[Bioc-devel] package rJava can not be loaded in build system OS X

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Fri Apr 26 00:03:59 CEST 2019

Hi Zheng,

We're working on this and will provide an update ASAP.

Note that this won't affect the release of the esATAC Mac binary, which is already available in BioC 3.9 (see at the bottom of the landing page):


This is because it already passed CHECK on celaya2 before we started to see the rJava problem on this machine. Keep in mind that a package is allowed to propagate as soon as it passes BUILD and CHECK (granted that its version is greater than the version of the package that is already available). If, for whatever reason, it starts to show errors on the daily build report, we typically don't remove the package that is currently available. What has propagated stays.

Hope this clarifies.


On 4/25/19 14:08, Zheng Wei wrote:

Dear all,

I find package rJava is not available in build system OS X.

My package esATAC depends on this package so it causes ERROR when building. The ERROR is pasted below.

Is there anyone can fix this problem?



** byte-compile and prepare package for lazy loading Error: .onLoad failed in loadNamespace() for 'rJava', details:   call: dyn.load(file, DLLpath = DLLpath, ...)   error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so':   dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib   Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so   Reason: image not found Execution halted ERROR: lazy loading failed for package ��esATAC�� * removing ��/Library/Frameworks/R.framework/Versions/3.6/Resources/library/esATAC��
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: hpages using fredhutch.org<mailto:hpages using fredhutch.org>
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