From 6200d0f5aadc7f537298bbc8de8abaf4bbc802de Mon Sep 17 00:00:00 2001 From: Ellis Hughes Date: Wed, 9 Dec 2020 16:16:43 -0800 Subject: [PATCH 01/24] clean up temp library path to be an object --- tests/testthat/test-document.R | 16 ++++++++------- tests/testthat/test-r-processing.R | 33 +++++++++++++++++------------- 2 files changed, 28 insertions(+), 21 deletions(-) diff --git a/tests/testthat/test-document.R b/tests/testthat/test-document.R index 37d4884..e9b0f75 100644 --- a/tests/testthat/test-document.R +++ b/tests/testthat/test-document.R @@ -10,11 +10,13 @@ test_that("documentation is built via document()", { force = TRUE, r_object_names = "cars_over_20" ) - package_build( - file.path(tempdir(), "subsetCars") - ) - dir.create(file.path(tempdir(),"lib")) - expect_true(document(file.path(tempdir(), "subsetCars"), lib = file.path(tempdir(),"lib"))) + + temp_libpath <- file.path(tempdir(), "lib") + dir.create(temp_libpath) + + package_build(file.path(tempdir(), "subsetCars")) + + expect_true(document(file.path(tempdir(), "subsetCars"), lib = temp_libpath)) docfile <- readLines(file.path( tempdir(), "subsetCars", "data-raw", "documentation.R" @@ -45,10 +47,10 @@ test_that("documentation is built via document()", { flush(connection) close(connection) expect_output( - document(file.path(tempdir(), "subsetCars"), lib = file.path(tempdir(),"lib")), + document(file.path(tempdir(), "subsetCars"), lib = temp_libpath), "Writing testmarkdownroxygen.Rd" ) - v <- vignette(package = "subsetCars", lib.loc = file.path(tempdir(),"lib")) + v <- vignette(package = "subsetCars", lib.loc = temp_libpath) expect_equal(v$results[, "Item"], "subsetCars") unlink(file.path(tempdir(), "subsetCars"), recursive = TRUE, diff --git a/tests/testthat/test-r-processing.R b/tests/testthat/test-r-processing.R index ecf72e4..96e2e36 100644 --- a/tests/testthat/test-r-processing.R +++ b/tests/testthat/test-r-processing.R @@ -1,9 +1,10 @@ context("R file script processing to vignette") test_that("R file processing works and creates vignettes", { + file <- system.file("extdata", "tests", "rfileTest.R", package = "DataPackageR" ) - dir.create(file.path(tempdir(),"lib")) + datapackage_skeleton( name = "rfiletest", path = tempdir(), @@ -11,24 +12,28 @@ test_that("R file processing works and creates vignettes", { force = TRUE, r_object_names = "data" ) + + temp_libpath <- file.path(tempdir(),"lib") + dir.create(temp_libpath) + expect_equal( - basename( - package_build( - file.path(tempdir(), "rfiletest"), - install = TRUE, - lib = file.path(tempdir(),"lib") - ) - ), + basename(package_build( + file.path(tempdir(), "rfiletest"), + install = TRUE, + lib = temp_libpath + )), "rfiletest_1.0.tar.gz" ) - v <- vignette(package = "rfiletest", lib.loc = file.path(tempdir(),"lib")) + + v <- vignette(package = "rfiletest", lib.loc = temp_libpath) + expect_equal(v$results[, "Item"], "rfileTest") expect_true(file_test("-f", file.path(tempdir(),"rfiletest","inst","doc","rfileTest.pdf"))) unlink(file.path(tempdir(), "rfiletest"), recursive = TRUE, force = TRUE ) - remove.packages("rfiletest", lib = file.path(tempdir(),"lib")) + remove.packages("rfiletest", lib = temp_libpath) file <- system.file("extdata", "tests", "rfileTest_noheader.R", package = "DataPackageR" ) @@ -39,23 +44,23 @@ test_that("R file processing works and creates vignettes", { force = TRUE, r_object_names = "data" ) - dir.create(file.path(tempdir(),"lib")) + dir.create(temp_libpath) expect_equal( basename( package_build( file.path(tempdir(), "rfiletest"), install = TRUE, - lib = file.path(tempdir(),"lib") + lib = temp_libpath ) ), "rfiletest_1.0.tar.gz" ) - v <- vignette(package = "rfiletest", lib.loc = file.path(tempdir(),"lib")) + v <- vignette(package = "rfiletest", lib.loc = temp_libpath) expect_equal(v$results[, "Item"], "rfileTest_noheader") unlink(file.path(tempdir(), "rfiletest"), recursive = TRUE, force = TRUE ) try(usethis::proj_set(NULL),silent = TRUE) #wrap in try for usethis 1.4 vs 1.5 - remove.packages("rfiletest",lib = file.path(tempdir(),"lib")) + remove.packages("rfiletest",lib = temp_libpath) }) From 49508f3d5366fad5c47865e4e8317893a8c4fc86 Mon Sep 17 00:00:00 2001 From: Ellis Hughes Date: Wed, 9 Dec 2020 16:17:35 -0800 Subject: [PATCH 02/24] Update code to unload package that it is trying to install. It gets loaded to namespace during building in prior step. --- R/build.R | 2 +- R/processData.R | 5 +++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/R/build.R b/R/build.R index fa17151..c7f5952 100644 --- a/R/build.R +++ b/R/build.R @@ -98,8 +98,8 @@ package_build <- function(packageName = NULL, ) # try to install and then reload the package in the current session if (install) { + devtools::unload(packageName) install.packages(location, repos = NULL, type = "source", ...) - devtools::reload(package_path) } .next_steps() return(location) diff --git a/R/processData.R b/R/processData.R index 7756c8e..ad174c3 100644 --- a/R/processData.R +++ b/R/processData.R @@ -834,9 +834,10 @@ document <- function(path = ".", install = TRUE, ...) { pkg = path, path = dirname(path), vignettes = FALSE, quiet = TRUE ) + # try to install and then reload the package in the current session if (install) { - install.packages(location, repos = NULL, type = "source", quiet = TRUE, ...) - devtools::reload(path, quiet = TRUE) + devtools::unload(basename(path)) + install.packages(location, repos = NULL, type = "source", ...) } return(TRUE) } From 310cc4a7e736c278105d5c15855a4b7656c3e6ca Mon Sep 17 00:00:00 2001 From: Marie Vendettuoli Date: Wed, 9 Dec 2020 19:45:30 -0800 Subject: [PATCH 03/24] update to run tests in interactive mode --- tests/testthat/test-news-update.R | 3 ++- tests/testthat/test-updating-datapackager-version.R | 12 ++++++------ vignettes/YAML_CONFIG.Rmd | 4 ++-- 3 files changed, 10 insertions(+), 9 deletions(-) diff --git a/tests/testthat/test-news-update.R b/tests/testthat/test-news-update.R index d86d5fa..52eadcf 100644 --- a/tests/testthat/test-news-update.R +++ b/tests/testthat/test-news-update.R @@ -10,11 +10,12 @@ test_that("news file is created", { force = TRUE, r_object_names = c("cars_over_20") ) + options(DataPackageR_interact = FALSE) package_build(file.path(tempdir(), "subsetCars")) expect_equal(readLines(file.path(tempdir(), "subsetCars", "NEWS.md"))[3], "Package built in non-interactive mode") # nolint unlink(file.path(tempdir(), "subsetCars"), recursive = TRUE, force = TRUE ) - expect_equal(.prompt_user_for_change_description(), "Package built in non-interactive mode") # nolint + expect_equal(DataPackageR:::.prompt_user_for_change_description(interact = FALSE), "Package built in non-interactive mode") # nolint }) diff --git a/tests/testthat/test-updating-datapackager-version.R