[ Started: 2026-07-10 20:28:25 CEST ] [ OmnipathR v3.18.4 for BioC-3.22 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_22 (efaae39 2026-01-20 15:40:26) ] * checking for file ‘./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 [2026-07-10 20:28:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-07-10 20:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-07-10 20:28:41] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-07-10 20:28:41] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-07-10 20:28:41] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-07-10 20:28:41] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-07-10 18:28:26 UTC; unix [2026-07-10 20:28:41] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-07-10 20:28:41] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-07-10 20:28:41] [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=2026-07-10; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-07-10 20:28:41] [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] [2026-07-10 20:28:41] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.27(2025-11-14); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.47(2026-06-16); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.3(2026-06-23); igraph 2.3.3(2026-06-26); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-07-10); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); 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 0.3.4(2026-01-17); Rcpp 1.1.2(2026-07-05); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.3.0(2026-07-05); rmarkdown 2.31(2026-03-26); RSQLite 3.53.3(2026-06-30); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.4(2026-06-04); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.3(2026-06-19); xfun 0.60(2026-07-09); XML 3.99-0.23(2026-03-20); xml2 1.6.0(2026-06-22); yaml 2.3.12(2025-12-10); zip 3.0.0(2026-06-10) [2026-07-10 20:28:41] [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 [2026-07-10 20:28:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-07-10 20:28:41] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-07-10 20:28:41] [TRACE] [OmnipathR] Contains 1 files. [2026-07-10 20:28:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-07-10 20:28:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-07-10 20:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-07-10 20:28:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-07-10 20:28:41] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-07-10 20:28:41] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpIvOwHC/Rinst35c12c563d4201/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-07-10 20:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-07-10 20:28:41] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpIvOwHC/Rinst35c12c563d4201/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-07-10 20:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-07-10 20:28:41] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpIvOwHC/Rinst35c12c563d4201/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-07-10 20:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-07-10 20:28:41] [TRACE] [OmnipathR] Reading JSON from `/tmp/RtmpIvOwHC/Rinst35c12c563d4201/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-07-10 20:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-07-10 20:28:41] [TRACE] [OmnipathR] Cache locked: FALSE [2026-07-10 20:28:41] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-07-10 20:28:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2026-07-10 20:28:41] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-07-10 20:28:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-07-10 20:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-07-10 20:28:41] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-07-10 20:28:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-07-10 20:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-07-10 20:28:41] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-07-10 20:28:41] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-07-10 20:28:41] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-07-10 20:28:41] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-07-10 