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Gradle plugin 3.5.0: "Failed to transform artifact", "Execution failed for JetifyTransform"

We updated Android Gradle plugin from 3.4.2 to 3.5.0 (and Gradle from 5.1.1 to 5.4.1).
After that, the build started failing in a few submodules. Trying to assemble any build variant yields this (same error on the command line and in Android Studio):
> Failed to transform artifact 'bottom-navigation.aar (project :bottom-navigation)' to match attributes {artifactType=jar}.
> Execution failed for JetifyTransform: <project_root>/bottom-navigation/build/outputs/aar/bottom-navigation-release.aar.
> Failed to transform '<project_root>/bottom-navigation/build/outputs/aar/bottom-navigation-release.aar' using Jetifier.
Reason: Cannot open a library at 'FileMapping(from=<project_root>/bottom-navigation/build/outputs/aar/bottom-navigation-release.aar, to=<project_root>/bottom-navigation/build/.transforms/9b2af95a5f0e0055110660c22ff05ab5/jetified-bottom-navigation-release.aar)'. (Run with --stacktrace for more details.)
Any ideas how to fix this?
What I've tried
"Invalidate caches" in AS and also clearing all Gradle caches in ~/.gradle/caches as suggested in this answer
All the advice in this somewhat similar question
I checked that the problematic modules use apply plugin:
'com.android.library' (instead of com.android.application)
I tried updating appcompat dependency to androidx.appcompat:appcompat:1.1.0 in affected modules and also removing that dependency
Update
It starts to look like something is wrong in Gradle plugin 3.5.0; builds behave erratically for me locally and on our CI machine.
For example, clean builds are failing: ./gradlew clean assembleBetaRelease fails while ./gradlew assembleBetaRelease works!
Also, sometimes I get AAPT: error: attribute ... not found instead of the above Failed to transform artifact error.
Reverting to Gradle plugin 3.4.2, all these problems disappear.
Edit Oct 2019: Still seeing this weird behaviour with Gradle plugin 3.5.1. Edit Nov 2019 And 3.5.2. Upgrading to Gradle 5.6 didn't help either.

A bit weird, but I got it working again. Apparently just a temporary glitch in Android Gradle plugin related to caching.
This answer helped me:
The simple way to solve this is to switch between your build variants. This refreshes the cached copies and resolves the issue.
I couldn't do that in Android Studio since the project sync was failing, but on the command line I tried another variant (in my case ./gradlew assembleBetaDebug having used ./gradlew assembleBetaRelease earlier). The build passed, and after that it worked for all all other variants too, and Gradle sync in Android Studio started working as well!
Edit: actually this is not completely solved; see updated question.
Update 12/2019: bundle* commands work fine, it's only assemble* that fails—still failing with Android Gradle plugin 3.5.3. Building in Android Studio works fine. Obviously this is not a common issue, and I don't know what exactly in the particular project I'm working on is causing this.
Update 04/2020: now with Android Gradle plugin 3.6.2 (and Gradle 5.6.4) builds work for me locally and I was able to update the project. On CircleCI, the build still occasionally fails with "Failed to transform artifact" but re-running fixes it. Go figure 🤔

NoClassDefFoundError when running unit test with Gradle task

I have a project using dynamic feature module, and I want to run my unit test in feature module via gradle task (for my CI purpose):
./gradlew :feature_product:test
But it always gives me NoClassDefFoundError for tests that have dependencies on classes from the base module:
com.example.android.feature.product.ProductViewTest > on vote change to negative FAILED
java.lang.NoClassDefFoundError: app.BaseView
ProductView class from the feature module extends BaseView from the base module.
Oddly, it succeeds when run in Android Studio, it works fine.
Then I notice something different in the logs, when I run via command line and when I run Android Studio. The first line in the Android Studio is generateDebugSources, something which absent when I run ./gradlew test
Executing tasks: [:lib_ui:generateDebugSources, ...]
How do I fix this? Does Android Studio has different command with the provided command ./gradlew test when I press Ctrl+Shift+R ?

