[ Started: 2025-10-13 20:06:53 CEST ] [ OmnipathR v3.17.6 for BioC-3.22 from https://github.com/saezlab/OmnipathR@devel (63cc07f 2025-09-23 14:44:35) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/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 ‘3.17.6’ * 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 20:07:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:07:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:07:26] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:07:26] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:05:40 UTC; omnipath [2025-10-13 20:07:26] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:07:26] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:06:56 UTC; unix [2025-10-13 20:07:26] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-13 20:07:26] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:07:26] [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 20:07:26] [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 20:07:26] [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 3.17.6(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 20:07:26] [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 20:07:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:07:26] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:07:26] [TRACE] [OmnipathR] Contains 1 files. [2025-10-13 20:07:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:07:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:07:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:07:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:07:26] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:07:26] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:07:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:07:26] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:07:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:07:26] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:07:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:07:26] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:07:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:07:26] [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 20:07:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:07:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:07:38] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:07:38] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:05:40 UTC; omnipath [2025-10-13 20:07:38] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:07:38] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:06:56 UTC; unix [2025-10-13 20:07:38] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-13 20:07:38] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:07:38] [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 20:07:38] [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 20:07:38] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); 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 3.17.6(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 20:07:38] [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 20:07:38] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:07:38] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:07:38] [TRACE] [OmnipathR] Contains 1 files. [2025-10-13 20:07:38] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:07:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:07:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:07:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:07:38] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:07:38] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:07:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:07:38] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:07:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:07:38] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:07:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:07:38] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:07:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:07:38] [TRACE] [OmnipathR] Cache locked: FALSE .cosmos_pkn: no visible global function definition for ‘metabolite_idsc’ cosmos_ksn: no visible binding for global variable ‘substrate_genesymbol’ cosmos_ksn: no visible binding for global variable ‘residue_type’ cosmos_ksn: no visible binding for global variable ‘residue_offset’ cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’ cosmos_ksn: no visible binding for global variable ‘mor’ recon3d_genes: no visible binding for global variable ‘notes’ recon3d_genes: no visible binding for global variable ‘annotation’ recon3d_genes: no visible binding for global variable ‘original_bigg_ids’ recon3d_metabolites: no visible binding for global variable ‘notes’ recon3d_metabolites: no visible binding for global variable ‘original_bigg_ids’ recon3d_metabolites: no visible binding for global variable ‘annotation’ recon3d_metabolites: no visible global function definition for ‘chalmers_gem_matlab_tibble’ recon3d_metabolites: no visible binding for global variable ‘hmdb’ recon3d_metabolites: no visible binding for global variable ‘metHMDBID’ recon3d_reactions: no visible binding for global variable ‘notes’ recon3d_reactions: no visible binding for global variable ‘metabolites’ recon3d_reactions: no visible binding for global variable ‘original_bigg_ids’ taxon_names_table: no visible binding for global variable ‘latin_name_uniprot’ taxon_names_table: no visible binding for global variable ‘latin_name_ensembl’ taxon_names_table: no visible binding for global variable ‘latin_name_oma’ taxon_names_table: no visible binding for global variable ‘common_name_ensembl’ taxon_names_table: no visible binding for global variable ‘common_name_uniprot’ Undefined global functions or variables: annotation chalmers_gem_matlab_tibble common_name_ensembl common_name_uniprot enzyme_genesymbol hmdb latin_name_ensembl latin_name_oma latin_name_uniprot metHMDBID metabolite_idsc metabolites mor notes original_bigg_ids residue_offset residue_type substrate_genesymbol * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘recon3d_raw’ ‘recon3d_raw_vmh’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'recon3d.Rd' ‘extra_hmdb’ Undocumented arguments in Rd file 'translate_ids_multi.Rd' ‘ramp’ ‘expand’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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: extra_attrs > ### Title: Extra attribute names in an interaction data frame > ### Aliases: extra_attrs > > ### ** Examples > > i <- omnipath(fields = "extra_attrs") [2025-10-13 20:11:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:11:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,datasets=omnipath] [2025-10-13 20:11:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:11:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,datasets=omnipath,query_type=interactions] [2025-10-13 20:11:15] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:11:15] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:11:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2025-10-13 20:11:15] [FATAL] [OmnipathR] Missing cache file: `/home/omnipath/.cache/OmnipathR/cd62310e6377458c15d1a9c58a97999a1b55be3e-1.rds`. Please run `omnipath_cache_clean_db()` and try again. Error in omnipath_cache_load(url = the_url) : Missing cache file: `/home/omnipath/.cache/OmnipathR/cd62310e6377458c15d1a9c58a97999a1b55be3e-1.rds`. Please run `omnipath_cache_clean_db()` and try again. Calls: omnipath ... omnipath_check_result -> do.call -> -> omnipath_cache_load 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 20:11:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:11:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:11:58] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:11:58] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:05:40 UTC; omnipath [2025-10-13 20:11:58] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:11:58] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:06:56 UTC; unix [2025-10-13 20:11:58] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-13 20:11:58] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:11:58] [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 20:11:58] [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 20:11:58] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.37.1(2025-08-03); 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 3.17.6(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 20:11:58] [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 20:11:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:11:58] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:11:58] [TRACE] [OmnipathR] Contains 19 files. [2025-10-13 