Run rcmdcheck as cran in CI

.github/workflows/deploy.yml

@@ -10,15 +10,31 @@ permissions:
 
 jobs:
   pre_deploy:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # macos-13 is an intel runner, macos-14 is apple silicon
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
     env:
       cache-version: 5
     steps:
       - uses: actions/checkout@v2
       - name: Set up libraries for Ubuntu
+        if: runner.os == 'Linux'
         run: |
           sudo apt-get update
           sudo apt-get install -y libsodium-dev libharfbuzz-dev libfribidi-dev libcurl4-openssl-dev texlive-latex-base texlive-fonts-extra pandoc libmagick++-dev libhdf5-dev
+      - name: Set up libraries for MacOS
+        if: runner.os == 'macOS'
+        run: |
+          brew install libsodium harfbuzz fribidi curl texlive pandoc imagemagick hdf5 basictex
+      - name: Set up libraries for Windows
+        if: runner.os == 'Windows'
+        run: |
+          choco install rtools
+          choco install pandoc
+          choco install tinytex
+          choco install imagemagick
       - name: Set up R 4.0
         uses: r-lib/actions/setup-r@v2
         with:
@@ -52,17 +68,26 @@ jobs:
       - name: rcmdcheck
         run: |
           rcmdcheck::rcmdcheck(
-            error_on = "error", # TODO: switch back to "warning"
+            error_on = "error",
             check_dir = "check"
           )
         shell: Rscript {0}
         env:
           _R_CHECK_FORCE_SUGGESTS_: false
+      - name: rcmdcheck as CRAN
+        run: |
+          rcmdcheck::rcmdcheck(
+            args = "--as-cran",
+            error_on = "warning",
+            check_dir = "cran_check"
+          )
+        shell: Rscript {0}
       - name: Run coverage report
         run: |
           covr::package_coverage()
         shell: Rscript {0}
       - name: Downgrade pkgdown
+        # Reference: https://github.com/r-lib/pkgdown/issues/2205#issuecomment-1377793532
         run: |
           remotes::install_version("pkgdown", "2.0.3")
         shell: Rscript {0}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: pizzarr
 Type: Package
-Title: Slice into Zarr arrays in R
+Title: Slice into Zarr Arrays in R
 Version: 0.1.0
 Authors@R: c(
     person(
@@ -39,7 +39,6 @@ RoxygenNote: 7.3.2
 Suggests: 
     testthat,
     knitr,
-    covr,
     bslib,
     pkgdown,
     rmarkdown,

R/numcodecs.R

@@ -61,7 +61,7 @@ ZstdCodec <- R6::R6Class("ZstdCodec",
     #' @param zarr_arr The ZarrArray instance.
     #' @return Compressed data.
     encode = function(buf, zarr_arr) {
-      # Reference: https://github.com/traversc/qs/blob/84e30f4/R/RcppExports.R#L16
+      # Reference: https://github.com/qsbase/qs/blob/84e30f4/R/RcppExports.R#L16
       result <- zstd_compress_raw(buf, self$level)
       return(result)
     },
@@ -114,7 +114,7 @@ Lz4Codec <- R6::R6Class("Lz4Codec",
      #' @param zarr_arr The ZarrArray instance.
      #' @return Compressed data.
      encode = function(buf, zarr_arr) {
-       # Reference: https://github.com/traversc/qs/blob/84e30f4/R/RcppExports.R#L24
+       # Reference: https://github.com/qsbase/qs/blob/84e30f4/R/RcppExports.R#L24
        body <- lz4_compress_raw(buf, self$acceleration)
 
        # The compressed output includes a 4-byte header storing the original size

R/zarr-array.R

@@ -79,7 +79,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
     #' oindex TODO
     #' @keywords internal
     oindex = NULL,
-    #' method_description
+    #' @description
     #' (Re)load metadata from store without synchronization (file locking).
     load_metadata_nosync = function() {
 
