[Bioc-devel] Issue with a package dependent on rJava

Anestis Gkanogiannis @ne@t|@ @end|ng |rom gk@nog|@nn|@@com
Mon Oct 10 02:02:52 CEST 2022


On line 1289 of melting.R you call the keyset() method of opts_melt (which is a HashMap).
This method in Java until 11, return a private AbstractSet (KeySet).
On line 1290 of melting.R you call iterator() method of the KeySet object you got on the previous line.

Problem is that this KeySet is private and this call through reflexion isn’t valid, hence the exception.

They changed this in java 11 where the returned AbstractSet is public.

So solution is either use java >11 
or change your code in melting.R to not call the iterator() method of keyset (which is a private AbstractSet).

Best regards,

Anestis Gkanogiannis, PhD

-----Original Message-----
From: Bioc-devel <bioc-devel-bounces using r-project.org> On Behalf Of DR J Aravind via Bioc-devel
Sent: 10 October 2022 00:33
To: bioc-devel using r-project.org
Cc: Aravind J (aravindj86 using yahoo.com) <aravindj86 using yahoo.com>
Subject: [Bioc-devel] Issue with a package dependent on rJava

Dear Bioconductor Developers,

My package  `rmelting` is failing to build on release (3.15) and devel (3.16) versions for the following systems.

Bioconductor 3.15
- palomino3 (Windows Server 2022 Datacenter / x64)

Bioconductor 3.15
- palomino4 (Windows Server 2022 Datacenter / x64)
- lconway (macOS 12.5.1 Monterey / x86_64)

The error message is as follows.

* creating vignettes ... ERROR
--- re-building 'Tutorial.Rmd' using rmarkdown_notangle

Quitting from lines 195-197 (Tutorial.Rmd)

Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:

java.lang.IllegalAccessException: class RJavaTools cannot access a member of class java.util.HashMap$KeySet (in module java.base) with modifiers "public final"

--- failed re-building 'Tutorial.Rmd'

SUMMARY: processing the following file failed:


I am unable to replicate the same on my end.

It seems to be an issue with java. The package is a low level interface to a software written in Java 1.5 using `rJava`. I have tried with different java versions upto 1.8.

Any pointers or suggestions to fix the same will be appreciated.

Best Regards,

J. Aravind

ICAR-National Bureau of Plant Genetic Resources
New Delhi, India

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