20:28:41] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-07-10 20:28:41] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-07-10 20:28:41] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-07-10 20:28:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-07-10 20:28:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-07-10 20:28:41] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-07-10 20:28:41] [TRACE] [OmnipathR] Sending HTTP request. [2026-07-10 20:28:41] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-07-10 20:28:41] [TRACE] [OmnipathR] No downlad stats available: no curl handle. [2026-07-10 20:28:41] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 10 Jul 2026 18:28:41 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Fri, 10 Jul 2026 19:28:41 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-07-10 20:28:41] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-07-10 20:28:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-07-10 20:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-07-10 20:28:41] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-07-10 20:28:41] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-07-10 20:28:41] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-07-10 20:28:41] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-07-10 20:28:41] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-07-10 20:28:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-07-10 20:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-07-10 20:28:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-07-10 20:28:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-07-10 20:28:42] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-07-10 20:28:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-07-10 20:28:42] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-07-10 20:28:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-07-10 20:28:42] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-07-10 20:28:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-07-10 20:28:42] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-07-10 20:28:42] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-07-10 20:28:42] [TRACE] [OmnipathR] Downloaded 31.7 Kb in 0.079904s from omabrowser.org (396.9 Kb/s); Redirect: 0s, DNS look up: 0.000603s, Connection: 0.006599s, Pretransfer: 0.040856s, First byte at: 0.079278s [2026-07-10 20:28:42] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 10 Jul 2026 18:28:42 GMT; content-type: text/plain; server: cloudflare; last-modified: Thu, 16 Apr 2026 06:12:03 GMT; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; etag: W/"69e07db3-657c0"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=EW1WpX97DxoE%2FnzxQ40gkOEXxD7Rgf6VuyhSCO%2B1CpdcZLfcbixnhpFuPrUkfsNLsBHNIpW86nV9a4csPPl0vbx8Ho7VZ3V%2BnK8HA3f3diL%2BFsPfVZzdXfMIgsJ1WP1n"}]}; cf-ray: a191a1332af3d394-FRA [2026-07-10 20:28:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-07-10 20:28:42] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-07-10 20:28:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-07-10 20:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-07-10 20:28:42] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. Quitting from bioc_workshop.Rmd:215-218 [network] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `map_int()`: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. --- Backtrace: ▆ 1. ├─OmnipathR::transcriptional() 2. │ ├─rlang::exec(omnipath_query, !!!args) 3. │ └─OmnipathR (local) ``(...) 4. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 5. ├─OmnipathR:::omnipath_check_param(.) 6. │ └─param$organisms %<>% map_int(ncbi_taxid) 7. ├─purrr::map_int(., ncbi_taxid) 8. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 9. │ ├─purrr:::with_indexed_errors(...) 10. │ │ └─base::withCallingHandlers(...) 11. │ ├─purrr:::call_with_cleanup(...) 12. │ └─OmnipathR (local) .f(.x[[i]], ...) 13. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 14. ├─purrr::map_int(., taxon_name, "ncbi") 15. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 16. │ ├─purrr:::with_indexed_errors(...) 17. │ │ └─base::withCallingHandlers(...) 18. │ ├─purrr:::call_with_cleanup(...) 