Merge branch '78_packrat_to_renv' into 'master'

78 packrat to renv See merge request !59

Merge branch '78_packrat_to_renv' into 'master'
989cbbcf · Johannes Boog · c7d53ad5 · 9a9bc838 · 989cbbcf · 989cbbcf
Commit 989cbbcf authored 1 year ago by Johannes Boog
--- a/.Rbuildignore
+++ b/.Rbuildignore
+^renv$
+^renv\.lock$
 ^.gitlab-ci.yml
 ^.*\.Rproj$
 ^\.Rproj\.user$
@@ -14,4 +16,4 @@
 ^Meta$
 ^packrat/
 ^public$
-^tmp$
\ No newline at end of file
+^tmp$
--- a/.Rprofile
+++ b/.Rprofile
+source("renv/activate.R")
--- a/.gitignore
+++ b/.gitignore
@@ -2,10 +2,11 @@
 .Rhistory
 .RData
 .Ruserdata
+.vscode
 config.yml
-packrat/lib*/
+ci/local_docker_test
 inst/doc
 inst/extdata/test_tempdirs
 Meta
+renv/settings.json
 tmp
-packrat/src/
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,21 +6,18 @@ stages:
  - test

 test:
-  image: $CI_REGISTRY_IMAGE:09092022
+  image: $CI_REGISTRY_IMAGE:24032023
  stage: test
  tags:
    - envinf2
  variables:
-    R_LIBS_USER: "$CI_PROJECT_DIR/ci/lib/"
-    RETICULATE_MINICONDA_PATH: "/root/.local/share/r-miniconda/" #default path
+    RETICULATE_MINICONDA_PATH: "/root/.local/share/r-miniconda/"
    RETICULATE_PYTHON_ENV: "/root/.local/share/r-miniconda/envs/r-reticulate/"
+    RENV_CONFIG_EXTERNAL_LIBRARIES: "/usr/local/lib/R/site-library:/usr/local/lib/R/library"
+    RENV_PATHS_LIBRARY: "$CI_PROJECT_DIR/ci/renv/library"
  script:
-    - if [ ! -d "$R_LIBS_USER" ]; then mkdir -p "$R_LIBS_USER"; fi
-    - R -e 'withr::with_libpaths(new = Sys.getenv("R_LIBS_USER"), devtools::install_deps(dependencies = T))'
-    # checks if the packages from the Imports, Suggests, LinkinTo field
-    # are already installed in the cache
-    - R -e '.libPaths(new = Sys.getenv("R_LIBS_USER"))'
-    - R -e 'withr::with_libpaths(new = Sys.getenv("R_LIBS_USER"), {install.packages("BiocManager"); BiocManager::install("rhdf5")})'
+    # Install deps or load from renv cache
+    - R -e 'renv::restore()'
    # Build and Check r2ogs6
    - R CMD build . --no-build-vignettes --no-manual
    - R CMD check $(ls -1t *.tar.gz | head -n 1) --no-build-vignettes --no-manual
@@ -31,7 +28,7 @@ test:
    key: "$CI_COMMIT_REF_SLUG"
    untracked: true
    paths:
-      - "$R_LIBS_USER"
+      - "$RENV_PATHS_LIBRARY"
  rules:
    - if: '$CI_PIPELINE_SOURCE == "merge_request_event" || $CI_PIPELINE_SOURCE == "web"'
    - if: '$CI_COMMIT_BRANCH == "master"'
\ No newline at end of file
--- a/ci/dockerfile
+++ b/ci/dockerfile
+FROM rocker/tidyverse:4.2.3
+ENV PATH="/root/miniconda3/bin:$PATH"
+ARG PATH="/root/miniconda3/bin:$PATH"
+ARG PROJECT_DIR="/root/test-bm"
+ARG GOVERSION="1.13.9"
+ARG OGS_VERSION="6.4.4"
+ARG SING_VERSION="3.5.3"
+
+# install linux dependencies
+RUN apt-get update && apt-get install -y build-essential libssl-dev uuid-dev libgpgme11-dev squashfs-tools libseccomp-dev pkg-config cryptsetup-bin
+
+# install go
+ARG OS=linux
+ARG ARCH=amd64
+RUN wget -O /tmp/go${GOVERSION}.${OS}-${ARCH}.tar.gz https://dl.google.com/go/go$GOVERSION.$OS-$ARCH.tar.gz
+RUN tar -C /usr/local -xzvf /tmp/go$GOVERSION.$OS-$ARCH.tar.gz
+RUN rm /tmp/go$GOVERSION.$OS-$ARCH.tar.gz
+
+# configure go
+ARG GOPATH="/root/go"
