"bookdown", "0.21",
"rticles", "0.18",
"rmdshower", "2.1.1",
"rJava", "0.9-13",
"xaringan", "0.19"
)
# R packages to be installed that aren't from apt
# Combination of informal requests & rocker image suggestions
# Some of these were already in datahub image
cran_packages = c(
"AER", "1.2-9",
"BH", "1.72.0-3",
"BiocManager", "1.30.10",
"DBI", "1.1.0",
"FNN", "1.1.3",
"IRkernel", "1.1.1",
"Matrix", "1.3-0",
"R.methodsS3", "1.8.1",
"R.oo", "1.24.0",
"R.utils", "2.10.1",
"RCSF", "1.0.2",
"RColorBrewer", "1.1-2",
"RCurl", "1.98-1.2",
"RNetCDF", "2.4-2",
"RandomFields", "3.3.8",
"RandomFieldsUtils", "0.5.3",
"Rcpp", "1.0.5",
"RcppProgress", "0.4.2",
"assertthat", "0.2.1",
"base64enc", "0.1-3",
"bibtex", "0.4.2.3",
"bindrcpp", "0.2.2",
"broom", "0.7.3",
"checkr", "0.5.0",
"clipr", "0.7.1",
"crayon", "1.3.4",
"crosstalk", "1.1.0.1",
"curl", "4.3",
"data.table", "1.13.6",
"dichromat", "2.0-0",
"digest", "0.6.27",
"docopt", "0.7.1",
"e1071", "1.7-4",
"evaluate", "0.14",
"forcats", "0.5.0",
"future", "1.21.0",
"gdalUtils", "2.0.3.2",
"gdtools", "0.2.3",
"geoR", "1.8-1",
"geometry", "0.4.5",
"geosphere", "1.5-10",
"gert", "1.0.2",
"ggplot2", "3.3.3",
"git2r", "0.27.1",
"globals", "0.14.0",
"glue", "1.4.2",
"gstat", "2.0-6",
"haven", "2.3.1",
"hdf5r", "1.3.3",
"here", "1.0.1",
"highr", "0.8",
"hms", "0.5.3",
"htmlwidgets", "1.5.3",
"httpuv", "1.5.4",
"httr", "1.4.2",
"intervals", "0.15.2",
"ivpack", "1.2",
"jsonlite", "1.7.2",
"knitr", "1.30",
"units", "0.6-7",
"leafem", "0.1.3",
"leaflet", "2.0.3",
"leafpop", "0.0.6",
"leafsync", "0.1.0",
"learnr", "0.11.2",
"lfe", "3.0-0",
"linprog", "0.9-2",
"listenv", "0.8.0",
"lpSolve", "5.6.15",
"lubridate", "1.7.9.2",
"lwgeom", "0.2-13",
"magic", "1.5-9",
"manipulateWidget", "0.10.1",
"mapdata", "2.3.0",
"mapproj", "1.2.7",
"maptools", "1.0-2",
"mapview", "2.9.0",
"markdown", "1.1",
"matrixStats", "0.57.0",
"memoise", "1.1.0",
"miniUI", "0.1.1.1",
"modelr", "0.1.8",
"ncdf4", "1.17",
"ncmeta", "0.3.0",
"nlme", "3.1-151",
"openssl", "1.4.3",
"packrat", "0.5.0",
"pander", "0.6.3",
"pbdZMQ", "0.3-4",
"pillar", "1.4.7",
"png", "0.1-7",
"praise", "1.0.0",
"proj4", "1.0-10",
"proto", "1.0.0",
"pryr", "0.1.4",
"rapportools", "1.0",
"raster", "3.4-5",
"rdrobust", "2.0.2",
"readr", "1.4.0",
"readxl", "1.3.1",
"redland", "1.0.17-14",
"rematch", "1.0.1",
"repr", "1.1.0",
"reprex", "0.3.0",
"reshape", "0.8.8",
"reticulate", "1.34.0",
"rgeos", "0.5-5",
"rgl", "0.103.5",
"rjson", "0.2.20",
"rlang", "0.4.10",
"rlas", "1.3.8",
"rlist", "0.4.6.1",
"rmarkdown", "2.6",
"rpart", "4.1-15",
"rprojroot", "2.0.2",
"rsconnect", "0.8.16",
"satellite", "1.0.2",
"selectr", "0.4-2",
"shiny", "1.5.0",
"sp", "1.4-4",
"spacetime", "1.2-3",
"spatialreg", "1.1-5",
"spatstat", "1.64-1",
"spatstat.data", "1.7-0",
"spdep", "1.1-5",
"splancs", "2.01-40",
"stargazer", "5.2.3",
"stars", "0.4-3",
"stringi", "1.5.3",
"stringr", "1.4.0",
"summarytools", "0.9.8",
"svglite", "1.2.3.2",
"systemfonts", "0.3.2",
"testit", "0.12",
"testthat", "3.0.4",
"tibble", "3.0.4",
"tidync", "0.2.4",
"tidyr", "1.1.2",
"tidyverse", "1.3.0",
"tmap", "3.2",
"tmaptools", "3.1",
"tufte", "0.9",
"utf8", "1.1.4",
"uuid", "0.1-4",
"viridis", "0.5.1",
"vroom", "1.3.2",
"whoami", "1.3.0",
"widgetframe", "0.3.1",
"withr", "2.3.0",
"xfun", "0.19",
"xml2", "1.3.2",
"xts", "0.12.1",
"yaml", "2.2.1"
)
class_libs_install_version("Base packages", cran_packages)
class_libs_install_version("dplyr packages", dplyr_packages)
class_libs_install_version("publishing packages", publishing_packages)
# Bioconductor packages present in rocker images
# FIXME: Find a way to version these?
# FIXME: Make sure these are binary installs?
BiocManager::install('rhdf5')
BiocManager::install('Rhdf5lib')