19. │ └─OmnipathR (local) .f(.x[[i]], ...) 20. │ ├─... %>% if_null_len0(NA) 21. │ └─OmnipathR::get_db("organisms") 22. │ └─OmnipathR::load_db(key, param = param) 23. │ ├─rlang::exec(loader, !!!param) 24. │ └─OmnipathR (local) ``() 25. │ └─... %>% ... 26. ├─OmnipathR:::if_null_len0(., NA) 27. │ └─value1 %>% is_empty_2 %>% if (value2) value1 28. ├─OmnipathR:::is_empty_2(.) 29. │ └─value %>% ... 30. ├─dplyr::pull(., name_type) 31. ├─dplyr::filter(...) 32. ├─dplyr::mutate(...) 33. ├─dplyr::full_join(...) 34. ├─dplyr::full_join(...) 35. ├─dplyr:::full_join.data.frame(...) 36. │ └─dplyr:::join_mutate(...) 37. │ └─dplyr:::join_cols(...) 38. │ └─dplyr:::check_join_vars(by$y, y_names, by$condition, "y", error_call = error_call) 39. │ └─rlang::abort(bullets, call = error_call) 40. │ └─rlang:::signal_abort(cnd, .file) 41. │ └─base::signalCondition(cnd) 42. └─purrr (local) ``(``) 43. └─cli::cli_abort(...) Caused by error in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- Backtrace: ▆ 1. ├─OmnipathR::transcriptional() 2. │ ├─rlang::exec(omnipath_query, !!!args) 3. │ └─OmnipathR (local) ``(...) 4. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 5. ├─OmnipathR:::omnipath_check_param(.) 6. │ └─param$organisms %<>% map_int(ncbi_taxid) 7. ├─purrr::map_int(., ncbi_taxid) 8. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 9. │ ├─purrr:::with_indexed_errors(...) 10. │ │ └─base::withCallingHandlers(...) 11. │ ├─purrr:::call_with_cleanup(...) 12. │ └─OmnipathR (local) .f(.x[[i]], ...) 13. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 14. ├─purrr::map_int(., taxon_name, "ncbi") 15. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 16. │ ├─purrr:::with_indexed_errors(...) 17. │ │ └─base::withCallingHandlers(...) 18. │ ├─purrr:::call_with_cleanup(...) 19. │ └─OmnipathR (local) .f(.x[[i]], ...) 20. │ ├─... %>% if_null_len0(NA) 21. │ └─OmnipathR::get_db("organisms") 22. │ └─OmnipathR::load_db(key, param = param) 23. │ ├─rlang::exec(loader, !!!param) 24. │ └─OmnipathR (local) ``() 25. │ └─... %>% ... 26. ├─OmnipathR:::if_null_len0(., NA) 27. │ └─value1 %>% is_empty_2 %>% if (value2) value1 28. ├─OmnipathR:::is_empty_2(.) 29. │ └─value %>% ... 30. ├─dplyr::pull(., name_type) 31. ├─dplyr::filter(...) 32. ├─dplyr::mutate(...) 33. ├─dplyr::full_join(...) 34. ├─dplyr::full_join(...) 35. └─dplyr:::full_join.data.frame(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- failed re-building ‘bioc_workshop.Rmd’ --- re-building ‘cosmos.Rmd’ using rmarkdown [2026-07-10 20:28:44] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2026-07-10 20:28:44] [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. [2026-07-10 20:28:45] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2026-07-10 20:28:45] [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. [2026-07-10 20:28:45] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2026-07-10 20:28:45] [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. [2026-07-10 20:28:45] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-07-10 20:28:45] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, latest version=1. [2026-07-10 20:28:45] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-07-10 20:28:45] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-07-10 20:28:45] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-07-10 20:28:45] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. Quitting from cosmos.Rmd:175-179 [omnipath] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `map_int()`: ℹ In index: 1. Caused by error in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- Backtrace: ▆ 1. ├─OmnipathR::omnipath_for_cosmos() 2. │ └─organism %<>% organism_for("omnipath") 3. ├─OmnipathR::organism_for(., "omnipath") 4. │ └─get(resource_info$check_by_id)(organism) 5. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 6. ├─purrr::map_int(., taxon_name, "ncbi") 7. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 8. │ ├─purrr:::with_indexed_errors(...) 9. │ │ └─base::withCallingHandlers(...) 10. │ ├─purrr:::call_with_cleanup(...) 11. │ └─OmnipathR (local) .f(.x[[i]], ...) 12. │ ├─... %>% if_null_len0(NA) 13. │ └─OmnipathR::get_db("organisms") 14. │ └─OmnipathR::load_db(key, param = param) 15. │ ├─rlang::exec(loader, !!!param) 16. │ └─OmnipathR (local) ``() 17. │ └─... %>% ... 