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Duplicate files during packaging of APK or UnsatisfiedLinkError Android

I have a Android project which uses libraries with interdependencies:
Android Application depends on the following native libraries
module tess-two (containing tesseract and leptonica)
module opencv4android
module mylibrary
mylibrary also depends on tess-two and opencv4android
The following is the build.gradle file of my Android Application:
apply plugin: 'com.android.application'
dependencies {
compile fileTree(include: '*.jar', dir: 'libs')
compile project(':libraries:opencv4android')
compile project(':libraries:tess-two')
compile project(':libraries:mylibrary')
}
android {
compileSdkVersion 19
buildToolsVersion "22.0.1"
defaultConfig {
minSdkVersion 14
targetSdkVersion 19
}
// packagingOptions {
// exclude 'lib/armeabi/liblept.so'
// exclude 'lib/armeabi/libtess.so'
// exclude 'lib/armeabi-v7a/liblept.so'
// exclude 'lib/armeabi-v7a/libtess.so'
// exclude 'lib/mips/liblept.so'
// exclude 'lib/mips/libtess.so'
// exclude 'lib/x86/liblept.so'
// exclude 'lib/x86/libtess.so'
// }
sourceSets {
main {
manifest.srcFile 'AndroidManifest.xml'
java.srcDirs = ['src']
resources.srcDirs = ['src']
aidl.srcDirs = ['src']
renderscript.srcDirs = ['src']
res.srcDirs = ['res']
assets.srcDirs = ['assets']
}
instrumentTest.setRoot('tests')
debug.setRoot('build-types/debug')
release.setRoot('build-types/release')
}
}
A gradle build on this configuration fails with duplicate files during packaging of APK error due to liblept.so and libtess.so being copied twice.
When I uncomment the packaging options I can build successfully, however, I get an UnsatisfiedLinkError at runtime since liblept.so and libtess.so are not contained in the apk at all.
How can I get liblept.so and libtess.so to be included in the apk exactly once?

I think I found the solution, however, I do not quite understand it.
The build.gradle files of both modules mylibrary and tess-two contained a definition for
android.sourceSets.main.jniLibs.srcDirs = ['libs']
Commenting this definition in tess-two resulted in libtess.soand liblept.so being copied to the apk only once.
If someone understands this solution please leave a comment or answer.
Edit:
In the meantime I found a better solution:
I added the following code to my main applications gradle.build file:
packagingOptions { // otherwise libtess.so and liblept.so are copied to apk twice resulting in an error
pickFirst('lib/*/liblept.so')
pickFirst('lib/*/libtess.so')
}

Missing allheaders.h in Android Studio Project

I am following the tutorial from this tesseract tutorial and had everything go smoothly up until my actual running of the Java code. When I try
new TessBaseApi();
It throws the following error
Error Code: 2
Output:
In file included from tesstwo/src/main/jni/com_googlecode_leptonica_android/box.cpp:17:0:
tesstwo/src/main/jni/com_googlecode_leptonica_android/common.h:22:24: fatal error: allheaders.h: No such file or directory
#include <allheaders.h>
^
compilation terminated.
make: ***
I have looked into /jni/com_googlecode_leptonica_android/src/src and find the allheaders.h file there. I have a feeling my paths are wrong, but I've tried almost everything and no avail. What's the issue?

I also ran into this problem with Android Studio. After googling some more i found this issue.
https://code.google.com/p/android/issues/detail?id=74132
Apparently the NDK plugin generates it's own Android.mk file and ignore any existing one, so the recommended way is to run ndk-build to generate the native .so files.
When I used ndk-build in the tess-two directory it compiles just fine and the .so files is created.
How you can include native libraries in gradle and android studio is described in this post: Add pre-built .so files in project using Android Gradle plugin 0.7.3

This works for me: https://coderwall.com/p/eurvaq/tesseract-with-andoird-and-gradle
But do not delete libs directory!
Set compileSdkVersion, buildToolsVersion, minSdkVersion and targetSdkVersio to the same values as in project buil.gradle
I also change classpath 'com.android.tools.build:gradle:0.9.+' to classpath 'com.android.tools.build:gradle:1.0.+'

At some point Android Studio suggests to set
jni.srcDirs = []
leading to following sourceSets in the gradle.build of my tess-two library project
sourceSets.main {
manifest.srcFile 'src/main/AndroidManifest.xml'
java.srcDirs = ['src/main/java']
resources.srcDirs = ['src/main/java']
res.srcDirs = ['src/main/res']
jni.srcDirs = []
jniLibs.srcDirs = ['src/main/libs']
}
With correct src path entered here this actualy works