20:11:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:11:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:11:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:11:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:11:58] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:11:58] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:11:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:11:58] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:11:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:11:58] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:11:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:11:58] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:11:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:11:58] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-13 20:11:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:11:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2025-10-13 20:11:58] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-13 20:11:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:11:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:11:59] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-13 20:11:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:11:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:11:59] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-13 20:11:59] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-13 20:11:59] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:11:59] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:11:59] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:11:59] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-13 20:11:59] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:11:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:11:59] [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 20:11:59] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:11:59] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:11:59] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:11:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:11:59] [TRACE] [OmnipathR] Downloaded 31.4 Kb in 0.187103s from www.ensembl.org (167.9 Kb/s); Redirect: 0s, DNS look up: 0.001546s, Connection: 0.019689s, Pretransfer: 0.074823s, First byte at: 0.164075s [2025-10-13 20:11:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:11:59 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 32161; 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 18:11:59 GMT; Set-cookie: ENSEMBL_HINX_SESSION=f8ecccf518110a720cb150c8693c5aef08f791ed1a02e341e2d1f5c2; 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 18:11:59 GMT; Set-cookie: ENSEMBL_HINX_SESSION=f8ecccf518110a720cb150c8693c5aef08f791ed1a02e341e2d1f5c2; 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 20:11:59] [TRACE] [OmnipathR] Response headers: [Date=Mon, 13 Oct 2025 18:11:59 GMT,Content-Type=text/html; charset=utf-8,Content-Length=32161,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 18:11:59 GMT,Set-cookie=ENSEMBL_HINX_SESSION=f8ecccf518110a720cb150c8693c5aef08f791ed1a02e341e2d1f5c2; 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 18:11:59 GMT,Set-cookie=ENSEMBL_HINX_SESSION=f8ecccf518110a720cb150c8693c5aef08f791ed1a02e341e2d1f5c2; 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 20:11:59] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-13 20:11:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:11:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:11:59] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-10-13 20:11:59] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:11:59] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:11:59] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:11:59] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:11:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:11:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:11:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:11:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:11:59] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-10-13 20:11:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:11:59] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:11:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:11:59] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:11:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:11:59] [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 20:11:59] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:11:59] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.059406s from omabrowser.org (146.3 Kb/s); Redirect: 0s, DNS look up: 0.001243s, Connection: 0.010649s, Pretransfer: 0.045055s, First byte at: 0.05923s [2025-10-13 20:11:59] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 13 Oct 2025 18:11:59 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 20:11:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:11:59] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-10-13 20:11:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:11:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:11:59] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-10-13 20:11:59] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:11:59] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-10-13 20:11:59] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:11:59] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-10-13 20:11:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:00] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2025-10-13 20:12:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-10-13 20:12:00] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:12:00] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:12:22] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-10-13 20:12:22] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2025-10-13 20:12:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:22] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2025-10-13 20:12:22] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-10-13 20:12:22] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:12:22] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:12:22] [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 20:12:22] [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 20:12:22] [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 20:12:22] [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 20:12:22] [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 20:12:22] [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 20:12:22] [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 20:12:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:12:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:12:22] [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 20:12:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:12:22] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.098268s from omnipathdb.org (159.4 Kb/s); Redirect: 0s, DNS look up: 0.001384s, Connection: 0.022016s, Pretransfer: 0.057451s, First byte at: 0.09782s [2025-10-13 20:12:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:12:22 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 19:12:22 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:12:23] [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 20:12:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:23] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2025-10-13 20:12:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2025-10-13 20:12:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2025-10-13 20:12:24] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2025-10-13 20:12:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:24] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. [2025-10-13 20:12:28] [SUCCESS] [OmnipathR] Downloaded 131398 interactions. [2025-10-13 20:12:32] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:12:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2025-10-13 20:12:32] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:12:32] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:12:32] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:12:32] [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 20:12:32] [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 20:12:32] [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 20:12:32] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:12:32] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:12:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:12:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:12:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:12:32] [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 20:12:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:12:32] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101799s