b/tests/testthat/test-updating-datapackager-version.R index f0da712..20171dc 100644 --- a/tests/testthat/test-updating-datapackager-version.R +++ b/tests/testthat/test-updating-datapackager-version.R @@ -1,6 +1,6 @@ context("updating datapackager API version") test_that("can update", { - + #setup, build example package file <- system.file("extdata", "tests", "subsetCars.Rmd", package = "DataPackageR" @@ -18,16 +18,16 @@ test_that("can update", { ) ) package_build(file.path(tempdir(), "subsetCars")) - + #remove news.md and modify with the digest so it thinks there has been an update when rebuilt file.remove(file.path(tempdir(),"subsetCars","news.md")) - oldDigest<-.parse_data_digest(file.path(tempdir(),"subsetCars")) + oldDigest<-DataPackageR:::.parse_data_digest(file.path(tempdir(),"subsetCars")) oldDigest$cars_over_20<-"123456789" DataPackageR:::.save_digest(oldDigest,file.path(tempdir(),"subsetCars")) - + expect_identical( try(package_build(file.path(tempdir(), "subsetCars"))), normalizePath(file.path(tempdir(),"subsetCars_1.0.tar.gz"),winslash = "/") )#if it passes, it returns the path to the tar file? - -}) \ No newline at end of file + +}) diff --git a/vignettes/YAML_CONFIG.Rmd b/vignettes/YAML_CONFIG.Rmd index 31d0a79..45f156f 100644 --- a/vignettes/YAML_CONFIG.Rmd +++ b/vignettes/YAML_CONFIG.Rmd @@ -8,7 +8,7 @@ output: toc: yes bibliography: bibliography.bib vignette: > - %\VignetteIndexEntry{DataPackageR YAML configuration.} + %\VignetteIndexEntry{The DataPackageR YAML configuration file.} %\VignetteEngine{knitr::rmarkdown} %\usepackage[utf8]{inputenc} %\usepackage{graphicx} @@ -216,4 +216,4 @@ yml_write(yml_oneobj, path = "path_to_package") ``` The `yml_oneobj` read by `yml_find()` carries an attribute -that is the path to the package. The user doesn't need to pass a `path` to `yml_write` if the config has been read by `yml_find`. \ No newline at end of file +that is the path to the package. The user doesn't need to pass a `path` to `yml_write` if the config has been read by `yml_find`. From cb323baa7c66433723e4d70e27116ff1364879af Mon Sep 17 00:00:00 2001 From: Jason Taylor Date: Tue, 15 Dec 2020 16:19:19 -0800 Subject: [PATCH 04/24] Delete travis and appveyor ci, add github actions. --- .github/.gitignore | 1 + .github/workflows/R-CMD-check.yaml | 84 ++++++++++++++++++++++++++++++ .travis.yml | 21 -------- appveyor.yml | 48 ----------------- 4 files changed, 85 insertions(+), 69 deletions(-) create mode 100644 .github/.gitignore create mode 100644 .github/workflows/R-CMD-check.yaml delete mode 100644 .travis.yml delete mode 100644 appveyor.yml diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..e7bad16 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,84 @@ +# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. +# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions +on: + push: + branches: + - main + - master + pull_request: + branches: + - main + - master + +name: R-CMD-check + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: windows-latest, r: 'release'} + - {os: macOS-latest, r: 'release'} + - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + + env: + R_REMOTES_NO_ERRORS_FROM_WARNINGS: true + RSPM: ${{ matrix.config.rspm }} + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + + steps: + - uses: actions/checkout@v2 + + - uses: r-lib/actions/setup-r@v1 + with: + r-version: ${{ matrix.config.r }} + + - uses: r-lib/actions/setup-pandoc@v1 + + - name: Query dependencies + run: | + install.packages('remotes') + saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) + writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + shell: Rscript {0} + + - name: Cache R packages + if: runner.os != 'Windows' + uses: actions/cache@v2 + with: + path: ${{ env.R_LIBS_USER }} + key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + + - name: Install system dependencies + if: runner.os == 'Linux' + run: | + while read -r cmd + do + eval sudo $cmd + done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') + + - name: Install dependencies + run: | + remotes::install_deps(dependencies = TRUE) + remotes::install_cran("rcmdcheck") + shell: Rscript {0} + + - name: Check + env: + _R_CHECK_CRAN_INCOMING_REMOTE_: false + run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") + shell: Rscript {0} + + - name: Upload check results + if: failure() + uses: actions/upload-artifact@main + with: + name: ${{ runner.os }}-r${{ matrix.config.r }}-results + path: check diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 1185943..0000000 --- a/.travis.yml +++ /dev/null @@ -1,21 +0,0 @@ -language: r -sudo: required -addons: - apt: - packages: - - libgit2-dev -matrix: - include: - - os: linux - r: release - - os: linux - r: devel - -cache: - packages: TRUE -r_github_packages: - - r-lib/covr - - r-lib/usethis -after_success: - - Rscript -e 'covr::codecov()' - diff --git a/appveyor.yml b/appveyor.yml deleted file mode 100644 index 226ff60..0000000 --- a/appveyor.yml +++ /dev/null @@ -1,48 +0,0 @@ -# DO NOT CHANGE the "init" and "install" sections below - -# Download script file from GitHub -init: - ps: | - $ErrorActionPreference = "Stop" - Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" - Import-Module '..\appveyor-tool.ps1' - -install: - ps: Bootstrap - -environment: - R_VERSION: release - -cache: - - C:\RLibrary - -# Adapt as necessary starting from here - -build_script: - - travis-tool.sh install_deps - -test_script: - - travis-tool.sh run_tests - -on_failure: - - 7z a failure.zip *.Rcheck\* - - appveyor PushArtifact failure.zip - -artifacts: - - path: '*.Rcheck\**\*.log' - name: Logs - - - path: '*.Rcheck\**\*.out' - name: Logs - - - path: '*.Rcheck\**\*.fail' - name: Logs - - - path: '*.Rcheck\**\*.Rout' - name: Logs - - - path: '\*_*.tar.gz' - name: Bits - - - path: '\*_*.zip' - name: Bits From a2992222c634202ac62346775b9954b3a2215397 Mon Sep 17 00:00:00 2001 From: Jason Taylor Date: Tue, 15 Dec 2020 17:04:57 -0800 Subject: [PATCH 05/24] Add covr::codecov() to workflow. --- .github/workflows/R-CMD-check.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index e7bad16..6b0c71e 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -68,6 +68,7 @@ jobs: run: | remotes::install_deps(dependencies = TRUE) remotes::install_cran("rcmdcheck") + remotes::install_cran("covr") shell: Rscript {0} - name: Check @@ -82,3 +83,7 @@ jobs: with: name: ${{ runner.os }}-r${{ matrix.config.r }}-results path: check + + - name: Test coverage + run: covr::codecov() + shell: Rscript {0} From 5cc195ab7c0fc393f80fa1ef2e6285c86c931e43 Mon Sep 17 00:00:00 2001 From: Jason Taylor Date: Fri, 18 Dec 2020 17:17:13 -0800 Subject: [PATCH 06/24] Actions yaml includes develop branch CI and statsrv R version. --- .github/workflows/R-CMD-check.