From dc7f7b8a8ca79e9fc9accb69d53bb53621f2feb3 Mon Sep 17 00:00:00 2001
From: ned-procogia <91500603+ned-procogia@users.noreply.github.com>
Date: Wed, 19 Jan 2022 14:22:52 -0800
Subject: [PATCH 1/2] bug fix - parallel error handling

catch parallel processes which fail and repeat - append to results
---
 R/NBthDE.R | 44 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/R/NBthDE.R b/R/NBthDE.R
index b9f6c1e..b429afd 100644
--- a/R/NBthDE.R
+++ b/R/NBthDE.R
@@ -350,6 +350,27 @@ fitNBthDE_funct =     function(form, annot,
             preci1, threshold_mean * probenum[features_high[start_index:end_index]], preci2,
             startpara, sizescalebythreshold, (iter == iterations))
         }, mc.cores = n_parallel)
+        bad = sapply(result,is.null)
+        to_retry = 1:n_parallel
+        to_retry = to_retry[bad]
+        print("need to retry")
+        print(to_retry)
+        if(sum(bad)>0){
+          more_results =  mclapply(to_retry, function(i) {
+            my_len = length(features_all)
+            start_index = (round(((i-1)*my_len/n_parallel))+1)
+            end_index = round(i*my_len/n_parallel)
+            NBthDE_paraOptall(
+              t(object[features_all, ])[,start_index:end_index], X, sizefact_BG, sizefact,
+              preci1, threshold_mean * probenum[features_all[start_index:end_index]], preci2,
+              startpara, sizescalebythreshold, (iter == iterations))
+          }, mc.cores = sum(bad)) 
+          for(i in 1:length(to_retry)){
+            print("changed entry")
+            print(to_retry[i])
+            result[to_retry[i]] = more_results[i]
+          }
+        }
         new_result= list('par'=matrix(,nrow=NROW(result[[1]]$par),ncol=0),
                          'hes',
                          'conv'=matrix(,nrow=0,ncol=1))
@@ -386,6 +407,27 @@ fitNBthDE_funct =     function(form, annot,
             preci1, threshold_mean * probenum[features_all[start_index:end_index]], preci2,
             startpara, sizescalebythreshold, (iter == iterations))
         }, mc.cores = n_parallel)
+        bad = sapply(result,is.null)
+        to_retry = 1:n_parallel
+        to_retry = to_retry[bad]
+        if(sum(bad)>0){
+          print("need to retry")
+          print(to_retry)
+          more_results =  mclapply(to_retry, function(i) {
+            my_len = length(features_all)
+            start_index = (round(((i-1)*my_len/n_parallel))+1)
+            end_index = round(i*my_len/n_parallel)
+            NBthDE_paraOptall(
+              t(object[features_all, ])[,start_index:end_index], X, sizefact_BG, sizefact,
+              preci1, threshold_mean * probenum[features_all[start_index:end_index]], preci2,
+              startpara, sizescalebythreshold, (iter == iterations))
+          }, mc.cores = sum(bad)) 
+          for(i in 1:length(to_retry)){
+            print("changed entry")
+            print(to_retry[i])
+            result[to_retry[i]] = more_results[i]
+          }
+        }
         new_result= list('par'=matrix(,nrow=NROW(result[[1]]$par),ncol=0),
                          'hes',
                          'conv'=matrix(,nrow=0,ncol=1))
@@ -397,6 +439,8 @@ fitNBthDE_funct =     function(form, annot,
         result=new_result
       }
       para <- result$par
+      print(length(para))
+      print(length(features_all))
       colnames(para) <- features_all
       conv <- result$conv
       names(conv) <- features_all

From 7006145ed6db5361a0638bd9badce3a68eb403c5 Mon Sep 17 00:00:00 2001
From: ned-procogia <91500603+ned-procogia@users.noreply.github.com>
Date: Wed, 19 Jan 2022 15:11:14 -0800
Subject: [PATCH 2/2] bug fix - parallel processing

---
 R/NBthDE.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/NBthDE.R b/R/NBthDE.R
index b429afd..e42bd54 100644
--- a/R/NBthDE.R
+++ b/R/NBthDE.R
@@ -353,9 +353,9 @@ fitNBthDE_funct =     function(form, annot,
         bad = sapply(result,is.null)
         to_retry = 1:n_parallel
         to_retry = to_retry[bad]
-        print("need to retry")
-        print(to_retry)
         if(sum(bad)>0){
+          print("need to retry")
+          print(to_retry)
           more_results =  mclapply(to_retry, function(i) {
             my_len = length(features_all)
             start_index = (round(((i-1)*my_len/n_parallel))+1)
@@ -402,7 +402,7 @@ fitNBthDE_funct =     function(form, annot,
           my_len = length(features_all)
           start_index = (round(((i-1)*my_len/n_parallel))+1)
           end_index = round(i*my_len/n_parallel)
-          NBthDE_paraOptall(
+          GeoDiff:::NBthDE_paraOptall(
             t(object[features_all, ])[,start_index:end_index], X, sizefact_BG, sizefact,
             preci1, threshold_mean * probenum[features_all[start_index:end_index]], preci2,
             startpara, sizescalebythreshold, (iter == iterations))
@@ -417,7 +417,7 @@ fitNBthDE_funct =     function(form, annot,
             my_len = length(features_all)
             start_index = (round(((i-1)*my_len/n_parallel))+1)
             end_index = round(i*my_len/n_parallel)
-            NBthDE_paraOptall(
+            GeoDiff:::NBthDE_paraOptall(
               t(object[features_all, ])[,start_index:end_index], X, sizefact_BG, sizefact,
               preci1, threshold_mean * probenum[features_all[start_index:end_index]], preci2,
               startpara, sizescalebythreshold, (iter == iterations))