fixing reset of options

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

@@ -1,21 +1,19 @@
-# NOTE: This workflow is overkill for most R packages
-# check-standard.yaml is likely a better choice
-# usethis::use_github_action("check-standard") will install it.
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 #
-# 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
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -26,80 +24,40 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
+
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: '3.6'}
-          - {os: ubuntu-16.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest", http-user-agent: "R/4.0.0 (ubuntu-16.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          - {os: ubuntu-16.04,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          # use 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: '4.1'}
+
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: 'oldrel-4'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - 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
+      - uses: r-lib/actions/setup-r-dependencies@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", "16.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

R/readGT3X.R

@@ -284,7 +284,7 @@ read.gt3x <- function(path, verbose = FALSE, asDataFrame = FALSE,
 
 
   accdata <- structure(accdata,
-                       class = c("activity", class(accdata)))
+                       class = unique(c("activity", class(accdata))))
 
   if (asDataFrame)
     accdata <- as.data.frame(accdata, verbose = verbose > 1)
@@ -383,7 +383,7 @@ as.data.frame.activity <- function(x, ..., verbose = FALSE,
     message("Done")
   }
   x <- structure(x,
-                 class = c("activity_df", class(x)),
+                 class = unique(c("activity_df", class(x))),
                  subject_name = all_attributes[["subject_name"]],
                  time_zone = all_attributes[["time_zone"]],
                  missingness = all_attributes[["missingness"]])
@@ -416,9 +416,8 @@ as.data.frame.activity <- function(x, ..., verbose = FALSE,
 #' @rdname print
 print.activity_df <- function(x, ...) {
 
-  old <- options()         # code line i
-  on.exit(options(old))    # code line i+1
-  options(digits = 15L, digits.secs = 3L)
+  old <- options(digits = 15L, digits.secs = 3L)     # code line i
+  on.exit(options(old))                              # code line i+1
 
   arglist <- list(...)
   if(! "n" %in% names(arglist)) {
@@ -436,6 +435,8 @@ print.activity_df <- function(x, ...) {
 #' @rdname print
 #' @export
 head.activity_df <- function(x, ...) {
+  old <- options(digits = 15L, digits.secs = 3L)     # code line i
+  on.exit(options(old))                              # code line i+1
   all_attr <- attributes(x)
   nattr <- names(all_attr)
   nattr <- setdiff(nattr, c("dim", "dimnames", "names", "rownames"))
@@ -444,7 +445,7 @@ head.activity_df <- function(x, ...) {
   for (iattr in nattr) {
     attr(x, iattr) <-  all_attr[[iattr]]
   }
-  class(x) <- c("activity_df", class(x))
+  class(x) <- unique(c("activity_df", class(x)))
 
   attr(x, "n_head") <- get_n_head(...)
   x
@@ -453,6 +454,8 @@ head.activity_df <- function(x, ...) {
 #' @rdname print
 #' @export
 print.activity <- function(x, ...) {
+  old <- options(digits = 15L, digits.secs = 3L)     # code line i
+  on.exit(options(old))                              # code line i+1
 
   arglist <- list(...)
   if(! "n" %in% names(arglist)) {
@@ -471,6 +474,9 @@ print.activity <- function(x, ...) {
 #' @importFrom utils head
 #' @export
 head.activity <- function(x, ...) {
+  old <- options(digits = 15L, digits.secs = 3L)     # code line i
+  on.exit(options(old))                              # code line i+1
+
   all_attr <- attributes(x)
   nattr <- names(all_attr)
   nattr <- setdiff(nattr, c("dim", "dimnames", "names", "rownames"))
@@ -479,7 +485,7 @@ head.activity <- function(x, ...) {
   for (iattr in nattr) {
     attr(x, iattr) <-  all_attr[[iattr]]
   }
-  class(x) <- c("activity", class(x))
+  class(x) <- unique(c("activity", class(x)))
 
   attr(x, "n_head") <- get_n_head(...)
 