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 6b0c71e..4e0f753 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -5,10 +5,12 @@ on: branches: - main - master + - develop pull_request: branches: - main - master + - develop name: R-CMD-check @@ -23,9 +25,9 @@ jobs: matrix: config: - {os: windows-latest, r: 'release'} - - {os: macOS-latest, r: 'release'} - - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: macOS-latest, r: 'release'} + - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true From db6ac45ebb3cb5774628755767d925b1cf948c36 Mon Sep 17 00:00:00 2001 From: Jason Taylor Date: Mon, 21 Dec 2020 16:34:15 -0800 Subject: [PATCH 07/24] Add older R for backwards compatibility. --- .github/workflows/R-CMD-check.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 4e0f753..2f93677 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -28,6 +28,11 @@ jobs: - {os: macOS-latest, r: 'release'} - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-18.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-18.04, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-18.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-18.04, r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-18.04, r: '3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true From 7786047d6fc1e534d7966acabc5ff288178e1bf3 Mon Sep 17 00:00:00 2001 From: Jason Taylor Date: Fri, 15 Jan 2021 16:55:28 -0800 Subject: [PATCH 08/24] Set CI ubuntu runners to only use ubuntu 20.04. --- .github/workflows/R-CMD-check.yaml | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 2f93677..453d18e 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -28,11 +28,10 @@ jobs: - {os: macOS-latest, r: 'release'} - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-18.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-18.04, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-18.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-18.04, r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-18.04, r: '3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-20.04, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-20.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-20.04, r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-20.04, r: '3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true From 4f621591328c8f5d1bf522eb6243ae9a3f640493 Mon Sep 17 00:00:00 2001 From: Jimmy Fulp Date: Tue, 19 Jan 2021 11:13:56 -0800 Subject: [PATCH 09/24] adding tinytex to workflow --- .github/workflows/R-CMD-check.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 453d18e..5f470d8 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -75,6 +75,9 @@ jobs: remotes::install_deps(dependencies = TRUE) remotes::install_cran("rcmdcheck") remotes::install_cran("covr") + install.packages("tinytex") + library(tinytex) + install_tinytex() shell: Rscript {0} - name: Check From fadf0dce27191237a3018f8540360e0cdae288ed Mon Sep 17 00:00:00 2001 From: Jason Taylor Date: Wed, 20 Jan 2021 06:50:50 -0800 Subject: [PATCH 10/24] Set working dir after unlinking of current dir. --- tests/testthat/test-edge-cases.R | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/testthat/test-edge-cases.R b/tests/testthat/test-edge-cases.R index c67ce25..30e6be0 100644 --- a/tests/testthat/test-edge-cases.R +++ b/tests/testthat/test-edge-cases.R @@ -115,6 +115,7 @@ test_that("package built in different edge cases", { recursive = TRUE, force = TRUE ) + setwd(old) yml <- DataPackageR:::construct_yml_config("foo.Rmd") expect_true(yml_enable_compile( From be6b26c414682ae7ddc451d1b710a044af386d25 Mon Sep 17 00:00:00 2001 From: jmtaylor-fhcrc <42221209+jmtaylor-fhcrc@users.noreply.github.com> Date: Thu, 21 Jan 2021 14:38:46 -0800 Subject: [PATCH 11/24] Remove all R versions < 3.5, update ubuntu rspm urls to focal Update CI: remove all R versions < 3.5, update Ubuntu rspm urls to focal --- .github/workflows/R-CMD-check.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 5f470d8..f598156 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -28,10 +28,8 @@ jobs: - {os: macOS-latest, r: 'release'} - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-20.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-20.04, r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-20.04, r: '3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} + - {os: ubuntu-20.04, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + - {os: ubuntu-20.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true From ac0813e6cba56eafb7aec30b75bf3436a3dc4327 Mon Sep 17 00:00:00 2001 From: Ellis Hughes Date: Tue, 9 Feb 2021 14:22:27 -0800 Subject: [PATCH 12/24] Add Ellis as maintainer. Add comment to Gregs section and remove maintainer status. Add Jimmy, Marie, and Jason as contributors --- DESCRIPTION | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e1b3684..95ae99e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,9 +2,15 @@ Package: DataPackageR Type: Package Title: Construct Reproducible Analytic Data Sets as R Packages Authors@R: - c(person(given = "Greg Finak", role=c("aut","cre","cph"), email="gfinak@fredhutch.org"), + c(person(given = "Greg Finak", + role=c("aut","cph"), + email="gfinak@fredhutch.org", + comment="Original author and creator of DataPackageR"), person(given = "Paul Obrecht", role=c("ctb")), - person(given = "Ellis Hughes", role=c("ctb")), + person(given = "Ellis Hughes", role=c("ctb","cre"), email = "ellishughes@live.com"), + person(given = "Jimmy Fulp", role=c("ctb")), + person(given = "Marie Vendettuoli", role=c("ctb")), + person(given = "Jason Taylor", role=c("ctb")), person("Kara", "Woo", role = "rev", comment = "Kara reviewed the package for ropensci, see "), person("William", "Landau", role = "rev", @@ -41,7 +47,7 @@ Imports: usethis, crayon VignetteBuilder: knitr -RoxygenNote: 7.1.0 +RoxygenNote: 7.1.1 Encoding: UTF-8 Suggests: spelling, From 1cb0fbc5474d40010c8a66be97be6441fc159cc5 Mon Sep 17 00:00:00 2001 From: Ellis Hughes Date: Tue, 16 Feb 2021 10:47:35 -0800 Subject: [PATCH 13/24] Update DESCRIPTION Update Greg's email Co-authored-by: Jimmy Fulp --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 95ae99e..571c6cd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -4,7 +4,7 @@ Title: Construct Reproducible Analytic Data Sets as R Packages Authors@R: c(person(given = "Greg Finak", role=c("aut","cph"), - email="gfinak@fredhutch.org", + email="greg.finak@gmail.com", comment="Original author and creator of DataPackageR"), person(given = "Paul Obrecht", role=c("ctb")), person(given = "Ellis Hughes", role=c("ctb","cre"), email = "ellishughes@live.com"), From c0cc1710cefbbc9d9539ec8d1f673e61242a9483 Mon Sep 17 00:00:00 2001 From: Ellis Hughes Date: Tue, 16 Feb 2021 10:47:45 -0800 Subject: [PATCH 14/24] Update DESCRIPTION Add Jimmy's email Co-authored-by: Jimmy Fulp --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 571c6cd..e1e04f7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -8,7 +8,7 @@ Authors@R: comment="Original author and creator of DataPackageR"), person(given = "Paul Obrecht", role=c("ctb")), person(given = "Ellis Hughes", role=c("ctb","cre"), email = "ellishughes@live.com"), - person(given = "Jimmy Fulp", role=c("ctb")), + person(given = "Jimmy Fulp", role=c("ctb"), email = "william.fulp@gmail.com"), person(given = "Marie Vendettuoli", role=c("ctb")), person(given = "Jason Taylor", role=c("ctb")), person("Kara", "Woo", role = "rev", From 4f418003295d59c0ad4899923db54c192b904c0c Mon Sep 17 00:00:00 2001 From: Ellis Hughes Date: Tue, 16 Feb 2021 17:29:07 -0800 Subject: [PATCH 15/24] use scharp emails --- DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e1e04f7..312ae5d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,8 +7,8 @@ Authors@R: email="greg.finak@gmail.com", comment="Original author and creator of DataPackageR"), person(given = "Paul Obrecht", role=c("ctb")), - person(given = "Ellis Hughes", role=c("ctb","cre"), email = "ellishughes@live.com"), - person(given = "Jimmy Fulp", role=c("ctb"), email = "william.fulp@gmail.com"), + person(given = "Ellis Hughes", role=c("ctb","cre"), email = "ehhughes@scharp.org"), + person(given = "Jimmy Fulp", role=c("ctb"), email = "wfulp@scharp.org"), person(given = "Marie Vendettuoli", role=c("ctb")), person(given = "Jason Taylor", role=c("ctb")), person("Kara", "Woo", role = "rev", From 2ad586387eaa9a508ee3ceb97bcd1d507383031a Mon Sep 17 00:00:00 2001 From: Marie Vendettuoli Date: Wed, 17 Feb 2021 07:36:12 -0800 Subject: [PATCH 16/24] add email --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 312ae5d..24941e6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,7 +9,7 @@ Authors@R: person(given = "Paul Obrecht", role=c("ctb")), person(given = "Ellis Hughes", role=c("ctb","cre"), email = "ehhughes@scharp.org"), person(given = "Jimmy Fulp", role=c("ctb"), email = "wfulp@scharp.org"), - person(given = "Marie Vendettuoli", role=c("ctb")), + person(given = "Marie Vendettuoli", role=c("ctb"), email = "mvendett@scharp.org"), person(given = "Jason Taylor", role=c("ctb")), person("Kara", "Woo", role = "rev", comment = "Kara reviewed the package for ropensci, see "), From 745e34cf154895d9ae5c00d0476a4d7992a02443 Mon Sep 17 00:00:00 2001 From: Ellis Hughes Date: Tue, 23 Feb 2021 08:50:34 -0800 Subject: [PATCH 17/24] update URL paths to https/ or corrected redirects --- .github/CONTRIBUTING.md | 2 +- DESCRIPTION | 4 +- README.Rmd | 18 ++--- README.md | 117 ++++++++++++++++---------------- vignettes/usingDataPackageR.Rmd | 4 +- 5 files changed, 74 insertions(+), 71 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index f66c762..0bd8a17 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -21,7 +21,7 @@ bug, create an associated issue and illustrate the bug with a minimal * Look at the Travis and AppVeyor build status before and after making changes. The `README` should contain badges for any continuous integration services used by the package. -* We recommend the tidyverse [style guide](http://style.tidyverse.org). +* We recommend the tidyverse [style guide](https://style.tidyverse.org). You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR. diff --git a/DESCRIPTION b/DESCRIPTION index 24941e6..7ff6060 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -54,8 +54,8 @@ Suggests: testthat, covr, data.tree, -URL: https://docs.ropensci.org/DataPackageR (website) - https://github.com/ropensci/DataPackageR +URL: https://docs.ropensci.org/DataPackageR/ (website) + https://github.com/ropensci/DataPackageR/ BugReports: https://github.com/ropensci/DataPackageR/issues SystemRequirements: pandoc (>= 1.12.3) - http://pandoc.org Language: en-US diff --git a/README.Rmd b/README.Rmd index c8dc738..cc9e10b 100644 --- a/README.Rmd +++ b/README.Rmd @@ -20,14 +20,14 @@ knitr::opts_chunk$set( DataPackageR is used to reproducibly process raw data into packaged, analysis-ready data sets. + [![CRAN](https://www.r-pkg.org/badges/version/DataPackageR)]( https://CRAN.R-project.org/package=DataPackageR) -[![Build Status](https://travis-ci.org/ropensci/DataPackageR.svg?branch=master)](https://travis-ci.org/ropensci/DataPackageR) - [![Coverage status](https://codecov.io/gh/ropensci/DataPackageR/branch/master/graph/badge.svg)](https://codecov.io/github/ropensci/DataPackageR?branch=master) - [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/5y004036wg2rh2dx?svg=true -)](https://ci.appveyor.com/project/gfinak/DataPackageR) +[![R-CMD-check](https://github.com/ropensci/DataPackageR/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/DataPackageR/actions) +[![Coverage status](https://codecov.io/gh/ropensci/DataPackageR/branch/master/graph/badge.svg)](https://codecov.io/github/ropensci/DataPackageR?branch=master) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) -[![](https://badges.ropensci.org/230_status.svg)](https://github.com/ropensci/onboarding/issues/230) +[![](https://badges.ropensci.org/230_status.svg)](https://github.com/ropensci/software-review/issues/230) [![DOI](https://zenodo.org/badge/29267435.svg)](https://doi.org/10.5281/zenodo.1292095) + - [yaml configuration guide](vignettes/YAML_CONFIG.md) - [a more detailed technical vignette](vignettes/usingDataPackageR.md) @@ -63,7 +63,7 @@ You have diverse raw data sets that you need to preprocess and tidy in order to: - **Documentation.** - R's package system allows us to document data objects. What's more, the `roxygen2` package makes this very easy to do with [markup tags](http://r-pkgs.had.co.nz/data.html). + R's package system allows us to document data objects. What's more, the `roxygen2` package makes this very easy to do with [markup tags](https://r-pkgs.org/data.html). That documentation is the equivalent of a data dictionary and can be extremely valuable when returning to a project after a period of time. - **Convenience.