from omnipathdb.org (153.9 Kb/s); Redirect: 0s, DNS look up: 0.00121s, Connection: 0.022792s, Pretransfer: 0.05807s, First byte at: 0.101512s [2025-10-13 20:12:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:12:32 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 19:12:32 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:12:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:12:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:32] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2025-10-13 20:12:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-10-13 20:12:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-10-13 20:12:33] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2025-10-13 20:12:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:33] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2025-10-13 20:12:34] [SUCCESS] [OmnipathR] Downloaded 47840 enzyme-substrate relationships. [2025-10-13 20:12:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:12:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions] [2025-10-13 20:12:35] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:12:35] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:12:35] [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 20:12:35] [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 20:12:35] [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 20:12:35] [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 20:12:35] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:12:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:12:35] [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 20:12:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:12:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:12:35] [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 20:12:35] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:12:35] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090487s from omnipathdb.org (173.1 Kb/s); Redirect: 0s, DNS look up: 0.001038s, Connection: 0.018727s, Pretransfer: 0.05454s, First byte at: 0.090221s [2025-10-13 20:12:35] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:12:35 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 19:12:35 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:12:36] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:12:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:36] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-10-13 20:12:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:12:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:12:36] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-10-13 20:12:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:36] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2025-10-13 20:12:39] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2025-10-13 20:12:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:12:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes] [2025-10-13 20:12:39] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:12:39] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:12:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic` [2025-10-13 20:12:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2025-10-13 20:12:39] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic` [2025-10-13 20:12:39] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic` [2025-10-13 20:12:39] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic` [2025-10-13 20:12:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2025-10-13 20:12:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2025-10-13 20:12:39] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:12:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:12:39] [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 20:12:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:12:39] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.104067s from omnipathdb.org (150.5 Kb/s); Redirect: 0s, DNS look up: 0.000966s, Connection: 0.023155s, Pretransfer: 0.059095s, First byte at: 0.103779s [2025-10-13 20:12:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:12:39 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 19:12:39 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:12:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic` [2025-10-13 20:12:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:40] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2025-10-13 20:12:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2025-10-13 20:12:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2025-10-13 20:12:40] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2025-10-13 20:12:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:40] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2025-10-13 20:12:40] [SUCCESS] [OmnipathR] Downloaded 52085 protein complexes. [2025-10-13 20:12:40] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:12:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2025-10-13 20:12:40] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:12:40] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:12:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:12:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:12:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:12:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:12:41] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:12:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:12:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:12:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:12:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:12:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:12:41] [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 20:12:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:12:41] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097875s from omnipathdb.org (160.1 Kb/s); Redirect: 0s, DNS look up: 0.001045s, Connection: 0.021031s, Pretransfer: 0.057304s, First byte at: 0.097581s [2025-10-13 20:12:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:12:41 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 19:12:41 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:12:41] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:12:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:41] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2025-10-13 20:12:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-10-13 20:12:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-10-13 20:12:42] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2025-10-13 20:12:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:42] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2025-10-13 20:12:42] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2025-10-13 20:12:42] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:12:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations] [2025-10-13 20:12:42] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:12:42] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:12:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:12:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:12:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:12:42] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:12:42] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:12:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:12:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:12:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:12:42] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:12:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:12:42] [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 20:12:42] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:12:42] [TRACE] [OmnipathR] Downloaded 60 bytes in 0.074556s from omnipathdb.org (804 bytes/s); Redirect: 0s, DNS look up: 0.000951s, Connection: 0.019221s, Pretransfer: 0.054956s, First byte at: 0.074538s [2025-10-13 20:12:42] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:12:42 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 19:12:42 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-10-13 20:12:42] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2025-10-13 20:12:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:42] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2025-10-13 20:12:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2025-10-13 20:12:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2025-10-13 20:12:42] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2025-10-13 20:12:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:42] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2025-10-13 20:12:42] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. [2025-10-13 