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gorpipe / gor

GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using declarative query language, in a parallel execution engine.
GNU Affero General Public License v3.0
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Warnings shown when running gorpipe #1

Closed gumson closed 4 years ago

gumson commented 4 years ago

There are several warning which popup when running gorpipe related to reflection. Gorpipe built using instructions from repo but still getting these errors.

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$1 (file:/Users/gummi/source/gor/gortools/build/install/gor-scripts/lib/guice-4.2.2.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of com.google.inject.internal.cglib.core.$ReflectUtils$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Chrom   gene_start  gene_end    Gene_Symbol
chr1    131024  134836  RP11-34P13.10

The operation finishes correctly, yet still an eyesore.

Shicheng-Guo commented 4 years ago

Hi Gumson, What's the final solution or comment to this satiation?

snorristurluson commented 4 years ago

This warning needs to be addressed in Guice, and it has taken longer for a fix to this than we expected (see https://github.com/google/guice/issues/1133).

A workaround is add this environment variable before running: export GOR_GORPIPE_OPTS="--add-opens java.base/java.lang=ALL-UNNAMED"

We'll look into our options, but we have not seen any adverse effects of this and hopefully we can upgrade Guice soon.

gmagnu commented 4 years ago

This has been fixed in GOR 2.6.