** @@ -77,7 +77,7 @@ You have diverse raw data sets that you need to preprocess and tidy in order to: R packages have a 5MB size limit, at least on CRAN. BioConductor has explicit [data package](https://www.bioconductor.org/developers/package-guidelines/#package-types) types that can be larger and use git LFS for very large files. - Sharing large volumes of raw data in an R package format is still not ideal, and there are public biological data repositories better suited for raw data: e.g., [GEO](https://www.ncbi.nlm.nih.gov/geo/), [SRA](https://www.ncbi.nlm.nih.gov/sra), [ImmPort](http://www.immport.org/immport-open/public/home/home), [ImmuneSpace](https://immunespace.org/), [FlowRepository](https://flowrepository.org/). + Sharing large volumes of raw data in an R package format is still not ideal, and there are public biological data repositories better suited for raw data: e.g., [GEO](https://www.ncbi.nlm.nih.gov/geo/), [SRA](https://www.ncbi.nlm.nih.gov/sra), [ImmPort](https://www.immport.org:443/shared/immport-open/public/home/home), [ImmuneSpace](https://immunespace.org/), [FlowRepository](https://flowrepository.org/). Tools like [datastorr](https://github.com/ropenscilabs/datastorr) can help with this and we hope to integrate the into DataPackageR in the future. @@ -142,11 +142,11 @@ There are a number of tools out there that address similar and complementary pro ## Installation -You can install the latest version of DataPackageR from [github](https://www.github.com/RGLab/DataPackageR) with: +You can install the latest version of DataPackageR from [github](https://www.github.com/ropensci/DataPackageR) with: ```{r, eval=FALSE} library(devtools) -devtools::install_github("RGLab/DataPackageR") +devtools::install_github("ropensci/DataPackageR") ``` ## Blog Post - building packages interactively. diff --git a/README.md b/README.md index 28831ca..9c0a6e8 100644 --- a/README.md +++ b/README.md @@ -4,28 +4,27 @@ README # DataPackageR DataPackageR is used to reproducibly process raw data into packaged, -analysis-ready data -sets. +analysis-ready data sets. + + [![CRAN](https://www.r-pkg.org/badges/version/DataPackageR)](https://CRAN.R-project.org/package=DataPackageR) -[![Build -Status](https://travis-ci.org/ropensci/DataPackageR.svg?branch=master)](https://travis-ci.org/ropensci/DataPackageR) +[![R-CMD-check](https://github.com/ropensci/DataPackageR/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/DataPackageR/actions) [![Coverage status](https://codecov.io/gh/ropensci/DataPackageR/branch/master/graph/badge.svg)](https://codecov.io/github/ropensci/DataPackageR?branch=master) -[![AppVeyor Build -Status](https://ci.appveyor.com/api/projects/status/5y004036wg2rh2dx?svg=true)](https://ci.appveyor.com/project/gfinak/DataPackageR) [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) -[![](https://badges.ropensci.org/230_status.svg)](https://github.com/ropensci/onboarding/issues/230) +[![](https://badges.ropensci.org/230_status.svg)](https://github.com/ropensci/software-review/issues/230) [![DOI](https://zenodo.org/badge/29267435.svg)](https://doi.org/10.5281/zenodo.1292095) + - - [yaml configuration guide](vignettes/YAML_CONFIG.md) - - [a more detailed technical vignette](vignettes/usingDataPackageR.md) +- [yaml configuration guide](vignettes/YAML_CONFIG.md) +- [a more detailed technical vignette](vignettes/usingDataPackageR.md) > **Important Note**: [datapack](https://github.com/ropensci/datapack) > is a *different package* that is used to “create, send and load data -> from common repositories such as DataONE into the R environment”. +> from common repositories such as DataONE into the R environment.” > **This package** is for processing raw data into tidy data sets and > bundling them into R packages. @@ -35,11 +34,11 @@ developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.re You have diverse raw data sets that you need to preprocess and tidy in order to: - - Perform data analysis - - Write a report - - Publish a paper - - Share data with colleagues and collaborators - - Save time in the future when you return to this project but have +- Perform data analysis +- Write a report +- Publish a paper +- Share data with colleagues and collaborators +- Save time in the future when you return to this project but have forgotten all about what you did. ### Why package data sets? @@ -47,31 +46,31 @@ order to: **Definition:** A *data package* is a formal R package whose sole purpose is to contain, access, and / or document data sets. - - **Reproducibility.** - +- **Reproducibility.** + As described [elsewhere](https://github.com/ropensci/rrrpkg), packaging your data promotes reproducibility. R’s packaging infrastructure promotes unit testing, documentation, a reproducible build system, and has many other benefits. Coopting it for packaging data sets is a natural fit. - - **Collaboration.** - +- **Collaboration.** + A data set packaged in R is easy to distribute and share amongst collaborators, and is easy to install and use. All the hard work you’ve put into documenting and standardizing the tidy data set comes right along with the data package. - - **Documentation.** - +- **Documentation.** + R’s package system allows us to document data objects. What’s more, the `roxygen2` package makes this very easy to do with [markup - tags](http://r-pkgs.had.co.nz/data.html). That documentation is the + tags](https://r-pkgs.org/data.html). That documentation is the equivalent of a data dictionary and can be extremely valuable when returning to a project after a period of time. - - **Convenience.** - +- **Convenience.** + Data pre-processing can be time consuming, depending on the data type and raw data sets may be too large to share conveniently in a packaged format. Packaging and sharing the small, tidied data saves @@ -79,34 +78,34 @@ purpose is to contain, access, and / or document data sets. ## Challenges. - - **Package size limits.** - +- **Package size limits.** + R packages have a 5MB size limit, at least on CRAN. BioConductor has explicit [data package](https://www.bioconductor.org/developers/package-guidelines/#package-types) types that can be larger and use git LFS for very large files. - + Sharing large volumes of raw data in an R package format is still not ideal, and there are public biological data repositories better suited for raw data: e.g., [GEO](https://www.ncbi.nlm.nih.gov/geo/), [SRA](https://www.ncbi.nlm.nih.gov/sra), - [ImmPort](http://www.immport.org/immport-open/public/home/home), + [ImmPort](https://www.immport.org:443/shared/immport-open/public/home/home), [ImmuneSpace](https://immunespace.org/), [FlowRepository](https://flowrepository.org/). - + Tools like [datastorr](https://github.com/ropenscilabs/datastorr) can help with this and we hope to integrate the into DataPackageR in the future. - - **Manual effort** - +- **Manual effort** + There is still a substantial manual effort to set up the correct directory structures for an R data package. This can dissuade many individuals, particularly new users who have never built an R package, from going this route. - - **Scale** - +- **Scale** + Setting up and building R data packages by hand is a workable solution for a small project or a small number of projects, but when dealing with many projects each involving many data sets, tools are @@ -116,23 +115,23 @@ purpose is to contain, access, and / or document data sets. DataPackageR provides a number of benefits when packaging your data. - - It aims to automate away much of the tedium of