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BUILD report for netDx on machv2

This page was generated on 2020-10-17 11:59:04 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE netDx PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1186/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netDx 1.0.4
Shraddha Pai
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/netDx
Branch: RELEASE_3_11
Last Commit: e08c71c
Last Changed Date: 2020-10-12 17:37:46 -0400 (Mon, 12 Oct 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  TIMEOUT  skipped  skipped 
machv2 macOS 10.14.6 Mojave / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: netDx
Version: 1.0.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data netDx
StartedAt: 2020-10-16 20:12:00 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 20:19:51 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 471.6 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data netDx
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* checking for file ‘netDx/DESCRIPTION’ ... OK
* preparing ‘netDx’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘BuildPredictor.Rmd’ using knitr
Oct16@20:15:07  INFO FileUtils:88->total number of identifiers loaded from mapping file: 265
Oct16@20:15:07  INFO ProfileToNetworkDriver:332->total gene records: 264
Oct16@20:15:07  INFO ProfileToNetworkDriver:333->total features: 10
Oct16@20:15:07  INFO ProfileToNetworkDriver:212->computing network
Oct16@20:15:07  INFO ProfileToNetworkDriver:506->Initializing correlation with profile
Oct16@20:15:07  INFO ProfileToNetworkDriver:510->Correlation initialized. Total time: 12
Oct16@20:15:08 DEBUG ProfileToNetworkDriver:598->level control at size limit of 50
Oct16@20:15:08  INFO ProfileToNetworkDriver:577->Total time for calculating: 88
Oct16@20:15:08  INFO ProfileToNetworkDriver:216->Total genes in resulting network (after filtering/averaging): 264
Oct16@20:15:08  INFO ProfileToNetworkDriver:217->Time to compute network from profile (ms): 116
Oct16@20:15:08  INFO ProfileToNetworkDriver:225->Total #interactions in network (including symmetric interactions): 18494
Oct16@20:15:08  INFO ProfileToNetworkDriver:226->network sparsity: 26.54%
Oct16@20:15:08  INFO ProfileToNetworkDriver:227->done
Oct16@20:15:08  INFO FileUtils:88->total number of identifiers loaded from mapping file: 265
Oct16@20:15:08  INFO ProfileToNetworkDriver:332->total gene records: 264
Oct16@20:15:08  INFO ProfileToNetworkDriver:333->total features: 12
Oct16@20:15:08  INFO ProfileToNetworkDriver:212->computing network
Oct16@20:15:08  INFO ProfileToNetworkDriver:506->Initializing correlation with profile
Oct16@20:15:08  INFO ProfileToNetworkDriver:510->Correlation initialized. Total time: 12
Oct16@20:15:08 DEBUG ProfileToNetworkDriver:598->level control at size limit of 50
Oct16@20:15:08  INFO ProfileToNetworkDriver:577->Total time for calculating: 86
Oct16@20:15:08  INFO ProfileToNetworkDriver:216->Total genes in resulting network (after filtering/averaging): 264
Oct16@20:15:08  INFO ProfileToNetworkDriver:217->Time to compute network from profile (ms): 114
Oct16@20:15:08  INFO ProfileToNetworkDriver:225->Total #interactions in network (including symmetric interactions): 19006
Oct16@20:15:08  INFO ProfileToNetworkDriver:226->network sparsity: 27.27%
Oct16@20:15:08  INFO ProfileToNetworkDriver:227->done
Oct16@20:15:09  INFO FileUtils:88->total number of identifiers loaded from mapping file: 265
Oct16@20:15:09  INFO ProfileToNetworkDriver:332->total gene records: 264
Oct16@20:15:09  INFO ProfileToNetworkDriver:333->total features: 17
Oct16@20:15:09  INFO ProfileToNetworkDriver:212->computing network
Oct16@20:15:09  INFO ProfileToNetworkDriver:506->Initializing correlation with profile
Oct16@20:15:09  INFO ProfileToNetworkDriver:510->Correlation initialized. Total time: 14
Oct16@20:15:09 DEBUG ProfileToNetworkDriver:598->level control at size limit of 50
Oct16@20:15:09  INFO ProfileToNetworkDriver:577->Total time for calculating: 77
Oct16@20:15:09  INFO ProfileToNetworkDriver:216->Total genes in resulting network (after filtering/averaging): 264
Oct16@20:15:09  INFO ProfileToNetworkDriver:217->Time to compute network from profile (ms): 105
Oct16@20:15:09  INFO ProfileToNetworkDriver:225->Total #interactions in network (including symmetric interactions): 19118
Oct16@20:15:09  INFO ProfileToNetworkDriver:226->network sparsity: 27.43%
Oct16@20:15:09  INFO ProfileToNetworkDriver:227->done
predictor
Oct16@20:15:11  INFO CacheBuilder:228->network dir: /tmp/RtmpbHy8mt/QEAYJ1252R/pred_output/rng1/tmp/INTERACTIONS
Oct16@20:15:11  INFO CacheBuilder:229->cache dir: cache
Oct16@20:15:11  INFO CacheBuilder:110->processing organism 1 predictor
Oct16@20:15:11  INFO AddOrganism:89->building node/index mapping for organism 1
Oct16@20:15:11  INFO AddOrganism:102->building empty network ids for organism 1
Oct16@20:15:11  INFO CacheBuilder:148->building network/index mapping for organism 1
Oct16@20:15:11  INFO CacheBuilder:195->building matrix for network 1 UREA_CYCLE.profile organism 1
Oct16@20:15:11  INFO Config:86->loading engine config from org/genemania/engine/Engine.properties
Oct16@20:15:11  INFO CacheBuilder:195->building matrix for network 2 CDP-DIACYLGLYCEROL_BIOSYNTHESIS_I.profile organism 1
Oct16@20:15:11  INFO CacheBuilder:195->building matrix for network 3 SUPERPATHWAY_OF_D-_I_MYO__I_-INOSITOL__1,4,5_-TRISPHOSPHATE_METABOLISM.profile organism 1
Oct16@20:15:11  INFO CacheBuilder:195->building matrix for network 4 age_cont.txt organism 1
Oct16@20:15:11  INFO CacheBuilder:195->building matrix for network 5 stage_cont.txt organism 1
Oct16@20:15:11  INFO AbstractEngineApp:494->done
Unrecognized option: -d64
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
Quitting from lines 405-418 (BuildPredictor.Rmd) 
Error: processing vignette 'BuildPredictor.Rmd' failed with diagnostics:
object 'dat' not found
--- failed re-building 'BuildPredictor.Rmd'

--- re-building 'Predict_CaseControl_from_CNV.Rmd' using knitr
starting worker pid=82501 on localhost:11499 at 20:15:34.005
Loading required package: netDx
loaded netDx and set parent environment
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loaded netDx and set parent environment
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Quitting from lines 194-202 (Predict_CaseControl_from_CNV.Rmd) 
Error: processing vignette 'Predict_CaseControl_from_CNV.Rmd' failed with diagnostics:
object 'dat' not found
--- failed re-building 'Predict_CaseControl_from_CNV.Rmd'

--- re-building 'ThreeWayClassifier.Rmd' using knitr
Quitting from lines 302-317 (ThreeWayClassifier.Rmd) 
Error: processing vignette 'ThreeWayClassifier.Rmd' failed with diagnostics:
object 'dat' not found
--- failed re-building 'ThreeWayClassifier.Rmd'

SUMMARY: processing the following files failed:
  'BuildPredictor.Rmd' 'Predict_CaseControl_from_CNV.Rmd'
  'ThreeWayClassifier.Rmd'

Error: Vignette re-building failed.
Execution halted