Merge pull request #19 from jhrcook/0.1.4

Minor changes to address issues on CRAN servers

.github/workflows/test-coverage.yaml

@@ -0,0 +1,58 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: test-coverage
+
+# Increment this version when we want to clear cache
+env:
+  cache-version: v1
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-18.04
+    env:
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/bionic/latest
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        id: install-r
+
+      - name: Install pak and query dependencies
+        run: |
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@v2
+        with:
+          path: |
+            ${{ env.R_LIBS_USER }}/*
+            !${{ env.R_LIBS_USER }}/pak
+          key: ubuntu-18.04-${{ steps.install-r.outputs.installed-r-version }}-${{ env.cache-version }}-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: ubuntu-18.04-${{ steps.install-r.outputs.installed-r-version }}-${{ env.cache-version }}-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          pak::local_system_requirements(execute = TRUE)
+          pak::pkg_system_requirements("covr", execute = TRUE)
+        shell: Rscript {0}
+
+      - name: Install dependencies
+        run: |
+          pak::local_install_dev_deps(upgrade = TRUE)
+          pak::pkg_install("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

DESCRIPTION

@@ -12,10 +12,14 @@ Authors@R:
              family = "Briggs",
              role = c("ctb"),
              email = "[email protected]"),
-     person(given = "Vinay",
-            family = "Viswanadham",
-            role = c("ctb"),
-            email = "[email protected]"))
+      person(given = "Vinay",
+             family = "Viswanadham",
+             role = c("ctb"),
+             email = "[email protected]"),
+      person(given = "Travers",
+             family = "Ching",
+             role = c("ctb"),
+             email = "[email protected]"))
 Description: A simple system for saving and loading objects in
     R. Long running computations can be stashed after the first run and
     then reloaded the next time. Dependencies can be added to ensure that
@@ -42,5 +46,4 @@ VignetteBuilder:
     knitr
 Encoding: UTF-8
 Language: en-US
-LazyData: true
 RoxygenNote: 7.1.1

NEWS.md

@@ -1,3 +1,10 @@
+# mustashe 0.1.4
+
+- Functional and verbose parameters in the 'stash()' function (@traversc).
+- Minor fixes for CRAN package checking process.
+- Tooling changes to add [pre-commit](https://pre-commit.com) and ['renv'](https://CRAN.R-project.org/package=renv) and remove AppVeyor and Travis CI (only using GitHub Actions, now).
+- Add code coverage report CI as a GitHub Action (based on implementation by ['ggplot2'](https://github.com/tidyverse/ggplot2/blob/master/.github/workflows/test-coverage.yaml))
+
 # mustashe 0.1.3
 
 - An error is raised if the '.mustashe' directory cannot be created (#9).

R/clear_stash.R

@@ -1,7 +1,7 @@
 #' Clear the stash
 #'
 #' Clears the hidden '.mustashe' directory.
-#' 
+#'
 #' @param verbose Whether to print action statements (default TRUE).
 #'
 #' @return Returns \code{NULL} (invisibly).
@@ -10,7 +10,9 @@
 #' clear_stash()
 #' @export clear_stash
 clear_stash <- function(verbose = TRUE) {
-  if (verbose) { message("Clearing stash.") }
+  if (verbose) {
+    message("Clearing stash.")
+  }
   file.remove(c(
     list.files(get_stash_dir(), full.names = TRUE, pattern = "qs$"),
     list.files(get_stash_dir(), full.names = TRUE, pattern = "hash$")

R/stash.R

@@ -8,7 +8,7 @@
 #' @param code The code to generate the object to be stashed.
 #' @param depends_on A vector of other objects that this one depends on. Changes
 #'   to these objects will cause the re-running of the code, next time.
-#' @param functional If TRUE, return the object rather than setting in the global environment (default FALSE). 
+#' @param functional If TRUE, return the object rather than setting in the global environment (default FALSE).
 #' @param verbose Whether to print action statements (default TRUE).
 #'
 #' @return Returns \code{NULL} (invisibly).
@@ -50,17 +50,23 @@ stash <- function(var, code, depends_on = NULL, functional = FALSE, verbose = TR
   if (has_been_stashed(var)) {
     old_hash_tbl <- get_hash_table(var)
     if (hash_tables_are_equivalent(old_hash_tbl, new_hash_tbl)) {
-      if (verbose) { message("Loading stashed object.") }
+      if (verbose) {
+        message("Loading stashed object.")
+      }
       res <- load_variable(var, functional)
     } else {
-      if (verbose) { message("Updating stash.") }
+      if (verbose) {
+        message("Updating stash.")
+      }
       res <- new_stash(var, formatted_code, new_hash_tbl, functional)
     }
   } else {
-    if (verbose) { message("Stashing object.") }
+    if (verbose) {
+      message("Stashing object.")
+    }
     res <- new_stash(var, formatted_code, new_hash_tbl, functional)
   }
-  
+
   invisible(res)
 }
 

R/unstash.R

@@ -23,10 +23,14 @@
 unstash <- function(var, verbose = TRUE) {
   f <- function(v) {
     if (has_been_stashed(v)) {
-      if (verbose) { message(paste0("Unstashing '", v, "'.")) }
+      if (verbose) {
+        message(paste0("Unstashing '", v, "'."))
+      }
       file.remove(unlist(stash_filename(v)))
     } else {
-      if (verbose) { message(paste0("No object '", v, "' in stash.")) }
+      if (verbose) {
+        message(paste0("No object '", v, "' in stash."))
+      }
     }
   }
   lapply(var, f)