20:12:42] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:12:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations] [2025-10-13 20:12:42] [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 20:12:43] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:12:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2025-10-13 20:12:43] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:12:43] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:12:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:12:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:12:43] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-10-13 20:12:43] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:12:43] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2025-10-13 20:12:43] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:12:43] [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 20:12:43] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:12:43] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:12:43] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:12:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:43] [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 20:12:43] [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 20:12:43] [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 20:12:43] [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 20:12:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-10-13 20:12:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-10-13 20:12:43] [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 20:12:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:12:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:12:43] [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 20:12:43] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:12:43] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089466s from omnipathdb.org (175.1 Kb/s); Redirect: 0s, DNS look up: 0.000917s, Connection: 0.018286s, Pretransfer: 0.053942s, First byte at: 0.089118s [2025-10-13 20:12:43] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:12:43 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 19:12:43 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:12:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2025-10-13 20:12:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:44] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`. [2025-10-13 20:12:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2025-10-13 20:12:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2025-10-13 20:12:44] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1] [2025-10-13 20:12:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:44] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`. [2025-10-13 20:12:44] [SUCCESS] [OmnipathR] Downloaded 3752 annotation records. [2025-10-13 20:12:44] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:12:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2025-10-13 20:12:44] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:12:44] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:12:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:12:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:12:44] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:12:44] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:12:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:12:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:12:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:12:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:12:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:12:44] [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 20:12:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:12:44] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088345s from omnipathdb.org (177.3 Kb/s); Redirect: 0s, DNS look up: 0.000911s, Connection: 0.017964s, Pretransfer: 0.05361s, First byte at: 0.088052s [2025-10-13 20:12:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:12:44 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 19:12:44 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:12:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:12:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:44] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2025-10-13 20:12:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-10-13 20:12:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-10-13 20:12:44] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2025-10-13 20:12:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:44] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2025-10-13 20:12:44] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2025-10-13 20:12:44] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:12:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-10-13 20:12:44] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:12:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-10-13 20:12:45] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:12:45] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:12:45] [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 20:12:45] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:12:45] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:12:48] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. [2025-10-13 20:12:48] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:12:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations] [2025-10-13 20:12:48] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:12:48] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:12:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:12:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:12:48] [FATAL] [OmnipathR] Missing cache file: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. Please run `omnipath_cache_clean_db()` and try again. Quitting from bioc_workshop.Rmd:367-372 [annotate-network] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `omnipath_cache_load()`: ! Missing cache file: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. Please run `omnipath_cache_clean_db()` and try again. --- Backtrace: ▆ 1. ├─OmnipathR::annotated_network(network, "SignaLink_pathway") 2. │ └─... %>% ... 3. ├─checkmate::assert_data_frame(.) 4. │ └─checkmate::checkDataFrame(...) 5. │ └─... %and% checkListTypes(x, types) 6. │ └─base::isTRUE(lhs) 7. ├─rlang::exec(annotations, resources = ., !!!annot_args) 8. ├─OmnipathR (local) ``(resources = "SignaLink_pathway") 9. │ ├─rlang::exec(omnipath_query, proteins = proteins, !!!args) 10. │ └─OmnipathR (local) ``(proteins = NULL, resources = "SignaLink_pathway", query_type = "annotations") 11. │ ├─do.call(omnipath_download, download_args) %>% ... 12. │ ├─base::do.call(omnipath_download, download_args) 13. │ └─OmnipathR (local) ``(...) 14. │ └─OmnipathR::omnipath_cache_load(url = the_url) 15. └─OmnipathR:::omnipath_post_download(...) 16. └─OmnipathR:::omnipath_check_result(result, url) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics: Missing cache file: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. Please run `omnipath_cache_clean_db()` and try again. --- failed re-building ‘bioc_workshop.Rmd’ --- re-building ‘cosmos.Rmd’ using rmarkdown [2025-10-13 20:12:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:50] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:12:50] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:05:40 UTC; omnipath [2025-10-13 20:12:50] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:12:50] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:06:56 UTC; unix [2025-10-13 20:12:50] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-13 20:12:50] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:12:50] [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 20:12:50] [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 20:12:50] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.37.1(2025-08-03); 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 3.17.6(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 20:12:50] [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 20:12:50] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:12:50] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:12:50] [TRACE] [OmnipathR] Contains 3 files. [2025-10-13 20:12:50] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:12:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:12:50] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:12:50] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:12:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:50] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:12:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:50] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:12:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:50] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:12:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:50] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-13 