bye bye packrat

.gitlab-ci.yml

@@ -16,58 +16,58 @@
 # GNU General Public License version 2.0 for more details.             #
 # ==================================================================== #
 
-# https://r-posts.com/gitlab-ci-for-r-package-development/
+# from https://stackoverflow.com/questions/51866926
+# and https://github.com/jangorecki/r.gitlab.ci
+# and https://docs.gitlab.com/ce/ci/yaml/README.html
+# how the Docker+R images work: https://hub.docker.com/r/rocker/r-ver/
+
+stages:
+  - build
+  - deploy
+
+image: debian:buster-slim
 
-image: rocker/r-base
 before_script:
   - apt-get update
   # install dependencies for package
-  - apt-get -y install libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev
+  - apt-get -y install libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev pandoc r-base
+  - Rscript -e 'install.packages(c("devtools", "rlang"), repos = "https://cran.rstudio.com")'
+  - Rscript -e 'devtools::install_dev_deps(repos = "https://cran.rstudio.com")'
 
-stages:
+R 3:
-  - setup
+  stage: build
-  - test
+  allow_failure: true
-  - deploy
-
-cache:
-  # Ommit key to use the same cache across all pipelines and branches
-  key: "$CI_COMMIT_REF_SLUG"
-  paths:
-    - packrat/lib/
-
-setup:
-  stage: setup
   script:
-    - R -e 'source("ci.R"); ci_setup()'
+    # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
-
+    - rm -rf vignettes
-check:
+    - Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
-  stage: test
+    # build package
-  dependencies:
+    - R CMD build . --no-build-vignettes --no-manual
-    - setup
+    - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
-  when: on_success
+    - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
-  script:
+    # code coverage
-    - R -e 'source("ci.R"); ci_check()'
+    - apt-get install --yes git
-
+    - Rscript -e 'cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = "50ffa0aa-fee0-4f8b-a11d-8c7edc6d32ca"); cat("Code coverage:", covr::percent_coverage(cc))'
-coverage:
-  stage: test
-  dependencies:
-    - setup
-  when: on_success
-  only:
-    - master
-  script:
-    - R -e 'source("ci.R"); ci_coverage()'
   coverage: '/Code coverage: \d+\.\d+/'
+  artifacts:
+    paths:
+      - '*.Rcheck/*.log'
+      - '*.Rcheck/*.out'
+      # - '*.Rcheck/*.fail'
+      - '*.Rcheck/*.Rout'
+    name: 'Rcheck log'
+    expire_in: '1 month'
 
 pages:
   stage: deploy
-  dependencies:
-    - setup
-  when: always
-  only:
-    - master
   script:
-    - R -e 'source("ci.R"); ci_pages()'
+    - Rscript -e "install.packages('pkgdown', repos = 'https://cran.rstudio.com')"
+    - Rscript -e "devtools::install(build = TRUE, upgrade = FALSE)"
+    # - R -e "pkgdown::build_favicon()"
+    - R -e "pkgdown::build_site(examples = FALSE, override = list(destination = 'public'))"
+  when: always
   artifacts:
     paths:
       - public
+  only:
+    - master

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
 Version: 0.5.0.9008
-Date: 2018-12-29
+Date: 2018-12-30
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(

ci.R

@@ -1,50 +0,0 @@
-# ==================================================================== #
-# TITLE                                                                #
-# Antimicrobial Resistance (AMR) Analysis                              #
-#                                                                      #
-# AUTHORS                                                              #
-# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)           #
-#                                                                      #
-# LICENCE                                                              #
-# This package is free software; you can redistribute it and/or modify #
-# it under the terms of the GNU General Public License version 2.0,    #
-# as published by the Free Software Foundation.                        #
-#                                                                      #
-# This R package is distributed in the hope that it will be useful,    #
-# but WITHOUT ANY WARRANTY; without even the implied warranty of       #
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the        #
-# GNU General Public License version 2.0 for more details.             #
-# ==================================================================== #
-
-install_if_needed <- function(package_to_install) {
-  package_path <- find.package(package_to_install, quiet = TRUE)
-
-  if(length(package_path) == 0){
-    # Only install if not present
-    install.packages(package_to_install, repos = "https://cran.rstudio.com/")
-  }
-}
-
-ci_setup <- function() {
-  install_if_needed("packrat")
-  packrat::restore()
-}
-
-ci_check <- function() {
-  install_if_needed("devtools")
-  install_if_needed("roxygen2")
-  devtools::check()
-}
-
-ci_coverage <- function() {
-  install_if_needed("covr")
-  devtools::install()
-  cc <- covr::package_coverage(type = c("tests", "examples"))
-  covr::codecov(coverage = cc, token = "50ffa0aa-fee0-4f8b-a11d-8c7edc6d32ca")
-  cat("Code coverage:", covr::percent_coverage(cc))
-}
-
-ci_pages <- function() {
-  install_if_needed("pkgdown")
-  pkgdown::build_site(examples = FALSE, override = list(destination = "public"))
-}

