Make non-tsv file import defunct

DESCRIPTION

@@ -43,8 +43,6 @@ Suggests:
     DBI,
     future,
     knitr,
-    readODS,
-    readxl,
     rmarkdown,
     RSQLite,
     testthat (>= 3.0.0),

Makefile

@@ -31,8 +31,6 @@ dev_deps:
 > ${RSCRIPT} -e "stopifnot(requireNamespace('jsonlite', quietly = TRUE))";\
 > ${RSCRIPT} -e "stopifnot(requireNamespace('knitr', quietly = TRUE))";\
 > ${RSCRIPT} -e "stopifnot(requireNamespace('pkgdown', quietly = TRUE))";\
-> ${RSCRIPT} -e "stopifnot(requireNamespace('readODS', quietly = TRUE))";\
-> ${RSCRIPT} -e "stopifnot(requireNamespace('readxl', quietly = TRUE))";\
 > ${RSCRIPT} -e "stopifnot(requireNamespace('rmarkdown', quietly = TRUE))";\
 > ${RSCRIPT} -e "stopifnot(requireNamespace('RSQLite', quietly = TRUE))";\
 > ${RSCRIPT} -e "stopifnot(requireNamespace('sf', quietly = TRUE))";\
@@ -51,7 +49,7 @@ sentinels/check: sentinels/pkgdown $(shell find tests -type f)
 > mkdir -p $(@D);\
 > touch $@
 
-sentinels/pkgdown: sentinels/vignettes README.md NEWS.md LICENSE sentinels/doc _pkgdown.yml $(shell find pkgdown -type f)
+sentinels/pkgdown: sentinels/vignettes README.md LICENSE sentinels/doc _pkgdown.yml $(shell find pkgdown -type f)
 > echo "options(rmarkdown.html_vignette.check_title = FALSE)" > .Rprofile;\
 > ${RSCRIPT} -e "pkgdown::build_site()";\
 > rm .Rprofile; \
@@ -62,17 +60,6 @@ sentinels/pkgdown: sentinels/vignettes README.md NEWS.md LICENSE sentinels/doc _
 README.md: README.Rmd DESCRIPTION
 > ${RSCRIPT} -e "knitr::knit('$<')"
 
-NEWS.md: inst/NEWS.Rd
-> ${RSCRIPT} -e "tools::Rd2HTML('$<', 'inst/NEWS.html')";\
-> sed -i 's/h2>/h1>/g' inst/NEWS.html;\
-> sed -i 's/h3>/h1>/g' inst/NEWS.html;\
-> sed -i 's/h4>/h2>/g' inst/NEWS.html;\
-> pandoc -s inst/NEWS.html -o inst/NEWS.md -t gfm;\
-> sed -i '1,8d' inst/NEWS.md;\
-> head -n -2 inst/NEWS.md > NEWS.md;\
-> sed -i 's/# ${PKGNM} version/# ${PKGNM}/g' NEWS.md;\
-> $(RM) inst/NEWS.html inst/NEWS.md
-
 sentinels/vignettes: $(shell find inst/vign -type f)
 > cd ..;\
 > R CMD build $(PKGSRC);\

NEWS.md

@@ -2,9 +2,10 @@
 
 # finbif 0.9.8.9000
 
-## NEW FEATURES
+## DEFUNCT
 
-  - This is the latest development version.
+  - Importing `.ods` and `.xlsx` occurrence data files is now defunct users
+    should use `.tsv` download files only.
 
 # finbif 0.9.8
 

R/finbif_occurrence_load.R

@@ -75,15 +75,6 @@ finbif_occurrence_load <- function(
   skip = 0
 ) {
 
-  nchars <- nchar(file)
-
-  file <- switch(
-    substring(file, nchars - 3L, nchars),
-    .ods = from_ods(file),
-    xlsx = from_xlsx(file),
-    file
-  )
-
   fb_records_obj <- list(
     file = file,
     n = as.integer(n),
@@ -1583,66 +1574,6 @@ open_tsv_connection <- function(connection_obj) {
 
 }
 
-#' @noRd
-
-from_ods <- function(file) {
-
-  warn <- Sys.getenv("DEPRECATION_WARNING", 0)
-
-  op <- options()
-
-  options(warn = as.integer(warn))
-
-  warning(
-    "Reading ODS file downloads has been deprecated in the {finbif} package ",
-    "and will unavailable in the next release. Please use TSV downloads ",
-    "instead.",
-    call. = FALSE
-  )
-
-  options(op)
-
-  stopifnot("Package {readODS} required for ODS files" = has_pkgs("readODS"))
-
-  df <- readODS::read_ods(file, col_types = NA)
-
-  write_tsv(df)
-
-}
-
-#' @noRd
-
-from_xlsx <- function(file) {
-
-  warn <- Sys.getenv("DEPRECATION_WARNING", 0)
-
-  op <- options()
-
-  options(warn = as.integer(warn))
-
-  warning(
-    "Reading XLSX file downloads has been deprecated in the {finbif} package ",
-    "and will unavailable in the next release. Please use TSV downloads ",
-    "instead.",
-    call. = FALSE
-  )
-
-  options(op)
-
-  stopifnot("Package {readxl} required for Excel files" = has_pkgs("readxl"))
-
-  df <- readxl::read_xlsx(
-    file,
-    progress = FALSE,
-    col_types = "text",
-    trim_ws = FALSE,
-    .name_repair = "minimal"
-  )
-
-  write_tsv(df)
-
-}
-
 #' @noRd
 #' @importFrom utils write.table
 

README.md

@@ -88,7 +88,7 @@ FinBIF itself and the contributed datasets please visit this link:
 To cite the finbif R package in publications please use:
 
   Morris, William K. (2024). Introduction to the finbif package. R
-  package version 0.9.8, https://doi.org/10.5281/zenodo.3612814
+  package version 0.9.8.9000, https://doi.org/10.5281/zenodo.3612814
 
 ----
 

codemeta.json

@@ -106,30 +106,6 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=knitr"
     },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "readODS",
-      "name": "readODS",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=readODS"
-    },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "readxl",
-      "name": "readxl",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=readxl"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "rmarkdown",
@@ -246,7 +222,7 @@
   "applicationCategory": "Biodiversity",
   "isPartOf": "https://species.fi",
   "keywords": ["api", "biodiversity", "biodiversity-informatics", "biodiversity-information", "finbif", "finbif-access", "occurrences", "r-package", "r-programming", "rstats", "species", "specimens", "taxon", "taxonomy", "web-services"],
-  "fileSize": "12047.358KB",
+  "fileSize": "11961.439KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",

docs/pkgdown.yml

@@ -7,7 +7,7 @@ articles:
   v03_selecting_variables: v03_selecting_variables.html
   v04_metadata: v04_metadata.html
   v05_filtering: v05_filtering.html
-last_built: 2024-08-19T10:30Z
+last_built: 2024-08-21T08:56Z
 urls:
   reference: https://finbif-docs-dev.netlify.app/reference
   article: https://finbif-docs-dev.netlify.app/articles