Merge pull request #236 from marouenbg/fix-crane-alpaca

update crane
netZoo · Jan 30, 2022 · 7a9c0d0 · 7a9c0d0
2 parents baa4bee + 14e87e9
commit 7a9c0d0
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Showing 2 changed files with 11 additions and 4 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -50,7 +50,16 @@ jobs:
             install.packages('reticulate', repos = "http://cran.us.r-project.org")
             library('reticulate')
         shell: Rscript {0}
-      - name: Install reticulate 2
+      - name: Install reticulate 2-1
+        if: matrix.os == 'macos-latest'
+        run: |
+            library('reticulate')
+            py_config()
+            use_python("/usr/local/bin/python3")
+            virtualenv_create("r-reticulate")
+        shell: sudo -E Rscript {0}
+      - name: Install reticulate 2-2
+        if: matrix.os == 'ubuntu-latest'
         run: |
             library('reticulate')
             py_config()
@@ -73,14 +82,12 @@ jobs:
       - name: Check
         run: |
             library('reticulate')
-            use_condaenv("r-reticulate")
             py_config()
             rcmdcheck::rcmdcheck(args = c("--no-manual","--ignore-vignettes"), error_on = "error", build_args="--no-build-vignettes")
         shell: sudo -E Rscript {0}
       - name: Report coverage
         run: |
             library('reticulate')
-            use_condaenv("r-reticulate")
             py_config()            
             covr::codecov()
         shell: sudo -E Rscript {0}

diff --git a/R/CRANE.R b/R/CRANE.R
@@ -81,7 +81,7 @@ alpacaCrane = function(input,alp,alpha=0.1,beta=0,iteration=30,isParallel=F){
     if (i %% round(iteration/5)==0){
       print(paste("Computing Differential Score",(i/iteration)*100,"%"))
     }
-    dwbm = computeDWBMmat.mscale(pos.table,ctrl.memb[V(pos.graph)$name])
+    dwbm = alpacaComputeDWBMmatmScale(pos.table,ctrl.memb[V(pos.graph)$name])
 
     miss_tf=setdiff(tfcheck,rownames(dwbm))
     miss_g=setdiff(gcheck,colnames(dwbm))