Merge pull request #104 from inbo/dev_nextrelease

Release version 0.4.2

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

@@ -23,10 +23,8 @@ jobs:
  fail-fast: false
  matrix:
  config:
- - {os: ubuntu-20.04, r: 'release'}
- - {os: ubuntu-20.04, r: 'devel'}
- - {os: ubuntu-18.04, r: 'release'}
- - {os: ubuntu-18.04, r: 'devel'}
+ # - {os: ubuntu-22.04, r: 'release'}
+ # - {os: ubuntu-22.04, r: 'devel'}
  - {os: windows-latest, r: 'release'}
  - {os: macOS-latest, r: 'release'}
 
@@ -35,13 +33,15 @@ jobs:
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
 
- - uses: r-lib/actions/setup-r@v1
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
  with:
  r-version: ${{ matrix.config.r }}
-
- - uses: r-lib/actions/setup-pandoc@v1
+ http-user-agent: ${{ matrix.config.http-user-agent }}
+  use-public-rspm: false
 
  - name: Query dependencies
  run: |
@@ -89,7 +89,7 @@ jobs:
 
  - name: Upload check results
  if: failure()
- uses: actions/upload-artifact@main
+ uses: actions/upload-artifact@v3
  with:
  name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
  path: check

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

@@ -2,6 +2,8 @@
 # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
 on:
  push:
+ branches:
+ - '*'
 
 name: R-CMD-check
 
@@ -15,71 +17,30 @@ jobs:
  fail-fast: false
  matrix:
  config:
- - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- - {os: ubuntu-18.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+ - {os: ubuntu-22.04, r: 'release'}
  - {os: windows-latest, r: 'release'}
- - {os: macOS-latest, r: 'release'}
+ - {os: macOS-latest,  r: 'release'}
 
  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@v3
 
- - uses: r-lib/actions/setup-r@v1
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - 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: Restore (or define new) R package cache
- uses: actions/cache@v2
+ - uses: r-lib/actions/setup-r-dependencies@v2
  with:
- path: ${{ env.R_LIBS_USER }}
- key: ${{ matrix.config.os }}-${{ secrets.CACHE_VERSION }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
- restore-keys: ${{ matrix.config.os }}-${{ secrets.CACHE_VERSION }}-${{ hashFiles('.github/R-version') }}-1-
-
- - name: Install system dependencies (Linux)
- if: runner.os == 'Linux'
- run: |
- while read -r cmd
- do
- eval sudo $cmd
- done < <(Rscript -e 'release <- system("lsb_release -rs", intern = TRUE); writeLines(remotes::system_requirements("ubuntu", release))')
+ cache-version: ${{ secrets.CACHE_VERSION }}
+ extra-packages: any::rcmdcheck
+ needs: check
 
- - name: Install system dependencies (macOS)
- if: runner.os == 'macOS'
- run: |
- brew install udunits
- brew install gdal
- brew install proj
-
- - name: Install package dependencies
- run: |
- remotes::install_deps(dependencies = TRUE)
- remotes::install_cran("rcmdcheck")
- shell: Rscript {0}
-
- - name: Check
- env:
- _R_CHECK_CRAN_INCOMING_REMOTE_: false
- run: |
- options(rmarkdown.html_vignette.check_title = FALSE)
- 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: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
- path: check
+ - uses: r-lib/actions/check-r-package@v2

.github/workflows/site-deploy.yaml

@@ -8,53 +8,23 @@ name: site-deploy
 
 jobs:
  site-deploy:
- runs-on: ${{ matrix.config.os }}
- name: ${{ matrix.config.os }} (${{ matrix.config.r }})
- strategy:
- matrix:
- config:
- - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+ runs-on: ubuntu-22.04
  env:
- RSPM: ${{ matrix.config.rspm }}
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
 
