[ Started: 2025-10-13 20:30:29 CEST ] [ OmnipathR v3.16.2 for BioC-3.21 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_21 (e923fc4 2025-08-30 11:55:56) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.16.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... OK * checking installed package size ... INFO installed size is 6.8Mb sub-directories of 1Mb or more: doc 5.4Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE [2025-10-13 20:31:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:31:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:31:18] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:31:18] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:29:01 UTC; omnipath [2025-10-13 20:31:18] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:31:18] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:30:32 UTC; unix [2025-10-13 20:31:18] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2 [2025-10-13 20:31:18] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:31:18] [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=2025-10-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-10-13 20:31:18] [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] [2025-10-13 20:31:18] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); 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 1.1.0(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 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-13 20:31:18] [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 [2025-10-13 20:31:18] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:31:18] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:31:18] [TRACE] [OmnipathR] Contains 2 files. [2025-10-13 20:31:18] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:31:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:31:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:31:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:31:18] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:31:18] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:31:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:31:18] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:31:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:31:18] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:31:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:31:18] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:31:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:31:18] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2025-10-13 20:31:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:31:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:31:31] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:31:31] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:29:01 UTC; omnipath [2025-10-13 20:31:31] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:31:31] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:30:32 UTC; unix [2025-10-13 20:31:31] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2 [2025-10-13 20:31:31] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:31:31] [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=2025-10-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-10-13 20:31:31] [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] [2025-10-13 20:31:31] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); 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 1.1.0(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 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-13 20:31:31] [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 [2025-10-13 20:31:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:31:31] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:31:31] [TRACE] [OmnipathR] Contains 1 files. [2025-10-13 20:31:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:31:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:31:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:31:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:31:31] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:31:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:31:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:31:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:31:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:31:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:31:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:31:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:31:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:31:31] [TRACE] [OmnipathR] Cache locked: FALSE * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > ### Name: kegg_conv > ### Title: Convert KEGG identifiers to/from outside identifiers > ### Aliases: kegg_conv > > ### ** Examples > > kegg_conv("compound", "pubchem") [2025-10-13 20:36:40] [INFO] [OmnipathR] Loading database `List of organisms in KEGG`. [2025-10-13 20:36:40] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:36:40] [TRACE] [OmnipathR] Looking up in cache: `https://rest.kegg.jp/list/organism`. [2025-10-13 20:36:40] [INFO] [OmnipathR] Cache record does not exist: `https://rest.kegg.jp/list/organism` [2025-10-13 20:36:40] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.kegg.jp/list/organism`. [2025-10-13 20:36:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:36:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:36:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:36:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:36:40] [INFO] [OmnipathR] Cache item `e7c3da8d7f582ca4c3a757f7408df807fbe91b47` version 1: status changed from `unknown` to `started`. [2025-10-13 20:36:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e7c3da8d7f582ca4c3a757f7408df807fbe91b47-1.rds`. [2025-10-13 20:36:40] [INFO] [OmnipathR] Retrieving URL: `https://rest.kegg.jp/list/organism` [2025-10-13 20:36:40] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.kegg.jp/list/organism` [2025-10-13 20:36:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:36:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:36:40] [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] [2025-10-13 20:36:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:36:41] [TRACE] [OmnipathR] Downloaded 4.1 Kb in 1.076044s from rest.kegg.jp (3.8 Kb/s); Redirect: 0s, DNS look up: 0.001098s, Connection: 0.241971s, Pretransfer: 0.728239s, First byte at: 1.07602s [2025-10-13 20:36:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:36:41 GMT; Server: Apache; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked [2025-10-13 20:36:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e7c3da8d7f582ca4c3a757f7408df807fbe91b47-1.rds`. [2025-10-13 20:36:46] [INFO] [OmnipathR] Download ready [key=e7c3da8d7f582ca4c3a757f7408df807fbe91b47, version=1] [2025-10-13 20:36:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:36:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:36:46] [INFO] [OmnipathR] Cache item `e7c3da8d7f582ca4c3a757f7408df807fbe91b47` version 1: status changed from `started` to `ready`. [2025-10-13 20:36:46] [SUCCESS] [OmnipathR] KEGG (rest.kegg.jp): downloaded 11233 records [2025-10-13 20:36:46] [INFO] [OmnipathR] Loaded database `List of organisms in KEGG`. [2025-10-13 20:36:46] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:36:46] [TRACE] [OmnipathR] Looking up in cache: `https://rest.kegg.jp/conv/compound/pubchem`. [2025-10-13 20:36:46] [INFO] [OmnipathR] Cache record does not exist: `https://rest.kegg.jp/conv/compound/pubchem` [2025-10-13 20:36:46] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.kegg.jp/conv/compound/pubchem`. [2025-10-13 20:36:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:36:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:36:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:36:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:36:46] [INFO] [OmnipathR] Cache item `df48f267c99a2d8dd3cb7ed031941afbedc22d48` version 1: status changed from `unknown` to `started`. [2025-10-13 20:36:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/df48f267c99a2d8dd3cb7ed031941afbedc22d48-1.rds`. [2025-10-13 20:36:46] [INFO] [OmnipathR] Retrieving URL: `https://rest.kegg.jp/conv/compound/pubchem` [2025-10-13 20:36:46] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.kegg.jp/conv/compound/pubchem` [2025-10-13 20:36:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:36:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:36:46] [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] [2025-10-13 20:36:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:36:47] [TRACE] [OmnipathR] Downloaded 4.1 Kb in 1.044949s from rest.kegg.jp (3.9 Kb/s); Redirect: 0s, DNS look up: 0.001155s, Connection: 0.242066s, Pretransfer: 0.728375s, First byte at: 1.044923s [2025-10-13 20:36:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:36:47 GMT; Server: Apache; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked Warning in gzfile(file, mode) : cannot open compressed file '/home/omnipath/.cache/OmnipathR/df48f267c99a2d8dd3cb7ed031941afbedc22d48-1.rds', probable reason 'No such file or directory' Error in gzfile(file, mode) : cannot open the connection Calls: kegg_conv ... -> %>% -> omnipath_cache_save -> saveRDS -> gzfile Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: --- re-building ‘bioc_workshop.Rmd’ using rmarkdown [2025-10-13 20:37:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:09] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:37:09] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:29:01 UTC; omnipath [2025-10-13 20:37:09] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:37:09] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:30:32 UTC; unix [2025-10-13 20:37:09] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2 [2025-10-13 20:37:09] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:37:09] [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=2025-10-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-10-13 20:37:09] [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] [2025-10-13 20:37:09] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.36.0(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 0.45(2025-10-03); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); 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 1.1.0(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 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-13 20:37:09] [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 [2025-10-13 20:37:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:37:09] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:37:09] [TRACE] [OmnipathR] Contains 14 files. [2025-10-13 20:37:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:37:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:37:09] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:37:09] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:37:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:09] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:37:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:09] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:37:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:09] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:37:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:09] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-13 20:37:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:37:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2025-10-13 20:37:09] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-13 20:37:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:09] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-13 20:37:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:09] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-13 20:37:09] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-13 20:37:09] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:37:09] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:37:09] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:37:09] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-13 20:37:09] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:37:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:09] [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] [2025-10-13 20:37:09] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:37:09] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:37:09] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:37:09] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:09] [TRACE] [OmnipathR] Downloaded 31.2 Kb in 0.182775s from www.ensembl.org (171 Kb/s); Redirect: 0s, DNS look up: 0.001426s, Connection: 0.019485s, Pretransfer: 0.074235s, First byte at: 0.15946s [2025-10-13 20:37:09] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:37:09 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31996; 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=Tue, 14 Oct 2025 18:37:09 GMT; Set-cookie: ENSEMBL_HINX_SESSION=45b032f67609b16c0fe2c12f693c60d50ba5cd054df432ca18aed2bf; 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=Tue, 14 Oct 2025 18:37:09 GMT; Set-cookie: ENSEMBL_HINX_SESSION=45b032f67609b16c0fe2c12f693c60d50ba5cd054df432ca18aed2bf; 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-p1m2-34.ebi.ac.uk [2025-10-13 20:37:09] [TRACE] [OmnipathR] Response headers: [Date=Mon, 13 Oct 2025 18:37:09 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31996,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=Tue, 14 Oct 2025 18:37:09 GMT,Set-cookie=ENSEMBL_HINX_SESSION=45b032f67609b16c0fe2c12f693c60d50ba5cd054df432ca18aed2bf; 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=Tue, 14 Oct 2025 18:37:09 GMT,Set-cookie=ENSEMBL_HINX_SESSION=45b032f67609b16c0fe2c12f693c60d50ba5cd054df432ca18aed2bf; 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-p1m2-34.ebi.ac.uk] [2025-10-13 20:37:09] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-13 20:37:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:09] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-10-13 20:37:09] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:37:10] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:37:10] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:37:10] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:37:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:10] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:37:10] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:37:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:37:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:10] [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] [2025-10-13 20:37:10] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:37:10] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.059472s from omabrowser.org (146.1 Kb/s); Redirect: 0s, DNS look up: 0.001168s, Connection: 0.010719s, Pretransfer: 0.045091s, First byte at: 0.05931s [2025-10-13 20:37:10] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 13 Oct 2025 18:37:10 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 [2025-10-13 20:37:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:37:10] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-10-13 20:37:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:10] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:10] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-10-13 20:37:10] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:37:10] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:37:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:37:10] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:37:10] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:37:10] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:37:10] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:37:10] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:37:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:37:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:10] [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] [2025-10-13 20:37:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:10] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094057s from omnipathdb.org (166.6 Kb/s); Redirect: 0s, DNS look up: 0.00104s, Connection: 0.020251s, Pretransfer: 0.054879s, First byte at: 0.093704s [2025-10-13 20:37:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:37:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:37:10 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:37:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:37:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:11] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2025-10-13 20:37:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2025-10-13 20:37:11] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2025-10-13 20:37:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:11] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:15] [SUCCESS] [OmnipathR] Downloaded 131398 interactions. [2025-10-13 20:37:19] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:37:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2025-10-13 20:37:19] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:37:19] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:37:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:19] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:19] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:19] [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] [2025-10-13 20:37:19] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:19] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097997s from omnipathdb.org (159.9 Kb/s); Redirect: 0s, DNS look up: 0.001088s, Connection: 0.021597s, Pretransfer: 0.056619s, First byte at: 0.097713s [2025-10-13 20:37:19] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:37:19 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:37:19 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:37:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:20] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-10-13 20:37:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-10-13 20:37:20] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2025-10-13 20:37:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:20] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:21] [SUCCESS] [OmnipathR] Downloaded 47840 enzyme-substrate relationships. [2025-10-13 20:37:22] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:37:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions] [2025-10-13 