packaging data sets +- It aims to automate away much of the tedium of packaging data sets without getting too much in the way, and keeps your processing workflow reproducible. - - It sets up the necessary package structure and files for a data +- It sets up the necessary package structure and files for a data package. - - It allows you to keep the large, raw data and only ship the packaged +- It allows you to keep the large, raw data and only ship the packaged tidy data, saving space and time consumers of your data set need to spend downloading and re-processing it. - - It maintains a reproducible record (vignettes) of the data +- It maintains a reproducible record (vignettes) of the data processing along with the package. Consumers of the data package can verify how the processing was done, increasing confidence in your data. - - It automates construction of the documentation and maintains a data +- It automates construction of the documentation and maintains a data set version and an md5 fingerprint of each data object in the package. If the data changes and the package is rebuilt, the data version is automatically updated. @@ -142,40 +141,40 @@ DataPackageR provides a number of benefits when packaging your data. There are a number of tools out there that address similar and complementary problems: - - **datastorr** [github +- **datastorr** [github repo](https://github.com/ropenscilabs/datastorr) - + Simple data retrieval and versioning using GitHub to store data. - - - Caches downloads and uses github releases to version data. - - Deal consistently with translating the file stored online into a + + - Caches downloads and uses github releases to version data. + - Deal consistently with translating the file stored online into a loaded data object - - Access multiple versions of the data at once - + - Access multiple versions of the data at once + `datastorrr` could be used with DataPackageR to store / access remote raw data sets, remotely store / access tidied data that are too large to fit in the package itself. - - **fst** [github repo](https://github.com/fstpackage/fst) - +- **fst** [github repo](https://github.com/fstpackage/fst) + `fst` provides lightning fast serialization of data frames. - - **The modern data package** +- **The modern data package** [pdf](https://github.com/noamross/2018-04-18-rstats-nyc/blob/master/Noam_Ross_ModernDataPkg_rstatsnyc_2018-04-20.pdf) - + A presentation from @noamross touching on modern tools for open science and reproducibility. Discusses `datastorr` and `fst` as well as standardized metadata and documentation. - - **rrrpkg** [github repo](https://github.com/ropensci/rrrpkg) - +- **rrrpkg** [github repo](https://github.com/ropensci/rrrpkg) + A document from ropensci describing using an R package as a research compendium. Based on ideas originally introduced by Robert Gentleman and Duncan Temple Lang (Gentleman and Lang (2004)) - - **template** [github repo](https://github.com/ropensci/rrrpkg) - +- **template** [github repo](https://github.com/ropensci/rrrpkg) + An R package template for data packages. See the [publication](#publication) for further discussion. @@ -183,11 +182,11 @@ See the [publication](#publication) for further discussion. ## Installation You can install the latest version of DataPackageR from -[github](https://www.github.com/RGLab/DataPackageR) with: +[github](https://www.github.com/ropensci/DataPackageR) with: ``` r library(devtools) -devtools::install_github("RGLab/DataPackageR") +devtools::install_github("ropensci/DataPackageR") ``` ## Blog Post - building packages interactively. @@ -234,16 +233,20 @@ datapackage_skeleton( # These will be added to the NEWS.md file along with the DataVersion in the package source directory. # If the build is run in non-interactive mode, the description will read # "Package built in non-interactive mode". You may update it later. -package_build(packageName = file.path(tempdir(),"mtcars20"), install = TRUE) +dir.create(file.path(tempdir(),"lib")) +package_build(packageName = file.path(tempdir(),"mtcars20"), install = TRUE, lib = file.path(tempdir(),"lib")) +#> Warning: package 'mtcars20' is in use and will not be installed # Update the autogenerated roxygen documentation in data-raw/documentation.R. # edit(file.path(tempdir(),"mtcars20","R","mtcars20.R")) # 4. Rebuild the documentation. -document(file.path(tempdir(),"mtcars20"), install = TRUE) +document(file.path(tempdir(),"mtcars20"), install = TRUE, lib = file.path(tempdir(),"lib")) +#> Warning: package 'mtcars20' is in use and will not be installed # Let's use the package we just created. install.packages(file.path(tempdir(),"mtcars20_1.0.tar.gz"), type = "source", repos = NULL) +#> Warning: package 'mtcars20' is in use and will not be installed library(mtcars20) data("cars_over_20") # load the data cars_over_20 # Now we can use it. diff --git a/vignettes/usingDataPackageR.Rmd b/vignettes/usingDataPackageR.Rmd index 14571ab..b034be3 100644 --- a/vignettes/usingDataPackageR.Rmd +++ b/vignettes/usingDataPackageR.Rmd @@ -35,7 +35,7 @@ In this vignette we will subset and package the `mtcars` data set. ## Set up a new data package. -We'll set up a new data package based on `mtcars` example in the [README](https://github.com/RGLab/DataPackageR/blob/master/README.md). +We'll set up a new data package based on `mtcars` example in the [README](https://github.com/ropensci/DataPackageR/blob/master/README.md). The `datapackage_skeleton()` API is used to set up a new package. The user needs to provide: @@ -413,7 +413,7 @@ You now have a data package source tree. This will let you version control your data processing code, and provide a mechanism for sharing your package with others. -For more details on using git and github with R, there is an excellent guide provided by Jenny Bryan: [Happy Git and GitHub for the useR](http://happygitwithr.com/) and Hadley Wickham's [book on R packages](http://r-pkgs.had.co.nz/). +For more details on using git and github with R, there is an excellent guide provided by Jenny Bryan: [Happy Git and GitHub for the useR](https://happygitwithr.com/) and Hadley Wickham's [book on R packages]( https://r-pkgs.org/). # Additional Details From 1d0d83492472cdc2142b12a2ab24c12aae33a864 Mon Sep 17 00:00:00 2001 From: Ellis Hughes Date: Tue, 23 Feb 2021 09:27:25 -0800 Subject: [PATCH 18/24] https://www.github.com -> https://github.com --- README.