I'm not sure if it works for you but in my case, here's what I've done:
1. In common.h: change #include <allheaders.h> into #include <src/src/allheaders.h>.
2. In the library project build.gradle: add this
sourceSets{
main {
manifest.srcFile 'AndroidManifest.xml'
jni.srcDirs = []
jniLibs.srcDirs = ['src/main/jniLibs']
resources.srcDirs = ['src']
res.srcDirs = ['res']
}
}

Ppl, After struggling a day.. finally got the solution
In build.gradle of tess-two module add the below code:
sourceSets.main {
manifest.srcFile 'src/main/AndroidManifest.xml'
java.srcDirs = ['src/main/java']
resources.srcDirs = ['src/main/java']
res.srcDirs = ['src/main/res']
jni.srcDirs = []
jniLibs.srcDirs = ['src/main/jniLibs']
}
Main thing is please check manually weather all those file paths specified in above code exists in tess-two module!!
Check in which path "liblept.so" and other ".so" files exist in tess-two library. For me it was inside /tesstwo/src/main/jniLibs/armeabi-v7a . Hence i have made jniLibs.srcDirs = ['src/main/jniLibs'] in above code. Hope it helps !!

Gradle android-library build fails. java.lang.IllegalArgumentException: already added

I'm trying to build my android library project, which contains sub test project. Command to build: gradle clean connectedCheck
After task :dexTest I got error:
UNEXPECTED TOP-LEVEL EXCEPTION:
java.lang.IllegalArgumentException: already added: Lorg/json/simple/ItemList;
UNEXPECTED TOP-LEVEL EXCEPTION:
java.lang.IllegalArgumentException: already added: Landroid/support/v4/accessibilityservice/AccessibilityServiceInfoCompat;
UNEXPECTED TOP-LEVEL EXCEPTION:
java.lang.IllegalArgumentException: already added: Lorg/apache/commons/lang3/CharRange$1;
Command gradle clean build ends successful. So my problem is that i can't run my tests. When i change plugin, in my build.gradle file, from 'android-library' to 'android' everything works fine.
Also, i'm added --info param and got this, before error
command: /home/username/adt-bundle/sdk/build-tools/18.1.1/dx --dex --output /home/username/android/build/libs/android-test.dex /home/username/android/build/classes/test /home/username/android/build/dependency-cache/test /home/username/android/libs/json_simple.jar /home/username/android/build/bundles/debug/classes.jar /home/username/android/build/bundles/debug/libs/json_simple.jar /home/username/android/libs/android-support-v4.jar /home/username/android/build/bundles/debug/libs/commons-lang3-3.1.jar /home/username/android/build/bundles/debug/libs/android-support-v4.jar /home/username/android/libs/commons-lang3-3.1.jar
What was that? Why it uses libraries from folder build/bundles/debug/libs/? This is the reason why I had error java.lang.IllegalArgumentException but why gradle takes libraries from that dir i don't understand.
Here my build.gradle file
buildscript {
repositories {
mavenCentral()
}
dependencies {
classpath 'com.android.tools.build:gradle:0.6.3'
}
}
apply plugin: 'android-library'
android {
compileSdkVersion 18
buildToolsVersion "18.1.1"
defaultConfig {
minSdkVersion 8
targetSdkVersion 18
testPackageName "ua.cooperok.stringcalc.tests"
testInstrumentationRunner "android.test.InstrumentationTestRunner"
}
sourceSets {
main {
manifest.srcFile file('AndroidManifest.xml')
java.srcDirs = ['src']
resources.srcDirs = ['src']
res.srcDirs = ['res']
assets.srcDirs = ['assets']
}
instrumentTest {
manifest.srcFile file('tests/AndroidManifest.xml')
java.srcDirs = ['tests/src']
resources.srcDirs = ['tests/src']
res.srcDirs = ['tests/res']
assets.srcDirs = ['tests/assets']
}
}
dependencies {
compile fileTree(dir: 'libs', include: '*.jar')
}
}
Maybe it's a bug in android-library plugin?

While I do not know exact answer to the question, my colleagues from JetBrains supporting gradle in IntelliJ IDEA advised to ask the question at https://code.google.com/p/android/ because it's clearly an issue (and may be a bug) in Google Android Gradle Plugin for Eclipse, given that you work in Eclipse, as far as I recall from our conversation.

Now problem is no longer relevant. In build tools from version 0.7.2 it is fixed.
Piece of updates from tech doc
- Solve issue with local jar when testing library projects.

