Fixed test-coverage CI failure when running pandaPy

.github/workflows/bioc-check.yml

@@ -61,7 +61,25 @@ jobs:
             libglpk-dev
 
       # Install dependencies using r-lib/actions (uses pak, handles R-devel well)
+      - name: Install dependencies on R devel, ignoring GOstats
+        if: matrix.r-version == 'devel'
+        run: |
+          install.packages("pak", repos = "https://cloud.r-project.org")
+          Sys.setenv(PKG_USE_BIOCONDUCTOR = "true")
+
+          pak::pkg_install(
+            c(
+              "deps::.",
+              "GOstats=?ignore",
+              "any::BiocCheck",
+              "any::rcmdcheck"
+            ),
+            dependencies = TRUE
+          )
+        shell: Rscript {0}
+
       - name: Install dependencies
+        if: matrix.r-version != 'devel'
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
@@ -163,10 +181,24 @@ jobs:
         with:
           extra-packages: |
             any::covr
+            any::reticulate
 
       - name: Test coverage
         run: |
           covr::codecov(quiet = FALSE)
         shell: Rscript {0}
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat failure logs
+        if: failure()
+        run: |
+          echo "=== Searching for Rout.fail files ==="
+          sudo find /tmp "$GITHUB_WORKSPACE" -name "*.Rout.fail" -print || true
+
+          echo "=== Printing Rout.fail files ==="
+          sudo find /tmp "$GITHUB_WORKSPACE" -name "*.Rout.fail" -exec sh -c '
+
+            echo "----- $1 -----"
+            cat "$1"
+          ' sh {} \;

R/PANDA.R

@@ -134,6 +134,21 @@ pandaPy <- function(expr_file, motif_file=NULL, ppi_file=NULL, computing="cpu",
 
   # source the pypanda from github raw website.
   pandapath <- system.file("extdata", "panda.py", package = "netZooR", mustWork = TRUE)
+  message("pandapath: ", pandapath)
+  message("exists: ", file.exists(pandapath))
+  message("python: ", reticulate::py_config()$python)
+  tryCatch(
+    reticulate::source_python(pandapath, convert = TRUE),
+    error = function(e) {
+      cat("source_python failed:")
+      cat(conditionMessage(e))
+
+      cat("reticulate Python error:")
+      cat(reticulate::py_last_error())
+      flush.console()
+      stop(e)
+    }
+  )
   reticulate::source_python(pandapath,convert = TRUE)
 
   # invoke Python script to create a Panda object