[ Started: 2025-07-26 19:19:16 CEST ] [ decoupleR v2.9.7 for BioC-3.22 from https://github.com/saezlab/decoupleR@devel (930b765 2025-02-15 00:00:59) ] * checking for file ‘./DESCRIPTION’ ... OK * preparing ‘decoupleR’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes * creating vignettes ... ERROR --- re-building ‘decoupleR.Rmd’ using rmarkdown --- finished re-building ‘decoupleR.Rmd’ --- re-building ‘pw_bk.Rmd’ using rmarkdown [2025-07-26 19:19:34] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-07-26 19:19:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:19:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:34] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-07-26 19:19:34] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-07-25 17:58:37 UTC; omnipath [2025-07-26 19:19:34] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-07-26 19:19:34] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-25 17:58:39 UTC; unix [2025-07-26 19:19:34] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-07-26 19:19:34] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-07-26 19:19:34] [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=2025-07-26; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-07-26 19:19:34] [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] [2025-07-26 19:19:34] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.26(2025-06-05); BiocParallel 1.43.4(2025-06-16); BiocStyle 2.37.0(2025-04-15); 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); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.9.7(2025-07-26); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.35.6(2025-07-09); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 3.5.2(2025-04-09); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); 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); magick 2.8.7(2025-06-06); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-07-25); parallelly 1.45.1(2025-07-24); pheatmap 1.0.13(2025-06-05); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); plyr 1.8.9(2023-10-02); 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); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); 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); tinytex 0.57(2025-04-15); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); 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) [2025-07-26 19:19:34] [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 [2025-07-26 19:19:34] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-07-26 19:19:34] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-07-26 19:19:34] [TRACE] [OmnipathR] Contains 1 files. [2025-07-26 19:19:34] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-07-26 19:19:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:19:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-07-26 19:19:34] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-07-26 19:19:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-07-26 19:19:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-07-26 19:19:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-07-26 19:19:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-07-26 19:19:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:34] [TRACE] [OmnipathR] Cache locked: FALSE [2025-07-26 19:19:34] [ERROR] [OmnipathR] cannot open the connection to 'https://omnipathdb.org/resources' [2025-07-26 19:19:34] [WARN] [OmnipathR] [decoupleR] Failed to check the list of available resources in OmniPath. Proceeding anyways. [2025-07-26 19:19:34] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-07-26 19:19:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:19:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:34] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-07-26 19:19:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:19:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:34] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-07-26 19:19:34] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-07-26 19:19:34] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-07-26 19:19:34] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-07-26 19:19:34] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-07-26 19:19:34] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-07-26 19:19:34] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-07-26 19:19:34] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-07-26 19:19:34] [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] [2025-07-26 19:19:34] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-07-26 19:19:34] [TRACE] [OmnipathR] Sending HTTP request. [2025-07-26 19:19:35] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-07-26 19:19:35] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-07-26 19:19:35] [TRACE] [OmnipathR] Downloaded 31.5 Kb in 0.285451s from www.ensembl.org (110.4 Kb/s); Redirect: 0s, DNS look up: 0.008684s, Connection: 0.037545s, Pretransfer: 0.127861s, First byte at: 0.248364s [2025-07-26 19:19:35] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Sat, 26 Jul 2025 17:19:35 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 32280; 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=Sun, 27 Jul 2025 17:19:35 GMT; Set-cookie: ENSEMBL_HINX_SESSION=86a1b9e06280da8d090c7e9268d4282702d61ef6c64ba86d1194a09c; 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=Sun, 27 Jul 2025 17:19:35 GMT; Set-cookie: ENSEMBL_HINX_SESSION=86a1b9e06280da8d090c7e9268d4282702d61ef6c64ba86d1194a09c; 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-p1m2-35.ebi.ac.uk [2025-07-26 19:19:35] [TRACE] [OmnipathR] Response headers: [Date=Sat, 26 Jul 2025 17:19:35 GMT,Content-Type=text/html; charset=utf-8,Content-Length=32280,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=Sun, 27 Jul 2025 17:19:35 GMT,Set-cookie=ENSEMBL_HINX_SESSION=86a1b9e06280da8d090c7e9268d4282702d61ef6c64ba86d1194a09c; 