fix some build issues

microbiomeDB · Feb 29, 2024 · 248ce01 · 248ce01
1 parent afca326
commit 248ce01
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -12,14 +12,15 @@ Authors@R:
            email = "[email protected]"))
 Imports:
     ape,
+    boot,
     data.table,
     DESeq2,
     Hmisc,
     jsonlite,
     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
@@ -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)