##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 OmnipathR
###
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* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* preparing ‘OmnipathR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
[2025-07-15 18:21:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 18:21:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:19] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-07-15 18:21:19] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-07-15 18:21:19] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-07-15
[2025-07-15 18:21:19] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-15 22:20:59 UTC; unix
[2025-07-15 18:21:19] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.3
[2025-07-15 18:21:19] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-07-15 18:21:19] [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); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-07-15; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-07-15 18:21:19] [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=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-07-15 18:21:19] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.37.0(2025-07-15); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.43(2025-04-15); 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); chromote 0.5.1(2025-04-24); 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); 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); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); 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); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); 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 18:21:19] [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 18:21:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-07-15 18:21:19] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-07-15 18:21:19] [TRACE]   [OmnipathR] Contains 1 files.
[2025-07-15 18:21:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-07-15 18:21:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 18:21:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-07-15 18:21:19] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-07-15 18:21:19] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpQg6KwZ/Rinst3058984e7e1ff7/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-07-15 18:21:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpQg6KwZ/Rinst3058984e7e1ff7/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpQg6KwZ/Rinst3058984e7e1ff7/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] Reading JSON from `/tmp/RtmpQg6KwZ/Rinst3058984e7e1ff7/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2025-07-15 18:21:20] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:20] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:20] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-07-15 18:21:20] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-15 18:21:20] [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 18:21:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-07-15 18:21:20] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] Downloaded 31.3 Kb in 1.036217s from www.ensembl.org (30.2 Kb/s); Redirect: 0.819029s, DNS look up: 0.024868s, Connection: 0.026671s, Pretransfer: 0.697521s, First byte at: 1.006818s
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Tue, 15 Jul 2025 22:21:20 GMT; Content-Type: text/html; charset=iso-8859-1; Content-Length: 288; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Location: //useast.ensembl.org/info/about/species.html?redirectsrc=//www.ensembl.org%2Finfo%2Fabout%2Fspecies.html; X-NGINX-MACHINE: wp-p1m2-35.ebi.ac.uk; HTTP/2 302 ; date: Tue, 15 Jul 2025 22:21:20 GMT; content-type: text/html; charset=iso-8859-1; content-length: 208; server: Apache; set-cookie: redirected_from_url=%2F%2Fwww.ensembl.org%252Finfo%252Fabout%252Fspecies.html; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; location: /info/about/species.html; x-nginx-machine: ip-10-25-25-86.us-east-2.compute.internal; HTTP/2 200 ; date: Tue, 15 Jul 2025 22:21:21 GMT; content-type: text/html; charset=utf-8; content-length: 32008; 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 22:15:58 GMT; set-cookie: ENSEMBL_WWW_SESSION=8296cc4d0ca1903b096d35e268c5ed1e055638d54462fa1ea2b1c26a; 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 22:15:58 GMT; set-cookie: ENSEMBL_WWW_SESSION=8296cc4d0ca1903b096d35e268c5ed1e055638d54462fa1ea2b1c26a; 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: ip-10-25-25-73.us-east-2.compute.internal
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] Response headers: [date=Tue, 15 Jul 2025 22:21:21 GMT,content-type=text/html; charset=utf-8,content-length=32008,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 22:15:58 GMT,set-cookie=ENSEMBL_WWW_SESSION=8296cc4d0ca1903b096d35e268c5ed1e055638d54462fa1ea2b1c26a; 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 22:15:58 GMT,set-cookie=ENSEMBL_WWW_SESSION=8296cc4d0ca1903b096d35e268c5ed1e055638d54462fa1ea2b1c26a; 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=ip-10-25-25-73.us-east-2.compute.internal]
[2025-07-15 18:21:21] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:21] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-07-15 18:21:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:21] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-07-15 18:21:21] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-07-15 18:21:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-07-15 18:21:21] [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 18:21:22] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-07-15 18:21:22] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.529705s from omabrowser.org (16.4 Kb/s); Redirect: 0s, DNS look up: 0.11374s, Connection: 0.11446s, Pretransfer: 0.443881s, First byte at: 0.52923s
[2025-07-15 18:21:22] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 15 Jul 2025 22:21:22 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 18:21:23] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-07-15 18:21:23] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-07-15 18:21:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 18:21:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:23] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-07-15 18:21:23] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-07-15 18:21:23] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-07-15 18:21:23] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-07-15 18:21:23] [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 18:21:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 18:21:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 18:21:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:23] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2025-07-15 18:21:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-07-15 18:21:23] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-07-15 18:21:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-07-15 18:21:51] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-07-15 18:21:51] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2025-07-15 18:21:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-15 18:21:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:51] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2025-07-15 18:21:51] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.

Quitting from bioc_workshop.Rmd:215-218 [network]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'bioc_workshop.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 ‘bioc_workshop.Rmd’

--- re-building ‘cosmos.Rmd’ using rmarkdown
[2025-07-15 18:21:52] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2025-07-15 18:21:52] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-07-15 18:21:52] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2025-07-15 18:21:52] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2025-07-15 18:21:52] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2025-07-15 18:21:52] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.

Quitting from cosmos.Rmd:175-179 [omnipath]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2025-07-15 18:21:52] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2025-07-15 18:21:52] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)

Quitting from db_manager.Rmd:66-69 [get]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2025-07-15 18:21:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-15 18:21:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2025-07-15 18:21:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-15 18:21:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]

Quitting from drug_targets.Rmd:45-51 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'drug_targets.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 ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2025-07-15 18:21:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-15 18:21:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]

Quitting from extra_attrs.Rmd:55-58 [load-interactions]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'extra_attrs.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 ‘extra_attrs.Rmd’

--- re-building ‘nichenet.Rmd’ using rmarkdown
--- finished re-building ‘nichenet.Rmd’

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2025-07-15 18:21:56] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-07-15 18:21:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-15 18:21:56] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-15 18:21:56] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2025-07-15 18:21:56] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-15 18:21:56] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]

Quitting from omnipath_intro.Rmd:166-175 [interactions]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'omnipath_intro.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 ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2025-07-15 18:21:56] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-07-15 18:21:56] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]

Quitting from paths.Rmd:55-67 [tfcensus-op]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'paths.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 ‘paths.Rmd’

SUMMARY: processing the following files failed:
  ‘bioc_workshop.Rmd’ ‘cosmos.Rmd’ ‘db_manager.Rmd’ ‘drug_targets.Rmd’ ‘extra_attrs.Rmd’
  ‘omnipath_intro.Rmd’ ‘paths.Rmd’

Error: Vignette re-building failed.
Execution halted