Back to Multiple platform build/check report for BioC 3.16
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2022-07-07 11:11:37 -0400 (Thu, 07 Jul 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4343
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4148
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4160
kjohnsonmacOS 12.4 Montereyarm644.2.0 Patched (2022-06-09 r82473) -- "Vigorous Calisthenics" 3115
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD results for netDx on kjohnson


To the developers/maintainers of the netDx package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netDx.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1308/2124HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netDx 1.9.0  (landing page)
Shraddha Pai
Snapshot Date: 2022-07-06 14:00:06 -0400 (Wed, 06 Jul 2022)
git_url: https://git.bioconductor.org/packages/netDx
git_branch: master
git_last_commit: 491b7a6
git_last_commit_date: 2022-04-26 12:02:19 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.2.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnsonmacOS 12.4 Monterey / arm64  OK    ERROR  skippedskipped

Summary

Package: netDx
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data netDx
StartedAt: 2022-07-07 01:05:47 -0400 (Thu, 07 Jul 2022)
EndedAt: 2022-07-07 01:11:26 -0400 (Thu, 07 Jul 2022)
EllapsedTime: 338.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data netDx
###
##############################################################################
##############################################################################


* checking for file ‘netDx/DESCRIPTION’ ... OK
* preparing ‘netDx’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RawDataConversion.Rmd’ using rmarkdown
Exception in thread "main" java.lang.ExceptionInInitializerError
	at net.sf.cglib.core.KeyFactory$Generator.generateClass(KeyFactory.java:166)
	at net.sf.cglib.core.DefaultGeneratorStrategy.generate(DefaultGeneratorStrategy.java:25)
	at net.sf.cglib.core.AbstractClassGenerator.create(AbstractClassGenerator.java:216)
	at net.sf.cglib.core.KeyFactory$Generator.create(KeyFactory.java:144)
	at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:116)
	at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:108)
	at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:104)
	at net.sf.cglib.proxy.Enhancer.<clinit>(Enhancer.java:69)
	at org.genemania.mediator.lucene.LuceneMediator.createOrganism(LuceneMediator.java:447)
	at org.genemania.mediator.lucene.LuceneOrganismMediator$2.handleHit(LuceneOrganismMediator.java:75)
	at org.genemania.mediator.lucene.AbstractCollector.collect(AbstractCollector.java:52)
	at org.apache.lucene.search.MultiSearcher$1.collect(MultiSearcher.java:258)
	at org.apache.lucene.search.TermScorer.score(TermScorer.java:78)
	at org.apache.lucene.search.TermScorer.score(TermScorer.java:70)
	at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:212)
	at org.apache.lucene.search.MultiSearcher.search(MultiSearcher.java:270)
	at org.apache.lucene.search.Searcher.search(Searcher.java:67)
	at org.genemania.mediator.lucene.LuceneMediator.search(LuceneMediator.java:201)
	at org.genemania.mediator.lucene.LuceneOrganismMediator.createOrganisms(LuceneOrganismMediator.java:70)
	at org.genemania.mediator.lucene.LuceneOrganismMediator.getAllOrganisms(LuceneOrganismMediator.java:65)
	at org.genemania.engine.apps.CacheBuilder.processAllOrganisms(CacheBuilder.java:87)
	at org.genemania.engine.apps.CacheBuilder.process(CacheBuilder.java:237)
	at org.genemania.engine.apps.CacheBuilder.main(CacheBuilder.java:260)
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make protected final java.lang.Class java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) throws java.lang.ClassFormatError accessible: module java.base does not "opens java.lang" to unnamed module @48f63233
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
	at java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:200)
	at java.base/java.lang.reflect.Method.setAccessible(Method.java:194)
	at net.sf.cglib.core.ReflectUtils$2.run(ReflectUtils.java:56)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:318)
	at net.sf.cglib.core.ReflectUtils.<clinit>(ReflectUtils.java:46)
	... 23 more
Quitting from lines 189-208 (RawDataConversion.Rmd) 
Error: processing vignette 'RawDataConversion.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘RawDataConversion.Rmd’

--- re-building ‘ThreeWayClassifier.Rmd’ using rmarkdown
Exception in thread "main" java.lang.ExceptionInInitializerError
	at net.sf.cglib.core.KeyFactory$Generator.generateClass(KeyFactory.java:166)
	at net.sf.cglib.core.DefaultGeneratorStrategy.generate(DefaultGeneratorStrategy.java:25)
	at net.sf.cglib.core.AbstractClassGenerator.create(AbstractClassGenerator.java:216)
	at net.sf.cglib.core.KeyFactory$Generator.create(KeyFactory.java:144)
	at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:116)
	at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:108)
	at net.sf.cglib.core.KeyFactory.create(KeyFactory.java:104)
	at net.sf.cglib.proxy.Enhancer.<clinit>(Enhancer.java:69)
	at org.genemania.mediator.lucene.LuceneMediator.createOrganism(LuceneMediator.java:447)
	at org.genemania.mediator.lucene.LuceneOrganismMediator$2.handleHit(LuceneOrganismMediator.java:75)
	at org.genemania.mediator.lucene.AbstractCollector.collect(AbstractCollector.java:52)
	at org.apache.lucene.search.MultiSearcher$1.collect(MultiSearcher.java:258)
	at org.apache.lucene.search.TermScorer.score(TermScorer.java:78)
	at org.apache.lucene.search.TermScorer.score(TermScorer.java:70)
	at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:212)
	at org.apache.lucene.search.MultiSearcher.search(MultiSearcher.java:270)
	at org.apache.lucene.search.Searcher.search(Searcher.java:67)
	at org.genemania.mediator.lucene.LuceneMediator.search(LuceneMediator.java:201)
	at org.genemania.mediator.lucene.LuceneOrganismMediator.createOrganisms(LuceneOrganismMediator.java:70)
	at org.genemania.mediator.lucene.LuceneOrganismMediator.getAllOrganisms(LuceneOrganismMediator.java:65)
	at org.genemania.engine.apps.CacheBuilder.processAllOrganisms(CacheBuilder.java:87)
	at org.genemania.engine.apps.CacheBuilder.process(CacheBuilder.java:237)
	at org.genemania.engine.apps.CacheBuilder.main(CacheBuilder.java:260)
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make protected final java.lang.Class java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain) throws java.lang.ClassFormatError accessible: module java.base does not "opens java.lang" to unnamed module @48f63233
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
	at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
	at java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:200)
	at java.base/java.lang.reflect.Method.setAccessible(Method.java:194)
	at net.sf.cglib.core.ReflectUtils$2.run(ReflectUtils.java:56)
	at java.base/java.security.AccessController.doPrivileged(AccessController.java:318)
	at net.sf.cglib.core.ReflectUtils.<clinit>(ReflectUtils.java:46)
	... 23 more
Quitting from lines 302-322 (ThreeWayClassifier.Rmd) 
Error: processing vignette 'ThreeWayClassifier.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'ThreeWayClassifier.Rmd'

SUMMARY: processing the following files failed:
  'RawDataConversion.Rmd' 'ThreeWayClassifier.Rmd'

Error: Vignette re-building failed.
Execution halted