20:37:22] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:37:22] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:37:22] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:22] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:22] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:22] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:22] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:22] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:22] [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] [2025-10-13 20:37:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:22] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094814s from omnipathdb.org (165.2 Kb/s); Redirect: 0s, DNS look up: 0.001056s, Connection: 0.020569s, Pretransfer: 0.055508s, First byte at: 0.094553s [2025-10-13 20:37:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:37:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:37:22 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:37:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:23] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:37:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:37:23] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-10-13 20:37:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:23] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:26] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2025-10-13 20:37:26] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:37:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes] [2025-10-13 20:37:26] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:37:26] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:37:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic` [2025-10-13 20:37:26] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2025-10-13 20:37:26] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic` [2025-10-13 20:37:26] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic` [2025-10-13 20:37:26] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic` [2025-10-13 20:37:26] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2025-10-13 20:37:26] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2025-10-13 20:37:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:26] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:26] [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] [2025-10-13 20:37:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:26] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090276s from omnipathdb.org (173.5 Kb/s); Redirect: 0s, DNS look up: 0.001004s, Connection: 0.018796s, Pretransfer: 0.054067s, First byte at: 0.090036s [2025-10-13 20:37:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:37:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:37:26 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:37:27] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic` [2025-10-13 20:37:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:27] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2025-10-13 20:37:27] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2025-10-13 20:37:27] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2025-10-13 20:37:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:27] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:27] [SUCCESS] [OmnipathR] Downloaded 52085 protein complexes. [2025-10-13 20:37:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:37:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2025-10-13 20:37:27] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:37:27] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:37:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:37:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:28] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:28] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:28] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:28] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:28] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:28] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:28] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:28] [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] [2025-10-13 20:37:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:28] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100346s from omnipathdb.org (156.1 Kb/s); Redirect: 0s, DNS look up: 0.000941s, Connection: 0.022278s, Pretransfer: 0.056897s, First byte at: 0.100044s [2025-10-13 20:37:28] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:37:28 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:37:28 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:37:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:28] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-10-13 20:37:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-10-13 20:37:28] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2025-10-13 20:37:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:28] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:28] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2025-10-13 20:37:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:37:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations] [2025-10-13 20:37:29] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:37:29] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:37:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:37:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:37:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:37:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:37:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:37:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:37:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:37:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:37:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:29] [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] [2025-10-13 20:37:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:29] [TRACE] [OmnipathR] Downloaded 60 bytes in 0.076823s from omnipathdb.org (781 bytes/s); Redirect: 0s, DNS look up: 0.001018s, Connection: 0.021278s, Pretransfer: 0.056325s, First byte at: 0.076805s [2025-10-13 20:37:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:37:29 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 60; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:37:29 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-10-13 20:37:29] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:37:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:29] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2025-10-13 20:37:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2025-10-13 20:37:29] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2025-10-13 20:37:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:29] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:29] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. [2025-10-13 20:37:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:37:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations] [2025-10-13 20:37:29] [FATAL] [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest. [2025-10-13 20:37:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:37:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2025-10-13 20:37:29] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:37:29] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:37:29] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:37:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:29] [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] [2025-10-13 20:37:30] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:30] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.119095s from omnipathdb.org (131.5 Kb/s); Redirect: 0s, DNS look up: 0.001038s, Connection: 0.019767s, Pretransfer: 0.055298s, First byte at: 0.11879s [2025-10-13 20:37:30] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:37:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:37:30 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:37:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:37:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:30] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-10-13 20:37:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-10-13 20:37:30] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2025-10-13 20:37:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:30] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:30] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2025-10-13 20:37:30] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:37:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations] [2025-10-13 20:37:30] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:37:30] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:37:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:37:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-10-13 20:37:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-10-13 20:37:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-10-13 20:37:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-10-13 20:37:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-10-13 20:37:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-10-13 20:37:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-10-13 20:37:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:31] [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] [2025-10-13 20:37:31] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:31] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.098171s from omnipathdb.org (159.6 Kb/s); Redirect: 0s, DNS look up: 0.00117s, Connection: 0.021593s, Pretransfer: 0.056596s, First byte at: 0.097817s [2025-10-13 20:37:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:37:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:37:31 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:37:31] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-10-13 20:37:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:31] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2025-10-13 20:37:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2025-10-13 20:37:31] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1] [2025-10-13 20:37:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:31] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:31] [SUCCESS] [OmnipathR] Downloaded 3752 annotation records. [2025-10-13 20:37:31] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:37:31] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2025-10-13 20:37:31] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:37:31] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:37:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:37:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:37:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:37:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:37:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:37:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:37:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:37:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:37:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:31] [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] [2025-10-13 20:37:31] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:31] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090765s from omnipathdb.org (172.6 Kb/s); Redirect: 0s, DNS look up: 0.001062s, Connection: 0.0189s, Pretransfer: 0.054391s, First byte at: 0.090458s [2025-10-13 20:37:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:37:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:37:31 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:37:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:37:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:32] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-10-13 20:37:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-10-13 20:37:32] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2025-10-13 20:37:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:32] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:32] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2025-10-13 20:37:32] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:37:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-10-13 20:37:32] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:37:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-10-13 20:37:32] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:37:32] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:37:32] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:32] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:32] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:32] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:32] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:32] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:32] [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] [2025-10-13 20:37:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:32] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100644s from omnipathdb.org (155.7 Kb/s); Redirect: 0s, DNS look up: 0.000999s, Connection: 0.022458s, Pretransfer: 0.057068s, First byte at: 0.100382s [2025-10-13 20:37:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:37:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:37:32 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:37:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:33] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:37:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:37:33] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-10-13 20:37:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:33] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:36] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2025-10-13 20:37:36] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:37:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations] [2025-10-13 20:37:36] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:37:36] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:37:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:37:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:37:36] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-10-13 20:37:36] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:37:36] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache. [2025-10-13 20:37:36] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:37:36] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:37:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic` [2025-10-13 20:37:36] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic` [2025-10-13 20:37:36] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic` [2025-10-13 20:37:36] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic` [2025-10-13 20:37:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic` [2025-10-13 20:37:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic` [2025-10-13 20:37:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic` [2025-10-13 20:37:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:36] [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] [2025-10-13 20:37:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:36] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.085566s from omnipathdb.org (183.1 Kb/s); Redirect: 0s, DNS look up: 0.001071s, Connection: 0.017193s, Pretransfer: 0.052642s, First byte at: 0.085249s [2025-10-13 20:37:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:37:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:37:36 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:37:38] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic` [2025-10-13 20:37:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:38] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:38] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2025-10-13 20:37:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2025-10-13 20:37:40] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1] [2025-10-13 20:37:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:40] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:40] [SUCCESS] [OmnipathR] Downloaded 388239 intercellular communication role records. [2025-10-13 20:37:41] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2025-10-13 20:37:41] [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. [2025-10-13 20:37:41] [TRACE] [OmnipathR] Bypassing call: `intercell_network()`. [2025-10-13 20:37:41] [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. [2025-10-13 20:37:41] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `. [2025-10-13 20:37:41] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`. [2025-10-13 20:37:41] [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. [2025-10-13 20:37:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:37:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:41] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:37:41] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:37:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:37:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:37:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2025-10-13 20:37:41] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2025-10-13 20:37:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2025-10-13 20:37:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:37:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:37:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:41] [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] [2025-10-13 20:37:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:41] [TRACE] [OmnipathR] Downloaded 9.4 Kb in 0.078706s from omnipathdb.org (119.3 Kb/s); Redirect: 0s, DNS look up: 0.001111s, Connection: 0.021707s, Pretransfer: 0.056516s, First byte at: 0.078525s [2025-10-13 20:37:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:37:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:37:41 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:37:42] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:37:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:42] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2025-10-13 20:37:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2025-10-13 20:37:42] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2025-10-13 