Dependencies missing in the pom

[pgrt]

Hello,

The dependencies commons-io:commons-io, com.google.guava:guava and org.apache.commons:commons-lang3 (test scope only for the last one) are missing in pom.xml, whereas they are needed by some files in the code.

Cheers,
Pierre

[mlathara]

@pgrt Can you elaborate on what steps you followed to find these missing dependencies? This doesn't trigger issues when we try to build a jar, so I'm trying to understand if building a specific target causes this issue, or perhaps I'm missing something

[pgrt]

Hello @mlathara and thanks for reading my report.

I met the issue when embedding the build of GenomicsDB in the Debian packaging workflow. The dependencies are searched for in other Debian packages, which can explain there might be discrepancies between the versions of the dependencies you are using and mine (and thus different transitive dependencies maybe...).

Anyway, if I fail to add the above discussed dependencies in the pom, I get

[ERROR] COMPILATION ERROR :
[INFO] -------------------------------------------------------------
[ERROR] /<>/src/test/java/org/genomicsdb/reader/GenomicsDBQueryTest.java:[28,37] package org.apache.commons.lang3.math does not exist
[ERROR] /<>/src/test/java/org/genomicsdb/importer/GenomicsDBImporterSpec.java:[38,29] package org.apache.commons.io does not exist
[ERROR] /<>/src/test/java/org/genomicsdb/GenomicsDBUtilsTest.java:[25,28] package com.google.common.io does not exist
[INFO] 3 errors

If there is no additional cost on your side, I would suggest yo add the dependencies in the pom; I guess today they are provided as part of some dependency chain, but this might break and obviously the packages are needed by the code, so it should be safe to include them explcitly...

But you can also ignore this suggestion if the outcome is uncertain to you. It is still OK to add them later if needed!

Best,
Pierre