@@ -135,27 +135,27 @@ ZarrArray <- R6::R6Class("ZarrArray",
       }
       private$dtype <- normalize_dtype(meta$dtype, object_codec = object_codec)
     },
-    #' method_description
+    #' @description
     #' Load or reload metadata from store.
     load_metadata = function() {
       private$load_metadata_nosync()
       # TODO: support for synchronization
     },
-    #' method_description
+    #' @description
     #' Referesh metadata if not cached without synchronization (file locking).
     refresh_metadata_nosync = function() {
       if(!private$cache_metadata && !private$is_view) {
         private$load_metadata_nosync()
       }
     },
-    #' method_description
+    #' @description
     #' Refresh metadata from store if not cached.
     refresh_metadata = function() {
       if(!private$cache_metadata) {
         private$load_metadata()
       }
     },
-    #' method_description
+    #' @description
     #' Write metadata to store without synchronization (file locking).
     flush_metadata_nosync = function() {
       if(private$is_view) {
@@ -188,13 +188,13 @@ ZarrArray <- R6::R6Class("ZarrArray",
       encoded_meta <- private$store$metadata_class$encode_array_metadata(zarray_meta)
       private$store$set_item(mkey, encoded_meta)
     },
-    #' method_description
+    #' @description
     #' TODO
     chunk_key = function(chunk_coords) {
       # Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/core.py#L2063
       return(paste0(private$key_prefix, do.call(paste, c(as.list(chunk_coords), sep = private$dimension_separator))))
     },
-    #' method_description
+    #' @description
     #' TODO
     compute_cdata_shape = function() {
       # Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/core.py#L428
@@ -212,7 +212,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
       cdata_shape <- as.numeric(cdata_shape)
       return(cdata_shape)
     },
-    #' method_description
+    #' @description
     #' Resize an array without synchronization (file locking)
     resize_nosync = function(...) {
       # Note: When resizing an array, the data are not rearranged in any way.
@@ -252,7 +252,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
         }
       }
     },
-    #' method_description
+    #' @description
     #' TODO
     get_basic_selection_zd = function(selection = NA, out = NA, fields = NA) {
       # Special case basic selection for zero-dimensional array
@@ -296,13 +296,13 @@ ZarrArray <- R6::R6Class("ZarrArray",
       }
       return(out)
     },
-    #' method_description
+    #' @description
     #' TODO
     get_basic_selection_nd = function(selection = NA, out = NA, fields = NA) {
       indexer <- BasicIndexer$new(selection, self)
       return(private$get_selection(indexer, out = out, fields = fields))
     },
-    #' method_description
+    #' @description
     #' TODO
     get_selection = function(indexer, out = NA, fields = NA) {
       # Reference: https://github.com/gzuidhof/zarr.js/blob/292804/src/core/index.ts#L304
@@ -369,7 +369,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
       return(out)
 
     },
-    #' method_description
+    #' @description
     #' TODO
     set_basic_selection_zd = function(selection, value, fields = NA) {
       # Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0e6cdc04c6413e14f57f61d389972ea937c/zarr/core.py#L1625
@@ -432,13 +432,13 @@ ZarrArray <- R6::R6Class("ZarrArray",
       c_data <- private$encode_chunk(chunk_raw)
       self$get_chunk_store()$set_item(c_key, c_data)
     },
-    #' method_description
+    #' @description
     #' TODO
     set_basic_selection_nd = function(selection, value, fields = NA) {
       indexer <- BasicIndexer$new(selection, self)
       return(private$set_selection(indexer, value = value, fields = fields))
     },
-    #' method_description
+    #' @description
     #' TODO
     set_selection = function(indexer, value, fields = NA) {
       # Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/core.py#L1682
@@ -515,13 +515,13 @@ ZarrArray <- R6::R6Class("ZarrArray",
         return()
       }
     },
-    #' method_description
+    #' @description
     #' TODO
     process_chunk = function(out, cdata, chunk_selection, drop_axes, out_is_ndarray, fields, out_selection, partial_read_decode = FALSE) {
       # Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/core.py#L1755
       # TODO
     },
-    #' method_description
+    #' @description
     #' TODO
     get_chunk_value = function(proj, indexer, value, selection_shape) {
       # Reference: https://github.com/gzuidhof/zarr.js/blob/15e3a3f00eb19f0133018fb65f002311ea53bb7c/src/core/index.ts#L550
@@ -541,12 +541,12 @@ ZarrArray <- R6::R6Class("ZarrArray",
       }
       return(chunk_value)
     },
-    #' method_description
+    #' @description
     #' TODO
     chunk_buffer_to_raw_array = function(decoded_chunk) {
       # TODO
     },
-    #' method_description
+    #' @description
     #' For parallel usage
     chunk_getitem_part1 = function(chunk_coords, chunk_selection, out, out_selection, drop_axes = NA, fields = NA) {
       if(length(chunk_coords) != length(private$chunks)) {
@@ -567,7 +567,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
       })
       return(result)
     },
-    #' method_description
+    #' @description
     #' For parallel usage
     chunk_getitem_part2 = function(part1_result, chunk_coords, chunk_selection, out, out_selection, drop_axes = NA, fields = NA) {
       c_key <- private$chunk_key(chunk_coords)
@@ -610,7 +610,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
         }
       }
     },
-    #' method_description
+    #' @description
     #' For non-parallel usage
     chunk_getitem = function(chunk_coords, chunk_selection, out, out_selection, drop_axes = NA, fields = NA) {
       # TODO
@@ -658,12 +658,12 @@ ZarrArray <- R6::R6Class("ZarrArray",
         }
       })
     },
-    #' method_description
+    #' @description
     #' TODO
     chunk_getitems = function(lchunk_coords, lchunk_selection, out, lout_selection, drop_axes = NA, fields = NA) {
       # TODO
     },
-    #' method_description
+    #' @description
     #' TODO
     chunk_setitem = function(chunk_coords, chunk_selection, value, fields = NA) {
       # Reference: https://github.com/gzuidhof/zarr.js/blob/15e3a3f00eb19f0133018fb65f002311ea53bb7c/src/core/index.ts#L625
@@ -741,30 +741,30 @@ ZarrArray <- R6::R6Class("ZarrArray",
       chunk_data <- private$encode_chunk(chunk_raw)
       self$get_chunk_store()$set_item(chunk_key, chunk_data)
     },
-    #' method_description
+    #' @description
     #' TODO
     chunk_setitem_nosync = function(chunk_coords, chunk_selection, value, fields = NA) {
       # TODO
     },
-    #' method_description
+    #' @description
     #' TODO
     chunk_setitems = function(lchunk_coords, lchunk_selection, values, fields = NA) {
       # TODO
     },
-    #' method_description
+    #' @description
     #' TODO
     process_for_setitem = function(ckey, chunk_selection, value, fields = NA) {
       # TODO
     },
     chunk_delitem = function(ckey) {
       # TODO
     },
-    #' method_description
+    #' @description
     #' TODO
     chunk_delitems = function(ckeys) {
       # TODO
     },
-    #' method_description
+    #' @description
     #' TODO
     decode_chunk = function(cdata, start = NA, nitems = NA, expected_shape = NA) {
       # Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0e6cdc04c6413e14f57f61d389972ea937c/zarr/core.py#L2066
@@ -806,7 +806,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
       # ensure correct chunk shape
       return(chunk)
     },
-    #' method_description
+    #' @description
     #' TODO
     encode_chunk = function(chunk_as_raw) {
       # Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0e6cdc04c6413e14f57f61d389972ea937c/zarr/core.py#L2105
@@ -837,7 +837,7 @@ ZarrArray <- R6::R6Class("ZarrArray",
 