20:37:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:42] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:42] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2025-10-13 20:37:42] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`. [2025-10-13 20:37:42] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2025-10-13 20:37:42] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2025-10-13 20:37:42] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:37:42] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2025-10-13 20:37:42] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-10-13 20:37:42] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2025-10-13 20:37:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:42] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-10-13 20:37:42] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-10-13 20:37:42] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-10-13 20:37:42] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:42] [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] [2025-10-13 20:37:42] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:37:42] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.344556s from rest.uniprot.org (124 bytes/s); Redirect: 0s, DNS look up: 0.001133s, Connection: 0.019478s, Pretransfer: 0.07419s, First byte at: 0.344525s [2025-10-13 20:37:42] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 08-August-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Mon, 13 Oct 2025 18:37:42 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_03; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 18-June-2025 [2025-10-13 20:37:51] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-10-13 20:37:51] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2025-10-13 20:37:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:51] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:51] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20420 records [2025-10-13 20:37:52] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2025-10-13 20:37:52] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-10-13 20:37:52] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2025-10-13 20:37:52] [TRACE] [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`. [2025-10-13 20:37:52] [TRACE] [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`. [2025-10-13 20:37:52] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`. [2025-10-13 20:37:52] [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. [2025-10-13 20:37:52] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`. [2025-10-13 20:37:52] [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. [2025-10-13 20:37:52] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`. [2025-10-13 20:37:52] [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. --- finished re-building ‘bioc_workshop.Rmd’ --- re-building ‘cosmos.Rmd’ using rmarkdown [2025-10-13 20:37:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:54] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:37:54] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:29:01 UTC; omnipath [2025-10-13 20:37:54] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:37:54] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:30:32 UTC; unix [2025-10-13 20:37:54] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2 [2025-10-13 20:37:54] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:37:54] [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=2025-10-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-10-13 20:37:54] [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] [2025-10-13 20:37:54] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.36.0(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 0.45(2025-10-03); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); 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 1.1.0(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 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-13 20:37:54] [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 [2025-10-13 20:37:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:37:54] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:37:54] [TRACE] [OmnipathR] Contains 9 files. [2025-10-13 20:37:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:37:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:37:54] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:37:54] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:37:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:54] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:37:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:54] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:37:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:54] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:37:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:54] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-13 20:37:54] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2025-10-13 20:37:54] [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. [2025-10-13 20:37:54] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2025-10-13 20:37:54] [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. [2025-10-13 20:37:54] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2025-10-13 20:37:54] [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. [2025-10-13 20:37:55] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-13 20:37:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:55] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-13 20:37:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:55] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-13 20:37:55] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-13 20:37:55] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:37:55] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:37:55] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:37:55] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-13 20:37:55] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:37:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:55] [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] [2025-10-13 20:37:55] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:37:55] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:37:55] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:37:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:55] [TRACE] [OmnipathR] Downloaded 31.3 Kb in 0.189124s from www.ensembl.org (165.7 Kb/s); Redirect: 0s, DNS look up: 0.001397s, Connection: 0.019543s, Pretransfer: 0.073683s, First byte at: 0.166094s [2025-10-13 20:37:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:37:55 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 32099; 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=Tue, 14 Oct 2025 18:37:55 GMT; Set-cookie: ENSEMBL_HINX_SESSION=c8fa17274a89e15a0bdc36cc693c61030f9b38b90fc0021681856b02; 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=Tue, 14 Oct 2025 18:37:55 GMT; Set-cookie: ENSEMBL_HINX_SESSION=c8fa17274a89e15a0bdc36cc693c61030f9b38b90fc0021681856b02; 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-p1m2-33.ebi.ac.uk [2025-10-13 20:37:55] [TRACE] [OmnipathR] Response headers: [Date=Mon, 13 Oct 2025 18:37:55 GMT,Content-Type=text/html; charset=utf-8,Content-Length=32099,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=Tue, 14 Oct 2025 18:37:55 GMT,Set-cookie=ENSEMBL_HINX_SESSION=c8fa17274a89e15a0bdc36cc693c61030f9b38b90fc0021681856b02; 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=Tue, 14 Oct 2025 18:37:55 GMT,Set-cookie=ENSEMBL_HINX_SESSION=c8fa17274a89e15a0bdc36cc693c61030f9b38b90fc0021681856b02; 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-p1m2-33.ebi.ac.uk] [2025-10-13 20:37:55] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-13 20:37:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:55] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-10-13 20:37:55] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:37:55] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:37:55] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:37:55] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:37:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:55] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:37:55] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:37:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:37:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:55] [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] [2025-10-13 20:37:55] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:37:55] [TRACE] [OmnipathR] Downloaded 7.8 Kb in 0.059988s from omabrowser.org (130.1 Kb/s); Redirect: 0s, DNS look up: 0.001065s, Connection: 0.010453s, Pretransfer: 0.044963s, First byte at: 0.059853s [2025-10-13 20:37:55] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 13 Oct 2025 18:37:55 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 [2025-10-13 20:37:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:37:55] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-10-13 20:37:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:55] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:55] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-10-13 20:37:56] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2025-10-13 20:37:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:37:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2025-10-13 20:37:56] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:37:56] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:37:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:37:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:56] [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] [2025-10-13 20:37:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:37:56] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089982s from omnipathdb.org (174.1 Kb/s); Redirect: 0s, DNS look up: 0.000884s, Connection: 0.018921s, Pretransfer: 0.053848s, First byte at: 0.089713s [2025-10-13 20:37:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:37:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:37:56 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:37:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:37:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:56] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:37:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:37:57] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-10-13 20:37:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:57] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2025-10-13 20:37:59] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2025-10-13 20:37:59] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2025-10-13 20:37:59] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2025-10-13 20:37:59] [TRACE] [OmnipathR] BioMart query: [2025-10-13 20:37:59] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:37:59] [TRACE] [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2025-10-13 20:37:59] [INFO] [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2025-10-13 20:37:59] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2025-10-13 20:37:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:37:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:37:59] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2025-10-13 20:37:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2025-10-13 20:37:59] [INFO] [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2025-10-13 20:37:59] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:37:59] [TRACE] [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2025-10-13 20:37:59] [TRACE] [OmnipathR] Preparing httr2 request to URL `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2025-10-13 20:37:59] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:37:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:37:59] [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] [2025-10-13 20:37:59] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:37:59] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:38:17] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:38:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:38:17] [TRACE] [OmnipathR] Downloaded 2 Mb in 17.626932s from www.ensembl.org (116.2 Kb/s); Redirect: 0s, DNS look up: 0.00121s, Connection: 0.019343s, Pretransfer: 0.019393s, First byte at: 0.084577s [2025-10-13 20:38:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: Apache; Content-Type: text/plain; charset=utf-8; Content-Security-Policy: frame-ancestors 'self'; Date: Mon, 13 Oct 2025 18:38:00 GMT; Transfer-Encoding: chunked; Connection: Keep-Alive; X-Frame-Options: SAMEORIGIN [2025-10-13 20:38:17] [TRACE] [OmnipathR] Response headers: [Server=Apache,Content-Type=text/plain; charset=utf-8,Content-Security-Policy=frame-ancestors 'self',Date=Mon, 13 Oct 2025 18:38:00 GMT,Transfer-Encoding=chunked,Connection=Keep-Alive,X-Frame-Options=SAMEORIGIN] [2025-10-13 20:38:17] [TRACE] [OmnipathR] Calling reader callback on response. [2025-10-13 20:38:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2025-10-13 20:38:18] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2025-10-13 20:38:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:18] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2025-10-13 20:38:18] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 244093 records [2025-10-13 20:38:18] [TRACE] [OmnipathR] Translating complexes: 612 complexes in data. [2025-10-13 20:38:18] [TRACE] [OmnipathR] 451 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-10-13 20:38:19] [TRACE] [OmnipathR] Translated 451 complexes to 451. [2025-10-13 20:38:19] [TRACE] [OmnipathR] 71139 rows before translation, 4827 uniprot IDs in column `source`. [2025-10-13 20:38:19] [TRACE] [OmnipathR] 71220 rows after translation; translated 4827 `uniprot` IDs in column `source` to 4663 `genesymbol` IDs in column `genesymbol_source`. [2025-10-13 20:38:19] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2025-10-13 20:38:19] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2025-10-13 20:38:19] [TRACE] [OmnipathR] BioMart query: [2025-10-13 20:38:19] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:38:19] [TRACE] [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2025-10-13 20:38:19] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2025-10-13 20:38:19] [SUCCESS] [OmnipathR] www.ensembl.org: loaded 244093 records from cache [2025-10-13 20:38:20] [TRACE] [OmnipathR] Translating complexes: 381 complexes in data. [2025-10-13 20:38:20] [TRACE] [OmnipathR] 229 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-10-13 20:38:20] [TRACE] [OmnipathR] Translated 229 complexes to 229. [2025-10-13 20:38:20] [TRACE] [OmnipathR] 71220 rows before translation, 5240 uniprot IDs in column `target`. [2025-10-13 20:38:20] [TRACE] [OmnipathR] 72796 rows after translation; translated 5240 `uniprot` IDs in column `target` to 5086 `genesymbol` IDs in column `genesymbol_target`. [2025-10-13 20:38:20] [INFO] [OmnipathR] OmniPath PPI for COSMOS PKN ready: 145749 interactions. --- finished re-building ‘cosmos.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2025-10-13 20:38:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:23] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:38:23] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:29:01 UTC; omnipath [2025-10-13 20:38:23] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:38:23] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:30:32 UTC; unix [2025-10-13 20:38:23] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2 [2025-10-13 20:38:23] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:38:23] [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=2025-10-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-10-13 20:38:23] [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] [2025-10-13 20:38:23] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.36.0(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 0.45(2025-10-03); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); 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 1.1.0(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 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-13 20:38:23] [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 [2025-10-13 20:38:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:38:23] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:38:23] [TRACE] [OmnipathR] Contains 10 files. [2025-10-13 20:38:23] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:38:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:38:23] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:38:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:38:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:38:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:38:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:38:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:23] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-13 20:38:23] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2025-10-13 20:38:23] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2025-10-13 20:38:23] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-13 20:38:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:23] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-13 20:38:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:23] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-13 20:38:23] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-13 20:38:23] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:38:23] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:38:23] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:38:23] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-13 20:38:23] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:38:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:38:23] [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] [2025-10-13 20:38:23] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:38:23] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:38:24] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:38:24] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:38:24] [TRACE] [OmnipathR] Downloaded 31.1 Kb in 0.198533s from www.ensembl.org (156.6 Kb/s); Redirect: 0s, DNS look up: 0.010306s, Connection: 0.028488s, Pretransfer: 0.083866s, First byte at: 0.175125s [2025-10-13 20:38:24] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:38:23 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31830; 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=Tue, 14 Oct 2025 18:38:23 GMT; Set-cookie: ENSEMBL_HINX_SESSION=3fd367af976fb6f30e5e2285693c611f0a192d19d606ef55e605355d; 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=Tue, 14 Oct 2025 18:38:23 GMT; Set-cookie: ENSEMBL_HINX_SESSION=3fd367af976fb6f30e5e2285693c611f0a192d19d606ef55e605355d; 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-p1m2-31.ebi.ac.uk [2025-10-13 20:38:24] [TRACE] [OmnipathR] Response headers: [Date=Mon, 13 Oct 2025 18:38:23 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31830,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=Tue, 14 Oct 2025 18:38:23 GMT,Set-cookie=ENSEMBL_HINX_SESSION=3fd367af976fb6f30e5e2285693c611f0a192d19d606ef55e605355d; 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=Tue, 14 Oct 2025 18:38:23 GMT,Set-cookie=ENSEMBL_HINX_SESSION=3fd367af976fb6f30e5e2285693c611f0a192d19d606ef55e605355d; 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-p1m2-31.ebi.ac.uk] [2025-10-13 20:38:24] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-13 20:38:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:24] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-10-13 20:38:24] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:38:24] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:38:24] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:38:24] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:38:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:24] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-10-13 20:38:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:38:24] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:38:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:38:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:38:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:38:24] [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] [2025-10-13 20:38:24] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:38:24] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.061648s from omabrowser.org (141 Kb/s); Redirect: 0s, DNS look up: 0.00105s, Connection: 0.01146s, Pretransfer: 0.046513s, First byte at: 0.061496s [2025-10-13 20:38:24] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 13 Oct 2025 18:38:24 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 [2025-10-13 20:38:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:38:24] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-10-13 20:38:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:24] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-10-13 20:38:24] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-10-13 20:38:24] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2025-10-13 20:38:24] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:38:24] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2025-10-13 20:38:24] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-10-13 20:38:24] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2025-10-13 20:38:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:24] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2025-10-13 20:38:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-10-13 20:38:24] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-10-13 20:38:24] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2025-10-13 20:38:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:38:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:38:24] [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] [2025-10-13 20:38:25] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:38:25] [TRACE] [OmnipathR] Downloaded 15.4 Kb in 0.097539s from rest.uniprot.org (157.6 Kb/s); Redirect: 0s, DNS look up: 0.001157s, Connection: 0.019342s, Pretransfer: 0.073324s, First byte at: 0.097303s [2025-10-13 20:38:25] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 08-August-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Mon, 13 Oct 2025 18:37:42 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_03; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 18-June-2025; content-length: 129293 [2025-10-13 20:38:25] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-10-13 20:38:25] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2025-10-13 20:38:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:25] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2025-10-13 20:38:25] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20420 records [2025-10-13 20:38:25] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2025-10-13 20:38:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:38] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:38:38] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:29:01 UTC; omnipath [2025-10-13 20:38:38] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:38:38] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:30:32 UTC; unix [2025-10-13 20:38:38] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2 [2025-10-13 20:38:38] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:38:38] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-10-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-10-13 20:38:38] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-10-13 20:38:38] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.36.0(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 0.45(2025-10-03); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); 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 2.2.0(2025-10-13); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); 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 1.1.0(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); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); S7 0.2.0(2024-11-07); 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 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-13 20:38:38] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-10-13 20:38:38] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:38:38] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:38:38] [TRACE] [OmnipathR] Contains 1 files. [2025-10-13 20:38:38] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:38:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:38:38] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:38:38] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:38:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:38] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:38:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:38] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:38:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:38] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:38:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:38] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-13 20:38:38] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:38:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-10-13 20:38:38] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:38:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-10-13 20:38:38] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-13 20:38:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:39] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-13 20:38:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:39] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-13 20:38:39] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-13 20:38:39] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:38:39] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:38:39] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:38:39] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-13 20:38:39] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:38:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:38:39] [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] [2025-10-13 20:38:39] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:38:39] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:38:39] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:38:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:38:39] [TRACE] [OmnipathR] Downloaded 31.3 Kb in 0.219284s from www.ensembl.org (142.9 Kb/s); Redirect: 0s, DNS look up: 0.007388s, Connection: 0.025506s, Pretransfer: 0.079194s, First byte at: 0.197751s [2025-10-13 20:38:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:38:39 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 32099; 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=Tue, 14 Oct 2025 18:38:39 GMT; Set-cookie: ENSEMBL_HINX_SESSION=39452fec3370bc900da3e185693c612f09e4f1cffda8133c4c9e664e; 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=Tue, 14 Oct 2025 18:38:39 GMT; Set-cookie: ENSEMBL_HINX_SESSION=39452fec3370bc900da3e185693c612f09e4f1cffda8133c4c9e664e; 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 [2025-10-13 20:38:39] [TRACE] [OmnipathR] Response headers: [Date=Mon, 13 Oct 2025 18:38:39 GMT,Content-Type=text/html; charset=utf-8,Content-Length=32099,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=Tue, 14 Oct 2025 18:38:39 GMT,Set-cookie=ENSEMBL_HINX_SESSION=39452fec3370bc900da3e185693c612f09e4f1cffda8133c4c9e664e; 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=Tue, 14 Oct 2025 18:38:39 GMT,Set-cookie=ENSEMBL_HINX_SESSION=39452fec3370bc900da3e185693c612f09e4f1cffda8133c4c9e664e; 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] [2025-10-13 20:38:39] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-13 20:38:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:39] [WARN] [OmnipathR] Failed to update cache: key `7332486db7400730697234bad76ca0c8e4d00799` does not exist. 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 in `path_to_connection()`: ! '/home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html' does not exist. --- failed re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2025-10-13 20:38:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:41] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:38:41] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:29:01 UTC; omnipath [2025-10-13 20:38:41] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:38:41] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:30:32 UTC; unix [2025-10-13 20:38:41] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2 [2025-10-13 20:38:41] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:38:41] [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=2025-10-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-10-13 20:38:41] [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] [2025-10-13 20:38:41] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.36.0(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 0.45(2025-10-03); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); 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 1.1.0(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 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-13 20:38:41] [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 [2025-10-13 20:38:41] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:38:41] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:38:41] [TRACE] [OmnipathR] Contains 1 files. [2025-10-13 20:38:41] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:38:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:38:41] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:38:41] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:38:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:41] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:38:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:41] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:38:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:41] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:38:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:41] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-13 20:38:41] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:38:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2025-10-13 20:38:41] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-13 20:38:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:41] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-13 20:38:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:41] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-13 20:38:41] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-13 20:38:41] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:38:41] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:38:41] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:38:41] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-13 20:38:41] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:38:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:38:41] [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] [2025-10-13 20:38:41] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:38:41] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:38:41] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:38:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:38:41] [TRACE] [OmnipathR] Downloaded 31.3 Kb in 0.192117s from www.ensembl.org (162.8 Kb/s); Redirect: 0s, DNS look up: 0.001227s, Connection: 0.019382s, Pretransfer: 0.074256s, First byte at: 0.171527s [2025-10-13 20:38:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:38:41 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 32035; 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=Tue, 14 Oct 2025 18:38:41 GMT; Set-cookie: ENSEMBL_HINX_SESSION=13256fdd0c4970a40b1d1aaf693c61310f5a0acb25370872de61b9c2; 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=Tue, 14 Oct 2025 18:38:41 GMT; Set-cookie: ENSEMBL_HINX_SESSION=13256fdd0c4970a40b1d1aaf693c61310f5a0acb25370872de61b9c2; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Vary: Accept-Encoding; Content-Encoding: gzip; X-Frame-Options: SAMEORIGIN; Content-Security-Policy: frame-ancestors 'self'; X-NGINX-MACHINE: wp-p1m2-32.ebi.ac.uk [2025-10-13 20:38:41] [TRACE] [OmnipathR] Response headers: [Date=Mon, 13 Oct 2025 18:38:41 GMT,Content-Type=text/html; charset=utf-8,Content-Length=32035,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=Tue, 14 Oct 2025 18:38:41 GMT,Set-cookie=ENSEMBL_HINX_SESSION=13256fdd0c4970a40b1d1aaf693c61310f5a0acb25370872de61b9c2; 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=Tue, 14 Oct 2025 18:38:41 GMT,Set-cookie=ENSEMBL_HINX_SESSION=13256fdd0c4970a40b1d1aaf693c61310f5a0acb25370872de61b9c2; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Vary=Accept-Encoding,Content-Encoding=gzip,X-Frame-Options=SAMEORIGIN,Content-Security-Policy=frame-ancestors 'self',X-NGINX-MACHINE=wp-p1m2-32.ebi.ac.uk] [2025-10-13 20:38:42] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-13 20:38:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:42] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-10-13 20:38:42] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:38:42] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:38:42] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:38:42] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:38:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:42] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-10-13 20:38:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:38:42] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:38:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:38:42] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:38:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:38:42] [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] [2025-10-13 20:38:42] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:38:42] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.058408s from omabrowser.org (148.8 Kb/s); Redirect: 0s, DNS look up: 0.000956s, Connection: 0.010415s, Pretransfer: 0.044193s, First byte at: 0.058249s [2025-10-13 20:38:42] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 13 Oct 2025 18:38:42 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 [2025-10-13 20:38:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:38:42] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-10-13 20:38:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:42] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-10-13 20:38:42] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-10-13 20:38:42] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:38:42] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:38:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-10-13 20:38:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-10-13 20:38:42] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-10-13 20:38:42] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-10-13 20:38:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-10-13 20:38:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-10-13 20:38:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-10-13 20:38:42] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:38:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:38:42] [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] [2025-10-13 20:38:42] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:38:42] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100061s from omnipathdb.org (156.6 Kb/s); Redirect: 0s, DNS look up: 0.000986s, Connection: 0.022804s, Pretransfer: 0.056696s, First byte at: 0.09978s [2025-10-13 20:38:42] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:38:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:38:42 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:38:43] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-10-13 20:38:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:43] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2025-10-13 20:38:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2025-10-13 20:38:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2025-10-13 20:38:44] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2025-10-13 20:38:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:38:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:38:44] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2025-10-13 20:38:44] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2025-10-13 20:38:53] [SUCCESS] [OmnipathR] Downloaded 139054 interactions. [2025-10-13 