18. ├─OmnipathR:::if_null_len0(., NA) 19. │ └─value1 %>% is_empty_2 %>% if (value2) value1 20. ├─OmnipathR:::is_empty_2(.) 21. │ └─value %>% ... 22. ├─dplyr::pull(., name_type) 23. ├─dplyr::filter(...) 24. ├─dplyr::mutate(...) 25. ├─dplyr::full_join(...) 26. ├─dplyr::full_join(...) 27. └─dplyr:::full_join.data.frame(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'cosmos.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- failed re-building ‘cosmos.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2026-07-10 20:28:45] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2026-07-10 20:28:45] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-07-10 20:28:45] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-07-10 20:28:45] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, latest version=1. [2026-07-10 20:28:45] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-07-10 20:28:45] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-07-10 20:28:45] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-07-10 20:28:45] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. Quitting from db_manager.Rmd:66-69 [get] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `map_int()`: ℹ In index: 1. Caused by error in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- Backtrace: ▆ 1. ├─OmnipathR::get_db("up_gs") 2. │ └─OmnipathR::load_db(key, param = param) 3. │ ├─rlang::exec(loader, !!!param) 4. │ └─OmnipathR (local) ``(to = "genesymbol", organism = 9606L) 5. │ └─... %>% trim_and_distinct 6. ├─OmnipathR:::trim_and_distinct(.) 7. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct 8. ├─dplyr::distinct(.) 9. ├─dplyr::mutate(., across(everything(), str_trim)) 10. ├─dplyr::filter(., !is.na(From) & !is.na(To)) 11. ├─tidyr::separate_rows(., To, sep = "[; ]") 12. ├─tidyr::separate_rows(., From, sep = "[; ]") 13. ├─dplyr::mutate(., From = strip_semicol(From), To = strip_semicol(To)) 14. ├─dplyr::rename(., From = 1, To = 2) 15. ├─OmnipathR::all_uniprots(., reviewed = reviewed, organism = organism) 16. │ └─organism %<>% ncbi_taxid 17. ├─OmnipathR::ncbi_taxid(.) 18. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 19. ├─purrr::map_int(., taxon_name, "ncbi") 20. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 21. │ ├─purrr:::with_indexed_errors(...) 22. │ │ └─base::withCallingHandlers(...) 23. │ ├─purrr:::call_with_cleanup(...) 24. │ └─OmnipathR (local) .f(.x[[i]], ...) 25. │ ├─... %>% if_null_len0(NA) 26. │ └─OmnipathR::get_db("organisms") 27. │ └─OmnipathR::load_db(key, param = param) 28. │ ├─rlang::exec(loader, !!!param) 29. │ └─OmnipathR (local) ``() 30. │ └─... %>% ... 31. ├─OmnipathR:::if_null_len0(., NA) 32. │ └─value1 %>% is_empty_2 %>% if (value2) value1 33. ├─OmnipathR:::is_empty_2(.) 34. │ └─value %>% ... 35. ├─dplyr::pull(., name_type) 36. ├─dplyr::filter(...) 37. ├─dplyr::mutate(...) 38. ├─dplyr::full_join(...) 39. ├─dplyr::full_join(...) 40. └─dplyr:::full_join.data.frame(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'db_manager.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- failed re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2026-07-10 20:28:47] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-07-10 20:28:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-07-10 20:28:47] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-07-10 20:28:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-07-10 20:28:47] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-07-10 20:28:47] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, latest version=1. [2026-07-10 20:28:47] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-07-10 20:28:47] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-07-10 20:28:47] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-07-10 20:28:47] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. Quitting from drug_targets.Rmd:45-51 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `map_int()`: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. --- Backtrace: ▆ 1. ├─omnipath() %>% as_tibble() 2. ├─tibble::as_tibble(.) 