- - uses: r-lib/actions/setup-r@v1
- with:
- r-version: ${{ matrix.config.r }}
-
- - uses: r-lib/actions/setup-pandoc@v1
+ - uses: r-lib/actions/setup-pandoc@v2
 
- - 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: Restore (or define new) R package cache
- uses: actions/cache@v2
+ - uses: r-lib/actions/setup-r@v2
  with:
- path: ${{ env.R_LIBS_USER }}
- key: ${{ matrix.config.os }}-${{ secrets.CACHE_VERSION }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+ use-public-rspm: true
 
- - name: Install system dependencies (Linux)
- run: |
- while read -r cmd
- do
- eval sudo $cmd
- done < <(Rscript -e 'release <- system("lsb_release -rs", intern = TRUE); writeLines(remotes::system_requirements("ubuntu", release))')
- sudo apt-get install -y libfribidi-dev libharfbuzz-dev
-
- - name: Install dependencies
- run: |
- remotes::install_deps(dependencies = TRUE)
- install.packages("pkgdown")
- shell: Rscript {0}
-
- - name: Install package
- run: R CMD INSTALL .
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ cache-version: ${{ secrets.CACHE_VERSION }}
+ extra-packages: local::., [email protected]
+ needs: website
 
  - name: Deploy package
  run: |

.github/workflows/site-devel.yaml

@@ -8,60 +8,30 @@ name: site-devel
 
 jobs:
  site-devel:
- runs-on: ${{ matrix.config.os }}
- name: ${{ matrix.config.os }} (${{ matrix.config.r }})
- strategy:
- matrix:
- config:
- - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+ runs-on: ubuntu-22.04
  env:
- RSPM: ${{ matrix.config.rspm }}
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
 
- - uses: r-lib/actions/setup-r@v1
- with:
- r-version: ${{ matrix.config.r }}
-
- - uses: r-lib/actions/setup-pandoc@v1
+ - uses: r-lib/actions/setup-pandoc@v2
 
- - 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: Restore (or define new) R package cache
- uses: actions/cache@v2
+ - uses: r-lib/actions/setup-r@v2
  with:
- path: ${{ env.R_LIBS_USER }}
- key: ${{ matrix.config.os }}-${{ secrets.CACHE_VERSION }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+ use-public-rspm: true
 
- - name: Install system dependencies (Linux)
- run: |
- while read -r cmd
- do
- eval sudo $cmd
- done < <(Rscript -e 'release <- system("lsb_release -rs", intern = TRUE); writeLines(remotes::system_requirements("ubuntu", release))')
- sudo apt-get install -y libfribidi-dev libharfbuzz-dev
-
- - name: Install dependencies
- run: |
- remotes::install_deps(dependencies = TRUE)
- install.packages("pkgdown")
- shell: Rscript {0}
-
- - name: Install package
- run: R CMD INSTALL .
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ cache-version: ${{ secrets.CACHE_VERSION }}
+ extra-packages: local::., [email protected]
+ needs: website
 
  - name: Build site
  run: |
  Rscript -e 'options(rmarkdown.html_vignette.check_title = FALSE); pkgdown::build_site()'
 
  - name: Upload pkgdown-site as artifact
- uses: actions/upload-artifact@main
+ uses: actions/upload-artifact@v3
  with:
  name: pkgdown-site
  path: docs

.zenodo.json

@@ -4,7 +4,7 @@
  "license": "GPL-3.0",
  "upload_type": "software",
  "access_right": "open",
- "version": "0.4.1",
+ "version": "0.4.2",
  "creators": [
  {
  "name": "Vanderhaeghe, Floris",

