[ Started: 2025-07-15 19:49:27 CEST ]
[ wppi v1.6.0 for BioC-3.22 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
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:38] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2025-07-15 19:49:38] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2025-07-15 17:08:41 UTC; omnipath
[2025-07-15 19:49:38] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2025-07-15 19:49:38] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-15 17:08:43 UTC; unix
[2025-07-15 19:49:38] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.3
[2025-07-15 19:49:38] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2025-07-15 19:49:38] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-07-15; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2025-07-15 19:49:38] [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]
[2025-07-15 19:49:38] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.0(2025-07-13); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.17.3(2025-07-15); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.1(2025-06-08); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); wppi 1.6.0(2025-07-15); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-07-15 19:49:38] [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
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] Contains 1 files.
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-07-15 19:49:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-07-15 19:49:39] [INFO]    [wppi] Executing WPPI workflow.
[2025-07-15 19:49:39] [INFO]    [wppi] Collecting database knowledge.
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-07-15 19:49:39] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:39] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-07-15 19:49:39] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-15 19:49:39] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-15 19:49:40] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-07-15 19:49:40] [TRACE]   [OmnipathR] Downloaded 14.8 Kb in 0.845717s from purl.obolibrary.org (17.5 Kb/s); Redirect: 0.689606s, DNS look up: 0.036808s, Connection: 0.053281s, Pretransfer: 0.152114s, First byte at: 0.844778s
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[2025-07-15 19:49:41] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-07-15 19:49:41] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:41] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2025-07-15 19:49:41] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 316793 records
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-07-15 19:49:41] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:41] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-07-15 19:49:41] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-15 19:49:41] [TRACE]   [OmnipathR] `gz` compressed file, downloading to temporary location: `/tmp/Rtmp2baXsc/goa_human.gaf.gz`
[2025-07-15 19:49:42] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-15 19:49:42] [TRACE]   [OmnipathR] Downloaded 14.7 Mb in 0.456321s from current.geneontology.org (32.2 Mb/s); Redirect: 0s, DNS look up: 0.058675s, Connection: 0.065862s, Pretransfer: 0.065954s, First byte at: 0.280611s
[2025-07-15 19:49:42] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Content-Type: application/gzip; Content-Length: 15423314; Connection: keep-alive; x-amz-meta-build-pipeline: release; x-amz-meta-build-number: 379; Last-Modified: Fri, 06 Jun 2025 23:42:54 GMT; Server: AmazonS3; Date: Tue, 15 Jul 2025 17:49:43 GMT; ETag: "2562cecdaf6a74ed6ff6e92964a9ec37-2"; X-Cache: RefreshHit from cloudfront; Via: 1.1 f996db233b87d6765cc5ad56701268d8.cloudfront.net (CloudFront); X-Amz-Cf-Pop: FRA56-P8; X-Amz-Cf-Id: NeEUNHXlq6AxsLiDd8_3fgTooH0SR5wdBsgo7b61uFDEp0Bm-j7Sfw==
[2025-07-15 19:49:50] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-07-15 19:49:50] [INFO]    [OmnipathR] Download ready [key=4dccec1f0141d8846ba49e6f0eada25ebf0253fa, version=1]
[2025-07-15 19:49:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:50] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `started` to `ready`.
[2025-07-15 19:49:51] [SUCCESS] [OmnipathR] Gene Ontology (current.geneontology.org): downloaded 993512 records
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [entity_types=protein,query_type=interactions]
[2025-07-15 19:49:51] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:51] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:51] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-07-15 19:49:51] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Downloaded 31.2 Kb in 0.215849s from www.ensembl.org (144.5 Kb/s); Redirect: 0s, DNS look up: 0.001524s, Connection: 0.019901s, Pretransfer: 0.073154s, First byte at: 0.192s
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Tue, 15 Jul 2025 17:49:51 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31929; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 16 Jul 2025 17:49:51 GMT; Set-cookie: ENSEMBL_HINX_SESSION=f6c600732748068d0896ed6168c5aebf014d05285fc40ec1100e71b5; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Wed, 16 Jul 2025 17:49:51 GMT; Set-cookie: ENSEMBL_HINX_SESSION=f6c600732748068d0896ed6168c5aebf014d05285fc40ec1100e71b5; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-32.ebi.ac.uk
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Response headers: [Date=Tue, 15 Jul 2025 17:49:51 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31929,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 16 Jul 2025 17:49:51 GMT,Set-cookie=ENSEMBL_HINX_SESSION=f6c600732748068d0896ed6168c5aebf014d05285fc40ec1100e71b5; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Wed, 16 Jul 2025 17:49:51 GMT,Set-cookie=ENSEMBL_HINX_SESSION=f6c600732748068d0896ed6168c5aebf014d05285fc40ec1100e71b5; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-32.ebi.ac.uk]
[2025-07-15 19:49:51] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:51] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-07-15 19:49:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:51] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-07-15 19:49:51] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] Downloaded 7.8 Kb in 0.065602s from omabrowser.org (118.9 Kb/s); Redirect: 0s, DNS look up: 0.000839s, Connection: 0.01241s, Pretransfer: 0.045467s, First byte at: 0.065472s
[2025-07-15 19:49:51] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 15 Jul 2025 17:49:51 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-07-15 19:49:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-07-15 19:49:52] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-07-15 19:49:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:52] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-07-15 19:49:52] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-07-15 19:49:52] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-07-15 19:49:52] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-07-15 19:49:52] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-07-15 19:49:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:49:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:49:52] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2025-07-15 19:49:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-07-15 19:49:52] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-07-15 19:49:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-07-15 19:50:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-07-15 19:50:14] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2025-07-15 19:50:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 19:50:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 19:50:14] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2025-07-15 19:50:14] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.

Quitting from wppi_workflow.Rmd:79-102 [workflow]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error:
! Can't coerce from a string to an integer.
--- failed re-building ‘wppi_workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
[ Finished: 2025-07-15 19:50:14 CEST ]