3. ├─OmnipathR::omnipath() 4. │ ├─rlang::exec(omnipath_interactions, !!!args) 5. │ └─OmnipathR (local) ``(datasets = "omnipath") 6. │ ├─rlang::exec(omnipath_query, !!!args) 7. │ └─OmnipathR (local) ``(datasets = "omnipath", query_type = "interactions") 8. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 9. ├─OmnipathR:::omnipath_check_param(.) 10. │ └─param$organisms %<>% map_int(ncbi_taxid) 11. ├─purrr::map_int(., ncbi_taxid) 12. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 13. │ ├─purrr:::with_indexed_errors(...) 14. │ │ └─base::withCallingHandlers(...) 15. │ ├─purrr:::call_with_cleanup(...) 16. │ └─OmnipathR (local) .f(.x[[i]], ...) 17. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 18. ├─purrr::map_int(., taxon_name, "ncbi") 19. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 20. │ ├─purrr:::with_indexed_errors(...) 21. │ │ └─base::withCallingHandlers(...) 22. │ ├─purrr:::call_with_cleanup(...) 23. │ └─OmnipathR (local) .f(.x[[i]], ...) 24. │ ├─... %>% if_null_len0(NA) 25. │ └─OmnipathR::get_db("organisms") 26. │ └─OmnipathR::load_db(key, param = param) 27. │ ├─rlang::exec(loader, !!!param) 28. │ └─OmnipathR (local) ``() 29. │ └─... %>% ... 30. ├─OmnipathR:::if_null_len0(., NA) 31. │ └─value1 %>% is_empty_2 %>% if (value2) value1 32. ├─OmnipathR:::is_empty_2(.) 33. │ └─value %>% ... 34. ├─dplyr::pull(., name_type) 35. ├─dplyr::filter(...) 36. ├─dplyr::mutate(...) 37. ├─dplyr::full_join(...) 38. ├─dplyr::full_join(...) 39. ├─dplyr:::full_join.data.frame(...) 40. │ └─dplyr:::join_mutate(...) 41. │ └─dplyr:::join_cols(...) 42. │ └─dplyr:::check_join_vars(by$y, y_names, by$condition, "y", error_call = error_call) 43. │ └─rlang::abort(bullets, call = error_call) 44. │ └─rlang:::signal_abort(cnd, .file) 45. │ └─base::signalCondition(cnd) 46. └─purrr (local) ``(``) 47. └─cli::cli_abort(...) Caused by error in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- Backtrace: ▆ 1. ├─omnipath() %>% as_tibble() 2. ├─tibble::as_tibble(.) 3. ├─OmnipathR::omnipath() 4. │ ├─rlang::exec(omnipath_interactions, !!!args) 5. │ └─OmnipathR (local) ``(datasets = "omnipath") 6. │ ├─rlang::exec(omnipath_query, !!!args) 7. │ └─OmnipathR (local) ``(datasets = "omnipath", query_type = "interactions") 8. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 9. ├─OmnipathR:::omnipath_check_param(.) 10. │ └─param$organisms %<>% map_int(ncbi_taxid) 11. ├─purrr::map_int(., ncbi_taxid) 12. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 13. │ ├─purrr:::with_indexed_errors(...) 14. │ │ └─base::withCallingHandlers(...) 15. │ ├─purrr:::call_with_cleanup(...) 16. │ └─OmnipathR (local) .f(.x[[i]], ...) 17. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 18. ├─purrr::map_int(., taxon_name, "ncbi") 19. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 20. │ ├─purrr:::with_indexed_errors(...) 21. │ │ └─base::withCallingHandlers(...) 22. │ ├─purrr:::call_with_cleanup(...) 23. │ └─OmnipathR (local) .f(.x[[i]], ...) 24. │ ├─... %>% if_null_len0(NA) 25. │ └─OmnipathR::get_db("organisms") 26. │ └─OmnipathR::load_db(key, param = param) 27. │ ├─rlang::exec(loader, !!!param) 28. │ └─OmnipathR (local) ``() 29. │ └─... %>% ... 30. ├─OmnipathR:::if_null_len0(., NA) 31. │ └─value1 %>% is_empty_2 %>% if (value2) value1 32. ├─OmnipathR:::is_empty_2(.) 33. │ └─value %>% ... 34. ├─dplyr::pull(., name_type) 35. ├─dplyr::filter(...) 36. ├─dplyr::mutate(...) 37. ├─dplyr::full_join(...) 38. ├─dplyr::full_join(...) 39. └─dplyr:::full_join.data.frame(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- failed re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2026-07-10 20:28:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-07-10 20:28:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2026-07-10 20:28:50] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-07-10 20:28:50] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, latest version=1. [2026-07-10 20:28:50] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-07-10 20:28:50] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-07-10 20:28:50] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-07-10 20:28:50] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. Quitting from extra_attrs.Rmd:55-58 [load-interactions] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `map_int()`: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. --- Backtrace: ▆ 1. ├─OmnipathR::post_translational(fields = "extra_attrs") 2. │ ├─rlang::exec(omnipath_query, !!!args) 3. │ └─OmnipathR (local) ``(fields = "extra_attrs", query_type = "interactions", datasets = ``) 4. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 5. ├─OmnipathR:::omnipath_check_param(.) 6. │ └─param$organisms %<>% map_int(ncbi_taxid) 7. ├─purrr::map_int(., ncbi_taxid) 8. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 9. │ ├─purrr:::with_indexed_errors(...) 10. │ │ └─base::withCallingHandlers(...) 11. │ ├─purrr:::call_with_cleanup(...) 12. │ └─OmnipathR (local) .f(.x[[i]], ...) 13. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 14. ├─purrr::map_int(., taxon_name, "ncbi") 15. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 16. │ ├─purrr:::with_indexed_errors(...) 17. │ │ └─base::withCallingHandlers(...) 18. │ ├─purrr:::call_with_cleanup(...) 19. │ └─OmnipathR (local) .f(.x[[i]], ...) 20. │ ├─... %>% if_null_len0(NA) 21. │ └─OmnipathR::get_db("organisms") 22. │ └─OmnipathR::load_db(key, param = param) 23. │ ├─rlang::exec(loader, !!!param) 24. │ └─OmnipathR (local) ``() 25. │ └─... %>% ... 26. ├─OmnipathR:::if_null_len0(., NA) 27. │ └─value1 %>% is_empty_2 %>% if (value2) value1 28. ├─OmnipathR:::is_empty_2(.) 29. │ └─value %>% ... 30. ├─dplyr::pull(., name_type) 31. ├─dplyr::filter(...) 32. ├─dplyr::mutate(...) 33. ├─dplyr::full_join(...) 34. ├─dplyr::full_join(...) 35. ├─dplyr:::full_join.data.frame(...) 36. │ └─dplyr:::join_mutate(...) 37. │ └─dplyr:::join_cols(...) 38. │ └─dplyr:::check_join_vars(by$y, y_names, by$condition, "y", error_call = error_call) 39. │ └─rlang::abort(bullets, call = error_call) 40. │ └─rlang:::signal_abort(cnd, .file) 41. │ └─base::signalCondition(cnd) 42. └─purrr (local) ``(``) 43. └─cli::cli_abort(...) Caused by error in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- Backtrace: ▆ 1. ├─OmnipathR::post_translational(fields = "extra_attrs") 2. │ ├─rlang::exec(omnipath_query, !!!args) 3. │ └─OmnipathR (local) ``(fields = "extra_attrs", query_type = "interactions", datasets = ``) 4. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 5. ├─OmnipathR:::omnipath_check_param(.) 6. │ └─param$organisms %<>% map_int(ncbi_taxid) 7. ├─purrr::map_int(., ncbi_taxid) 8. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 9. │ ├─purrr:::with_indexed_errors(...) 10. │ │ └─base::withCallingHandlers(...) 11. │ ├─purrr:::call_with_cleanup(...) 12. │ └─OmnipathR (local) .f(.x[[i]], ...) 13. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 14. ├─purrr::map_int(., taxon_name, "ncbi") 15. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 16. │ ├─purrr:::with_indexed_errors(...) 17. │ │ └─base::withCallingHandlers(...) 18. │ ├─purrr:::call_with_cleanup(...) 19. │ └─OmnipathR (local) .f(.x[[i]], ...) 20. │ ├─... %>% if_null_len0(NA) 21. │ └─OmnipathR::get_db("organisms") 22. │ └─OmnipathR::load_db(key, param = param) 23. │ ├─rlang::exec(loader, !!!param) 24. │ └─OmnipathR (local) ``() 25. │ └─... %>% ... 26. ├─OmnipathR:::if_null_len0(., NA) 27. │ └─value1 %>% is_empty_2 %>% if (value2) value1 28. ├─OmnipathR:::is_empty_2(.) 29. │ └─value %>% ... 30. ├─dplyr::pull(., name_type) 31. ├─dplyr::filter(...) 32. ├─dplyr::mutate(...) 33. ├─dplyr::full_join(...) 34. ├─dplyr::full_join(...) 35. └─dplyr:::full_join.data.frame(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- failed re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown [2026-07-10 20:28:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-07-10 20:28:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-07-10 20:28:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-07-10 20:28:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2026-07-10 20:28:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-07-10 20:28:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2026-07-10 20:28:54] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-07-10 20:28:54] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, latest version=1. [2026-07-10 20:28:54] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-07-10 20:28:54] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-07-10 20:28:54] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-07-10 20:28:54] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. Quitting from omnipath_intro.Rmd:166-175 [interactions] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `map_int()`: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. --- Backtrace: ▆ 1. ├─OmnipathR::omnipath(...) 