After searching further about this issue, I found it also being reported in the android-test and app-bundle-samples projects and there is also an issue in the issue tracker.
It turns out this issue fixed in the Android Gradle Plugin 4.1.0 as per comment in the issue tracker.
If you don't want to update AGP to 4.1.0 which is still in alpha, adding this to the feature module's build.gradle fixed the issue for me, as per this comment:
testRuntimeOnly(files("$projectDir/../b_app/build/intermediates/app_classes/debug/classes.jar"))

If it is a missing task that you believe is necessary then calling it first like below should do the trick:
./gradlew :lib_ui:generateDebugSources :feature_product:test
I would even go full on and assemble the dependencies if necessary though that might take more time:
./gradlew :lib_ui:assemble :feature_product:assemble :feature_product:test

Gradle: No tests found

When I am trying to run Android tests by executing:
./gradlew connectedDebugAndroidTest
The following error occurs:
com.android.builder.testing.ConnectedDevice > No tests found.[devicename] FAILED
No tests found. This usually means that your test classes are not in the form that your test runner expects (e.g. don't inherit from TestCase or lack #Test annotations).
:connectedDebugAndroidTest FAILED
FAILURE: Build failed with an exception.
I have not made any changes to build.gradle or gradle-wrapper.properties files.
The issue can't be solved by updating everything to the latest version (gradle, android plugin, build tools, etc.)
All tests were previously successful. What could cause this mystic regression? Thanks.

One possible reason for this error message is that you get a crash in the app early in the test Runner. In such cases the exception stack will be in logcat but not in the gradle output.

I had the issue, try upgrading the test runner. Upgrading it to 0.5 from 0.4.x solved it. Ensure you have these lines in your build.gradle:
androidTestCompile "junit:junit:4.12"
androidTestCompile "com.android.support.test:runner:0.5"

I faced this exact issue today. Please do feel free to use all the other worthy solutions as mentioned above but what specifically worked for me was to delete the ".gradle" folder (found under the project panel on the left in Android Studio) entirely, followed by a clean build. A simple clean build didn't work for me.

This can happen if the tests are placed in the test or androidTest directory without a package. The path should be something like /src/androidTest/kotlin/yourPackageName/yourTestClass.

You can check if individually, all tests pass. Could be some test(s) is(are) failing. Had a similar issue and that was my case

I solved this by deleting androidTests folders from unneeded modules - /common and /data in my case.

"Could not initialize class" error running lint target from gradle

I'm working on an Android project with two projects inside it. When trying to run a build with gradlew (./gradlew build), I see the following error:
Execution failed for task ':example:lint'.
Could not initialize class
com.android.build.gradle.tasks.Lint$LintGradleIssueRegistry
With stacktrace enabled, this is listed as a java.lang.NoClassDefFoundError.
Oddly, the first time I ran this (which downloaded dependencies), the build failed with a different error:
Execution failed for task ':example:lint'.
lombok/ast/Node
The gradle wrapper that Android SDK created for the project is using Gradle 2.8.
Could this be a configuration issue with the project or my dev machine? I'm trying to avoid using the Android SDK lint tool as this complains about the projects using Gradle (and I hear it may miss some parts of these projects).

Turned out this was a configuration issue in our build.gradle. The following line had been added for testing and never removed:
configurations.classpath.exclude group: 'com.android.tools.external.lombok'
As such, the classes needed for linting were missing.
The following discussion pointed us in the right direction, in case it's useful to anyone else:
https://github.com/evant/gradle-retrolambda/issues/96

Gradle Android task crashing with unclear error

I am trying to run a Gradle Android task generated by libGDX utility (the desktop task runs fine) in IntelliJ IDEA, but I'm only getting this nonspecific error message. What is the issue, or where are the logs, or how to enabled logs?
Information:Gradle: Executing tasks: [:core:assemble, :android:assembleDebug]
Information:24. 10. 2015 16:58 - Compilation completed with 1 error and 0 warnings in 9s 415ms
Error:Gradle: Execution failed for task ':android:proguardDebug'.
> java.io.IOException: Please correct the above warnings first.
PS: Not sure if it is relevant, but I have modified build files and ProGuard file to support Scala as described there.

I did not find a way of getting any useful logs from IntelliJ IDEA. I solved the problem by running Gradle from console.
gradlew assemble --stacktrace --info
Problem was Gradle could not find tools.jar. Adding system environment variable JAVA_HOME pointing to Java SDK directory fixed the issue.