packrat/init.R

@@ -1,226 +0,0 @@
-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% rownames(available.packages())) {
-        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",
-      "--slave",
-      "-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 0.5.0"
-
-    ## -- 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")
-
-  }
-
-})

packrat/packrat.lock

@@ -1,354 +0,0 @@
-PackratFormat: 1.4
-PackratVersion: 0.5.0
-RVersion: 3.5.2
-Repos: CRAN=https://cloud.r-project.org
-
-Package: BH
-Source: CRAN
-Version: 1.66.0-1
-Hash: 4cc8883584b955ed01f38f68bc03af6d
-
-Package: R6
-Source: CRAN
-Version: 2.3.0
-Hash: 8eccabbf292b5aba632985cde6406fc3
-
-Package: RColorBrewer
-Source: CRAN
-Version: 1.1-2
-Hash: c0d56cd15034f395874c870141870c25
-
-Package: Rcpp
-Source: CRAN
-Version: 1.0.0
-Hash: c7273c0f0bc9f5e41f4c52a8cf571f0f
-
-Package: assertthat
-Source: CRAN
-Version: 0.2.0
-Hash: e8805df54c65ac96d50235c44a82615c
-
-Package: backports
-Source: CRAN
-Version: 1.1.2
-Hash: 5ae7b3466e529e4400951ca18c137e40
-
-Package: base64enc
-Source: CRAN
-Version: 0.1-3
-Hash: c590d29e555926af053055e23ee79efb
-
-Package: cli
-Source: CRAN
-Version: 1.0.1
-Hash: a742a3229dbf7085c3a737af10e5065b
-Requires: assertthat, crayon
-
-Package: colorspace
-Source: CRAN
-Version: 1.3-2
-Hash: 0bf8618b585fa98eb23414cd3ab95118
-
-Package: covr
-Source: CRAN
-Version: 3.2.1
-Hash: b1dab7f44fae6114c222cee94d6acd63
-Requires: crayon, digest, httr, jsonlite, rex, withr
-
-Package: crayon
-Source: CRAN
-Version: 1.3.4
-Hash: ff2840dd9b0d563fc80377a5a45510cd
-
-Package: curl
-Source: CRAN
-Version: 3.2
-Hash: 82a7cf5bb702ef52329b6d23ea6132a7
-
-Package: data.table
-Source: CRAN
-Version: 1.11.8
-Hash: 67c877937c790a0cadb71284febb6b34
-
-Package: digest
-Source: CRAN
-Version: 0.6.18
-Hash: 65f62365ec69ddd17230d2ffe891a6ab
-
-Package: dplyr
-Source: github
-Version: 0.7.99.9000
-Hash: 2ad5ae0fa33abb1278da08b574c03c74
-Requires: BH, R6, Rcpp, assertthat, glue, magrittr, pkgconfig, plogr,
-    rlang, tibble, tidyselect
-GithubRepo: dplyr
-GithubUsername: tidyverse
-GithubRef: master
-GithubSha1: 45894214a543e63c01f66e8b1fb4cc77a5978f40
-RemoteHost: api.github.com
-RemoteRepo: dplyr
-RemoteUsername: tidyverse
-RemoteRef: master
-RemoteSha: 45894214a543e63c01f66e8b1fb4cc77a5978f40
-
-Package: evaluate
-Source: CRAN
-Version: 0.12
-Hash: c32505adba4f6eca5aa20dd32300b019
-
-Package: fansi
-Source: CRAN
-Version: 0.4.0
-Hash: f147621f72b561485bfffcae78c4f5d5
-
-Package: ggplot2
-Source: CRAN
-Version: 3.1.0
-Hash: ef541b05dda10b209d509b5bbaf46ea3