20:45:42] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:45:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations] [2025-10-13 20:45:42] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:45:42] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:45:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:45:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-10-13 20:45:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-10-13 20:45:42] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-10-13 20:45:42] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-10-13 20:45:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-10-13 20:45:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-10-13 20:45:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-10-13 20:45:42] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:45:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:45:42] [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] [2025-10-13 20:45:42] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:45:42] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.104353s from omnipathdb.org (150.1 Kb/s); Redirect: 0s, DNS look up: 0.001207s, Connection: 0.022815s, Pretransfer: 0.059369s, First byte at: 0.103122s [2025-10-13 20:45:42] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:45:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:45:42 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:45:43] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2025-10-13 20:45:43] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:45:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:43] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:45:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:43] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2025-10-13 20:45:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2025-10-13 20:45:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2025-10-13 20:45:44] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2025-10-13 20:45:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:44] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2025-10-13 20:45:44] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records. [2025-10-13 20:45:45] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:45:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub] [2025-10-13 20:45:45] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:45:45] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:45:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-10-13 20:45:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-10-13 20:45:45] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-10-13 20:45:45] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-10-13 20:45:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-10-13 20:45:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-10-13 20:45:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-10-13 20:45:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:45:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:45:45] [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] [2025-10-13 20:45:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:45:45] [TRACE] [OmnipathR] Downloaded 11.6 Kb in 0.140099s from omnipathdb.org (82.8 Kb/s); Redirect: 0s, DNS look up: 0.010636s, Connection: 0.028404s, Pretransfer: 0.104466s, First byte at: 0.140058s [2025-10-13 20:45:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:45:45 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 11882; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:45:45 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-10-13 20:45:46] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2025-10-13 20:45:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:46] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2025-10-13 20:45:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2025-10-13 20:45:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2025-10-13 20:45:46] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2025-10-13 20:45:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:46] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2025-10-13 20:45:46] [SUCCESS] [OmnipathR] Downloaded 164 enzyme-substrate relationships. --- finished re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown [2025-10-13 20:45:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:52] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:45:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:29:01 UTC; omnipath [2025-10-13 20:45:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:45:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:30:32 UTC; unix [2025-10-13 20:45:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2 [2025-10-13 20:45:52] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:45:52] [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=2025-10-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-10-13 20:45:52] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-10-13 20:45:52] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.36.0(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 0.45(2025-10-03); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-13 20:45:52] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-10-13 20:45:52] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:45:52] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:45:52] [TRACE] [OmnipathR] Contains 3 files. [2025-10-13 20:45:52] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:45:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:45:52] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:45:52] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:45:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:52] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:45:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:53] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:45:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:53] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:45:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:53] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-13 20:45:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:45:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:45:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2025-10-13 20:45:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:45:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2025-10-13 20:45:55] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-13 20:45:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:55] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-13 20:45:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:55] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-13 20:45:55] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-13 20:45:55] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:45:55] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:45:55] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:45:55] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-13 20:45:55] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:45:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:45:55] [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] [2025-10-13 20:45:55] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:45:55] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:45:55] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:45:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:45:55] [TRACE] [OmnipathR] Downloaded 31.3 Kb in 0.235681s from www.ensembl.org (132.7 Kb/s); Redirect: 0s, DNS look up: 0.026338s, Connection: 0.044552s, Pretransfer: 0.127311s, First byte at: 0.21448s [2025-10-13 20:45:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:45:55 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 32025; 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=Tue, 14 Oct 2025 18:45:55 GMT; Set-cookie: ENSEMBL_HINX_SESSION=8fae0bbb25f41e720cdde7b7693c62e3089acb2f67ee093fafec0d3a; 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=Tue, 14 Oct 2025 18:45:55 GMT; Set-cookie: ENSEMBL_HINX_SESSION=8fae0bbb25f41e720cdde7b7693c62e3089acb2f67ee093fafec0d3a; 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 [2025-10-13 20:45:55] [TRACE] [OmnipathR] Response headers: [Date=Mon, 13 Oct 2025 18:45:55 GMT,Content-Type=text/html; charset=utf-8,Content-Length=32025,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=Tue, 14 Oct 2025 18:45:55 GMT,Set-cookie=ENSEMBL_HINX_SESSION=8fae0bbb25f41e720cdde7b7693c62e3089acb2f67ee093fafec0d3a; 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=Tue, 14 Oct 2025 18:45:55 GMT,Set-cookie=ENSEMBL_HINX_SESSION=8fae0bbb25f41e720cdde7b7693c62e3089acb2f67ee093fafec0d3a; 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] [2025-10-13 20:45:56] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-13 20:45:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:56] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-10-13 20:45:56] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:45:56] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:45:56] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:45:56] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:45:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:56] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-10-13 20:45:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:45:56] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:45:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:45:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:45:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:45:56] [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] [2025-10-13 20:45:56] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:45:56] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.093943s from omabrowser.org (92.5 Kb/s); Redirect: 0s, DNS look up: 0.032167s, Connection: 0.042501s, Pretransfer: 0.078398s, First byte at: 0.093728s [2025-10-13 20:45:56] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 13 Oct 2025 18:45:56 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 [2025-10-13 20:45:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:45:56] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-10-13 20:45:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:56] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-10-13 20:45:56] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-10-13 20:45:56] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:45:56] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:45:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:45:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:45:57] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:45:57] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:45:57] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:45:57] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:45:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:45:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:45:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:45:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:45:57] [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] [2025-10-13 20:45:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:45:57] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094495s from omnipathdb.org (165.8 Kb/s); Redirect: 0s, DNS look up: 0.000989s, Connection: 0.02048s, Pretransfer: 0.054573s, First byte at: 0.09424s [2025-10-13 20:45:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:45:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:45:57 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:45:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:45:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:57] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2025-10-13 20:45:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2025-10-13 20:45:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2025-10-13 20:45:57] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2025-10-13 20:45:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:45:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:45:58] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:00] [SUCCESS] [OmnipathR] Downloaded 67773 interactions. [2025-10-13 20:46:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra] [2025-10-13 20:46:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions] [2025-10-13 20:46:04] [TRACE] [OmnipathR] Organism(s): 10090 [2025-10-13 20:46:04] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:46:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:04] [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] [2025-10-13 20:46:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:04] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.106743s from omnipathdb.org (146.8 Kb/s); Redirect: 0s, DNS look up: 0.001171s, Connection: 0.022194s, Pretransfer: 0.063967s, First byte at: 0.106426s [2025-10-13 20:46:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:04 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:05] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2025-10-13 20:46:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2025-10-13 20:46:05] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1] [2025-10-13 20:46:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:05] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:06] [SUCCESS] [OmnipathR] Downloaded 41476 interactions. [2025-10-13 20:46:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra] [2025-10-13 20:46:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions] [2025-10-13 20:46:07] [TRACE] [OmnipathR] Organism(s): 10116 [2025-10-13 20:46:07] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:46:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:07] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:07] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:07] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:07] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:07] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:07] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:07] [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] [2025-10-13 20:46:07] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:07] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.152778s from omnipathdb.org (102.5 Kb/s); Redirect: 0s, DNS look up: 0.013423s, Connection: 0.035075s, Pretransfer: 0.109232s, First byte at: 0.152507s [2025-10-13 20:46:07] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:07 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:08] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2025-10-13 20:46:08] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2025-10-13 20:46:08] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2025-10-13 20:46:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:08] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:08] [SUCCESS] [OmnipathR] Downloaded 11083 interactions. [2025-10-13 20:46:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra] [2025-10-13 20:46:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions] [2025-10-13 20:46:09] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:09] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:46:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:09] [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] [2025-10-13 20:46:09] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:09] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097318s from omnipathdb.org (161 Kb/s); Redirect: 0s, DNS look up: 0.001076s, Connection: 0.021078s, Pretransfer: 0.056713s, First byte at: 0.097035s [2025-10-13 20:46:09] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:09 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:09 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:09] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2025-10-13 20:46:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2025-10-13 20:46:09] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2025-10-13 20:46:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:09] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:09] [SUCCESS] [OmnipathR] Downloaded 2840 interactions. [2025-10-13 20:46:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-10-13 20:46:09] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:09] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-10-13 20:46:09] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:09] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:09] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:09] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:09] [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] [2025-10-13 20:46:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:10] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.134052s from omnipathdb.org (116.9 Kb/s); Redirect: 0s, DNS look up: 0.011296s, Connection: 0.03449s, Pretransfer: 0.086149s, First byte at: 0.13374s [2025-10-13 20:46:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:10 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:12] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:46:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:46:12] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-10-13 20:46:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:12] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:15] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2025-10-13 20:46:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea] [2025-10-13 20:46:17] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:17] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:46:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:46:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:46:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:46:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:46:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:46:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:46:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:17] [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] [2025-10-13 20:46:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:17] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094488s from omnipathdb.org (165.8 Kb/s); Redirect: 0s, DNS look up: 0.000912s, Connection: 0.020032s, Pretransfer: 0.056214s, First byte at: 0.094237s [2025-10-13 20:46:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:17 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic` [2025-10-13 20:46:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:17] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2025-10-13 20:46:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2025-10-13 20:46:17] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1] [2025-10-13 20:46:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:17] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:17] [SUCCESS] [OmnipathR] Downloaded 6128 interactions. [2025-10-13 20:46:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget] [2025-10-13 20:46:18] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:18] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:46:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:18] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:18] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:18] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:18] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:18] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:18] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:18] [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] [2025-10-13 20:46:18] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:18] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.157691s from omnipathdb.org (99.4 Kb/s); Redirect: 0s, DNS look up: 0.016869s, Connection: 0.038441s, Pretransfer: 0.114601s, First byte at: 0.157374s [2025-10-13 20:46:18] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:18 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:19] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:19] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2025-10-13 20:46:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2025-10-13 20:46:19] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1] [2025-10-13 20:46:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:20] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:20] [SUCCESS] [OmnipathR] Downloaded 648 interactions. [2025-10-13 20:46:20] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule] [2025-10-13 20:46:20] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:20] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-10-13 20:46:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-10-13 20:46:20] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-10-13 20:46:20] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-10-13 20:46:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-10-13 20:46:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-10-13 20:46:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-10-13 20:46:20] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:20] [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] [2025-10-13 20:46:20] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:20] [TRACE] [OmnipathR] Downloaded 189 bytes in 0.120715s from omnipathdb.org (1.5 Kb/s); Redirect: 0s, DNS look up: 0.001408s, Connection: 0.0216s, Pretransfer: 0.099194s, First byte at: 0.12069s [2025-10-13 20:46:20] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:20 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 189; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:20 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-10-13 20:46:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2025-10-13 20:46:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:21] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2025-10-13 20:46:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2025-10-13 20:46:21] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1] [2025-10-13 20:46:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:21] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:21] [SUCCESS] [OmnipathR] Downloaded 0 interactions. [2025-10-13 20:46:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:46:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:21] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2025-10-13 20:46:21] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:21] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:21] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:21] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:21] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:21] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:21] [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] [2025-10-13 20:46:21] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:21] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09811s from omnipathdb.org (159.7 Kb/s); Redirect: 0s, DNS look up: 0.000977s, Connection: 0.021554s, Pretransfer: 0.0564s, First byte at: 0.097787s [2025-10-13 20:46:21] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:21 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:22] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:22] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-10-13 20:46:22] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-10-13 20:46:22] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2025-10-13 20:46:22] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:46:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:22] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:46:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:22] [WARN] [OmnipathR] Failed to update cache: key `a6f560033dff45b503a8016c14c974c4c04b5967` does not exist. [2025-10-13 20:46:23] [SUCCESS] [OmnipathR] Downloaded 47840 enzyme-substrate relationships. [2025-10-13 20:46:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-10-13 20:46:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-10-13 20:46:24] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:24] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:24] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:24] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:24] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:24] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:24] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:24] [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] [2025-10-13 20:46:24] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:24] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.143799s from omnipathdb.org (109 Kb/s); Redirect: 0s, DNS look up: 0.001186s, Connection: 0.020805s, Pretransfer: 0.084508s, First byte at: 0.143522s [2025-10-13 20:46:24] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:24 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:24 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:26] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:46:26] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:46:26] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-10-13 20:46:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:26] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:29] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2025-10-13 20:46:30] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub] [2025-10-13 20:46:30] [TRACE] [OmnipathR] Organism(s): 10090 [2025-10-13 20:46:30] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:46:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:30] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:30] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:31] [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] [2025-10-13 20:46:31] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:31] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.10621s from omnipathdb.org (147.5 Kb/s); Redirect: 0s, DNS look up: 0.001088s, Connection: 0.024228s, Pretransfer: 0.059807s, First byte at: 0.105903s [2025-10-13 20:46:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:31 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:31] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:46:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:31] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2025-10-13 20:46:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2025-10-13 20:46:31] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1] [2025-10-13 20:46:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:31] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:32] [SUCCESS] [OmnipathR] Downloaded 19838 enzyme-substrate relationships. [2025-10-13 20:46:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:46:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:32] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes] [2025-10-13 20:46:32] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:32] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:46:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:32] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:46:32] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:46:32] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:46:32] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:46:32] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:46:32] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:46:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:46:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:32] [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] [2025-10-13 20:46:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:32] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.10866s from omnipathdb.org (144.2 Kb/s); Redirect: 0s, DNS look up: 0.001256s, Connection: 0.020805s, Pretransfer: 0.068857s, First byte at: 0.10844s [2025-10-13 20:46:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:32 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:33] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:46:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:33] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2025-10-13 20:46:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2025-10-13 20:46:33] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1] [2025-10-13 20:46:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:33] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:33] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes. [2025-10-13 20:46:34] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:46:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:34] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,...],wide=FALSE,query_type=annotations] [2025-10-13 20:46:34] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:34] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:34] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-10-13 20:46:34] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-10-13 20:46:34] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-10-13 20:46:34] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-10-13 20:46:34] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-10-13 20:46:34] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-10-13 20:46:34] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-10-13 20:46:34] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:34] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:34] [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] [2025-10-13 20:46:34] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:34] [TRACE] [OmnipathR] Downloaded 15.2 Kb in 0.085914s from omnipathdb.org (177.1 Kb/s); Redirect: 0s, DNS look up: 0.000912s, Connection: 0.017038s, Pretransfer: 0.053538s, First byte at: 0.085592s [2025-10-13 20:46:34] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:34 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:34 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:34] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic` [2025-10-13 20:46:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:34] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2025-10-13 20:46:34] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2025-10-13 20:46:34] [INFO] [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1] [2025-10-13 20:46:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:34] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:34] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records. [2025-10-13 20:46:34] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations] [2025-10-13 20:46:34] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:34] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:34] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:46:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:35] [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] [2025-10-13 20:46:35] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:35] [TRACE] [OmnipathR] Downloaded 5.8 Kb in 0.094031s from omnipathdb.org (61.8 Kb/s); Redirect: 0s, DNS look up: 0.003402s, Connection: 0.019228s, Pretransfer: 0.076583s, First byte at: 0.094011s [2025-10-13 20:46:35] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:35 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 5949; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:35 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-10-13 20:46:35] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:35] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2025-10-13 20:46:35] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2025-10-13 20:46:35] [INFO] [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1] [2025-10-13 20:46:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:35] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:35] [SUCCESS] [OmnipathR] Downloaded 86 annotation records. [2025-10-13 20:46:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations] [2025-10-13 20:46:35] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:35] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:46:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:35] [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] [2025-10-13 20:46:35] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:35] [TRACE] [OmnipathR] Downloaded 17.9 Kb in 0.091593s from omnipathdb.org (195.5 Kb/s); Redirect: 0s, DNS look up: 0.001008s, Connection: 0.019023s, Pretransfer: 0.055157s, First byte at: 0.091556s [2025-10-13 20:46:35] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:35 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 18335; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:35 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-10-13 20:46:36] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic` [2025-10-13 20:46:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:36] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2025-10-13 20:46:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2025-10-13 20:46:36] [INFO] [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1] [2025-10-13 20:46:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:36] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:36] [SUCCESS] [OmnipathR] Downloaded 366 annotation records. [2025-10-13 20:46:36] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2025-10-13 20:46:36] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:36] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:46:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:46:36] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:46:36] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:46:36] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:46:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:46:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:46:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:46:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:36] [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] [2025-10-13 20:46:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:36] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094305s from omnipathdb.org (166.1 Kb/s); Redirect: 0s, DNS look up: 0.001041s, Connection: 0.019996s, Pretransfer: 0.055538s, First byte at: 0.093984s [2025-10-13 20:46:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:36 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:36] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:46:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:36] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-10-13 20:46:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-10-13 20:46:36] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2025-10-13 20:46:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:36] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:36] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2025-10-13 20:46:37] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:37] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:46:37] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:46:37] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2025-10-13 20:46:37] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2025-10-13 20:46:37] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2025-10-13 20:46:37] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:46:37] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:46:37] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:37] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:37] [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] [2025-10-13 20:46:37] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:37] [TRACE] [OmnipathR] Downloaded 9.4 Kb in 0.076817s from omnipathdb.org (122.2 Kb/s); Redirect: 0s, DNS look up: 0.001062s, Connection: 0.020317s, Pretransfer: 0.055816s, First byte at: 0.076631s [2025-10-13 20:46:37] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:37 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:37 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:37] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:46:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:37] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2025-10-13 20:46:37] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2025-10-13 20:46:37] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2025-10-13 20:46:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:37] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:37] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2025-10-13 