       return(cdata)
     },
-    #' method_description
+    #' @description
     #' TODO
     append_nosync = function(data, axis = 0) {
       # Reference: https://github.com/zarr-developers/zarr-python/blob/5dd4a0/zarr/core.py#L2141

README.md

@@ -67,7 +67,7 @@ print(selection$data)
 | `Unicode`             |            ✔ / ✔             |  Converted to `character` in R.               |
 | `void *`              |            ❌ / ❌             |                                                                                                                                                                                 |
 | Structured data types |            ❌ / ❌             |   |
-| Object data type - [VLenUTF8](https://numcodecs.readthedocs.io/en/stable/vlen.html#vlenutf8) |            ✔ / ✔             | Converted to `character` in R. |
+| Object data type - [VLenUTF8](https://numcodecs.readthedocs.io/en/stable/other/vlen.html) |            ✔ / ✔             | Converted to `character` in R. |
 
 
 Note: no effort is made to assess loss of precision due to conversion.
@@ -120,14 +120,14 @@ pkgdown::build_site()
   - Note: `pizzarr` has an optional dependency on Rarr for Blosc (de)compression.
 - R package development
   - [R packages](https://r-pkgs.org/)
-  - [roxygen2 syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html)
+  - [roxygen2 syntax](https://CRAN.R-project.org/package=roxygen2/vignettes/rd-formatting.html)
   - [R6](https://r6.r-lib.org/index.html)
   - [R6 roxygen2 syntax](https://www.tidyverse.org/blog/2019/11/roxygen2-7-0-0/#r6-documentation)
   - [pkgdown](https://pkgdown.r-lib.org/)
 - Zarr implementation
   - [zarr_implementations](https://github.com/zarr-developers/zarr_implementations)
   - [zarr-python](https://github.com/zarr-developers/zarr-python)
-  - [LZ4 and ZSTD compression in R](https://github.com/traversc/qs)
+  - [LZ4 and ZSTD compression in R](https://github.com/qsbase/qs)
   - [zarr.js](https://github.com/gzuidhof/zarr.js)
   - [zarrita.js](https://github.com/manzt/zarrita.js)
   - [v2 spec](https://zarr.readthedocs.io/en/stable/spec/v2.html)