2. │ ├─rlang::exec(omnipath_interactions, !!!args) 3. │ └─OmnipathR (local) ``(resources = ``, datasets = "omnipath") 4. │ ├─rlang::exec(omnipath_query, !!!args) 5. │ └─OmnipathR (local) ``(datasets = "omnipath", resources = ``, query_type = "interactions") 6. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 7. ├─OmnipathR:::omnipath_check_param(.) 8. │ └─param$organisms %<>% map_int(ncbi_taxid) 9. ├─purrr::map_int(., ncbi_taxid) 10. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 11. │ ├─purrr:::with_indexed_errors(...) 12. │ │ └─base::withCallingHandlers(...) 13. │ ├─purrr:::call_with_cleanup(...) 14. │ └─OmnipathR (local) .f(.x[[i]], ...) 15. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 16. ├─purrr::map_int(., taxon_name, "ncbi") 17. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 18. │ ├─purrr:::with_indexed_errors(...) 19. │ │ └─base::withCallingHandlers(...) 20. │ ├─purrr:::call_with_cleanup(...) 21. │ └─OmnipathR (local) .f(.x[[i]], ...) 22. │ ├─... %>% if_null_len0(NA) 23. │ └─OmnipathR::get_db("organisms") 24. │ └─OmnipathR::load_db(key, param = param) 25. │ ├─rlang::exec(loader, !!!param) 26. │ └─OmnipathR (local) ``() 27. │ └─... %>% ... 28. ├─OmnipathR:::if_null_len0(., NA) 29. │ └─value1 %>% is_empty_2 %>% if (value2) value1 30. ├─OmnipathR:::is_empty_2(.) 31. │ └─value %>% ... 32. ├─dplyr::pull(., name_type) 33. ├─dplyr::filter(...) 34. ├─dplyr::mutate(...) 35. ├─dplyr::full_join(...) 36. ├─dplyr::full_join(...) 37. ├─dplyr:::full_join.data.frame(...) 38. │ └─dplyr:::join_mutate(...) 39. │ └─dplyr:::join_cols(...) 40. │ └─dplyr:::check_join_vars(by$y, y_names, by$condition, "y", error_call = error_call) 41. │ └─rlang::abort(bullets, call = error_call) 42. │ └─rlang:::signal_abort(cnd, .file) 43. │ └─base::signalCondition(cnd) 44. └─purrr (local) ``(``) 45. └─cli::cli_abort(...) Caused by error in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- Backtrace: ▆ 1. ├─OmnipathR::omnipath(...) 2. │ ├─rlang::exec(omnipath_interactions, !!!args) 3. │ └─OmnipathR (local) ``(resources = ``, datasets = "omnipath") 4. │ ├─rlang::exec(omnipath_query, !!!args) 5. │ └─OmnipathR (local) ``(datasets = "omnipath", resources = ``, query_type = "interactions") 6. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 7. ├─OmnipathR:::omnipath_check_param(.) 8. │ └─param$organisms %<>% map_int(ncbi_taxid) 9. ├─purrr::map_int(., ncbi_taxid) 10. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 11. │ ├─purrr:::with_indexed_errors(...) 12. │ │ └─base::withCallingHandlers(...) 13. │ ├─purrr:::call_with_cleanup(...) 14. │ └─OmnipathR (local) .f(.x[[i]], ...) 15. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 16. ├─purrr::map_int(., taxon_name, "ncbi") 17. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 18. │ ├─purrr:::with_indexed_errors(...) 19. │ │ └─base::withCallingHandlers(...) 20. │ ├─purrr:::call_with_cleanup(...) 21. │ └─OmnipathR (local) .f(.x[[i]], ...) 22. │ ├─... %>% if_null_len0(NA) 23. │ └─OmnipathR::get_db("organisms") 24. │ └─OmnipathR::load_db(key, param = param) 25. │ ├─rlang::exec(loader, !!!param) 26. │ └─OmnipathR (local) ``() 27. │ └─... %>% ... 28. ├─OmnipathR:::if_null_len0(., NA) 29. │ └─value1 %>% is_empty_2 %>% if (value2) value1 30. ├─OmnipathR:::is_empty_2(.) 31. │ └─value %>% ... 32. ├─dplyr::pull(., name_type) 33. ├─dplyr::filter(...) 34. ├─dplyr::mutate(...) 35. ├─dplyr::full_join(...) 36. ├─dplyr::full_join(...) 