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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data wppi
###
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* 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
[2025-02-09 18:51:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-09 18:51:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 18:51:32] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-09 18:51:32] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-09 18:51:32] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-09
[2025-02-09 18:51:32] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-09 20:27:39 UTC; unix
[2025-02-09 18:51:32] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-09 18:51:32] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-09 18:51:32] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-22 r87618); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-09; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-02-09 18:51:33] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.42 2022-12-11; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-02-09 18:51:33] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 18:51:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-09 18:51:33] [INFO]    [wppi] Executing WPPI workflow.
[2025-02-09 18:51:33] [INFO]    [wppi] Collecting database knowledge.
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-02-09 18:51:33] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 18:51:33] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-02-09 18:51:33] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-02-09 18:51:33] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-09 18:51:35] [TRACE]   [OmnipathR] Downloaded 18.8 Mb in 0.998833s from purl.obolibrary.org (18.9 Mb/s); Redirect: 0.429479s, DNS look up: 0.03482s, Connection: 0.056616s, Pretransfer: 0.087256s, First byte at: 0.50389s
[2025-02-09 18:51:36] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-02-09 18:51:36] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2025-02-09 18:51:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-09 18:51:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 18:51:36] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2025-02-09 18:51:36] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 316589 records
[2025-02-09 18:51:36] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-09 18:51:36] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-02-09 18:51:36] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-09 18:51:36] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-02-09 18:51:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-09 18:51:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 18:51:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-09 18:51:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 18:51:36] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2025-02-09 18:51:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-02-09 18:51:36] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-09 18:51:36] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-09 18:51:36] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-09 18:51:39] [WARN]    [OmnipathR] Failed to download `http://current.geneontology.org/annotations/goa_human.gaf.gz` (attempt 1/3); error: embedded nul in string: '\037\x8b\b\b\x903)g\0\003goa_human.gaf\0ԝ[s\xdb8\xb2ǟ5\x9f\x82\xf3\xb6[u\xe8\020\027\x82\xa4\xab\u0383-ٱ\xe3K\024\xdbq./S\xb2L\xdb:#\x89^IΎ\xab\xf2\xe1\017H\xf0&'
[2025-02-09 18:51:44] [TRACE]   [OmnipathR] Attempt 2/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-09 18:51:44] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-09 18:51:45] [WARN]    [OmnipathR] Failed to download `http://current.geneontology.org/annotations/goa_human.gaf.gz` (attempt 2/3); error: embedded nul in string: '\037\x8b\b\b\x903)g\0\003goa_human.gaf\0ԝ[s\xdb8\xb2ǟ5\x9f\x82\xf3\xb6[u\xe8\020\027\x82\xa4\xab\u0383-ٱ\xe3K\024\xdbq./S\xb2L\xdb:#\x89^IΎ\xab\xf2\xe1\017H\xf0&'
[2025-02-09 18:51:50] [TRACE]   [OmnipathR] Attempt 3/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-09 18:51:50] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-09 18:51:51] [ERROR]   [OmnipathR] Failed to download `http://current.geneontology.org/annotations/goa_human.gaf.gz` (attempt 3/3); error: embedded nul in string: '\037\x8b\b\b\x903)g\0\003goa_human.gaf\0ԝ[s\xdb8\xb2ǟ5\x9f\x82\xf3\xb6[u\xe8\020\027\x82\xa4\xab\u0383-ٱ\xe3K\024\xdbq./S\xb2L\xdb:#\x89^IΎ\xab\xf2\xe1\017H\xf0&'
[2025-02-09 18:51:51] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-09 18:51:51] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-09
[2025-02-09 18:51:51] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-09 20:27:39 UTC; unix
[2025-02-09 18:51:51] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-09 18:51:51] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-09 18:51:51] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-22 r87618); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-09; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-02-09 18:51:51] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.42 2022-12-11; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-02-09 18:51:51] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE

Quitting from lines 80-102 [workflow] (wppi_workflow.Rmd)
Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics:
embedded nul in string: '\037\x8b\b\b\x903)g\0\003goa_human.gaf\0ԝ[s\xdb8\xb2ǟ5\x9f\x82\xf3\xb6[u\xe8\020\027\x82\xa4\xab\u0383-ٱ\xe3K\024\xdbq./S\xb2L\xdb:#\x89^IΎ\xab\xf2\xe1\017H\xf0&'
--- failed re-building ‘wppi_workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted