Merge pull request #88 from ropensci/cran_submission_v0.15.8

Cran submission v0.15.8

.Rbuildignore

@@ -17,3 +17,4 @@ bibliography.bib
 cran-comments.md
 ^revdep$
 ^$
+^cran-comments\.md$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.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.  

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,96 @@
+# 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
+      - develop
+  pull_request:
+    branches:
+      - main
+      - master
+      - develop
+
+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"}
+          - {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
+      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")
+          remotes::install_cran("covr")
+          install.packages("tinytex")
+          library(tinytex)
+          install_tinytex()
+        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
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

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 96c7270).

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="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")),
+      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"), email = "mvendett@scharp.org"),
+      person(given = "Jason Taylor", role=c("ctb")),
       person("Kara", "Woo", role = "rev",
       comment = "Kara reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/230>"),
       person("William", "Landau", role = "rev",
@@ -41,15 +47,15 @@ Imports:
     usethis,
     crayon
 VignetteBuilder: knitr
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Encoding: UTF-8
 Suggests:
     spelling,
     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

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)

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)

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)
 }

README.Rmd

@@ -20,17 +20,17 @@ knitr::opts_chunk$set(
 
 DataPackageR is used to reproducibly process raw data into packaged, analysis-ready data sets.
 
+<!-- badges: start -->
 [![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)
+<!-- badges: end -->
 
-- [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".
 
@@ -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://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.
@@ -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