Code analysis not working after MacOS 12.5 update

After upgrading my Mac to Catalina 12.5 the code analysis no longer seems to work. The top-right corner of the IDE says either 'paused' or 'analyzing' when I click the pause message, but nothing seems to happen. I checked to see if maybe this was a MacOS permission issue, but PHPStorm does have read-write permissions on my project folders.

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There are some severe issues in my log file, not sure if they are related:

2022-07-31 21:18:24,581 [ 769958] SEVERE - #c.i.p.i.s.PsiFileImpl - readOrBuilt roots = {PhpFileStubImpl Language: PHP}; , stubBindingRoot = PhpFileImpl, languages = [PHP, HTML], fileTypes = [PHP, HTML], files = [PhpFileImpl, HtmlFileImpl], roots = [(php.FILE, Language: PHP -> PhpFileImpl), (FILE, Language: HTML -> HtmlFileImpl)], indexingInfo = indexing timestamp = 1650294859702, binary = false, byte size = 0, char size = 0, isTooLarge = false
java.lang.Throwable: readOrBuilt roots = {PhpFileStubImpl Language: PHP}; , stubBindingRoot = PhpFileImpl, languages = [PHP, HTML], fileTypes = [PHP, HTML], files = [PhpFileImpl, HtmlFileImpl], roots = [(php.FILE, Language: PHP -> PhpFileImpl), (FILE, Language: HTML -> HtmlFileImpl)], indexingInfo = indexing timestamp = 1650294859702, binary = false, byte size = 0, char size = 0, isTooLarge = false
    at com.intellij.openapi.diagnostic.Logger.error(Logger.java:182)
    at com.intellij.psi.impl.source.PsiFileImpl.getStubTree(PsiFileImpl.java:653)
    at com.intellij.psi.impl.source.PsiFileImpl.getGreenStubTree(PsiFileImpl.java:956)
    at com.intellij.psi.impl.source.PsiFileImpl.getGreenStub(PsiFileImpl.java:611)
    at com.jetbrains.php.lang.psi.PhpPsiUtil.findClasses(PhpPsiUtil.java:516)
    at com.jetbrains.php.lang.psi.PhpPsiUtil.findAllClasses(PhpPsiUtil.java:552)
    at com.jetbrains.php.projectView.PhpFileNode.getClasses(PhpFileNode.java:35)
    at com.jetbrains.php.projectView.PhpFileNode.isDeprecated(PhpFileNode.java:60)
    at com.intellij.ide.projectView.impl.nodes.AbstractPsiBasedNode.lambda$doUpdate$1(AbstractPsiBasedNode.java:165)
    at com.intellij.openapi.application.impl.ApplicationImpl.runReadAction(ApplicationImpl.java:907)
    at com.intellij.ide.projectView.impl.nodes.AbstractPsiBasedNode.doUpdate(AbstractPsiBasedNode.java:148)
    at com.intellij.ide.projectView.impl.nodes.AbstractPsiBasedNode.lambda$update$0(AbstractPsiBasedNode.java:144)
    at com.intellij.util.AstLoadingFilter.lambda$toComputable$2(AstLoadingFilter.java:172)
    at com.intellij.util.AstLoadingFilter.disallowTreeLoading(AstLoadingFilter.java:130)
    at com.intellij.util.AstLoadingFilter.disallowTreeLoading(AstLoadingFilter.java:119)
    at com.intellij.util.AstLoadingFilter.disallowTreeLoading(AstLoadingFilter.java:109)
    at com.intellij.ide.projectView.impl.nodes.AbstractPsiBasedNode.update(AbstractPsiBasedNode.java:144)
    at com.intellij.ide.util.treeView.PresentableNodeDescriptor.getUpdatedPresentation(PresentableNodeDescriptor.java:78)
    at com.intellij.ide.util.treeView.PresentableNodeDescriptor.update(PresentableNodeDescriptor.java:30)
    at com.intellij.ui.tree.StructureTreeModel$Node.update(StructureTreeModel.java:458)
    at com.intellij.ui.tree.StructureTreeModel$Node.<init>(StructureTreeModel.java:439)
    at com.intellij.ui.tree.StructureTreeModel$Node.<init>(StructureTreeModel.java:432)
    at com.intellij.ui.tree.StructureTreeModel.getValidChildren(StructureTreeModel.java:390)
    at com.intellij.ui.tree.StructureTreeModel.validateChildren(StructureTreeModel.java:299)
    at com.intellij.ui.tree.StructureTreeModel$Node.isModelLeaf(StructureTreeModel.java:557)
    at com.intellij.ui.tree.StructureTreeModel.isLeaf(StructureTreeModel.java:335)
    at com.intellij.ui.tree.LeafState.get(LeafState.java:64)
    at com.intellij.ui.tree.AsyncTreeModel$CmdGetChildren.load(AsyncTreeModel.java:574)
    at com.intellij.ui.tree.AsyncTreeModel$CmdGetChildren.getNode(AsyncTreeModel.java:547)
    at com.intellij.ui.tree.AsyncTreeModel$Command.get(AsyncTreeModel.java:440)
    at com.intellij.ui.tree.AsyncTreeModel$Command.get(AsyncTreeModel.java:406)
    at com.intellij.util.concurrency.Invoker$Task.run(Invoker.java:314)
    at com.intellij.openapi.application.impl.ApplicationImpl.tryRunReadAction(ApplicationImpl.java:1152)
    at com.intellij.openapi.progress.util.ProgressIndicatorUtils.lambda$runInReadActionWithWriteActionPriority$0(ProgressIndicatorUtils.java:75)
    at com.intellij.openapi.progress.util.ProgressIndicatorUtils.runActionAndCancelBeforeWrite(ProgressIndicatorUtils.java:158)
    at com.intellij.openapi.progress.util.ProgressIndicatorUtils.lambda$runWithWriteActionPriority$1(ProgressIndicatorUtils.java:115)
    at com.intellij.openapi.progress.ProgressManager.lambda$runProcess$0(ProgressManager.java:58)
    at com.intellij.openapi.progress.impl.CoreProgressManager.lambda$runProcess$2(CoreProgressManager.java:189)
    at com.intellij.openapi.progress.impl.CoreProgressManager.lambda$executeProcessUnderProgress$12(CoreProgressManager.java:608)
    at com.intellij.openapi.progress.impl.CoreProgressManager.registerIndicatorAndRun(CoreProgressManager.java:683)
    at com.intellij.openapi.progress.impl.CoreProgressManager.computeUnderProgress(CoreProgressManager.java:639)
    at com.intellij.openapi.progress.impl.CoreProgressManager.executeProcessUnderProgress(CoreProgressManager.java:607)
    at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeProcessUnderProgress(ProgressManagerImpl.java:60)
    at com.intellij.openapi.progress.impl.CoreProgressManager.runProcess(CoreProgressManager.java:176)
    at com.intellij.openapi.progress.ProgressManager.runProcess(ProgressManager.java:58)
    at com.intellij.openapi.progress.util.ProgressIndicatorUtils.runWithWriteActionPriority(ProgressIndicatorUtils.java:112)
    at com.intellij.openapi.progress.util.ProgressIndicatorUtils.runInReadActionWithWriteActionPriority(ProgressIndicatorUtils.java:75)
    at com.intellij.util.concurrency.Invoker.invokeSafely(Invoker.java:203)
    at com.intellij.util.concurrency.Invoker.lambda$offerSafely$0(Invoker.java:181)
    at com.intellij.util.concurrency.Invoker$Background.lambda$offer$0(Invoker.java:481)
    at com.intellij.util.concurrency.BoundedTaskExecutor.doRun(BoundedTaskExecutor.java:241)
    at com.intellij.util.concurrency.BoundedTaskExecutor.access$200(BoundedTaskExecutor.java:31)
    at com.intellij.util.concurrency.BoundedTaskExecutor$1.execute(BoundedTaskExecutor.java:214)
    at com.intellij.util.ConcurrencyUtil.runUnderThreadName(ConcurrencyUtil.java:212)
    at com.intellij.util.concurrency.BoundedTaskExecutor$1.run(BoundedTaskExecutor.java:203)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    at java.base/java.util.concurrent.Executors$PrivilegedThreadFactory$1$1.run(Executors.java:668)
    at java.base/java.util.concurrent.Executors$PrivilegedThreadFactory$1$1.run(Executors.java:665)
    at java.base/java.security.AccessController.doPrivileged(Native Method)
    at java.base/java.util.concurrent.Executors$PrivilegedThreadFactory$1.run(Executors.java:665)
    at java.base/java.lang.Thread.run(Thread.java:829)
2022-07-31 21:18:24,582 [ 769959] SEVERE - #c.i.p.i.s.PsiFileImpl - PhpStorm 2022.1.4  Build #PS-221.6008.16
2022-07-31 21:18:24,582 [ 769959] SEVERE - #c.i.p.i.s.PsiFileImpl - JDK: 11.0.15; VM: OpenJDK 64-Bit Server VM; Vendor: JetBrains s.r.o.
2022-07-31 21:18:24,582 [ 769959] SEVERE - #c.i.p.i.s.PsiFileImpl - OS: Mac OS X
2022-07-31 21:18:24,585 [ 769962] SEVERE - #c.i.p.i.s.PsiFileImpl - readOrBuilt roots = {PhpFileStubImpl Language: PHP}; , stubBindingRoot = PhpFileImpl, languages = [PHP, HTML], fileTypes = [PHP, HTML], files = [PhpFileImpl, HtmlFileImpl], roots = [(php.FILE, Language: PHP -> PhpFileImpl), (FILE, Language: HTML -> HtmlFileImpl)], indexingInfo = indexing timestamp = 1650294859702, binary = false, byte size = 0, char size = 0, isTooLarge = false
java.lang.Throwable: readOrBuilt roots = {PhpFileStubImpl Language: PHP}; , stubBindingRoot = PhpFileImpl, languages = [PHP, HTML], fileTypes = [PHP, HTML], files = [PhpFileImpl, HtmlFileImpl], roots = [(php.FILE, Language: PHP -> PhpFileImpl), (FILE, Language: HTML -> HtmlFileImpl)], indexingInfo = indexing timestamp = 1650294859702, binary = false, byte size = 0, char size = 0, isTooLarge = false