-Requires: digest, gtable, lazyeval, plyr, reshape2, rlang, scales,
-    tibble, viridisLite, withr
-
-Package: glue
-Source: CRAN
-Version: 1.3.0
-Hash: 1fbde6dec830370be696eee8ef31c9e4
-
-Package: gtable
-Source: CRAN
-Version: 0.2.0
-Hash: cd78381a9d3fea966ac39bd0daaf5554
-
-Package: highr
-Source: CRAN
-Version: 0.7
-Hash: 20757f5c393ed0ecf96c9e8e6d8d514c
-
-Package: hms
-Source: CRAN
-Version: 0.4.2
-Hash: b4096a4f6a6736138e9a825c2baaacf0
-Requires: pkgconfig, rlang
-
-Package: htmltools
-Source: CRAN
-Version: 0.3.6
-Hash: 9707abea0a9b7406e98fb1242e97e1f6
-Requires: Rcpp, digest
-
-Package: httr
-Source: CRAN
-Version: 1.3.1
-Hash: 2d32e01e53d532c812052e27a1021441
-Requires: R6, curl, jsonlite, mime, openssl
-
-Package: jsonlite
-Source: CRAN
-Version: 1.5
-Hash: 9c51936d8dd00b2f1d4fe9d10499694c
-
-Package: knitr
-Source: CRAN
-Version: 1.20
-Hash: 9c6b215d1d02b97586c8232e94533e6a
-Requires: evaluate, highr, markdown, stringr, yaml
-
-Package: labeling
-Source: CRAN
-Version: 0.3
-Hash: ecf589b42cd284b03a4beb9665482d3e
-
-Package: lazyeval
-Source: CRAN
-Version: 0.2.1
-Hash: 88926ad9c43581fd0822a37c8ed09f05
-
-Package: magrittr
-Source: CRAN
-Version: 1.5
-Hash: bdc4d48c3135e8f3b399536ddf160df4
-
-Package: markdown
-Source: CRAN
-Version: 0.8
-Hash: 045d7c594d503b41f1c28946d076c8aa
-Requires: mime
-
-Package: mime
-Source: CRAN
-Version: 0.6
-Hash: 2ed8f98b8284ad733f3907fc6e2f1334
-
-Package: munsell
-Source: CRAN
-Version: 0.5.0
-Hash: 38d0efee9bb99bef143bde41c4ce715c
-Requires: colorspace
-
-Package: openssl
-Source: CRAN
-Version: 1.0.2
-Hash: 12a42cbd5aecdb887782247856ccbafd
-
-Package: packrat
-Source: CRAN
-Version: 0.5.0
-Hash: 498643e765d1442ba7b1160a1df3abf9
-
-Package: pillar
-Source: CRAN
-Version: 1.3.1
-Hash: 9ed4c2a5d3047bfba3e852ad5e806d91
-Requires: cli, crayon, fansi, rlang, utf8
-
-Package: pkgconfig
-Source: CRAN
-Version: 2.0.2
-Hash: b0fd6ed908e150b77e5f00c6478bd58c
-
-Package: plogr
-Source: CRAN
-Version: 0.2.0
-Hash: 81a8008a5e7858552503935f1abe48aa
-
-Package: plyr
-Source: CRAN
-Version: 1.8.4
-Hash: ec185c885aab7ec91693d78c20cb5d1a
-Requires: Rcpp
-
-Package: praise
-Source: CRAN
-Version: 1.0.0
-Hash: 77da8f1df873a4b91e5c4a68fe2fb1b6
-
-Package: purrr
-Source: CRAN
-Version: 0.2.5
-Hash: 8b0c16db10c7e20b70cd37779a673a8b
-Requires: magrittr, rlang, tibble
-
-Package: reshape2
-Source: CRAN
-Version: 1.4.3
-Hash: c950c8ac85b81209635acb3ce21b4cce
-Requires: Rcpp, plyr, stringr
-
-Package: rex
-Source: CRAN
-Version: 1.1.2
-Hash: 57541aaae58f1a284a398f5c62c95097
-Requires: lazyeval, magrittr