20:46:37] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:37] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:46:37] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:46:37] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:46:37] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:46:37] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:46:37] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:46:37] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:46:37] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:37] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:37] [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] [2025-10-13 20:46:37] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:37] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.098967s from omnipathdb.org (158.3 Kb/s); Redirect: 0s, DNS look up: 0.001148s, Connection: 0.021532s, Pretransfer: 0.057327s, First byte at: 0.098603s [2025-10-13 20:46:37] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:37 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:37 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:38] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:46:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:38] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:38] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2025-10-13 20:46:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2025-10-13 20:46:40] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1] [2025-10-13 20:46:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:40] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:40] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records. [2025-10-13 20:46:41] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2025-10-13 20:46:41] [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. [2025-10-13 20:46:41] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`. [2025-10-13 20:46:41] [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. --- finished re-building ‘omnipath_intro.Rmd’ --- re-building ‘paths.Rmd’ using rmarkdown [2025-10-13 20:46:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:44] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:46:44] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:29:01 UTC; omnipath [2025-10-13 20:46:44] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:46:44] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:30:32 UTC; unix [2025-10-13 20:46:44] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2 [2025-10-13 20:46:44] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:46:44] [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=2025-10-13; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-10-13 20:46:44] [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] [2025-10-13 20:46:44] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.36.0(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 0.45(2025-10-03); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); 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 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); 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 1.1.0(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 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-10-13 20:46:44] [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 [2025-10-13 20:46:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:46:44] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:46:44] [TRACE] [OmnipathR] Contains 10 files. [2025-10-13 20:46:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:46:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:46:44] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:46:44] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:46:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:44] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:46:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:44] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:46:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:44] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:46:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:44] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-13 20:46:44] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2025-10-13 20:46:44] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-13 20:46:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:44] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-13 20:46:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:44] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-13 20:46:44] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-13 20:46:44] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:46:44] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:46:44] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:46:44] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-13 20:46:44] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:46:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:44] [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] [2025-10-13 20:46:44] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:46:44] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:46:44] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:46:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:44] [TRACE] [OmnipathR] Downloaded 31.2 Kb in 0.202585s from www.ensembl.org (153.9 Kb/s); Redirect: 0s, DNS look up: 0.001284s, Connection: 0.019445s, Pretransfer: 0.076158s, First byte at: 0.180429s [2025-10-13 20:46:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:46:44 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31917; 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=Tue, 14 Oct 2025 18:46:44 GMT; Set-cookie: ENSEMBL_HINX_SESSION=577bd4f1c55b97be0eb97ee8693c63140afe51ffbc34d98aea736c37; 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=Tue, 14 Oct 2025 18:46:44 GMT; Set-cookie: ENSEMBL_HINX_SESSION=577bd4f1c55b97be0eb97ee8693c63140afe51ffbc34d98aea736c37; 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-p1m2-31.ebi.ac.uk [2025-10-13 20:46:44] [TRACE] [OmnipathR] Response headers: [Date=Mon, 13 Oct 2025 18:46:44 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31917,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=Tue, 14 Oct 2025 18:46:44 GMT,Set-cookie=ENSEMBL_HINX_SESSION=577bd4f1c55b97be0eb97ee8693c63140afe51ffbc34d98aea736c37; 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=Tue, 14 Oct 2025 18:46:44 GMT,Set-cookie=ENSEMBL_HINX_SESSION=577bd4f1c55b97be0eb97ee8693c63140afe51ffbc34d98aea736c37; 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-p1m2-31.ebi.ac.uk] [2025-10-13 20:46:44] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-13 20:46:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:44] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-10-13 20:46:44] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:46:44] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:46:44] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:46:45] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:46:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:45] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:46:45] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:46:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:46:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:45] [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] [2025-10-13 20:46:45] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:46:45] [TRACE] [OmnipathR] Downloaded 7.8 Kb in 0.060588s from omabrowser.org (128.8 Kb/s); Redirect: 0s, DNS look up: 0.000997s, Connection: 0.010359s, Pretransfer: 0.045419s, First byte at: 0.060451s [2025-10-13 20:46:45] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 13 Oct 2025 18:46:45 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 [2025-10-13 20:46:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:46:45] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-10-13 20:46:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:45] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:45] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-10-13 20:46:45] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:45] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:46:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:45] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:46:45] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:46:45] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:46:45] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:46:45] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:46:45] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:46:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:46:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:45] [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] [2025-10-13 20:46:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:45] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101607s from omnipathdb.org (154.2 Kb/s); Redirect: 0s, DNS look up: 0.001288s, Connection: 0.023009s, Pretransfer: 0.057266s, First byte at: 0.101275s [2025-10-13 20:46:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:45 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:46:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:45] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2025-10-13 20:46:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2025-10-13 20:46:45] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2025-10-13 20:46:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:45] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:45] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records. [2025-10-13 20:46:45] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:46:45] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2025-10-13 20:46:45] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2025-10-13 20:46:45] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2025-10-13 20:46:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:45] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2025-10-13 20:46:45] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2025-10-13 20:46:45] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2025-10-13 20:46:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:45] [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] [2025-10-13 20:46:46] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:46:46] [TRACE] [OmnipathR] Downloaded 3.4 Kb in 0.088851s from static-content.springer.com (38.8 Kb/s); Redirect: 0s, DNS look up: 0.009615s, Connection: 0.018156s, Pretransfer: 0.051439s, First byte at: 0.088818s [2025-10-13 20:46:46] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; content-type: application/octet-stream; x-guploader-uploadid: AAwnv3KkFYuK6SNu41VJCyLvd7vrAixTj2RNozcEVbGdiezDUcrv08RNtB8v96VWvn0PXrP7mgvEK5o; cache-control: private, max-age=86400; last-modified: Thu, 16 Nov 2023 16:51:13 GMT; etag: "daa03c1eafd00cad9456b660ca85b849"; x-goog-generation: 1700153472991609; x-goog-metageneration: 1; x-goog-stored-content-encoding: identity; x-goog-stored-content-length: 160972; x-goog-hash: crc32c=v/3p0Q==; x-goog-hash: md5=2qA8Hq/QDK2UVrZgyoW4SQ==; x-goog-storage-class: MULTI_REGIONAL; server: UploadServer; x-cdn-origin: GCS, SNPaaS; accept-ranges: bytes; age: 48157; date: Mon, 13 Oct 2025 18:46:46 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230136-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1760381206.064306,VS0,VE7; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972 [2025-10-13 20:46:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2025-10-13 20:46:46] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2025-10-13 20:46:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:46] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:46] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2025-10-13 20:46:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions] [2025-10-13 20:46:46] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:46] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-10-13 20:46:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-10-13 20:46:46] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-10-13 20:46:46] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-10-13 20:46:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-10-13 20:46:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-10-13 20:46:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-10-13 20:46:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:46] [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] [2025-10-13 20:46:46] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:46] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101227s from omnipathdb.org (154.8 Kb/s); Redirect: 0s, DNS look up: 0.000983s, Connection: 0.022832s, Pretransfer: 0.057012s, First byte at: 0.100974s [2025-10-13 20:46:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:46 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:47] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic` [2025-10-13 20:46:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:47] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2025-10-13 20:46:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2025-10-13 20:46:47] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1] [2025-10-13 20:46:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:47] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:51] [SUCCESS] [OmnipathR] Downloaded 124225 interactions. [2025-10-13 20:46:51] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations] [2025-10-13 20:46:51] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:51] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:46:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-10-13 20:46:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-10-13 20:46:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-10-13 20:46:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-10-13 20:46:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-10-13 20:46:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-10-13 20:46:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-10-13 20:46:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:51] [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] [2025-10-13 20:46:51] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:51] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095665s from omnipathdb.org (163.8 Kb/s); Redirect: 0s, DNS look up: 0.001091s, Connection: 0.020986s, Pretransfer: 0.055117s, First byte at: 0.095287s [2025-10-13 20:46:51] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:51 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:52] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-10-13 20:46:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:52] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2025-10-13 20:46:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2025-10-13 20:46:54] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1] [2025-10-13 20:46:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:54] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:54] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records. [2025-10-13 20:46:54] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:54] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:46:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:46:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:46:54] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:46:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:46:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:46:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:46:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:54] [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] [2025-10-13 20:46:54] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:54] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.086875s from omnipathdb.org (180.3 Kb/s); Redirect: 0s, DNS look up: 0.00108s, Connection: 0.018028s, Pretransfer: 0.05204s, First byte at: 0.086466s [2025-10-13 20:46:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:54 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:46:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:55] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2025-10-13 20:46:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2025-10-13 20:46:55] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1] [2025-10-13 20:46:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:55] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:55] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records. [2025-10-13 20:46:55] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:55] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:46:55] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:46:55] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:46:55] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:46:55] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:46:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:46:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:46:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:55] [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] [2025-10-13 20:46:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:55] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.143679s from omnipathdb.org (109 Kb/s); Redirect: 0s, DNS look up: 0.000997s, Connection: 0.020769s, Pretransfer: 0.054773s, First byte at: 0.14334s [2025-10-13 20:46:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:55 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:46:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:55] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-10-13 20:46:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-10-13 20:46:56] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2025-10-13 20:46:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:56] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:56] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records. [2025-10-13 20:46:56] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:56] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-10-13 20:46:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-10-13 20:46:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-10-13 20:46:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-10-13 20:46:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-10-13 20:46:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-10-13 20:46:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-10-13 