+ENV GOPATH=${GOPATH}
+ENV PATH="/usr/local/go/bin:${PATH}:${GOPATH}/bin"
+
+# install singularity
+RUN mkdir -p ${GOPATH}/src/github.com/sylabs
+RUN cd ${GOPATH}/src/github.com/sylabs && git clone https://github.com/sylabs/singularity.git
+RUN cd ${GOPATH}/src/github.com/sylabs/singularity && git checkout v${SING_VERSION} && ./mconfig
+RUN cd ${GOPATH}/src/github.com/sylabs/singularity/builddir && make && make install
+RUN singularity version
+
+# get ogs
+RUN if [ ! -d "$PROJECT_DIR" ]; then mkdir -p "$PROJECT_DIR"; fi
+RUN git clone --branch ${OGS_VERSION} https://gitlab.opengeosys.org/ogs/ogs.git/ /root/ogs
+RUN wget -nv -P /root https://ogsstorage.blob.core.windows.net/binaries/ogs6/${OGS_VERSION}/ogs-${OGS_VERSION}-serial.sif
+
+# install R dependencies
+RUN R -e 'install.packages("reticulate")'
+RUN R -e 'reticulate::install_miniconda()'
+RUN R -e 'reticulate::py_install(c("numpy==1.19.1", "vtk==8.2.0"), python_version="3.7")'
\ No newline at end of file
--- a/ci/env.list
+++ b/ci/env.list
-R_LIBS_USER="/root/r2ogs6/ci/lib/"
-RETICULATE_MINICONDA_PATH="/root/.local/share/r-miniconda/"
-RETICULATE_PYTHON_ENV="/root/.local/share/r-miniconda/envs/r-reticulate/"
\ No newline at end of file
--- a/packrat/init.R
+++ b/packrat/init.R
-local({
-
-  ## Helper function to get the path to the library directory for a
-  ## given packrat project.
-  getPackratLibDir <- function(projDir = NULL) {
-    path <- file.path("packrat", "lib", R.version$platform, getRversion())
-
-    if (!is.null(projDir)) {
-
-      ## Strip trailing slashes if necessary
-      projDir <- sub("/+$", "", projDir)
-
-      ## Only prepend path if different from current working dir
-      if (!identical(normalizePath(projDir), normalizePath(getwd())))
-        path <- file.path(projDir, path)
-    }
-
-    path
-  }
-
-  ## Ensure that we set the packrat library directory relative to the
-  ## project directory. Normally, this should be the working directory,
-  ## but we also use '.rs.getProjectDirectory()' if necessary (e.g. we're
-  ## rebuilding a project while within a separate directory)
-  libDir <- if (exists(".rs.getProjectDirectory"))
-    getPackratLibDir(.rs.getProjectDirectory())
-  else
-    getPackratLibDir()
-
-  ## Unload packrat in case it's loaded -- this ensures packrat _must_ be
-  ## loaded from the private library. Note that `requireNamespace` will
-  ## succeed if the package is already loaded, regardless of lib.loc!
-  if ("packrat" %in% loadedNamespaces())
-    try(unloadNamespace("packrat"), silent = TRUE)
-
-  if (suppressWarnings(requireNamespace("packrat", quietly = TRUE, lib.loc = libDir))) {
-
-    # Check 'print.banner.on.startup' -- when NA and RStudio, don't print
-    print.banner <- packrat::get_opts("print.banner.on.startup")
-    if (print.banner == "auto" && is.na(Sys.getenv("RSTUDIO", unset = NA))) {
-      print.banner <- TRUE
-    } else {
-      print.banner <- FALSE
-    }
-    return(packrat::on(print.banner = print.banner))
-  }
-
-  ## Escape hatch to allow RStudio to handle bootstrapping. This
-  ## enables RStudio to provide print output when automagically
-  ## restoring a project from a bundle on load.
