From a2cbf1dbd34a9b19af69b658668b7d60916581fd Mon Sep 17 00:00:00 2001
From: Travers <traversc@gmail.com>
Date: Fri, 3 May 2024 00:57:24 -0700
Subject: [PATCH] suggests/tests fix

---
 ChangeLog                |  3 +++
 DESCRIPTION              |  4 ++--
 Makefile                 |  4 ++--
 tests/test_RadixForest.R |  9 +++++++++
 tests/test_RadixTree.R   |  8 ++++++++
 tests/test_pairwise.R    | 11 +++++++++++
 6 files changed, 35 insertions(+), 4 deletions(-)

diff --git a/ChangeLog b/ChangeLog
index 0cc616f..9159a26 100644
--- a/ChangeLog
+++ b/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
diff --git a/DESCRIPTION b/DESCRIPTION
index 1b9fe18..e057677 100644
--- a/DESCRIPTION
+++ b/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 = "traversc@gmail.com", role = c("aut", "cre", "cph")),
     person("Martin", "Moene", role = c("ctb", "cph"), comment = "span-lite C++ library"),
diff --git a/Makefile b/Makefile
index 6b86447..8450271 100644
--- a/Makefile
+++ b/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)
diff --git a/tests/test_RadixForest.R b/tests/test_RadixForest.R
index 3c5218c..b76e402 100755
--- a/tests/test_RadixForest.R
+++ b/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))
     })  
 }
+
+}
diff --git a/tests/test_RadixTree.R b/tests/test_RadixTree.R
index afeafd9..dad5db6 100755
--- a/tests/test_RadixTree.R
+++ b/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) {
     })
   
 }
+
+}
diff --git a/tests/test_pairwise.R b/tests/test_pairwise.R
index 89e4ed0..ff17cc9 100755
--- a/tests/test_pairwise.R
+++ b/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))
     })
 }
+
+}