introduction of Packrat

2024-12-26 06:06:12 +01:00 · 2018-12-30 08:40:40 +01:00 · 2018-12-30 08:40:40 +01:00 · fd646fe1fc
commit fd646fe1fc
parent cf44d94552
10 changed files with 750 additions and 58 deletions
--- a/.Rbuildignore
+++ b/.Rbuildignore
@ -1,17 +1,20 @@
-^Meta$
-^doc$
-^CRAN-RELEASE$
 ^.*\.Rproj$
+^\.gitlab-ci.yml$
+^\.Rprofile$
 ^\.Rproj\.user$
 ^\.travis.yml$
-^appveyor.yml$
-^\.gitlab-ci.yml$
 ^\.zenodo.json$
 ^_noinclude$
-^cran-comments\.md$
-^git.sh$
-^public$
-^docs$
 ^_pkgdown\.yml$
-^pkgdown$
+^appveyor.yml$
+^ci.R$
+^cran-comments\.md$
+^CRAN-RELEASE$
+^doc$
+^docs$
+^git.sh$
 ^index\.md$
+^Meta$
+^packrat/
+^pkgdown$
+^public$
--- a/.gitignore
+++ b/.gitignore
@ -15,5 +15,8 @@ _noinclude
 *.dll
 vignettes/*.R
 .DS_Store
+.Rprofile
 ^CRAN-RELEASE$
 git.sh
+packrat/lib*/
+packrat/src/
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@ -1,54 +1,69 @@
-# 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/
+# ==================================================================== #
+# 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.             #
+# ==================================================================== #
+
+# https://r-posts.com/gitlab-ci-for-r-package-development/
+
+image: rocker/r-base

 stages:
-  - build
+  - setup
+  - test
  - deploy

-image: rocker/r-ver:3 # test on R v3.*.*
-
-before_script:
-  - apt-get update
-  # install dependencies for package
-  - apt-get install --yes --no-install-recommends libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev pandoc
-  - Rscript -e 'install.packages(c("devtools", "rlang"), repos = "https://cran.rstudio.com")'
-  - Rscript -e 'devtools::install_dev_deps(repos = "https://cran.rstudio.com")'
-
-R 3:
-  stage: build
-  allow_failure: true
-  script:
-    # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
-    - rm -rf vignettes
-    - Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
-    # build package
-    - R CMD build . --no-build-vignettes --no-manual
-    - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
-    - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
-    # code coverage
-    - 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: '/Code coverage: \d+\.\d+/'
-  artifacts:
+cache:
+  # Ommit key to use the same cache across all pipelines and branches
+  key: "$CI_COMMIT_REF_SLUG"
  paths:
-      - '*.Rcheck/*.log'
-      - '*.Rcheck/*.out'
-      # - '*.Rcheck/*.fail'
-      - '*.Rcheck/*.Rout'
-    name: 'Rcheck log'
-    expire_in: '1 month'
+    - packrat/lib/
+
+setup:
+  stage: setup
+  script:
+    - R -e 'source("ci.R"); ci_setup()'
+
+check:
+  stage: test
+  dependencies:
+    - setup
+  when: on_success
+  script:
+    - R -e 'source("ci.R"); ci_check()'
+
+coverage:
+  stage: test
+  dependencies:
+    - setup
+  when: on_success
+  only:
+    - master
+  script:
+    - R -e 'source("ci.R"); ci_coverage()'
+  coverage: '/Code coverage: \d+\.\d+/'

 pages:
  stage: deploy
+   dependencies:
+    - setup
+  when: on_success
+  only:
+    - master
  script:
-    - 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'))"
+    - R -e 'source("ci.R"); ci_pages()'
  artifacts:
    paths:
      - public
-  only:
-    - master
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@ -1,3 +1,21 @@
+# ==================================================================== #
+# 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.             #
+# ==================================================================== #
+
 url: https://msberends.gitlab.io

 title: 'AMR (for R)'
--- a/ci.R
+++ b/ci.R
@ -0,0 +1,48 @@
+# ==================================================================== #
+# 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)
+  }
+}
+
+ci_setup <- function() {
+  install_if_needed("packrat")
+  packrat::restore()
+}
+
+ci_check <- function() {
+  install_if_needed("devtools")
+  devtools::check()
+}
+
+ci_coverage <- function() {
+  install_if_needed("covr")
+  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"))
+}
--- a/index.md
+++ b/index.md
@ -10,30 +10,35 @@ We created this package for academic research at the Faculty of Medical Sciences

 This package is ready-to-use for a professional environment by specialists in the following fields:

-* Medical Microbiology
+Medical Microbiology:
+
  * Epidemiologists (both clinical microbiological and research)
  * Research Microbiologists
  * Biomedical Researchers
  * Research Pharmacologists
  
-* Veterinary Microbiology
+Veterinary Microbiology:
+
  * Research Veterinarians
  * Veterinary Epidemiologists
  * Biomedical Researchers

-* Microbial Ecology
+Microbial Ecology:
+
  * Soil Microbiologists
  * Extremophile Researchers
  * Astrobiologists

-* Other specialists in any of the above fields:
+Other specialists in any of the above fields:
+
  * Data Scientists/Data Analysts
  * Biotechnologists
  * Biochemists
  * Geneticists
  * Molecular Biologists/Microbiologists

-* Developers
+Developers:
+
  * Package developers for R 
  * Software developers
  * Web application developers
--- a/packrat/init.R
+++ b/packrat/init.R
@ -0,0 +1,226 @@
+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")
+
+  }
+
+})
--- a/packrat/packrat.lock
+++ b/packrat/packrat.lock
@ -0,0 +1,354 @@
+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
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+Requires: base64enc, evaluate, htmltools, jsonlite, knitr, mime,
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+Requires: cli, crayon, pillar, rlang
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+Hash: 9ff92b9b3c11dfcd94d179b75b85c668
+Requires: Rcpp, dplyr, glue, magrittr, purrr, rlang, stringi, tibble,
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+Requires: Rcpp, glue, purrr, rlang
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+Hash: d534108bcd5f34ec73e9eb523751ba20
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--- a/packrat/packrat.opts
+++ b/packrat/packrat.opts
@ -0,0 +1,19 @@
+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
--- a/pkgdown/extra.js
+++ b/pkgdown/extra.js
@ -2,7 +2,8 @@
 $('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.6.3/css/all.css" integrity="sha384-UHRtZLI+pbxtHCWp1t77Bi1L4ZtiqrqD80Kn4Z8NTSRyMA2Fd33n5dQ8lWUE00s/" crossorigin="anonymous">');

 /* edit footer */
-var footer_txt = $('footer .copyright p').html();
-footer_txt = footer_txt.replace("Developed by", "Developed at the University of Groningen. Authors:");
-$('footer').html('<p>' + footer_txt + '</p>');
+$('footer').html('<p>' +
+                 $('footer .copyright p').html().replace("Developed by",
+                                                         "<code>AMR</code> (for R). Developed at the University of Groningen.<br>Authors:") +
+                 '</p>');
 //$('footer').prepend("<div class='university'/>");