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=Sun, 27 Jul 2025 17:19:35 GMT,Set-cookie=ENSEMBL_HINX_SESSION=86a1b9e06280da8d090c7e9268d4282702d61ef6c64ba86d1194a09c; 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-p1m2-35.ebi.ac.uk] [2025-07-26 19:19:35] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-07-26 19:19:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:19:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:35] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-07-26 19:19:35] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-07-26 19:19:35] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-07-26 19:19:35] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-07-26 19:19:35] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-07-26 19:19:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:19:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:19:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:35] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-07-26 19:19:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-07-26 19:19:35] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-07-26 19:19:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-07-26 19:19:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-07-26 19:19:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-07-26 19:19:35] [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] [2025-07-26 19:19:35] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-07-26 19:19:35] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.068906s from omabrowser.org (126.1 Kb/s); Redirect: 0s, DNS look up: 0.000934s, Connection: 0.011393s, Pretransfer: 0.053539s, First byte at: 0.068762s [2025-07-26 19:19:35] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 26 Jul 2025 17:19:35 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 [2025-07-26 19:19:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-07-26 19:19:36] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-07-26 19:19:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:19:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:36] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-07-26 19:19:36] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-07-26 19:19:36] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-07-26 19:19:36] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-07-26 19:19:36] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-07-26 19:19:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:19:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:19:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:36] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2025-07-26 19:19:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-07-26 19:19:36] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-07-26 19:19:36] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-07-26 19:19:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-07-26 19:19:58] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2025-07-26 19:19:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:19:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:19:58] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2025-07-26 19:19:58] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-07-26 19:19:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-07-26 19:19:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2025-07-26 19:19:58] [TRACE] [OmnipathR] Organism(s): 9606 [2025-07-26 19:19:58] [TRACE] [OmnipathR] Orthology targets: [2025-07-26 19:19:59] [ERROR] [OmnipathR] cannot open the connection to 'https://omnipathdb.org/resources' [2025-07-26 19:19:59] [WARN] [OmnipathR] Accessing `PROGENy` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues. [2025-07-26 19:19:59] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-07-26 19:19:59] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-07-26 19:19:59] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-07-26 19:19:59] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-07-26 19:19:59] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-07-26 19:20:00] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-07-26 19:20:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:20:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:20:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:20:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:20:00] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `unknown` to `started`. [2025-07-26 19:20:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2025-07-26 19:20:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2025-07-26 19:20:02] [INFO] [OmnipathR] Download ready [key=103f85125e0134e3d65e4e63d22c339270d103e8, version=1] [2025-07-26 19:20:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:20:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:20:02] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `started` to `ready`. [2025-07-26 19:20:02] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records. Warning: ggrepel: 445 unlabeled data points (too many overlaps). Consider increasing max.overlaps --- finished re-building ‘pw_bk.Rmd’ --- re-building ‘pw_sc.Rmd’ using rmarkdown [2025-07-26 19:20:16] [ERROR] [OmnipathR] cannot open the connection to 'https://omnipathdb.org/resources' [2025-07-26 19:20:16] [WARN] [OmnipathR] [decoupleR] Failed to check the list of available resources in OmniPath. Proceeding anyways. [2025-07-26 19:20:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-07-26 19:20:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2025-07-26 19:20:16] [TRACE] [OmnipathR] Organism(s): 9606 [2025-07-26 19:20:16] [TRACE] [OmnipathR] Orthology targets: [2025-07-26 19:20:16] [ERROR] [OmnipathR] cannot open the connection to 