From 469b145d8c93aca24233201f10887011ba34cc01 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Sun, 30 Dec 2018 12:00:53 +0100 Subject: [PATCH] bye bye packrat --- .gitlab-ci.yml | 82 +++++----- DESCRIPTION | 2 +- ci.R | 50 ------ packrat/init.R | 226 --------------------------- packrat/packrat.lock | 354 ------------------------------------------- packrat/packrat.opts | 19 --- 6 files changed, 42 insertions(+), 691 deletions(-) delete mode 100644 ci.R delete mode 100644 packrat/init.R delete mode 100644 packrat/packrat.lock delete mode 100644 packrat/packrat.opts diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 33d2857b..54c1fc3d 100644 --- a/.gitlab-ci.yml +++ b/.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: - - setup - - test - - deploy - -cache: - # Ommit key to use the same cache across all pipelines and branches - key: "$CI_COMMIT_REF_SLUG" - paths: - - packrat/lib/ - -setup: - stage: setup +R 3: + stage: build + allow_failure: true script: - - R -e 'source("ci.R"); ci_setup()' - -check: - stage: test - dependencies: - - setup - when: on_success - script: - - R -e 'source("ci.R"); ci_check()' - -coverage: - stage: test - dependencies: - - setup - when: on_success - only: - - master - script: - - R -e 'source("ci.R"); ci_coverage()' + # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file + - rm -rf vignettes + - Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")' + # build package + - R CMD build . --no-build-vignettes --no-manual + - PKG_FILE_NAME=$(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: + 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 diff --git a/DESCRIPTION b/DESCRIPTION index 0d78cb01..72f4246c 100755 --- a/DESCRIPTION +++ b/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( diff --git a/ci.R b/ci.R deleted file mode 100644 index 48e6c695..00000000 --- a/ci.R +++ /dev/null @@ -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")) -} diff --git a/packrat/init.R b/packrat/init.R deleted file mode 100644 index 5901a331..00000000 --- a/packrat/init.R +++ /dev/null @@ -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") - - } - -}) diff --git a/packrat/packrat.lock b/packrat/packrat.lock deleted file mode 100644 index 11a43058..00000000 --- a/packrat/packrat.lock +++ /dev/null @@ -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 - 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data - inst -quiet.package.installation: TRUE -snapshot.recommended.packages: FALSE -snapshot.fields: - Imports - Depends - LinkingTo -symlink.system.packages: TRUE