20:46:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:56] [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] [2025-10-13 20:46:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:56] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089167s from omnipathdb.org (175.7 Kb/s); Redirect: 0s, DNS look up: 0.001074s, Connection: 0.018597s, Pretransfer: 0.053446s, First byte at: 0.088846s [2025-10-13 20:46:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:56 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-10-13 20:46:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:56] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2025-10-13 20:46:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2025-10-13 20:46:56] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1] [2025-10-13 20:46:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:56] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:56] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records. [2025-10-13 20:46:56] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:56] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:46:56] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-10-13 20:46:56] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:46:56] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2025-10-13 20:46:56] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:56] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:46:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:46:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:46:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:46:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:46:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:46:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:46:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:56] [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] [2025-10-13 20:46:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:57] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096317s from omnipathdb.org (162.7 Kb/s); Redirect: 0s, DNS look up: 0.001125s, Connection: 0.02082s, Pretransfer: 0.055866s, First byte at: 0.095994s [2025-10-13 20:46:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:56 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:46:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:57] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2025-10-13 20:46:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2025-10-13 20:46:57] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1] [2025-10-13 20:46:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:57] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:57] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records. [2025-10-13 20:46:57] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:57] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:46:57] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-10-13 20:46:57] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:46:57] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2025-10-13 20:46:57] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:57] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-10-13 20:46:57] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-10-13 20:46:57] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-10-13 20:46:57] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-10-13 20:46:57] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-10-13 20:46:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-10-13 20:46:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-10-13 20:46:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:57] [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] [2025-10-13 20:46:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:57] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.085579s from omnipathdb.org (183.1 Kb/s); Redirect: 0s, DNS look up: 0.001051s, Connection: 0.017347s, Pretransfer: 0.052136s, First byte at: 0.085281s [2025-10-13 20:46:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:57 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-10-13 20:46:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:57] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2025-10-13 20:46:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2025-10-13 20:46:58] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1] [2025-10-13 20:46:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:58] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`. [2025-10-13 20:46:58] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records. [2025-10-13 20:46:58] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:58] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:46:58] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-10-13 20:46:58] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:46:58] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2025-10-13 20:46:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein] [2025-10-13 20:46:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:46:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions] [2025-10-13 20:46:58] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:46:58] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:46:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:46:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:46:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:46:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:46:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:46:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:46:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:46:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:46:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:46:58] [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] [2025-10-13 20:46:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:46:58] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090921s from omnipathdb.org (172.3 Kb/s); Redirect: 0s, DNS look up: 0.001008s, Connection: 0.019217s, Pretransfer: 0.053546s, First byte at: 0.090664s [2025-10-13 20:46:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:46:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:46:58 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:46:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:46:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:58] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2025-10-13 20:46:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2025-10-13 20:46:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2025-10-13 20:46:59] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2025-10-13 20:46:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:46:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:46:59] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2025-10-13 20:47:00] [SUCCESS] [OmnipathR] Downloaded 32281 interactions. [2025-10-13 20:47:00] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:47:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations] [2025-10-13 20:47:00] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:47:00] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:47:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:47:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:47:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:47:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:47:00] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:47:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:47:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:47:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:47:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:47:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:47:00] [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] [2025-10-13 20:47:00] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:47:00] [TRACE] [OmnipathR] Downloaded 13.1 Kb in 0.088235s from omnipathdb.org (148.6 Kb/s); Redirect: 0s, DNS look up: 0.000957s, Connection: 0.018151s, Pretransfer: 0.053289s, First byte at: 0.087998s [2025-10-13 20:47:00] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:47:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:47:00 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:47:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:47:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:00] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2025-10-13 20:47:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2025-10-13 20:47:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2025-10-13 20:47:00] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2025-10-13 20:47:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:00] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2025-10-13 20:47:00] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records. [2025-10-13 20:47:00] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:47:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations] [2025-10-13 20:47:01] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:47:01] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:47:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:47:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:47:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:47:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:47:01] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:47:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:47:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:47:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:47:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:47:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:47:01] [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] [2025-10-13 20:47:01] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:47:01] [TRACE] [OmnipathR] Downloaded 12.2 Kb in 0.089506s from omnipathdb.org (136 Kb/s); Redirect: 0s, DNS look up: 0.00094s, Connection: 0.018796s, Pretransfer: 0.053463s, First byte at: 0.089281s [2025-10-13 20:47:01] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:47:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:47:01 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:47:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:47:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:01] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`. [2025-10-13 20:47:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2025-10-13 20:47:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2025-10-13 20:47:01] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1] [2025-10-13 20:47:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:01] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`. [2025-10-13 20:47:01] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records. [2025-10-13 20:47:02] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`. [2025-10-13 20:47:02] [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. [2025-10-13 20:47:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:47:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions] [2025-10-13 20:47:02] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:47:02] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:47:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:47:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:47:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:47:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:47:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:47:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:47:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:47:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:47:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:47:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:47:02] [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] [2025-10-13 20:47:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:47:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.08503s from omnipathdb.org (184.3 Kb/s); Redirect: 0s, DNS look up: 0.001105s, Connection: 0.017222s, Pretransfer: 0.052195s, First byte at: 0.084758s [2025-10-13 20:47:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:47:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:47:02 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:47:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2025-10-13 20:47:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:02] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`. [2025-10-13 20:47:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2025-10-13 20:47:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2025-10-13 20:47:02] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1] [2025-10-13 20:47:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:02] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`. [2025-10-13 20:47:03] [SUCCESS] [OmnipathR] Downloaded 4242 interactions. [2025-10-13 20:47:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:47:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2025-10-13 20:47:03] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:47:03] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:47:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:47:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:47:03] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:47:03] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:47:03] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:47:03] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:47:03] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:47:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:47:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:47:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:47:03] [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] [2025-10-13 20:47:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:47:03] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091333s from omnipathdb.org (171.5 Kb/s); Redirect: 0s, DNS look up: 0.000873s, Connection: 0.019216s, Pretransfer: 0.053959s, First byte at: 0.091039s [2025-10-13 20:47:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:47:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:47:03 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:47:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:47:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:03] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2025-10-13 20:47:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-10-13 20:47:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-10-13 20:47:04] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2025-10-13 20:47:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:04] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2025-10-13 20:47:04] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2025-10-13 20:47:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:47:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2025-10-13 20:47:04] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:47:04] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:47:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:47:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:47:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:47:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:47:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:47:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:47:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:47:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:47:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:47:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:47:04] [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] [2025-10-13 20:47:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:47:04] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095283s from omnipathdb.org (164.4 Kb/s); Redirect: 0s, DNS look up: 0.001005s, Connection: 0.02077s, Pretransfer: 0.055098s, First byte at: 0.094981s [2025-10-13 20:47:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:47:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 13 Oct 2025 19:47:04 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:47:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:47:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:05] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`. [2025-10-13 20:47:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-10-13 20:47:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-10-13 20:47:05] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1] [2025-10-13 20:47:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:47:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:05] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`. [2025-10-13 20:47:05] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records. [2025-10-13 20:47:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:47:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2025-10-13 20:47:07] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:47:07] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:47:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:47:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:07] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:47:07] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-10-13 20:47:07] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:47:07] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2025-10-13 20:47:07] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:47:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2025-10-13 20:47:07] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:47:07] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:47:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:47:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:47:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:47:08] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-10-13 20:47:08] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:47:08] [SUCCESS] [OmnipathR] Loaded 2102 annotation records from cache. --- finished re-building ‘paths.Rmd’ SUMMARY: processing the following file failed: ‘drug_targets.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 2 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.21/2025-10-13_2017/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2025-10-13 20:47:17 CEST ]