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It may sound as a generic suggestion but have you tried to Invalidate caches already?https://www.jetbrains.com/help/phpstorm/invalidate-caches.html

 

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Thanks for the tip Vasily,

The code analysis issue seems to be in a single project. And invalidating the caches has not reolved the problem. The project folders take forever to fold open when I click them in the prject browser. Is there any additional analysis I can run to further pinpoint the problem?

 

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It would be great if you could collect & share the log files pack (Help > Collect Logs) and contact the support team.
Or you may upload the log files pack to the JetBrains Upload service and let me know the upload id:
https://uploads.jetbrains.com/

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Thanks! The upload id is 2022_08_01_7g5641HZauY1CiErihrUnC

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Thank you for sharing the log files pack. At the very first glance, your scenario resembles the following issue:
https://youtrack.jetbrains.com/issue/WI-59893

However, the issue seems to fixed some versions ago, so it is surprising to see it again.
By the way, we have finally released PhpStorm 2022.2 yesterday, would it be possible to install it and check if this behaviour is still reproducible there?

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Yes the behaviour is still the same. I saw the latest PHPStorm update come available yesterday and hoped this would fix the issue. And the linked issue does seem very similar indeed.

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Thank you for trying the new version.

Would it be possible to share the affected project privately? I would suggest submitting a support request, so we may proceed from there.

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Yes I think that's possible, I will submit the support request and share the details with you

 

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