-
-Package: rlang
-Source: CRAN
-Version: 0.3.0.1
-Hash: 35fb7a51d5d756c56f793ed9c381fb84
-
-Package: rmarkdown
-Source: CRAN
-Version: 1.10
-Hash: 02f1aac33000c63986c6b5585e36e7ae
-Requires: base64enc, evaluate, htmltools, jsonlite, knitr, mime,
-    rprojroot, stringr, tinytex, yaml
-
-Package: rprojroot
-Source: CRAN
-Version: 1.3-2
-Hash: a25c3f70c166fb3fbabc410eb32b6366
-Requires: backports
-
-Package: rstudioapi
-Source: CRAN
-Version: 0.8
-Hash: 9ba7fe76dcaf96966c449527ca04bb78
-
-Package: rvest
-Source: CRAN
-Version: 0.3.2
-Hash: c69f7526520bad66fd2111ebe8b1364b
-Requires: httr, magrittr, selectr, xml2
-
-Package: scales
-Source: CRAN
-Version: 1.0.0
-Hash: 7d9b717abcec656ae7c5c982d72b75e5
-Requires: R6, RColorBrewer, Rcpp, labeling, munsell, viridisLite
-
-Package: selectr
-Source: CRAN
-Version: 0.4-1
-Hash: b12802c11e35dec9d16a74d30ed0f3ed
-Requires: R6, stringr
-
-Package: stringi
-Source: CRAN
-Version: 1.2.4
-Hash: 03ab60ef7fa4627b38ad67c95ce6b04c
-
-Package: stringr
-Source: CRAN
-Version: 1.3.1
-Hash: 9f417a1d899ed1f080942ab36998e8b5
-Requires: glue, magrittr, stringi
-
-Package: testthat
-Source: CRAN
-Version: 2.0.1
-Hash: 777eb6e94f5a62bf6320fecf0175bbbb
-Requires: R6, cli, crayon, digest, magrittr, praise, rlang, withr
-
-Package: tibble
-Source: CRAN
-Version: 1.4.2
-Hash: 83895360ce4f8d2ce92eee00526b5b0b
-Requires: cli, crayon, pillar, rlang
-
-Package: tidyr
-Source: CRAN
-Version: 0.8.2
-Hash: 9ff92b9b3c11dfcd94d179b75b85c668
-Requires: Rcpp, dplyr, glue, magrittr, purrr, rlang, stringi, tibble,
-    tidyselect
-
-Package: tidyselect
-Source: CRAN
-Version: 0.2.5
-Hash: fad1cf10c5c4996fca6ca68e0716d2e6
-Requires: Rcpp, glue, purrr, rlang
-
-Package: tinytex
-Source: CRAN
-Version: 0.9
-Hash: a4ffe98c58eace5a95644d8fd6ca5a50
-Requires: xfun
-
-Package: utf8
-Source: CRAN
-Version: 1.1.4
-Hash: f3f97ce59092abc8ed3fd098a59e236c
-
-Package: viridisLite
-Source: CRAN
-Version: 0.3.0
-Hash: 78bb072c4f9e729a283d4c40ec93f9c6
-
-Package: withr
-Source: CRAN
-Version: 2.1.2
-Hash: d534108bcd5f34ec73e9eb523751ba20
-
-Package: xfun
-Source: CRAN
-Version: 0.4
-Hash: 76004125b45195c0330ec71904849995
-
-Package: xml2
-Source: CRAN
-Version: 1.2.0
-Hash: 3f00e5347a6d7ccad2237fe1bc1df6d0
-Requires: Rcpp
-
-Package: yaml
-Source: CRAN
-Version: 2.2.0
-Hash: a5ad5616d83d89f8d84cbf3cf4034e13

packrat/packrat.opts

@@ -1,19 +0,0 @@
-auto.snapshot: TRUE
-use.cache: FALSE
-print.banner.on.startup: auto
-vcs.ignore.lib: TRUE
-vcs.ignore.src: TRUE
-external.packages: 
-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