suggests/tests fix

ChangeLog

@@ -1,3 +1,6 @@
+Version 0.2.8 (2024-05-03)
+   * Conditionally run tests if required packages are installed
+
 Version 0.2.7 (2024-01-25)
    * Add Ankerl unordered_dense conditional on C++17 support
    * Add `pwalign` package to suggests field which is responsible for pairwiseAlignment in the biostrings package in BioC 3.19

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: seqtrie
 Title: Radix Tree and Trie-Based String Distances
-Version: 0.2.7
-Date: 2024-04-30
+Version: 0.2.8
+Date: 2024-05-03
 Authors@R: c(
     person("Travers", "Ching", email = "[email protected]", role = c("aut", "cre", "cph")),
     person("Martin", "Moene", role = c("ctb", "cph"), comment = "span-lite C++ library"),

Makefile

@@ -6,10 +6,10 @@ BUILD   := $(PACKAGE)_$(VERSION).tar.gz
 .PHONY: doc build install test vignette $(BUILD)
 
 check: $(BUILD)
-	R CMD check --as-cran $<
+	export _R_CHECK_FORCE_SUGGESTS_=false && R CMD check --as-cran $<
 
 check-no-vignette: $(BUILD)
-	R CMD check --as-cran --no-build-vignettes --ignore-vignettes --no-manual $<
+	export _R_CHECK_FORCE_SUGGESTS_=false && R CMD check --as-cran --no-build-vignettes --ignore-vignettes --no-manual $<
 
 
 check-cran: $(BUILD)

tests/test_RadixForest.R

@@ -2,6 +2,13 @@
 # 1) That insertion and deletion produce the correct results with random strings
 # 2) That search (hamming, levenshtein and anchored) produce the same results as the internal `dist_matrix` and `dist_pairwise` functions
 
+if(requireNamespace("seqtrie", quietly=TRUE) &&
+   requireNamespace("stringi", quietly=TRUE) &&
+   requireNamespace("stringdist", quietly=TRUE) &&
+   requireNamespace("dplyr", quietly=TRUE)
+) {
+
+
 library(seqtrie)
 library(stringdist)
 library(stringi)
@@ -152,3 +159,5 @@ for(. in 1:NITER) {
       stopifnot(identical(results_frac, sd_frac))
     })  
 }
+
+}

tests/test_RadixTree.R

@@ -2,6 +2,12 @@
 # 1) That insertion and deletion produce the correct results with random strings
 # 2) That search (hamming, levenshtein and anchored) produce the same results as the internal `dist_matrix` and `dist_pairwise` functions
 
+if(requireNamespace("seqtrie", quietly=TRUE) &&
+   requireNamespace("stringi", quietly=TRUE) &&
+   requireNamespace("stringdist", quietly=TRUE) &&
+   requireNamespace("dplyr", quietly=TRUE)
+) {
+
 library(seqtrie)
 library(stringdist)
 library(stringi)
@@ -294,3 +300,5 @@ for(. in 1:NITER) {
     })
 
 }
+
+}

tests/test_pairwise.R

@@ -2,6 +2,15 @@
 # These two functions are simple dynamic programming algorithms for computing pairwise distances and are themselves used to validate
 # the RadixTree imeplementation (see test_radix_tree.R)
 
+if(requireNamespace("seqtrie", quietly=TRUE) &&
+   requireNamespace("stringi", quietly=TRUE) &&
+   requireNamespace("stringdist", quietly=TRUE) &&
+   requireNamespace("Biostrings", quietly=TRUE) &&
+   requireNamespace("dplyr", quietly=TRUE) && 
+   # pwalign is only required for Biostrings >= 2.72.0 in R 4.4+
+   ( (packageVersion("Biostrings") < "2.72.0") || requireNamespace("pwalign", quietly=TRUE) )
+) {
+
 library(seqtrie)
 library(stringi)
 library(stringdist)
@@ -261,3 +270,5 @@ for(. in 1:NITER) {
       stopifnot(all(results_seqtrie == results_biostrings))
     })
 }
+
+}