Fix samr error options

DESCRIPTION

@@ -4,7 +4,7 @@ Version: 2.6.0
 Authors@R: person("Jakob", "Russel", email = "[email protected]", role = c("aut", "cre"))
 Description: What the title says.
 Depends: R (>= 3.2.5)
-Imports: foreach, doParallel, doSNOW, snow, MASS, pROC, ggplot2, cowplot, lme4, nlme, stats, methods, statmod, pscl, samr, minqa, nloptr, venneuler 
+Imports: foreach, doParallel, doSNOW, snow, MASS, pROC, ggplot2, cowplot, lme4, nlme, stats, methods, utils, statmod, pscl, samr, minqa, nloptr, venneuler 
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true

R/DA.sam.R

@@ -10,8 +10,6 @@
 #' @export
 DA.sam <- function(data, predictor, paired = NULL, fdr.output = 0.05, allResults = FALSE, ...){
 
-  library(samr, quietly = TRUE)
-
   # Extract from phyloseq
   if(class(data) == "phyloseq"){
     if(length(predictor) > 1 | length(paired) > 1) stop("When data is a phyloseq object predictor and paired should only contain the name of the variables in sample_data")
@@ -29,21 +27,21 @@ DA.sam <- function(data, predictor, paired = NULL, fdr.output = 0.05, allResults
 
   if(is.numeric(predictor)){
     # Quantitative
-    res <- SAMseq(count_table, predictor, resp.type = "Quantitative", genenames = rownames(count_table), fdr.output = fdr.output, ...)
+    res <- samr::SAMseq(count_table, predictor, resp.type = "Quantitative", genenames = rownames(count_table), fdr.output = fdr.output, ...)
   } else {
     # Categorical
     predictor <- as.numeric(as.factor(predictor))
 
     if(length(levels(as.factor(predictor))) == 2){
       if(is.null(paired)){
-        res <- SAMseq(count_table, predictor, resp.type = "Two class unpaired", genenames = rownames(count_table), fdr.output = fdr.output)
+        res <- samr::SAMseq(count_table, predictor, resp.type = "Two class unpaired", genenames = rownames(count_table), fdr.output = fdr.output)
       } else {
         predictor[predictor == 2] <- -1
         predictor <- as.numeric(as.factor(paired)) * predictor
-        res <- SAMseq(count_table, predictor, resp.type = "Two class paired", genenames = rownames(count_table), fdr.output = fdr.output, ...)
+        res <- samr::SAMseq(count_table, predictor, resp.type = "Two class paired", genenames = rownames(count_table), fdr.output = fdr.output, ...)
       }
     } else {
-      res <- SAMseq(count_table, predictor, resp.type = "Multiclass", genenames = rownames(count_table), fdr.output = fdr.output, ...)
+      res <- samr::SAMseq(count_table, predictor, resp.type = "Multiclass", genenames = rownames(count_table), fdr.output = fdr.output, ...)
     }
   }
 

R/testDA.R

@@ -110,7 +110,7 @@
 #'  \item run.times - A dataframe with average run times of the different methods
 #' }
 #' 
-#' @import snow doSNOW foreach
+#' @import snow doSNOW foreach utils
 #' @importFrom parallel detectCores
 #' @importFrom pROC roc
 #' @export

R/zzz.R

@@ -0,0 +1,6 @@
+# Fix samr options problem
+
+.onLoad <- function(libname, pkgname){
+  options(error=utils::dump.frames)
+}
+