[ Started: 2025-02-05 20:45:41 CET ]
[ wppi v1.6.0 for BioC-3.20 from https://github.com/AnaGalhoz37/wppi@main (9b574a4 2022-11-02 08:18:02) ]

* checking for file ‘./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
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 20:45:52] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-02-05 20:45:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-04 17:36:54 UTC; omnipath
[2025-02-05 20:45:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-05 20:45:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.4.1; ; 2025-02-04 17:36:55 UTC; unix
[2025-02-05 20:45:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-05 20:45:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-05 20:45:52] [INFO]    [OmnipathR] Session info: [version=R version 4.4.1 (2024-06-14); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-05; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-05 20:45:52] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-05 20:45:52] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 20:45:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.20/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-05 20:45:52] [INFO]    [wppi] Executing WPPI workflow.
[2025-02-05 20:45:52] [INFO]    [wppi] Collecting database knowledge.
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-02-05 20:45:52] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 20:45:52] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-02-05 20:45:52] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-05 20:45:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-05 20:45:54] [TRACE]   [OmnipathR] Downloaded 18.8 Mb in 1.209409s from purl.obolibrary.org (15.6 Mb/s); Redirect: 0.650565s, DNS look up: 0.026858s, Connection: 0.043239s, Pretransfer: 0.140018s, First byte at: 0.791125s
[2025-02-05 20:45:55] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-02-05 20:45:55] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2025-02-05 20:45:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 20:45:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 20:45:55] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2025-02-05 20:45:55] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 316589 records
[2025-02-05 20:45:55] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-05 20:45:55] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-02-05 20:45:55] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-05 20:45:55] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-02-05 20:45:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 20:45:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 20:45:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 20:45:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-05 20:45:55] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2025-02-05 20:45:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-02-05 20:45:55] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-05 20:45:55] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-05 20:45:55] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-05 20:45:55] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-05 20:45:55] [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&'
[2025-02-05 20:46:00] [TRACE]   [OmnipathR] Attempt 2/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-05 20:46:00] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-05 20:46:00] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-05 20:46:00] [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&'
[2025-02-05 20:46:05] [TRACE]   [OmnipathR] Attempt 3/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-05 20:46:05] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-05 20:46:05] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-05 20:46:06] [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&'
[2025-02-05 20:46:06] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-02-04 17:36:54 UTC; omnipath
[2025-02-05 20:46:06] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-02-05 20:46:06] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.4.1; ; 2025-02-04 17:36:55 UTC; unix
[2025-02-05 20:46:06] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-05 20:46:06] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-02-05 20:46:06] [INFO]    [OmnipathR] Session info: [version=R version 4.4.1 (2024-06-14); os=Ubuntu 24.04 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-02-05; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-02-05 20:46:06] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-05 20:46:06] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; 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
[ Finished: 2025-02-05 20:46:06 CET ]