'https://omnipathdb.org/resources' [2025-07-26 19:20:16] [WARN] [OmnipathR] Accessing `PROGENy` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues. [2025-07-26 19:20:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-07-26 19:20:17] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2025-07-26 19:20:17] [INFO] [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-07-26 19:20:17] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘pw_sc.Rmd’ --- re-building ‘tf_bk.Rmd’ using rmarkdown [2025-07-26 19:20:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-07-26 19:20:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-07-26 19:20:23] [TRACE] [OmnipathR] Organism(s): 9606 [2025-07-26 19:20:23] [TRACE] [OmnipathR] Orthology targets: [2025-07-26 19:20:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-07-26 19:20:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-07-26 19:20:23] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-07-26 19:20:23] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-07-26 19:20:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-07-26 19:20:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-07-26 19:20:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-07-26 19:20:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-07-26 19:20:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-07-26 19:20:23] [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] [2025-07-26 19:20:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-07-26 19:20:23] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095271s from omnipathdb.org (164.4 Kb/s); Redirect: 0s, DNS look up: 0.000927s, Connection: 0.020563s, Pretransfer: 0.055409s, First byte at: 0.094879s [2025-07-26 19:20:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 26 Jul 2025 17:20:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 26 Jul 2025 18:20:23 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-07-26 19:20:24] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-07-26 19:20:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:20:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:20:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:20:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:20:24] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`. [2025-07-26 19:20:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`. [2025-07-26 19:20:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`. [2025-07-26 19:20:24] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1] [2025-07-26 19:20:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-26 19:20:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-26 19:20:24] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`. [2025-07-26 19:20:26] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2025-07-26 19:20:26] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-07-26 19:20:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna] [2025-07-26 19:20:26] [TRACE] [OmnipathR] Organism(s): 9606 [2025-07-26 19:20:26] [TRACE] [OmnipathR] Orthology targets: [2025-07-26 19:20:26] [ERROR] [OmnipathR] cannot open the connection to 'https://omnipathdb.org/resources' [2025-07-26 19:20:26] [ERROR] [OmnipathR] [decoupleR] Failed to download TF-miRNA interactions from OmniPath. For more information, see the OmnipathR log. Quitting from tf_bk.Rmd:117-120 [collectri] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `value[[3L]]()`: ! [decoupleR] Failed to download TF-miRNA interactions from OmniPath. For more information, see the OmnipathR log. --- Backtrace: ▆ 1. └─decoupleR::get_collectri(organism = "human", split_complexes = FALSE) 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'tf_bk.Rmd' failed with diagnostics: [decoupleR] Failed to download TF-miRNA interactions from OmniPath. For more information, see the OmnipathR log. --- failed re-building ‘tf_bk.Rmd’ --- re-building ‘tf_sc.Rmd’ using rmarkdown [2025-07-26 19:20:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-07-26 19:20:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-07-26 19:20:27] [TRACE] [OmnipathR] Organism(s): 9606 [2025-07-26 19:20:27] [TRACE] [OmnipathR] Orthology targets: [2025-07-26 19:20:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-07-26 19:20:27] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`. [2025-07-26 19:20:27] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-07-26 19:20:29] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache. [2025-07-26 19:20:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-07-26 19:20:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna] [2025-07-26 19:20:29] [TRACE] [OmnipathR] Organism(s): 9606 [2025-07-26 19:20:29] [TRACE] [OmnipathR] Orthology targets: [2025-07-26 19:20:29] [ERROR] [OmnipathR] cannot open the connection to 'https://omnipathdb.org/resources' [2025-07-26 19:20:29] [ERROR] [OmnipathR] [decoupleR] Failed to download TF-miRNA interactions from OmniPath. For more information, see the OmnipathR log. Quitting from tf_sc.Rmd:85-88 [collectri] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `value[[3L]]()`: ! [decoupleR] Failed to download TF-miRNA interactions from OmniPath. For more information, see the OmnipathR log. --- Backtrace: ▆ 1. └─decoupleR::get_collectri(organism = "human", split_complexes = FALSE) 2. └─base::tryCatch(...) 3. └─base (local) tryCatchList(expr, classes, parentenv, handlers) 4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) 5. └─value[[3L]](cond) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'tf_sc.Rmd' failed with diagnostics: [decoupleR] Failed to download TF-miRNA interactions from OmniPath. For more information, see the OmnipathR log. --- failed re-building ‘tf_sc.Rmd’ SUMMARY: processing the following files failed: ‘tf_bk.Rmd’ ‘tf_sc.Rmd’ Error: Vignette re-building failed. Execution halted [ Finished: 2025-07-26 19:20:29 CEST ]