From 248ce014e9a602809a4408cea8036159a74f2df7 Mon Sep 17 00:00:00 2001
From: Danielle Callan <dcallan@upenn.edu>
Date: Thu, 29 Feb 2024 15:43:59 -0500
Subject: [PATCH] fix some build issues

---
 DESCRIPTION            | 3 ++-
 R/method-correlation.R | 8 ++++----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4682e4e..3a66c98 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -12,6 +12,7 @@ Authors@R:
            email = "annsize@upenn.edu"))
 Imports:
     ape,
+    boot,
     data.table,
     DESeq2,
     Hmisc,
@@ -19,7 +20,7 @@ Imports:
     Maaslin2,
     methods,
     Rcpp (>= 0.11.0),
-    SpiecEasi,
+    SpiecEasi (>= 1.1.1),
     stringi,
     vegan,
     veupathUtils,
diff --git a/R/method-correlation.R b/R/method-correlation.R
index 266aa71..1cba150 100644
--- a/R/method-correlation.R
+++ b/R/method-correlation.R
@@ -14,7 +14,7 @@ selfCorrelationGeneric <- getGeneric("selfCorrelation", package = "veupathUtils"
 #' @param stdDevThreshold numeric threshold to filter features by standard deviation across samples
 #' @return a ComputeResult object
 #' @export
-setMethod("correlation", signature("AbundanceData", "missing"), 
+setMethod(correlationGeneric, signature("AbundanceData", "missing"), 
 function(data1, data2, method = c('spearman','pearson'), format  = c('ComputeResult', 'data.table'), verbose = c(TRUE, FALSE), proportionNonZeroThreshold = 0.5, varianceThreshold = 0, stdDevThreshold = 0) {
   
   format <- veupathUtils::matchArg(format)
@@ -53,7 +53,7 @@ function(data1, data2, method = c('spearman','pearson'), format  = c('ComputeRes
 #' @return ComputeResult object
 #' @import veupathUtils
 #' @export
-setMethod("selfCorrelation", signature("AbundanceData"), 
+setMethod(selfCorrelationGeneric, signature("AbundanceData"), 
 function(data, method = c('spearman','pearson','sparcc'), format = c('ComputeResult', 'data.table'), verbose = c(TRUE, FALSE), proportionNonZeroThreshold = 0.5, varianceThreshold = 0, stdDevThreshold = 0) {
   
   format <- veupathUtils::matchArg(format)
@@ -89,7 +89,7 @@ function(data, method = c('spearman','pearson','sparcc'), format = c('ComputeRes
 #' @return ComputeResult object
 #' @import veupathUtils
 #' @export
-setMethod("selfCorrelation", signature("SampleMetadata"), 
+setMethod(selfCorrelationGeneric, signature("SampleMetadata"), 
 function(data, method = c('spearman','pearson','sparcc'), format = c('ComputeResult', 'data.table'), verbose = c(TRUE, FALSE)) {
 
   format <- veupathUtils::matchArg(format)
@@ -122,7 +122,7 @@ function(data, method = c('spearman','pearson','sparcc'), format = c('ComputeRes
 #' @param stdDevThreshold numeric threshold to filter features by standard deviation across samples
 #' @return ComputeResult object
 #' @export
-setMethod("correlation", signature("AbundanceData", "AbundanceData"), 
+setMethod(correlationGeneric, signature("AbundanceData", "AbundanceData"), 
 function(data1, data2, method = c('spearman','pearson'), format = c('ComputeResult', 'data.table'), verbose = c(TRUE, FALSE), proportionNonZeroThreshold = 0.5, varianceThreshold = 0, stdDevThreshold = 0) {
   
   format <- veupathUtils::matchArg(format)