Gradle import issues - Android

I am currently attempting to switch my project over to using gradle builds. While using the old build system I linked to the private/internal/hidden android API's by compiling the source and linking the classes.jar files before the Android libraries. I am currently trying to do the same thing in gradle with no luck at all.
With my current build.gradle file I receive the following error:
Gradle: A problem occurred evaluating project ':Launcher2'.
> Could not find method external() for arguments [file collection] on project ':Launcher2'.
If I remove these lines before "apply plugin: android"
dependencies {
compile files('libraries/classes.jar')
}
I receive errors about missing com.android.internal and com.android.common packages which are located in my classes.jar file.
Here's my build.gradle file.
buildscript {
repositories {
mavenCentral()
}
dependencies {
classpath 'com.android.tools.build:gradle:0.5.6'
}
}
dependencies {
compile files('libraries/classes.jar')
}
plugin: 'android'
android {
buildToolsVersion "17.0"
compileSdkVersion 10
dependencies {
compile fileTree(dir: 'libraries', include: '*.jar')
compile project(':ActiveAndroid')
}
sourceSets {
main {
manifest.srcFile 'AndroidManifest.xml'
java.srcDirs = ['src']
resources.srcDirs = ['src']
aidl.srcDirs = ['src']
renderscript.srcDirs = ['src']
res.srcDirs = ['res']
assets.srcDirs = ['assets']
}
}
}
Edit: After reading the gradle documentation a bit more I was able to successfully link the libraries into the project but the order of dependencies is wrong. The equivalent to what I am trying to do is adding both .jar files to the top of the classpath so that they are declared before the android SDK jar files.
I was digging through the source for the android gradle plugin, it seems that this may not be possible. The code seems incomplete and will not build. If anyone has any insight I would really appreciate it. Otherwise it looks like I will have to switch back to using Ant for now.

Can't build project, problems with gradle?

I'm trying to switch from eclipse to android studio for my android development.
However, I still haven't found the right way to import my existing project.
I don't know if it is important: but I'm using a mac
I did the export step in eclipse, imported this gradle build in Android Studio, but when I try to build my project, it gives me this error:
Gradle:
FAILURE: Could not determine which tasks to execute.
* What went wrong:
Task 'assembleDebug' not found in project ':ProjectName'.
* Try:
Run gradle tasks to get a list of available tasks.
Could not execute build using Gradle installation '/Users/<username>/Development/Build/gradle-1.6'.
This is the build.gradle file that eclipse gave me:
buildscript {
repositories {
mavenCentral()
}
dependencies {
classpath 'com.android.tools.build:gradle:0.4.+'
}
}
apply plugin: 'android'
dependencies {
compile project(':ProjectName:library:ActionBarSherlock')
compile project(':ProjectName:library:facebook')
compile files('../../../../../../../ProjectName/libs/gcm.jar')
compile files('../../../../../../../ProjectName/libs/libGoogleAnalyticsV2.jar')
compile files('../../../../../../../ProjectName/libs/commons-lang3-3.1.jar')
compile files('../../../../../../../ProjectName/libs/actionbarsherlock-plugin-maps-4.2.0.jar')
compile files('../../../../../../../NiteOwl/libs/volley.jar')
compile project(':ProjectName:library:PullToRefresh')
compile project(':ProjectName:library:google-play-services_lib')
}
android {
compileSdkVersion 17
buildToolsVersion "17"
defaultConfig {
minSdkVersion 8
targetSdkVersion 17
}
sourceSets {
main {
manifest.srcFile 'AndroidManifest.xml'
java.srcDirs = ['src']
resources.srcDirs = ['src']
aidl.srcDirs = ['src']
renderscript.srcDirs = ['src']
res.srcDirs = ['res']
assets.srcDirs = ['assets']
}
instrumentTest.setRoot('tests')
}
}
I've seen a lot of possible solutions, but none of them worked for me, any idea what I'm doing wrong?
The path to the project has no spaces in it
jar libraries => ProjectName/libs
android libraries => ProjectName/library
all of this was working in eclipse

We recently moved our project to gradle as well. We ran into issues due to the library projects.
To solve it we added a settings.gradle file in the root of your project with
include ':libs:actionbarsherlock'
include ':yourprojectname'
Add all your library projects from eclipse into the settings.gradle
We also made a build.gradle file for each of the library Projects.
AFAIK the export from eclipse doesn't deal well with library projects.

In the build.gradle at the root of your project (the one that's probably mostly empty), add the following line:
task assemble{}
Found at https://code.google.com/p/android/issues/detail?id=57531

I've had this error appear when I had a stray empty flavors stanza in my build.gradle:
productFlavors {
}