inst/doc/Require.R

In Require: Installing and Loading R Packages for Reproducible Workflows

## ----eval=FALSE---------------------------------------------------------------
#  library(Require)
#  Require::Install(
#    c("PredictiveEcology/reproducible@development (HEAD)",
#      "PredictiveEcology/SpaDES.core@development (>=2.0.5.9004)"))

## ----eval=FALSE,message=FALSE-------------------------------------------------
#  Require::Install("knn")
#  
#  try(pak::pkg_install(c("knn")))

## ----eval=FALSE,message=TRUE--------------------------------------------------
#  library(Require)
#  # Fails because of a) packages taken off CRAN & multiple GitHub branches requested within the nested dependencies
#  pkgs <- c("reproducible", "PredictiveEcology/SpaDES@development")
#  dirTmp <- tempdir2(sub = "first")
#  .libPaths(dirTmp)
#  install.packages("pak") # need this in the library; can't use personal library version
#  try(pak::pkg_install(pkgs))
#  # ✔ Loading metadata database ... done
#  # Error : ! error in pak subprocess
#  # Caused by error:
#  # ! Could not solve package dependencies:
#  # * reproducible: dependency conflict
#  # * PredictiveEcology/SpaDES@development: Can't install dependency PredictiveEcology/reproducible@development (>=  2.0.10)
#  # * PredictiveEcology/reproducible@development: Conflicts with reproducible
#  pkgsAny <- c("any::reproducible", "PredictiveEcology/SpaDES@development")
#  try(pak::pkg_install(pkgsAny))
#  
#  # Fine
#  dirTmp <- tempdir2(sub = "second")
#  .libPaths(dirTmp)
#  Require::Install(pkgs)

## ----eval=FALSE,message=TRUE--------------------------------------------------
#  # Fails
#  try(pk <- pak::pak(c("PredictiveEcology/LandR@development", "PredictiveEcology/LandR@main")))
#  # Error : ! error in pak subprocess
#  # Caused by error:
#  # ! Could not solve package dependencies:
#  # * PredictiveEcology/LandR@development: Conflicts with PredictiveEcology/LandR@main
#  # * PredictiveEcology/LandR@main: Conflicts with PredictiveEcology/LandR@development
#  
#  # Fine -- takes in order, so main first in this example
#  rq <- Require::Install(c("PredictiveEcology/LandR@main", "PredictiveEcology/LandR@development"))
#  
#  # Fine -- takes by version requirement, so takes development,
#  #    which is the only one that fulfills requirement on Jul 25, 2024
#  rq <- Require::Install(c("PredictiveEcology/LandR@main", "PredictiveEcology/LandR@development (>=1.1.5)"))
#  

## ----eval=FALSE,message=FALSE-------------------------------------------------
#  try(gg <- pak::pkg_deps("PredictiveEcology/LandR@development", dependencies = TRUE))
#  ff <- Require::pkgDep("PredictiveEcology/LandR@development", dependencies = TRUE)

## ----eval=FALSE---------------------------------------------------------------
#  # The following has no version specifications,
#  #   so CRAN version will be installed or none installed if already installed
#  Require::Install(c("PredictiveEcology/reproducible@development", "reproducible"))
#  
#  # The following specifies "HEAD" after the Github package name. This means the
#  #   tip of the development branch of reproducible will be installed if not already installed
#  Require::Install(c("PredictiveEcology/reproducible@development (HEAD)", "reproducible"))
#  
#  # The following specifies "HEAD" after the package name. This means the
#  #   tip of the development branch of reproducible
#  Require::Install(c("PredictiveEcology/reproducible@development", "reproducible (HEAD)"))
#  
#  # Not a problem because version number specifies
#  Require::Install(c("PredictiveEcology/reproducible@modsForLargeArchives (>=2.0.10.9010)",
#                     "PredictiveEcology/reproducible (>= 2.0.10)"))
#  
#  # Even if branch does not exist, if later version requirement specifies a different branch, no error
#  Require::Install(c("PredictiveEcology/reproducible@modsForLargeArchives (>=2.0.10.9010)",
#                     "PredictiveEcology/reproducible@validityTest (>= 2.0.9)"))

