More debugging efforts

Author: bbimber

jbrowse/package-lock.json

@@ -11,7 +11,7 @@
     "build-prod": "npm run clean && cross-env NODE_ENV=production PROD_SOURCE_MAP=source-map webpack --config ./config/prod.config.js --progress --profile",
     "clean": "rimraf resources/web/gen && rimraf resources/web/jbrowse/gen && rimraf resources/views/gen",
     "prepareCli": "rimraf ./buildCli && rimraf ./resources/external/jb-cli && npm install @jbrowse/cli@1.7.4 --prefix ./buildCli",
-    "jb-pkg": "npm run prepareCli && npx pkg --outdir=./resources/external/jb-cli ./buildCli/node_modules/@jbrowse/cli && rimraf ./buildCli"
+    "jb-pkg": "npm run prepareCli && npx pkg --debug --outdir=./resources/external/jb-cli ./buildCli/node_modules/@jbrowse/cli && rimraf ./buildCli"
   },
   "dependencies": {
     "@gmod/vcf": "^6.0.9",
@@ -24,7 +24,7 @@
     "@labkey/api": "^1.39.0",
     "@labkey/components": "^6.32.2",
     "@mui/x-data-grid": "^7.28.1",
-    "@yao-pkg/pkg": "^6.3.2",
+    "@yao-pkg/pkg": "^6.6.0",
     "assert": "^2.1.0",
     "browserify-zlib": "^0.2.0",
     "buffer": "^6.0.3",

jbrowse/package.json

@@ -243,33 +243,34 @@ public void testJBrowseCli() throws Exception
             wrapper.setLogPath(true);
             wrapper.setThrowNonZeroExits(false);
 
+            File node = AbstractCommandWrapper.resolveFileInPath("node", null, false);
+            if (node == null)
+            {
+                _log.info("Unable to find node in PATH, trying node.exe");
+                node = AbstractCommandWrapper.resolveFileInPath("node.exe", null, false);
+                if (node == null)
+                {
+                    _log.info("Unable to find node.exe in PATH");
+                }
+            }
+            _log.info("node executable location: " + node);
+
             String output = wrapper.executeWithOutput(Arrays.asList(exe.getPath(), "help"));
             if (wrapper.getLastReturnCode() != 0)
             {
                 _log.error("Non-zero exit from testJBrowseCli: " + wrapper.getLastReturnCode());
                 wrapper.getCommandsExecuted().forEach(_log::error);
                 _log.error("NODE_PATH: " + System.getenv("NODE_PATH"));
 
-                File node = AbstractCommandWrapper.resolveFileInPath("node", null, false);
-                if (node == null)
-                {
-                    _log.info("Unable to find node in PATH, trying node.exe");
-                    node = AbstractCommandWrapper.resolveFileInPath("node.exe", null, false);
-                    if (node == null)
-                    {
-                        _log.info("Unable to find node.exe in PATH");
-                    }
-                }
-
-                _log.info("node executable location: " + node);
-
                 _log.error("output: ");
                 _log.error(output);
 
                 // Repeat without output going direct to the server log:
                 try
                 {
-                    _log.info("Retrying without all output direct to the system log:");
+                    // NOTE: this is only useful if "npx pkg --debug" is used when building the executables
+                    _log.info("Retrying without all output direct to the system log and DEBUG_PKG=1:");
+                    wrapper.addToEnvironment("DEBUG_PKG", "1");
                     wrapper.execute(Arrays.asList(exe.getPath(), "help"));
                 }
                 catch (Exception e)