-  if (!is.na(Sys.getenv("RSTUDIO", unset = NA)) &&
-      is.na(Sys.getenv("RSTUDIO_PACKRAT_BOOTSTRAP", unset = NA))) {
-    Sys.setenv("RSTUDIO_PACKRAT_BOOTSTRAP" = "1")
-    setHook("rstudio.sessionInit", function(...) {
-      # Ensure that, on sourcing 'packrat/init.R', we are
-      # within the project root directory
-      if (exists(".rs.getProjectDirectory")) {
-        owd <- getwd()
-        setwd(.rs.getProjectDirectory())
-        on.exit(setwd(owd), add = TRUE)
-      }
-      source("packrat/init.R")
-    })
-    return(invisible(NULL))
-  }
-
-  ## Bootstrapping -- only performed in interactive contexts,
-  ## or when explicitly asked for on the command line
-  if (interactive() || "--bootstrap-packrat" %in% commandArgs(TRUE)) {
-
-    needsRestore <- "--bootstrap-packrat" %in% commandArgs(TRUE)
-
-    message("Packrat is not installed in the local library -- ",
-            "attempting to bootstrap an installation...")
-
-    ## We need utils for the following to succeed -- there are calls to functions
-    ## in 'restore' that are contained within utils. utils gets loaded at the
-    ## end of start-up anyhow, so this should be fine
-    library("utils", character.only = TRUE)
-
-    ## Install packrat into local project library
-    packratSrcPath <- list.files(full.names = TRUE,
-                                 file.path("packrat", "src", "packrat")
-    )
-
-    ## No packrat tarballs available locally -- try some other means of installation
-    if (!length(packratSrcPath)) {
-
-      message("> No source tarball of packrat available locally")
-
-      ## There are no packrat sources available -- try using a version of
-      ## packrat installed in the user library to bootstrap
-      if (requireNamespace("packrat", quietly = TRUE) && packageVersion("packrat") >= "0.2.0.99") {
-        message("> Using user-library packrat (",
-                packageVersion("packrat"),
-                ") to bootstrap this project")
-      }
-
-      ## Couldn't find a user-local packrat -- try finding and using devtools
-      ## to install
-      else if (requireNamespace("devtools", quietly = TRUE)) {
-        message("> Attempting to use devtools::install_github to install ",
-                "a temporary version of packrat")
-        library(stats) ## for setNames
-        devtools::install_github("rstudio/packrat")
-      }
-
-      ## Try downloading packrat from CRAN if available
-      else if ("packrat" %in% available.packages()[, "Package"]) {
-        message("> Installing packrat from CRAN")
-        install.packages("packrat")
-      }
-
-      ## Fail -- couldn't find an appropriate means of installing packrat
-      else {
-        stop("Could not automatically bootstrap packrat -- try running ",
-             "\"'install.packages('devtools'); devtools::install_github('rstudio/packrat')\"",
-             "and restarting R to bootstrap packrat.")
-      }
-
-      # Restore the project, unload the temporary packrat, and load the private packrat
-      if (needsRestore)
-        packrat::restore(prompt = FALSE, restart = TRUE)
-
-      ## This code path only reached if we didn't restart earlier
-      unloadNamespace("packrat")
-      requireNamespace("packrat", lib.loc = libDir, quietly = TRUE)
-      return(packrat::on())
-
-    }
-
-    ## Multiple packrat tarballs available locally -- try to choose one
