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BUILD report for paxtoolsr on merida2

This page was generated on 2018-10-17 08:53:45 -0400 (Wed, 17 Oct 2018).

Package 1066/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
paxtoolsr 1.14.0
Augustin Luna
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/paxtoolsr
Branch: RELEASE_3_7
Last Commit: e20a1a7
Last Changed Date: 2018-04-30 10:35:34 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
merida2 OS X 10.11.6 El Capitan / x86_64  OK [ ERROR ] skipped  skipped 

Summary

Package: paxtoolsr
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data paxtoolsr
StartedAt: 2018-10-16 17:39:18 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 17:39:41 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 22.8 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 paxtoolsr
###
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* checking for file ‘paxtoolsr/DESCRIPTION’ ... OK
* preparing ‘paxtoolsr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Loading required package: rJava
Loading required package: XML
2018-10-16 17:39:29,043 1562 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2018-10-16 17:39:29,207 1726 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)

Attaching package: 'plyr'

The following object is masked from 'package:paxtoolsr':

    summarize

Quitting from lines 218-233 (using_paxtoolsr.Rmd) 
Error: processing vignette 'using_paxtoolsr.Rmd' failed with diagnostics:
XML content does not seem to be XML: '{"propertyPath":"ProteinReference/entityFeature:ModificationFeature","version":"10","traverseEntry":[{"uri":"http://identifiers.org/uniprot/P31749","value":["http://pathwaycommons.org/pc2/ModificationFeature_01696e37142d7d4e695ca728f4a23304","http://pathwaycommons.org/pc2/ModificationFeature_cbd93b4c45efae1d3e95c377f5a75851","http://pathwaycommons.org/pc2/ModificationFeature_95cbd7039bd2a68180c0bb57bce9b995","http://pathwaycommons.org/pc2/ModificationFeature_1d9a0475e0ec0a464ae1b4c312862807","http://pathwaycommons.org/pc2/ModificationFeature_3822bddb1a9319e273f180903f6440e1","http://pathwaycommons.org/pc2/ModificationFeature_dd35f02813e403d9809fdd09738ed8c7","http://pathwaycommons.org/pc2/ModificationFeature_fa22523ffc0ad03502e7dd9a04b9d79d","http://pathwaycommons.org/pc2/ModificationFeature_c331ff0905dc3993147b47ac0a42bf54","http://pathwaycommons.org/pc2/ModificationFeature
Execution halted