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


* checking for file ‘wppi/DESCRIPTION’ ... OK
* preparing ‘wppi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘wppi_workflow.Rmd’ using rmarkdown
[2022-07-07 07:20:20] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2022-07-07 07:20:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2022-07-07 07:20:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2022-07-07 07:20:20] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-07-07 07:20:20] [TRACE]   [OmnipathR] Cache locked: FALSE
[2022-07-07 07:20:20] [INFO]    [wppi] Executing WPPI workflow.
[2022-07-07 07:20:20] [INFO]    [wppi] Collecting database knowledge.
[2022-07-07 07:20:20] [TRACE]   [OmnipathR] Looking up in cache: `https://ci.monarchinitiative.org/job/hpo.annotations/lastSuccessfulBuild/artifact/rare-diseases/util/annotation/genes_to_phenotype.txt`.
[2022-07-07 07:20:20] [INFO]    [OmnipathR] Cache record does not exist: `https://ci.monarchinitiative.org/job/hpo.annotations/lastSuccessfulBuild/artifact/rare-diseases/util/annotation/genes_to_phenotype.txt`
[2022-07-07 07:20:20] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ci.monarchinitiative.org/job/hpo.annotations/lastSuccessfulBuild/artifact/rare-diseases/util/annotation/genes_to_phenotype.txt`.
[2022-07-07 07:20:20] [INFO]    [OmnipathR] Cache item `79506c32d59251577fdd7a183eb3eca3cd1ec56b` version 1: status changed from `unknown` to `started`.
[2022-07-07 07:20:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/79506c32d59251577fdd7a183eb3eca3cd1ec56b-1.rds`.
[2022-07-07 07:20:20] [INFO]    [OmnipathR] Retrieving URL: `https://ci.monarchinitiative.org/job/hpo.annotations/lastSuccessfulBuild/artifact/rare-diseases/util/annotation/genes_to_phenotype.txt`
[2022-07-07 07:20:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://ci.monarchinitiative.org/job/hpo.annotations/lastSuccessfulBuild/artifact/rare-diseases/util/annotation/genes_to_phenotype.txt`
[2022-07-07 07:20:29] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/79506c32d59251577fdd7a183eb3eca3cd1ec56b-1.rds`.
[2022-07-07 07:20:29] [INFO]    [OmnipathR] Download ready [key=79506c32d59251577fdd7a183eb3eca3cd1ec56b, version=1]
[2022-07-07 07:20:29] [INFO]    [OmnipathR] Cache item `79506c32d59251577fdd7a183eb3eca3cd1ec56b` version 1: status changed from `started` to `ready`.
[2022-07-07 07:20:30] [SUCCESS] [OmnipathR] Human Phenotype Ontology (ci.monarchinitiative.org): downloaded 256738 records
[2022-07-07 07:20:30] [TRACE]   [OmnipathR] Looking up in cache: `http://geneontology.org/gene-associations/goa_human.gaf.gz`.
[2022-07-07 07:20:30] [INFO]    [OmnipathR] Cache record does not exist: `http://geneontology.org/gene-associations/goa_human.gaf.gz`
[2022-07-07 07:20:30] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://geneontology.org/gene-associations/goa_human.gaf.gz`.
[2022-07-07 07:20:30] [INFO]    [OmnipathR] Cache item `184816e75bc7a2b57e2a2e3a86b90b3e30189e01` version 1: status changed from `unknown` to `started`.
[2022-07-07 07:20:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/184816e75bc7a2b57e2a2e3a86b90b3e30189e01-1.rds`.