-    ## TODO: read lock file and infer most appropriate from there; low priority because
-    ## after bootstrapping packrat a restore should do the right thing
-    if (length(packratSrcPath) > 1) {
-      warning("Multiple versions of packrat available in the source directory;",
-              "using packrat source:\n- ", shQuote(packratSrcPath))
-      packratSrcPath <- packratSrcPath[[1]]
-    }
-
-
-    lib <- file.path("packrat", "lib", R.version$platform, getRversion())
-    if (!file.exists(lib)) {
-      dir.create(lib, recursive = TRUE)
-    }
-
-    message("> Installing packrat into project private library:")
-    message("- ", shQuote(lib))
-
-    surround <- function(x, with) {
-      if (!length(x)) return(character())
-      paste0(with, x, with)
-    }
-
-
-    ## Invoke install.packages() in clean R session
-    peq <- function(x, y) paste(x, y, sep = " = ")
-    installArgs <- c(
-      peq("pkgs", surround(packratSrcPath, with = "'")),
-      peq("lib", surround(lib, with = "'")),
-      peq("repos", "NULL"),
-      peq("type", surround("source", with = "'"))
-    )
-
-    fmt <- "utils::install.packages(%s)"
-    installCmd <- sprintf(fmt, paste(installArgs, collapse = ", "))
-
-    ## Write script to file (avoid issues with command line quoting
-    ## on R 3.4.3)
-    installFile <- tempfile("packrat-bootstrap", fileext = ".R")
-    writeLines(installCmd, con = installFile)
-    on.exit(unlink(installFile), add = TRUE)
-
-    fullCmd <- paste(
-      surround(file.path(R.home("bin"), "R"), with = "\""),
-      "--vanilla",
-      "-s",
-      "-f",
-      surround(installFile, with = "\"")
-    )
-    system(fullCmd)
-
-    ## Tag the installed packrat so we know it's managed by packrat
-    ## TODO: should this be taking information from the lockfile? this is a bit awkward
-    ## because we're taking an un-annotated packrat source tarball and simply assuming it's now
-    ## an 'installed from source' version
-
-    ## -- InstallAgent -- ##
-    installAgent <- "InstallAgent: packrat 0.6.0"
-
-    ## -- InstallSource -- ##
-    installSource <- "InstallSource: source"
-
-    packratDescPath <- file.path(lib, "packrat", "DESCRIPTION")
-    DESCRIPTION <- readLines(packratDescPath)
-    DESCRIPTION <- c(DESCRIPTION, installAgent, installSource)
-    cat(DESCRIPTION, file = packratDescPath, sep = "\n")
-
-    # Otherwise, continue on as normal
-    message("> Attaching packrat")
-    library("packrat", character.only = TRUE, lib.loc = lib)
-
-    message("> Restoring library")
-    if (needsRestore)
-      packrat::restore(prompt = FALSE, restart = FALSE)
-
-    # If the environment allows us to restart, do so with a call to restore
-    restart <- getOption("restart")
-    if (!is.null(restart)) {
-      message("> Packrat bootstrap successfully completed. ",
-              "Restarting R and entering packrat mode...")
-      return(restart())
-    }
-
-    # Callers (source-erers) can define this hidden variable to make sure we don't enter packrat mode
-    # Primarily useful for testing
-    if (!exists(".__DONT_ENTER_PACKRAT_MODE__.") && interactive()) {
-      message("> Packrat bootstrap successfully completed. Entering packrat mode...")
-      packrat::on()
-    }
-
-    Sys.unsetenv("RSTUDIO_PACKRAT_BOOTSTRAP")
-
-  }
-
-})
--- a/packrat/packrat.lock
+++ b/packrat/packrat.lock
-PackratFormat: 1.4
-PackratVersion: 0.6.0
-RVersion: 4.1.0