## ----eval=FALSE---------------------------------------------------------------
#  ## FAILS - can't specify version requirements
#  try(pak::pkg_install(
#      c("PredictiveEcology/reproducible@modsForLargeArchives (>=2.0.10.9010)",
#        "PredictiveEcology/reproducible (>= 2.0.10)")))

## ----eval=FALSE---------------------------------------------------------------
#  # In this example, it is `terra` that generally needs to be installed from source on Linux
#  if (Require:::isUbuntuOrDebian()) {
#    Require::setLinuxBinaryRepo()
#    pkgs <- c("terra", "PSPclean")
#    pkgFullName <- "ianmseddy/PSPclean@development"
#    try(remove.packages(pkgs))
#    pak::cache_delete() # make sure a locally built one is not present in the cache
#    try(pak::pkg_install(pkgFullName))
#    # ✔ Loading metadata database ... done
#    #
#    # → Will install 2 packages.
#    # → Will download 2 packages with unknown size.
#    # + PSPclean   0.1.4.9005 [bld][cmp][dl] (GitHub: fed9253)
#    # + terra      1.7-71     [dl] + ✔ libgdal-dev, ✔ gdal-bin, ✔ libgeos-dev, ✔ libproj-dev, ✔ libsqlite3-dev
#    # ✔ All system requirements are already installed.
#    #
#    # ℹ Getting 2 pkgs with unknown sizes
#    # ✔ Got PSPclean 0.1.4.9005 (source) (43.29 kB)
#    # ✔ Got terra 1.7-71 (x86_64-pc-linux-gnu-ubuntu-22.04) (4.24 MB)
#    # ✔ Downloaded 2 packages (4.28 MB) in 2.9s
#    # ✔ Installed terra 1.7-71  (61ms)
#    # ℹ Packaging PSPclean 0.1.4.9005
#    # ✔ Packaged PSPclean 0.1.4.9005 (420ms)
#    # ℹ Building PSPclean 0.1.4.9005
#    # ✖ Failed to build PSPclean 0.1.4.9005 (3.7s)
#    # Error:
#    # ! error in pak subprocess
#    # Caused by error in `stop_task_build(state, worker)`:
#    # ! Failed to build source package PSPclean.
#    # Type .Last.error to see the more details.
#  
#  
#    # Works fine because the `sourcePkgs()`
#  
#    try(remove.packages(pkgs)) # uninstall to make sure it is a clean install for this test
#    Require::cacheClearPackages(pkgs, ask = FALSE) # remove any existing local packages
#    Require::Install(pkgFullName)
#  }

## ----eval=FALSE---------------------------------------------------------------
#  depPak <- pak::pkg_deps("PredictiveEcology/LandR@LandWeb")
#  depRequire <- Require::pkgDep("PredictiveEcology/LandR@LandWeb") # Slightly different default in Require
#  
#  # Same
#  pakDepsClean <- setdiff(Require::extractPkgName(depPak$ref), Require:::.basePkgs)
#  requireDepsClean <- setdiff(Require::extractPkgName(depRequire[[1]]), Require:::.basePkgs)
#  setdiff(pakDepsClean, requireDepsClean)
#  setdiff(requireDepsClean, pakDepsClean) # does not report "RcppArmadillo", "RcppEigen", "cpp11" which are LinkingTo
#  

## ----eval=FALSE---------------------------------------------------------------
#  gg <- pak::pkg_deps("PredictiveEcology/LandR@development", dependencies = TRUE)
#  # Error:
#  # ! error in pak subprocess
#  # Caused by error:
#  # ! Could not solve package dependencies:
#  # * PredictiveEcology/LandR@development: Can't install dependency BioSIM
#  # * BioSIM: Can't find package called BioSIM.
#  # Type .Last.error to see the more details.
#  ff <- Require::pkgDep("PredictiveEcology/LandR@development", dependencies = TRUE)
#  # $`PredictiveEcology/LandR@development`
#  #  [1] "BH"                                                      "BIEN"
#  #  [3] "BioSIM"                                                  "DBI (>= 0.8)"
#  #  [5] "Deriv"                                                   "ENMeval"
#  #  ...