[2022-07-07 07:20:30] [INFO]    [OmnipathR] Retrieving URL: `http://geneontology.org/gene-associations/goa_human.gaf.gz`
[2022-07-07 07:20:30] [TRACE]   [OmnipathR] Attempt 1/3: `http://geneontology.org/gene-associations/goa_human.gaf.gz`
[2022-07-07 07:20:30] [WARN]    [OmnipathR] Failed to download `http://geneontology.org/gene-associations/goa_human.gaf.gz` (attempt 1/3); error: embedded nul in string: '\037\x8b\b\b\x9c\xa6\xbfb\0\003goa_human.gaf\0ԝ\xd9r\xe3\xb8Ҡ\xaf\xd9O\xc1\xbe\x9b\x89h\xba\x88\x85 鉹\xd0⭼\xa9l\x97\xbb\xabo*h\x99\xb65-\x89\xfe\xb5T\037\x9f\xf0\xc3\017\xc0M\022EI\\\022\\:\xa2\xcan\x95\x8d\xfc\x90H$\xd6D\xfe\xfe\xea\xbch\xbf\xdc\xd9|\xe4M\x8fU|\x84\177\xfb\xfd\xb7\xdf_ݩ;s\026\xee\xb3\xf6\xf4q\xac\x9e\xdd\xf6ć\xcf\xfc\003-\xfe\027\xfe\xb3:ƚnj:~\xd0ѱa\x8b\x9f9w\x9dgw\xa6\xbe̼\x89:\xf7\x96\xb3\xa1\xab:\xf3\xb97\0349\v^\xbe\xfa2\032\xbbǿ\xfd\xfe\177\017\xfd\x97\x9f\001= r\xac\x93$ë\xe7\xfc|[N\x9ciY\x9a\x877W\x9d\xbb\v\xd5{Q\xdfg\xde\xc2\035MUg8t\xe7Bmsu4\035\x8e\x97\xcf\xee3\xffF]\xbc\x8d\xe6~\xd1*\xff\xfa\xe4\xcc\xf9\xa7\\\xd6\xf7\xe9h\xc0\177O\x9d\xb9/\xee̝r\022\xbf\030o\xe2\xce\xffP\xff}\033'
[2022-07-07 07:20:35] [TRACE]   [OmnipathR] Attempt 2/3: `http://geneontology.org/gene-associations/goa_human.gaf.gz`
[2022-07-07 07:20:36] [WARN]    [OmnipathR] Failed to download `http://geneontology.org/gene-associations/goa_human.gaf.gz` (attempt 2/3); error: embedded nul in string: '\037\x8b\b\b\x9c\xa6\xbfb\0\003goa_human.gaf\0ԝ\xd9r\xe3\xb8Ҡ\xaf\xd9O\xc1\xbe\x9b\x89h\xba\x88\x85 鉹\xd0⭼\xa9l\x97\xbb\xabo*h\x99\xb65-\x89\xfe\xb5T\037\x9f\xf0\xc3\017\xc0M\022EI\\\022\\:\xa2\xcan\x95\x8d\xfc\x90H$\xd6D\xfe\xfe\xea\xbch\xbf\xdc\xd9|\xe4M\x8fU|\x84\177\xfb\xfd\xb7\xdf_ݩ;s\026\xee\xb3\xf6\xf4q\xac\x9e\xdd\xf6ć\xcf\xfc\003-\xfe\027\xfe\xb3:ƚnj:~\xd0ѱa\x8b\x9f9w\x9dgw\xa6\xbe̼\x89:\xf7\x96\xb3\xa1\xab:\xf3\xb97\0349\v^\xbe\xfa2\032\xbbǿ\xfd\xfe\177\017\xfd\x97\x9f\001= r\xac\x93$ë\xe7\xfc|[N\x9ciY\x9a\x877W\x9d\xbb\v\xd5{Q\xdfg\xde\xc2\035MUg8t\xe7Bmsu4\035\x8e\x97\xcf\xee3\xffF]\xbc\x8d\xe6~\xd1*\xff\xfa\xe4\xcc\xf9\xa7\\\xd6\xf7\xe9h\xc0\177O\x9d\xb9/\xee̝r\022\xbf\030o\xe2\xce\xffP\xff}\033'