README.Rmd

@@ -21,8 +21,6 @@ mustashe::clear_stash()
 [![CRAN status](https://www.r-pkg.org/badges/version/mustashe)](https://CRAN.R-project.org/package=mustashe)
 [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/mustashe)](https://cran.r-project.org/package=mustashe)
 [![R build status](https://github.com/jhrcook/mustashe/workflows/R-CMD-check/badge.svg)](https://github.com/jhrcook/mustashe/actions)
-[![Travis build status](https://travis-ci.org/jhrcook/mustashe.svg?branch=master)](https://travis-ci.org/jhrcook/mustashe)
-[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/jhrcook/mustashe?branch=master&svg=true)](https://ci.appveyor.com/project/jhrcook/mustashe)
 [![Codecov test coverage](https://codecov.io/gh/jhrcook/mustashe/branch/master/graph/badge.svg)](https://codecov.io/gh/jhrcook/mustashe?branch=master)
 [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 <!-- badges: end -->

README.md

@@ -11,10 +11,6 @@ status](https://www.r-pkg.org/badges/version/mustashe)](https://CRAN.R-project.o
 downloads](http://cranlogs.r-pkg.org/badges/grand-total/mustashe)](https://cran.r-project.org/package=mustashe)
 [![R build
 status](https://github.com/jhrcook/mustashe/workflows/R-CMD-check/badge.svg)](https://github.com/jhrcook/mustashe/actions)
-[![Travis build
-status](https://travis-ci.org/jhrcook/mustashe.svg?branch=master)](https://travis-ci.org/jhrcook/mustashe)
-[![AppVeyor build
-status](https://ci.appveyor.com/api/projects/status/github/jhrcook/mustashe?branch=master&svg=true)](https://ci.appveyor.com/project/jhrcook/mustashe)
 [![Codecov test
 coverage](https://codecov.io/gh/jhrcook/mustashe/branch/master/graph/badge.svg)](https://codecov.io/gh/jhrcook/mustashe?branch=master)
 [![License: GPL
@@ -71,7 +67,7 @@ stash("rnd_vals", {
 })
 #> Stashing object.
 tictoc::toc()
-#> random simulation: 3.481 sec elapsed
+#> random simulation: 3.638 sec elapsed
 ```
 
 Now, if we come back tomorrow and continue working on the same analysis,
@@ -87,7 +83,7 @@ stash("rnd_vals", {
 })
 #> Loading stashed object.
 tictoc::toc()
-#> random simulation: 0.02 sec elapsed
+#> random simulation: 0.016 sec elapsed
 ```
 
 ## Dependencies

_pkgdown.yml

@@ -24,16 +24,16 @@ navbar:
     articles:
       text: Articles
       menu:
-      - text: Getting Started
+      - text: Getting started
         href: articles/getting-started.html
       - text: How 'mustashe' works
         href: articles/how-mustashe-works.html
     news:
       text: News
       href: news/index.html
     github:
-      icon: fa-github fa-lg
-      href: https://github.com/jhrcook/stashR
+      icon: fab fa-github fa-lg
+      href: https://github.com/jhrcook/mustashe
     twitter:
       icon: fab fa-twitter fa-lg
       href: https://twitter.com/JoshDoesa

cran-comments.md

@@ -1,22 +1,39 @@
-# mustashe
+# 'mustashe' 0.1.4
 
-## Bug fix and minor version release
+May 15, 2021
 
-Brian Ripley reported that the tests for this package failed on the CRAN macOS servers.
-I was unable to reproduce this on my machine running macOS 10.15.2, and it seems like this problem only occured on versions of macOS 10.12 and older.
-We were able able to correct the problem without changing any of the tests or package as it was caused by how the time of last modification was reported for files written and read by the `stash()` function.
+## Test environments
 
-This is also a minor version release because we have switched to using the 'qs: Quick Serialization of R Objects' package for reading and writing files instead of using RDS files.
+- (developed on) macOS Catalina 10.15.2, 4.0.5
+- macOS x86_64-apple-darwin15.6.0 (64-bit) (on GitHub Actions), R 3.6.3
+- macOS x86_64-apple-darwin15.6.0 (64-bit) (on GitHub Actions), R 4.0.5
+- Ubuntu 16.04 (on GitHub Actions), R 3.5.3
+- Ubuntu 16.04 (on GitHub Actions), R 3.6.3
+- Ubuntu 16.04 (on GitHub Actions), R 4.0.5
+- Microsoft Windows Server 2019 (on GitHub Actions), R 3.6.3
+- Microsoft Windows Server 2019 (on GitHub Actions), R 4.0.5
 
-## Test environments
+## `R CMD check --as-cran` results
+
+There were no ERRORs nor WARNINGs. There was 1 NOTE about how this package has previously been archived:
+
+```
+* checking CRAN incoming feasibility ... NOTE
+Maintainer: ‘Joshua H Cook <[email protected]>’
+
+New submission
+
+Package was archived on CRAN
+
+CRAN repository db overrides:
+  X-CRAN-Comment: Archived on 2021-04-28 as check problems were not
+    corrected in time.
 
-- local macOS Catalina v10.15.2
-    - R version 3.6.1 (2019-07-05)
-- Ubuntu 16.04.6 LTS
-    - R version 3.6.2 (2017-01-27)
-- Windows Server 2012 R2 x64 (build 9600)
-    - R version 3.6.3 Patched (2020-03-11 r78011)
+  Suggests: packages not used conditionally.
+```
 
-## R CMD check results
+## Changes
 
-There were no ERRORs,  WARNINGs, or NOTES
+This update to 'mustashe' addresses issues on CRAN serves.
+This package was previously archived, but I believe the issues have been fixed.
+No new features.