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.Rmd b/README.Rmd index cc9e10b..c8c242d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -142,7 +142,7 @@ There are a number of tools out there that address similar and complementary pro ## Installation -You can install the latest version of DataPackageR from [github](https://www.github.com/ropensci/DataPackageR) with: +You can install the latest version of DataPackageR from [github](https://github.com/ropensci/DataPackageR) with: ```{r, eval=FALSE} library(devtools) From 30db659997319df940106013850e43ffb19d5526 Mon Sep 17 00:00:00 2001 From: Ellis Hughes Date: Tue, 16 Mar 2021 13:16:18 -0700 Subject: [PATCH 19/24] update cran comments --- .Rbuildignore | 1 + README.md | 2 +- cran-comments.md | 40 +++++++++++++++++++++++++++------------- 3 files changed, 29 insertions(+), 14 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index ffd8238..09f18ee 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -17,3 +17,4 @@ bibliography.bib cran-comments.md ^revdep$ ^$ +^cran-comments\.md$ diff --git a/README.md b/README.md index 9c0a6e8..cdac9ea 100644 --- a/README.md +++ b/README.md @@ -182,7 +182,7 @@ See the [publication](#publication) for further discussion. ## Installation You can install the latest version of DataPackageR from -[github](https://www.github.com/ropensci/DataPackageR) with: +[github](https://github.com/ropensci/DataPackageR) with: ``` r library(devtools) diff --git a/cran-comments.md b/cran-comments.md index b4d5e56..7f3671e 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,27 +1,41 @@ ## Submission 0.15.8 -* Fix a test associated with usethis 1.5.1.9000 +* Fix tests that were failing. This should resolve the failures identified by CRAN +* Change maintainer to Ellis Hughes from Greg Finak ## Test environments -* Local linux (x86_64-pc-linux-gnu), R 3.6.1 (2019-07-05) -* Local rhub docker (rhub/ubuntu-gcc-devel) -* Local rhub docker (rhub/ubuntu-gcc-release) -* Local rhub docker (rhub/ubuntu-rchk) -* Windows 10 enterprise v1607 14393.2906 (R 4.0.0 2020-04-09 v78186) -* rhub macOS 10.11 El Capitan, R-release (experimental) -* rhub fedora-gcc-devel +* local R installation, R 4.0.3 +* github actions/ windows-latest - R Release +* github actions/ macOS-latest - R Release +* github actions/ ubuntu-20.04 - R Release +* github actions/ ubuntu-20.04 - R devel +* github actions/ ubuntu-20.04 - R 3.6 +* github actions/ ubuntu-20.04 - R 3.5 +* rhub/windows-x86_64- R devel +* rhub/ubuntu-gcc - R release +* rhub/fedora-clang - R devel +* win-builder (devel) + ## R CMD check results There were no ERRORs or WARNINGs -One NOTE -─ checking CRAN incoming feasibility ... Note_to_CRAN_maintainers (1.4s) - Maintainer: 'Greg Finak ' +One NOTE: + +Maintainer: 'Ellis Hughes ' + +New submission + +Package was archived on CRAN + +CRAN repository db overrides: + X-CRAN-Comment: Archived on 2020-04-25 as check problems were not + corrected in time. -On rhub/fedora-gcc-devel one test fails because the texlive-framed package is not installed and is needed for rmarkdown. +This package was archived earlier due to not resolving check errors. With this +upload, this should resolve any errors. -I observe two test failures on rhub windows systems that I am unable to reproduce on windows systems I have avaialble to me with R 4.0.0. ## Downstream dependencies From 029a6c0c1764c9ff88cb38619917b71f82862cc4 Mon Sep 17 00:00:00 2001 From: Ellis Hughes Date: Tue, 16 Mar 2021 13:28:10 -0700 Subject: [PATCH 20/24] update NEWS.md with updates --- NEWS.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/NEWS.md b/NEWS.md index 6f2da8b..2af6c51 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,9 @@ # DataPackageR 0.15.8 * Fix to datapackager_object_read that was causing a test to break. `get` needs to have `inherits=FALSE`. * Other fixes for `usethis` 1.6.0 +* Fixes to tests that were failing on CRAN +* In `package_build`, remove `devtools::reload` and put `devtools::unload` and in front of install.packages +* in `document`, remove `devtools::reload` and put in `devtools::unload` and install.packages # DataPackageR 0.15.7 * Fix test and vignette bugs related to upcoming version of usethis (1.5) From 32b467b0a7e8095a2089c088521d6425ddbaeee3 Mon Sep 17 00:00:00 2001 From: Ellis Hughes Date: Tue, 16 Mar 2021 13:39:36 -0700 Subject: [PATCH 21/24] update codemeta.json --- codemeta.json | 49 ++++++++++++++++++++++++++++++------------------- 1 file changed, 30 insertions(+), 19 deletions(-) diff --git a/codemeta.json b/codemeta.json index e2903cb..b60faaf 100644 --- a/codemeta.json +++ b/codemeta.json @@ -7,22 +7,21 @@ "identifier": "DataPackageR", "description": "A framework to help construct R data packages in a \n reproducible manner. Potentially time consuming processing of \n raw data sets into analysis ready data sets is done in a reproducible \n manner and decoupled from the usual R CMD build process so that\n data sets can be processed into R objects in the data package and \n the data package can then be shared, built, and installed by others\n without the need to repeat computationally costly data processing.\n The package maintains data provenance by turning the data processing\n scripts into package vignettes, as well as enforcing documentation \n and version checking of included data objects. Data packages can be\n version controlled in github, and used to share data for manuscripts,\n collaboration and general reproducibility.", "name": "DataPackageR: Construct Reproducible Analytic Data Sets as R Packages", - "codeRepository": "https://github.com/ropensci/DataPackageR", + "codeRepository": "https://github.com/ropensci/DataPackageR/", "issueTracker": "https://github.com/ropensci/DataPackageR/issues", "license": "https://spdx.org/licenses/MIT", - "version": "0.15.7", + "version": "0.15.8", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", - "version": "3.6.0", "url": "https://r-project.org" }, - "runtimePlatform": "R Under development (unstable) (2019-03-20 r76254)", + "runtimePlatform": "R version 4.0.3 (2020-10-10)", "author": [ { "@type": "Organization", "name": "Greg Finak", - "email": "gfinak@fredhutch.org" + "email": "greg.finak@gmail.com" } ], "contributor": [ @@ -32,21 +31,36 @@ }, { "@type": "Organization", - "name": "Ellis Hughes" + "name": "Ellis Hughes", + "email": "ehhughes@scharp.org" + }, + { + "@type": "Organization", + "name": "Jimmy Fulp", + "email": "wfulp@scharp.org" + }, + { + "@type": "Organization", + "name": "Marie Vendettuoli", + "email": "mvendett@scharp.org" + }, + { + "@type": "Organization", + "name": "Jason Taylor" } ], "copyrightHolder": [ { "@type": "Organization", "name": "Greg Finak", - "email": "gfinak@fredhutch.org" + "email": "greg.finak@gmail.com" } ], "maintainer": [ { "@type": "Organization", - "name": "Greg Finak", - "email": "gfinak@fredhutch.org" + "name": "Ellis Hughes", + "email": "ehhughes@scharp.org" } ], "softwareSuggestions": [ @@ -287,17 +301,13 @@ } ], "releaseNotes": "https://github.com/ropensci/DataPackageR/blob/master/NEWS.md", - "readme": "https://github.com/ropensci/DataPackageR/blob/master/README.md", - "contIntegration": [ - "https://travis-ci.org/ropensci/DataPackageR", - "https://codecov.io/github/ropensci/DataPackageR?branch=master", - "https://ci.appveyor.com/project/RGLab/DataPackageR" - ], + "readme": "https://github.com/ropensci/DataPackageR/blob/main/README.md", + "contIntegration": "https://codecov.io/github/ropensci/DataPackageR?branch=master", "developmentStatus": "https://www.repostatus.org/#active", "review": { "@type": "Review", - "url": "https://github.com/ropensci/onboarding/issues/230", - "provider": "http://ropensci.org" + "url": "https://github.com/ropensci/software-review/issues/230", + "provider": "https://ropensci.org" }, "provider": { "@id": "https://cran.r-project.org", @@ -305,7 +315,7 @@ "name": "Comprehensive R Archive Network (CRAN)", "url": "https://cran.r-project.org" }, - "relatedLink": "https://CRAN.R-project.org/package=DataPackageR", + "relatedLink": ["https://CRAN.R-project.org/package=DataPackageR", "https://docs.ropensci.org/DataPackageR/"], "keywords": [ "r", "r-package", @@ -313,5 +323,6 @@ "rstats", "peer-reviewed" ], - "funder": {} + "funder": {}, + "fileSize": "1356.682KB" } From 14c0af2f0eaae4ebc23c01e136f88dbbd512fd04 Mon Sep 17 00:00:00 2001 From: Ellis Hughes Date: Tue, 16 Mar 2021 13:57:03 -0700 Subject: [PATCH 22/24] Add updated CRAN-RELEASE --- CRAN-RELEASE | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CRAN-RELEASE b/CRAN-RELEASE index 92cd9a9..f2c85ce 100644 --- a/CRAN-RELEASE +++ b/CRAN-RELEASE @@ -1,2 +1,2 @@ -This package was submitted to CRAN on 2019-03-30. -Once it is accepted, delete this file and tag the release (commit 56af129a9c). +This package was submitted to CRAN on 2021-03-16. +Once it is accepted, delete this file and tag the release (commit 32b467b). From 96c7270d4203c67d01848da436c52f5e40574cb6 Mon Sep 17 00:00:00 2001 From: Ellis Hughes Date: Tue, 16 Mar 2021 21:53:42 -0700 Subject: [PATCH 23/24] Update paths based on CRAN comments --- README.Rmd | 6 +++--- README.md | 10 ++++++---- vignettes/usingDataPackageR.Rmd | 4 ++-- 3 files changed, 11 insertions(+), 9 deletions(-) diff --git a/README.Rmd b/README.Rmd index c8c242d..6fcb38c 100644 --- a/README.Rmd +++ b/README.Rmd @@ -29,8 +29,8 @@ DataPackageR is used to reproducibly process raw data into packaged, analysis-re [![DOI](https://zenodo.org/badge/29267435.svg)](https://doi.org/10.5281/zenodo.1292095) -- [yaml configuration guide](vignettes/YAML_CONFIG.md) -- [a more detailed technical vignette](vignettes/usingDataPackageR.md) +- [yaml configuration guide](https://github.com/ropensci/DataPackageR/blob/main/vignettes/YAML_CONFIG.md) +- [a more detailed technical vignette](https://github.com/ropensci/DataPackageR/blob/main/vignettes/usingDataPackageR.md) > **Important Note**: [datapack](https://github.com/ropensci/datapack) is a *different package* that is used to "create, send and load data from common repositories such as DataONE into the R environment". @@ -259,7 +259,7 @@ The preprint is on [biorxiv](https://doi.org/10.1101/342907). ## Code of conduct -Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). +Please note that this project is released with a [Contributor Code of Conduct](https://github.com/ropensci/DataPackageR/blob/main/CODE_OF_CONDUCT.md). By participating in this project you agree to abide by its terms. ### References diff --git a/README.md b/README.md index cdac9ea..00aad97 100644 --- a/README.md +++ b/README.md @@ -19,8 +19,10 @@ developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.re [![DOI](https://zenodo.org/badge/29267435.svg)](https://doi.org/10.5281/zenodo.1292095) -- [yaml configuration guide](vignettes/YAML_CONFIG.md) -- [a more detailed technical vignette](vignettes/usingDataPackageR.md) +- [yaml configuration + guide](https://github.com/ropensci/DataPackageR/blob/main/vignettes/YAML_CONFIG.md) +- [a more detailed technical + vignette](https://github.com/ropensci/DataPackageR/blob/main/vignettes/usingDataPackageR.md) > **Important Note**: [datapack](https://github.com/ropensci/datapack) > is a *different package* that is used to “create, send and load data @@ -309,8 +311,8 @@ The preprint is on [biorxiv](https://doi.org/10.1101/342907). ## Code of conduct Please note that this project is released with a [Contributor Code of -Conduct](CODE_OF_CONDUCT.md). By participating in this project you agree -to abide by its terms. +Conduct](https://github.com/ropensci/DataPackageR/blob/main/CODE_OF_CONDUCT.md). +By participating in this project you agree to abide by its terms. ### References diff --git a/vignettes/usingDataPackageR.Rmd b/vignettes/usingDataPackageR.Rmd index b034be3..7cf06fe 100644 --- a/vignettes/usingDataPackageR.Rmd +++ b/vignettes/usingDataPackageR.Rmd @@ -117,7 +117,7 @@ The objects must be listed in the yaml configuration file. `datapackage_skeleton DataPackageR provides an API for modifying this file, so it does not need to be done by hand. -Further information on the contents of the YAML configuration file, and the API are in the [YAML Configuration Details](YAML_CONFIG.md) +Further information on the contents of the YAML configuration file, and the API are in the [YAML Configuration Details](YAML_CONFIG.html) ### Where do I put my raw datasets? @@ -298,7 +298,7 @@ assert_data_version(data_package_name = "mtcars20", Version 1.12.0 has moved away from controlling the build process using `datasets.R` and an additional `masterfile` argument. -The build process is now controlled via a `datapackager.yml` configuration file located in the package root directory. (see [YAML Configuration Details](YAML_CONFIG.md)) +The build process is now controlled via a `datapackager.yml` configuration file located in the package root directory. (see [YAML Configuration Details](YAML_CONFIG.html)) ### Create a datapackager.yml file From 97ab510ebf3c56e5c4966e2157e220f3ea719d74 Mon Sep 17 00:00:00 2001 From: Ellis Hughes Date: Tue, 16 Mar 2021 22:01:22 -0700 Subject: [PATCH 24/24] Update cran comments and release --- CRAN-RELEASE | 2 +- cran-comments.md | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/CRAN-RELEASE b/CRAN-RELEASE index f2c85ce..94e27c3 100644 --- a/CRAN-RELEASE +++ b/CRAN-RELEASE @@ -1,2 +1,2 @@ This package was submitted to CRAN on 2021-03-16. -Once it is accepted, delete this file and tag the release (commit 32b467b). +Once it is accepted, delete this file and tag the release (commit 96c7270). diff --git a/cran-comments.md b/cran-comments.md index 7f3671e..7f654f9 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,6 +1,7 @@ ## Submission 0.15.8 * Fix tests that were failing. This should resolve the failures identified by CRAN * Change maintainer to Ellis Hughes from Greg Finak +* update filepaths/URLS based on request from CRAN ## Test environments