README.Rmd

@@ -18,6 +18,7 @@ knitr::opts_chunk$set(
 [![R-CMD-check](https://github.com/THLfi/read.gt3x/workflows/R-CMD-check/badge.svg)](https://github.com/THLfi/read.gt3x/actions)
 [![CRAN status](https://www.r-pkg.org/badges/version/read.gt3x)](https://CRAN.R-project.org/package=read.gt3x)
 [![CRAN RStudio mirror downloads](https://cranlogs.r-pkg.org/badges/last-month/read.gt3x?color=blue)](https://r-pkg.org/pkg/read.gt3x)
+[![R-CMD-check](https://github.com/THLfi/read.gt3x/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/THLfi/read.gt3x/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 The `read.gt3x` R package implements a high performance C++ parser for ActiGraph's `.gt3x` data format. Read the binary accelerometer data (.gt3x) into an R data frame in a few seconds.

README.md

@@ -10,6 +10,7 @@
 status](https://www.r-pkg.org/badges/version/read.gt3x)](https://CRAN.R-project.org/package=read.gt3x)
 [![CRAN RStudio mirror
 downloads](https://cranlogs.r-pkg.org/badges/last-month/read.gt3x?color=blue)](https://r-pkg.org/pkg/read.gt3x)
+[![R-CMD-check](https://github.com/THLfi/read.gt3x/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/THLfi/read.gt3x/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 The `read.gt3x` R package implements a high performance C++ parser for
@@ -24,8 +25,7 @@ are used by both individuals and researchers to track movement. The
 devices measures [proper
 acceleration](https://en.wikipedia.org/wiki/Proper_acceleration) in
 three directions: X (right-left), Y (forward-backward), Z (up-down). The
-measurement unit is the gravitational unit,
-*g* = 9.81*m*/*s*<sup>2</sup>
+measurement unit is the gravitational unit, $g = 9.81 m / s^2$
 
 Data from the wearable ActiGraph devices is usually extracted and
 analyzed via a software called *ActiLife*. When data is extracted from
@@ -55,9 +55,9 @@ modification is done to the raw data. The package implements an
 efficient C++ parser which reads activity samples directly from the
 binary log.bin file inside the .gt3x archive. This allows for
 
--   Storing of the data in original binary format to reserve space  
--   Fast access to the accelerometer’s measurements  
--   Circumvent ActiLife’s filtering algorithms
+- Storing of the data in original binary format to reserve space  
+- Fast access to the accelerometer’s measurements  
+- Circumvent ActiLife’s filtering algorithms
 
 ## Installation
 
@@ -110,8 +110,14 @@ head(X)
 #> [4,] 0.016 -0.012 1.012
 #> [5,] 0.016 -0.008 1.008
 #> [6,] 0.008 -0.008 1.008
+```
+
+``` r
 head(attributes(X)$time_index)
 #> [1] 0 1 2 3 4 5
+```
+
+``` r
 attributes(X)[setdiff(names(attributes(X)), c("dim", "dimnames", "time_index"))]
 #> $missingness
 #>                           time n_missing
@@ -213,13 +219,16 @@ head(df)
 #> Sampling Rate: 100Hz
 #> Firmware Version: 1.7.2
 #> Serial Number Prefix: TAS
-#>                     time     X      Y     Z
-#> 1 2019-09-17 18:40:00.00 0.000  0.008 0.996
-#> 2 2019-09-17 18:40:00.00 0.016  0.000 1.008
-#> 3 2019-09-17 18:40:00.01 0.020 -0.008 1.004
-#> 4 2019-09-17 18:40:00.02 0.016 -0.012 1.012
-#> 5 2019-09-17 18:40:00.03 0.016 -0.008 1.008
-#> 6 2019-09-17 18:40:00.04 0.008 -0.008 1.008
+#>                  time     X      Y     Z
+#> 1 2019-09-17 18:40:00 0.000  0.008 0.996
+#> 2 2019-09-17 18:40:00 0.016  0.000 1.008
+#> 3 2019-09-17 18:40:00 0.020 -0.008 1.004
+#> 4 2019-09-17 18:40:00 0.016 -0.012 1.012
+#> 5 2019-09-17 18:40:00 0.016 -0.008 1.008
+#> 6 2019-09-17 18:40:00 0.008 -0.008 1.008
+```
+
+``` r
 attributes(df)[setdiff(names(attributes(df)), c("names", "row.names"))]
 #> $class
 #> [1] "activity_df" "data.frame"