-Repos: CRAN=https://cran.rstudio.com/
-
-Package: BH
-Source: CRAN
-Version: 1.72.0-3
-Hash: fc53be86f0b712d3de03fef95893d710
-
-Package: DT
-Source: CRAN
-Version: 0.16
-Hash: 7e8655053f400ece08a7e3782c59bcaa
-Requires: crosstalk, htmltools, jsonlite, htmlwidgets, magrittr,
-    promises
-
-Package: R6
-Source: CRAN
-Version: 2.5.0
-Hash: 25ebbd2664a276c915984da5c820c404
-
-Package: RCurl
-Source: CRAN
-Version: 1.98-1.2
-Hash: a0f856720001c4d75974c65e0aa437be
-Requires: bitops
-
-Package: Rcpp
-Source: CRAN
-Version: 1.0.5
-Hash: f6e400231df42179d6ce8fb35e52bf3f
-
-Package: XML
-Source: CRAN
-Version: 3.99-0.5
-Hash: 4d72b5b21762d6ddd4fe0f1db77a51f0
-
-Package: askpass
-Source: CRAN
-Version: 1.1
-Hash: 6f6c430e3cd0dd7d48f447700f4d7e7f
-Requires: sys
-
-Package: assertthat
-Source: CRAN
-Version: 0.2.1
-Hash: 622be49032fe50bd42e96aaef613e209
-
-Package: base64enc
-Source: CRAN
-Version: 0.1-3
-Hash: c590d29e555926af053055e23ee79efb
-
-Package: bitops
-Source: CRAN
-Version: 1.0-6
-Hash: 67d0775189fd0041d95abca618c5c07e
-
-Package: brew
-Source: CRAN
-Version: 1.0-6
-Hash: 931f9972deae0f205e1c78a51f33149b
-
-Package: brio
-Source: CRAN
-Version: 1.1.0
-Hash: 6935ba0d343d8901caf6b0a524749b4a
-
-Package: callr
-Source: CRAN
-Version: 3.5.1
-Hash: f9c95688940b93248943b187e998d743
-Requires: R6, processx
-
-Package: cli
-Source: CRAN
-Version: 2.2.0
-Hash: 38b61c4b8af7c1a3d9b260f3e5ef8018
-Requires: assertthat, crayon, fansi, glue
-
-Package: clipr
-Source: CRAN
-Version: 0.7.1
-Hash: 50bca21c0c36d24984b051077cb15cf3
-
-Package: commonmark
-Source: CRAN
-Version: 1.7
-Hash: 77f4ba718e2bad1877ef26e48cf8fa43
-
-Package: config
-Source: CRAN
-Version: 0.3.1
-Hash: 771e14360e686e2bb75e4a25e1f95cea
-Requires: yaml
-
-Package: covr
-Source: CRAN
-Version: 3.5.1
-Hash: 9fb31c09c7fdf51fef20371e3ffbf247
-Requires: crayon, yaml, digest, httr, jsonlite, rex, withr
-
-Package: cpp11
-Source: CRAN
-Version: 0.2.4
-Hash: 5374c8908db1d918b1c7fc6f2ec065da
-
-Package: crayon
-Source: CRAN
-Version: 1.3.4
-Hash: ff2840dd9b0d563fc80377a5a45510cd
-
-Package: crosstalk
-Source: CRAN
-Version: 1.1.0.1
-Hash: 0074e4967b2db46d003c5d23e4519306
-Requires: R6, jsonlite, lazyeval, htmltools
-
-Package: curl
-Source: CRAN
-Version: 4.3
-Hash: 3916ae5637dbaf5996dbde80ea92a047
-
-Package: data.table
-Source: CRAN
-Version: 1.13.4
-Hash: 8d29414760f530b50ff0bcb06f8ec8e3
-
-Package: desc
-Source: CRAN
-Version: 1.2.0
-Hash: a0a3ca939997679a52816bae4ed6aaae
-Requires: R6, assertthat, crayon, rprojroot
-
-Package: devtools
-Source: CRAN
-Version: 2.3.2
-Hash: f67347d7cd70a1037b25eea3237edf8f
-Requires: callr, cli, covr, desc, httr, jsonlite, rlang, withr, DT,
-    ellipsis, memoise, pkgbuild, pkgload, rcmdcheck, remotes, roxygen2,
-    rstudioapi, rversions, sessioninfo, testthat, usethis
-
-Package: diffobj
-Source: CRAN
-Version: 0.3.2
-Hash: 7872e6de15afd8b5233d7d382b8ec340
-Requires: crayon
-
-Package: digest
-Source: CRAN
-Version: 0.6.27
-Hash: 8ba156629c1537635b39332c93d8ed33
-
-Package: doParallel
-Source: CRAN
-Version: 1.0.16
-Hash: 0bfafffe940c8fc4bc4f785018b17dde
-Requires: foreach, iterators
-
-Package: dplyr
-Source: CRAN
-Version: 1.0.2
-Hash: ea54da55bb8474c5f1e7852ea3315c22
-Requires: R6, ellipsis, glue, lifecycle, magrittr, rlang, tibble,
-    vctrs, generics, tidyselect
-
-Package: ellipsis
-Source: CRAN
-Version: 0.3.1
-Hash: b294fcc92985c6235df03c1c34f25e99
-Requires: rlang