37. └─dplyr:::full_join.data.frame(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- failed re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2026-07-10 20:28:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-07-10 20:28:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2026-07-10 20:28:56] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-07-10 20:28:56] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, latest version=1. [2026-07-10 20:28:56] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-07-10 20:28:56] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-07-10 20:28:56] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-07-10 20:28:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. Quitting from paths.Rmd:55-67 [tfcensus-op] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `map_int()`: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. --- Backtrace: ▆ 1. ├─... %>% unique 2. ├─base::unique(.) 3. ├─dplyr::pull(., genesymbol) 4. ├─OmnipathR::annotations(resources = "TFcensus", entity_types = "protein") 5. │ ├─rlang::exec(omnipath_query, proteins = proteins, !!!args) 6. │ └─OmnipathR (local) ``(...) 7. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 8. ├─OmnipathR:::omnipath_check_param(.) 9. │ └─param$organisms %<>% map_int(ncbi_taxid) 10. ├─purrr::map_int(., ncbi_taxid) 11. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 12. │ ├─purrr:::with_indexed_errors(...) 13. │ │ └─base::withCallingHandlers(...) 14. │ ├─purrr:::call_with_cleanup(...) 15. │ └─OmnipathR (local) .f(.x[[i]], ...) 16. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 17. ├─purrr::map_int(., taxon_name, "ncbi") 18. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 19. │ ├─purrr:::with_indexed_errors(...) 20. │ │ └─base::withCallingHandlers(...) 21. │ ├─purrr:::call_with_cleanup(...) 22. │ └─OmnipathR (local) .f(.x[[i]], ...) 23. │ ├─... %>% if_null_len0(NA) 24. │ └─OmnipathR::get_db("organisms") 25. │ └─OmnipathR::load_db(key, param = param) 26. │ ├─rlang::exec(loader, !!!param) 27. │ └─OmnipathR (local) ``() 28. │ └─... %>% ... 29. ├─OmnipathR:::if_null_len0(., NA) 30. │ └─value1 %>% is_empty_2 %>% if (value2) value1 31. ├─OmnipathR:::is_empty_2(.) 32. │ └─value %>% ... 33. ├─dplyr::pull(., name_type) 34. ├─dplyr::filter(...) 35. ├─dplyr::mutate(...) 36. ├─dplyr::full_join(...) 37. ├─dplyr::full_join(...) 38. ├─dplyr:::full_join.data.frame(...) 39. │ └─dplyr:::join_mutate(...) 40. │ └─dplyr:::join_cols(...) 41. │ └─dplyr:::check_join_vars(by$y, y_names, by$condition, "y", error_call = error_call) 42. │ └─rlang::abort(bullets, call = error_call) 43. │ └─rlang:::signal_abort(cnd, .file) 44. │ └─base::signalCondition(cnd) 45. └─purrr (local) ``(``) 46. └─cli::cli_abort(...) Caused by error in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- Backtrace: ▆ 1. ├─... %>% unique 2. ├─base::unique(.) 3. ├─dplyr::pull(., genesymbol) 4. ├─OmnipathR::annotations(resources = "TFcensus", entity_types = "protein") 5. │ ├─rlang::exec(omnipath_query, proteins = proteins, !!!args) 6. │ └─OmnipathR (local) ``(...) 7. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 8. ├─OmnipathR:::omnipath_check_param(.) 9. │ └─param$organisms %<>% map_int(ncbi_taxid) 10. ├─purrr::map_int(., ncbi_taxid) 11. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 12. │ ├─purrr:::with_indexed_errors(...) 13. │ │ └─base::withCallingHandlers(...) 14. │ ├─purrr:::call_with_cleanup(...) 15. │ └─OmnipathR (local) .f(.x[[i]], ...) 16. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 17. ├─purrr::map_int(., taxon_name, "ncbi") 18. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 19. │ ├─purrr:::with_indexed_errors(...) 20. │ │ └─base::withCallingHandlers(...) 21. │ ├─purrr:::call_with_cleanup(...) 22. │ └─OmnipathR (local) .f(.x[[i]], ...) 23. │ ├─... %>% if_null_len0(NA) 24. │ └─OmnipathR::get_db("organisms") 25. │ └─OmnipathR::load_db(key, param = param) 26. │ ├─rlang::exec(loader, !!!param) 27. │ └─OmnipathR (local) ``() 28. │ └─... %>% ... 29. ├─OmnipathR:::if_null_len0(., NA) 30. │ └─value1 %>% is_empty_2 %>% if (value2) value1 31. ├─OmnipathR:::is_empty_2(.) 32. │ └─value %>% ... 33. ├─dplyr::pull(., name_type) 34. ├─dplyr::filter(...) 35. ├─dplyr::mutate(...) 36. ├─dplyr::full_join(...) 37. ├─dplyr::full_join(...) 38. └─dplyr:::full_join.data.frame(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 in `full_join()`: ! Join columns in `y` must be present in the data. ✖ Problem with `ncbi_tax_id`. --- 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 [ Finished: 2026-07-10 20:28:59 CEST ]