update GHA

mritchielab · Nov 25, 2024 · 626135b · 626135b
1 parent efc10e4
commit 626135b
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Showing 2 changed files with 21 additions and 14 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -80,6 +80,10 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@v3
 
+      - name: Temporary workaround for macOS-latest
+        if: matrix.config.os == 'macOS-latest'
+        run: brew uninstall pkg-config@0.29.2
+
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
@@ -129,6 +133,8 @@ jobs:
           brew install libxml2
           echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
 
+          brew install libjpeg
+
           ## Required to install magick as noted at
           ## /~https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
           brew install imagemagick@6
@@ -142,8 +148,12 @@ jobs:
           ## Required for tcltk
           brew install xquartz --cask
 
-          brew install minimap2
-          brew install samtools 
+          ## Temporary fix for libraries not found
+          ## https://pat-s.me/transitioning-from-x86-to-arm64-on-macos-experiences-of-an-r-user/
+          sudo ln -s /opt/homebrew/opt/* /usr/local/opt/
+          mkdir ~/.R
+          echo 'CFLAGS=-I/opt/homebrew/include -I/opt/homebrew/opt/jpeg/include' > ~/.R/Makevars
+          echo 'LDFLAGS+=-L/opt/homebrew/opt/jpeg/lib' >> ~/.R/Makevars
 
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
@@ -182,6 +192,13 @@ jobs:
         continue-on-error: true
         shell: Rscript {0}
 
+        # - name: Debug with SSH
+        #   if: matrix.config.os == 'macOS-latest'
+        #   uses: owenthereal/action-upterm@v1
+        #   with:
+        #     limit-access-to-actor: true
+        #     limit-access-to-users: ChangqingW
+
       - name: Install dependencies pass 2
         run: |
           ## Pass #2 at installing dependencies

diff --git a/src/main-functions/pileup_readid.cpp b/src/main-functions/pileup_readid.cpp
@@ -38,9 +38,7 @@ bool within_edit_dist(const std::string &s1, const std::string &s2) {
   for (std::size_t j = 1; j < len2; ++j)
     dist_holder[j] = j; //[0][j];
   for (std::size_t i = 1; i < len1; ++i)
-    dist_holder[i * len2] = 0; //[i][0];
-
-  unsigned int best = len2;
+    dist_holder[i * len2] = i; //[i][0];
 
   // loop over the distance matrix elements and calculate running distance
   for (std::size_t j = 1; j < len2; ++j) {
@@ -58,20 +56,12 @@ bool within_edit_dist(const std::string &s1, const std::string &s2) {
 
       if (min_value <= MAX_EDIT_DISTANCE)
         any_below_threshold = true;
-      if (j == (len2 - 1) && min_value < best) {
-        // if this is the last row in j
-        // check if this is the best running score
-        best = min_value;
-        if (best <= MAX_EDIT_DISTANCE) {
-          return true;
-        }
-      }
     }
     if (!any_below_threshold) { // early exit to save time.
       return false;
     }
   }
-  return best <= MAX_EDIT_DISTANCE;
+  return dist_holder.back() <= MAX_EDIT_DISTANCE;
 }
 
 // barcode -> UMI -> array of allele counts (A, T, C, G, -)