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: watina
 Title: Querying and Processing Data from the INBO Watina Database
-Version: 0.4.1
+Version: 0.4.2
 Description: The R-package watina contains functions to query
  and process data from the Watina database at the Research Institute for
  Nature and Forest (INBO). This database primarily provides
@@ -23,7 +23,6 @@ Imports:
  assertthat,
  dplyr,
  inbodb,
- KSgeneral,
  lubridate,
  rlang,
  stringr,
@@ -32,6 +31,7 @@ Imports:
 Suggests:
  DBI,
  knitr,
+ KSgeneral,
  purrr,
  rmarkdown,
  sf,
@@ -41,5 +41,5 @@ Remotes:
  inbo/inbodb
 LazyData: true
 Encoding: UTF-8
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 VignetteBuilder: knitr

NAMESPACE

@@ -13,7 +13,6 @@ export(get_locs)
 export(get_xg3)
 export(selectlocs_chem)
 export(selectlocs_xg3)
-importFrom(KSgeneral,disc_ks_test)
 importFrom(assertthat,assert_that)
 importFrom(assertthat,has_args)
 importFrom(assertthat,has_name)

NEWS.md

@@ -1,3 +1,9 @@
+# watina 0.4.2 (2023-09-15)
+
+- Move package {KSgeneral} to `Suggests` (#103).
+This avoids package breaking when {KSgeneral} is not available on CRAN.
+For the moment not taking further measures to protect against it, as the package is currently back on CRAN.
+
 # watina 0.4.1 (2021-06-11)
 
 - Fixed non-working `get_xg3()` and `get_chem()` for dataframe input, by avoiding the currently defunct `dbplyr::db_drop_table()` (#89, [08bc66d](https:/inbo/watina/commit/08bc66d)).

R/eval.R

@@ -354,8 +354,6 @@ qualify_xg3 <- function(data,
 #' @importFrom rlang .data
 #' @importFrom assertthat
 #' assert_that
-#' @importFrom KSgeneral
-#' disc_ks_test
 #' @importFrom stringr
 #' str_detect
 #' @importFrom stats
@@ -382,6 +380,8 @@ eval_xg3_series <- function(data,
  max_gap,
  min_dur) {
 
+ require_pkgs("KSgeneral")
+
  if (missing(xg3_type)) {
  xg3_type <- match.arg(xg3_type)} else {
  assert_that(all(xg3_type %in%
@@ -410,11 +410,13 @@ eval_xg3_series <- function(data,
  ser_rel_nryears = .data$ser_nryears / .data$ser_length,
  ser_firstyear = min(.data$hydroyear),
  ser_lastyear = max(.data$hydroyear),
- ser_pval_uniform = disc_ks_test(.data$hydroyear,
- ecdf(seq(.data$ser_firstyear,
- .data$ser_lastyear)),
- exact = TRUE) %>%
- .$p.value
+ ser_pval_uniform = KSgeneral::disc_ks_test(
+ .data$hydroyear,
+ ecdf(seq(.data$ser_firstyear,
+ .data$ser_lastyear)),
+ exact = TRUE
+ ) %>%
+ .$p.value
  ) %>%
  ungroup
  },
@@ -650,6 +652,8 @@ eval_chem <- function(data,
  type = c("avail", "num", "both"),
  uniformity_test = FALSE) {
 
+ require_pkgs("KSgeneral")
+
  type <- match.arg(type)
 
  assert_that(inherits(data, what = c("tbl_lazy", "data.frame")),
@@ -774,13 +778,15 @@ date, lab_sample_id, chem_variable, value, unit, below_loq."
  df %>%
  summarise(
  nryears = sum(.data$available),
- pval_uniform_totalspan = ifelse(.data$nryears > 0,
- disc_ks_test(.data$year[.data$available],
- ecdf(seq(firstyear,
- lastyear)),
- exact = TRUE) %>%
- .$p.value,
- NA)
+ pval_uniform_totalspan = ifelse(
+ .data$nryears > 0,
+ KSgeneral::disc_ks_test(.data$year[.data$available],
+ ecdf(seq(firstyear,
+ lastyear)),
+ exact = TRUE) %>%
+ .$p.value,
+ NA
+ )
  ) %>%
  select(-.data$nryears) %>%
  ungroup