-
-Package: evaluate
-Source: CRAN
-Version: 0.14
-Hash: 18306cc3bc1aec7b7360eea8a0eb0ee1
-
-Package: fansi
-Source: CRAN
-Version: 0.4.1
-Hash: fc0a252b8e427847d13e89f56ab4665e
-
-Package: foreach
-Source: CRAN
-Version: 1.5.1
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-Requires: iterators
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-Package: fs
-Source: CRAN
-Version: 1.5.0
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-
-Package: generics
-Source: CRAN
-Version: 0.1.0
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-
-Package: gh
-Source: CRAN
-Version: 1.2.0
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-Package: git2r
-Source: CRAN
-Version: 0.27.1
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-Package: gitcreds
-Source: CRAN
-Version: 0.1.1
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-Package: glue
-Source: CRAN
-Version: 1.4.2
-Hash: afa798ba9deec3676e20300b79094749
-
-Package: highr
-Source: CRAN
-Version: 0.8
-Hash: 16aa2cc98d7b68c9d148c263c8dcdbcd
-
-Package: hms
-Source: CRAN
-Version: 0.5.3
-Hash: a0709e1b17b4bc1c27f5235177543e07
-Requires: pkgconfig, rlang, vctrs
-
-Package: htmltools
-Source: CRAN
-Version: 0.5.0
-Hash: 79070a001acba57f88692d17e859bac5
-Requires: base64enc, digest, rlang
-
-Package: htmlwidgets
-Source: CRAN
-Version: 1.5.2
-Hash: 7019eab39b9b7560e649c1218ab6a357
-Requires: htmltools, jsonlite, yaml
-
-Package: httr
-Source: CRAN
-Version: 1.4.2
-Hash: 2ad813eba37ce1f357434789aa8b6132
-Requires: R6, curl, jsonlite, mime, openssl
-
-Package: ini
-Source: CRAN
-Version: 0.3.1
-Hash: 9d6de5178c1cedabfb24e7d2acc9a092
-
-Package: iterators
-Source: CRAN
-Version: 1.0.13
-Hash: 750adbdf6750e2dbcf2066c443d64892
-
-Package: jsonlite
-Source: CRAN
-Version: 1.7.1
-Hash: 313e0917dfcfbc98bb87d79da0d85aaa
-
-Package: knitr
-Source: CRAN
-Version: 1.30
-Hash: 1a622820d7dd1ec61bb95ecf40fb166e
-Requires: yaml, evaluate, highr, markdown, stringr, xfun
-
-Package: later
-Source: CRAN
-Version: 1.1.0.1
-Hash: 0c6d0dbad70a1b8698919b5d70e8a430
-Requires: BH, Rcpp, rlang
-
-Package: lazyeval
-Source: CRAN
-Version: 0.2.2
-Hash: 563563691bea3cde6945a98996d7c166
-
-Package: lifecycle
-Source: CRAN
-Version: 0.2.0
-Hash: df8649860c43571aab68cc73a2a02807
-Requires: glue, rlang
-
-Package: magrittr
-Source: CRAN
-Version: 2.0.1
-Hash: d3c166b0573ae8c918edf7221dfe7380
-
-Package: markdown
-Source: CRAN
-Version: 1.1
-Hash: 1b6a18fd395589425e338a47b999099f
-Requires: mime, xfun
-
-Package: memoise
-Source: CRAN
-Version: 1.1.0
-Hash: 410fcd334bc626db100237cc1370f2e9
-Requires: digest
-
-Package: mime
-Source: CRAN
-Version: 0.9
-Hash: f3388735b4ddea072aff3be44f7f4968
-
-Package: openssl
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--- a/packrat/packrat.opts
+++ b/packrat/packrat.opts
-auto.snapshot: FALSE
-use.cache: FALSE
-print.banner.on.startup: auto
-vcs.ignore.lib: TRUE
-vcs.ignore.src: TRUE
-external.packages: packrat
-local.repos: 
-load.external.packages.on.startup: TRUE
-ignored.packages: 
-ignored.directories:
-    data
-    inst
-quiet.package.installation: TRUE
-snapshot.recommended.packages: FALSE
-snapshot.fields:
-    Imports
-    Depends
-    LinkingTo
-symlink.system.packages: TRUE
--- a/renv.lock
+++ b/renv.lock
--- a/renv/.gitignore
+++ b/renv/.gitignore
+library/
+local/
+cellar/
+lock/
+python/
+sandbox/
+staging/
--- a/renv/activate.R
+++ b/renv/activate.R