gradle does not fetch dependencies after upgrade from 5.1.1 to 6.4.1

I have several services that uses gradle 5.1.1 with java 8.

As we want to upgrade to Java 13, we first need to upgrade to gradle 6after doing so, some dependencies are not fetched.

Those dependencies are listed with compile() under a dependency which is our jar library and still built with gradle 5.1.1

our libraries are stored in a S3 bucket and we use shadowjar to generate the end jar.

so, for example:

I have project A which I want to upgrdae. Project A has project B as a dependency (compile) Project B has google guava as a dependency (also with compile)

Now, project A, that under gradle 5.1.1 had fetched guava with no problems, alerting me that it is missing guava after upgrading to gradle 6.

I use local computer installed gradle (not wrapper).

Here are the important build.gradle parts:

buildscript {

    repositories {
        jcenter()
        maven {
            url "https://plugins.gradle.org/m2/"
        }
    }

    ext.ver = [
            'springboot': '2.2.0.RELEASE',
            'slf4j'     : '1.7.12'
    ]

    dependencies {
        classpath "org.springframework.boot:spring-boot-gradle-plugin:${ver.springboot}"
        classpath 'io.spring.gradle:dependency-management-plugin:1.0.7.BUILD-SNAPSHOT'
        classpath 'com.github.jengelman.gradle.plugins:shadow:5.2.0'
        classpath 'com.amazonaws:aws-java-sdk-core:1.11.5'
    }
}

apply plugin: 'java'
apply plugin: 'idea'
apply plugin: 'maven'
apply plugin: 'com.github.johnrengelman.shadow'
apply plugin: 'maven-publish'
apply plugin: 'org.springframework.boot'
apply plugin: 'io.spring.dependency-management'

compileJava {
    sourceCompatibility = JavaVersion.VERSION_1_8
}

configurations {
    compile.exclude module: 'spring-boot-starter-logging'
    testCompile.exclude module: 'spring-boot-starter-logging'
    runtime.exclude module: 'spring-boot-starter-logging'

    compile.exclude group: 'ch.qos.logback'
}

configurations.all {
    resolutionStrategy.cacheDynamicVersionsFor 10, 'seconds'
    resolutionStrategy.cacheChangingModulesFor 10, 'seconds'
}

dependencyManagement {
    applyMavenExclusions = false
}

repositories {
    mavenLocal()
    maven {
        url "s3://bucket"
        credentials(AwsCredentials) {
            accessKey = awsCredentials.AWSAccessKeyId
            secretKey = awsCredentials.AWSSecretKey
        }
        metadataSources {
            artifact()
        }
    }
    mavenCentral()
}


dependencies {
    compile("com.test:projectB:1.0.0")
     ...
}

import com.github.jengelman.gradle.plugins.shadow.transformers.PropertiesFileTransformer

shadowJar {
    classifier = ''
    baseName = 'project-A'
    manifest {
        attributes 'Main-Class': 'com.test.projectA.Starter'
    }
    mergeServiceFiles()
    append 'META-INF/spring.handlers'
    append 'META-INF/spring.schemas'
    append 'META-INF/spring.tooling'
    transform(PropertiesFileTransformer) {
        paths = ['META-INF/spring.factories']
        mergeStrategy = "append"
    }
}

Could this be because project B was not built with new gradle?

unfortunately, I cannot create a real reproducer as those libraries are real code of the company I work at.

Thanks and Regards, Ido