[2022-07-07 07:20:41] [TRACE]   [OmnipathR] Attempt 3/3: `http://geneontology.org/gene-associations/goa_human.gaf.gz`
[2022-07-07 07:20:41] [ERROR]   [OmnipathR] Failed to download `http://geneontology.org/gene-associations/goa_human.gaf.gz` (attempt 3/3); error: embedded nul in string: '\037\x8b\b\b\x9c\xa6\xbfb\0\003goa_human.gaf\0ԝ\xd9r\xe3\xb8Ҡ\xaf\xd9O\xc1\xbe\x9b\x89h\xba\x88\x85 鉹\xd0⭼\xa9l\x97\xbb\xabo*h\x99\xb65-\x89\xfe\xb5T\037\x9f\xf0\xc3\017\xc0M\022EI\\\022\\:\xa2\xcan\x95\x8d\xfc\x90H$\xd6D\xfe\xfe\xea\xbch\xbf\xdc\xd9|\xe4M\x8fU|\x84\177\xfb\xfd\xb7\xdf_ݩ;s\026\xee\xb3\xf6\xf4q\xac\x9e\xdd\xf6ć\xcf\xfc\003-\xfe\027\xfe\xb3:ƚnj:~\xd0ѱa\x8b\x9f9w\x9dgw\xa6\xbe̼\x89:\xf7\x96\xb3\xa1\xab:\xf3\xb97\0349\v^\xbe\xfa2\032\xbbǿ\xfd\xfe\177\017\xfd\x97\x9f\001= r\xac\x93$ë\xe7\xfc|[N\x9ciY\x9a\x877W\x9d\xbb\v\xd5{Q\xdfg\xde\xc2\035MUg8t\xe7Bmsu4\035\x8e\x97\xcf\xee3\xffF]\xbc\x8d\xe6~\xd1*\xff\xfa\xe4\xcc\xf9\xa7\\\xd6\xf7\xe9h\xc0\177O\x9d\xb9/\xee̝r\022\xbf\030o\xe2\xce\xffP\xff}\033'
Quitting from lines 80-102 (wppi_workflow.Rmd) 
Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics:
Failed to download `http://geneontology.org/gene-associations/goa_human.gaf.gz` (attempt 3/3); error: embedded nul in string: '\037\x8b\b\b\x9c\xa6\xbfb\0\003goa_human.gaf\0ԝ\xd9r\xe3\xb8Ҡ\xaf\xd9O\xc1\xbe\x9b\x89h\xba\x88\x85 鉹\xd0⭼\xa9l\x97\xbb\xabo*h\x99\xb65-\x89\xfe\xb5T\037\x9f\xf0\xc3\017\xc0M\022EI\\\022\\:\xa2\xcan\x95\x8d\xfc\x90H$\xd6D\xfe\xfe\xea\xbch\xbf\xdc\xd9|\xe4M\x8fU|\x84\177\xfb\xfd\xb7\xdf_ݩ;s\026\xee\xb3\xf6\xf4q\xac\x9e\xdd\xf6ć\xcf\xfc\003-\xfe\027\xfe\xb3:ƚnj:~\xd0ѱa\x8b\x9f9w\x9dgw\xa6\xbe̼\x89:\xf7\x96\xb3\xa1\xab:\xf3\xb97\0349\v^\xbe\xfa2\032\xbbǿ\xfd\xfe\177\017\xfd\x97\x9f\001= r\xac\x93$ë\xe7\xfc|[N\x9ciY\x9a\x877W\x9d\xbb\v\xd5{Q\xdfg\xde\xc2\035MUg8t\xe7Bmsu4\035\x8e\x97\xcf\xee3\xffF]\xbc\x8d\xe6~\xd1*\xff\xfa\xe4\xcc\xf9\xa7\\\xd6\xf7\xe9h\xc0\177O\x9d\xb9/\xee̝r\022\xbf\030o\xe2\xce\xffP\xff}\033'
--- failed re-building ‘wppi_workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘wppi_workflow.Rmd’

Error: Vignette re-building failed.
Execution halted