Hi Andreas, Apologies for newbie assumptions in the following.
I've had a quick look at the nextflow build (not in a debian context) and compared with your output. Assuming the build attempt is happening in a non-networked environment, the gradle build is complaining about not being able to auto-download the io.codearte.nexus-staging plugin, which it will be trying to get from the Gradle Central Plugin Repository (where io.codearte.nexus-staging now resides). Despite what it says about having searched there (this is the same error message I get when running a gradle build with no network). I remember you saying the debian build process has some way of getting around maven dynamic dependencies without network. This plugin can also be found in mvnrepository (https://mvnrepository.com/artifact/io.codearte.nexus-staging/io.codearte.nexus-staging.gradle.plugin/0.21.2) so perhaps it can be obtained by that route? A locally compiled version of the plugin could be picked up within the nextflow build.gradle by adding repositories { maven { url 'file:///path/to/local/plugins' } } to build.gradle. I fear that given the highly dynamic dependencies of gradle projects and their plugins, this will lead to more such problems. You can see a list of dependencies that gradle downloads by (in a git clone of nextflow) deleting ~/.gradle, git clean -dfx, gradle build --info. The nextflow runtime dependencies shown is not a short list but you might recognise if most can be dealt with in a similar way. Hopefully some of that makes sense? Keep safe, Ben ________________________________ From: Andreas Tille <andr...@an3as.eu> Sent: 28 April 2020 10:05 To: Debian Java List <debian-java@lists.debian.org> Cc: Debian Med Project List <debian-...@lists.debian.org> Subject: [covid-19] Gradle help for nextflow needed Hi, in our COVID-19 effort the Debian Med team intends to package some workflows that are useful to detect viruses. A common workflow tool is nextflow which I in injected into Salsa[1]. The build system uses gradle where I do not have any experience in. The build log of my weak attempt is running into: ... Evaluating root project 'nextflow-prj' using build file '/build/nextflow-20.04.1-edge/build.gradle'. Compiling build file '/build/nextflow-20.04.1-edge/build.gradle' using SubsetScriptTransformer. Creating new cache for metadata-2.36/module-metadata, path /build/nextflow-20.04.1-edge/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@19705650 FAILURE: Build failed with an exception. * Where: Build file '/build/nextflow-20.04.1-edge/build.gradle' line: 18 * What went wrong: Plugin [id: 'io.codearte.nexus-staging', version: '0.21.2'] was not found in any of the following sources: - Gradle Core Plugins (plugin is not in 'org.gradle' namespace) - Plugin Repositories (could not resolve plugin artifact 'io.codearte.nexus-staging:io.codearte.nexus-staging.gradle.plugin:0.21.2') Searched in the following repositories: Gradle Central Plugin Repository * Try: Run with --debug option to get more log output. Run with --scan to get full insights. * Exception is: org.gradle.api.plugins.UnknownPluginException: Plugin [id: 'io.codearte.nexus-staging', version: '0.21.2'] was not found in any of the following sources: - Gradle Core Plugins (plugin is not in 'org.gradle' namespace) - Plugin Repositories (could not resolve plugin artifact 'io.codearte.nexus-staging:io.codearte.nexus-staging.gradle.plugin:0.21.2') Searched in the following repositories: Gradle Central Plugin Repository at org.gradle.plugin.use.internal.DefaultPluginRequestApplicator.resolveToFoundResult(DefaultPluginRequestApplicator.java:262) at org.gradle.plugin.use.internal.DefaultPluginRequestApplicator.access$100(DefaultPluginRequestApplicator.java:63) at org.gradle.plugin.use.internal.DefaultPluginRequestApplicator$1.transform(DefaultPluginRequestApplicator.java:91) at org.gradle.plugin.use.internal.DefaultPluginRequestApplicator$1.transform(DefaultPluginRequestApplicator.java:88) at org.gradle.util.CollectionUtils.collect(CollectionUtils.java:203) at org.gradle.util.CollectionUtils.collect(CollectionUtils.java:198) ... Any help for a kickstart would be really appreciated. Kind regards Andreas. [1] https://salsa.debian.org/med-team/nextflow -- http://fam-tille.de The University of Dundee is a registered Scottish Charity, No: SC015096