20:12:50] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2025-10-13 20:12:50] [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 20:12:51] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2025-10-13 20:12:51] [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 20:12:51] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2025-10-13 20:12:51] [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 20:12:51] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-13 20:12:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:51] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-13 20:12:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:51] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-13 20:12:51] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-13 20:12:51] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:12:51] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:12:51] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:12:51] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-13 20:12:51] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:12:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:12:51] [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 20:12:51] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:12:51] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:12:51] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:12:51] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:12:51] [TRACE] [OmnipathR] Downloaded 31.3 Kb in 0.199315s from www.ensembl.org (157.2 Kb/s); Redirect: 0s, DNS look up: 0.001345s, Connection: 0.019528s, Pretransfer: 0.073841s, First byte at: 0.181435s [2025-10-13 20:12:51] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:12:51 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 32082; 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 18:12:51 GMT; Set-cookie: ENSEMBL_HINX_SESSION=091597ae929502c70ea8f2dd693c5b230aee3113b58692cb6008582e; 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 18:12:51 GMT; Set-cookie: ENSEMBL_HINX_SESSION=091597ae929502c70ea8f2dd693c5b230aee3113b58692cb6008582e; 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 20:12:51] [TRACE] [OmnipathR] Response headers: [Date=Mon, 13 Oct 2025 18:12:51 GMT,Content-Type=text/html; charset=utf-8,Content-Length=32082,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 18:12:51 GMT,Set-cookie=ENSEMBL_HINX_SESSION=091597ae929502c70ea8f2dd693c5b230aee3113b58692cb6008582e; 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 18:12:51 GMT,Set-cookie=ENSEMBL_HINX_SESSION=091597ae929502c70ea8f2dd693c5b230aee3113b58692cb6008582e; 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 20:12:51] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-13 20:12:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:51] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-10-13 20:12:51] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:12:51] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:12:51] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:12:51] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:12:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:51] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-10-13 20:12:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:12:51] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:12:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:12:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:12:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:12:51] [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 20:12:51] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:12:51] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.061252s from omabrowser.org (141.9 Kb/s); Redirect: 0s, DNS look up: 0.00104s, Connection: 0.011358s, Pretransfer: 0.04552s, First byte at: 0.061091s [2025-10-13 20:12:51] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 13 Oct 2025 18:12:51 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip [2025-10-13 20:12:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:12:52] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-10-13 20:12:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:52] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-10-13 20:12:52] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:12:52] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-10-13 20:12:52] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:12:52] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-10-13 20:12:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:12:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:12:52] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2025-10-13 20:12:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-10-13 20:12:52] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:12:52] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:13:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-10-13 20:13:13] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2025-10-13 20:13:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:13] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `ready` to `ready`. [2025-10-13 20:13:13] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-10-13 20:13:13] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2025-10-13 20:13:13] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:13:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2025-10-13 20:13:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:13:13] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:13:13] [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 20:13:13] [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 20:13:13] [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 20:13:13] [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 20:13:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:13:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:13:13] [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 20:13:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:13:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:13:13] [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 20:13:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:13:13] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099566s from omnipathdb.org (157.4 Kb/s); Redirect: 0s, DNS look up: 0.002235s, Connection: 0.020775s, Pretransfer: 0.056437s, First byte at: 0.099308s [2025-10-13 20:13:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:13:13 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 19:13:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:13:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:13:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:14] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-10-13 20:13:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:13:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:13:15] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-10-13 20:13:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:15] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2025-10-13 20:13:17] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2025-10-13 20:13:17] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2025-10-13 20:13:17] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2025-10-13 20:13:18] [TRACE] [OmnipathR] BioMart query: [2025-10-13 20:13:18] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:13:18] [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 20:13:18] [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 20:13:18] [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 20:13:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:18] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2025-10-13 20:13:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2025-10-13 20:13:18] [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 20:13:18] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:13:18] [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 20:13:18] [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 20:13:18] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:13:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:13:18] [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 20:13:18] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:13:18] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:13:36] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:13:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:13:36] [TRACE] [OmnipathR] Downloaded 2 Mb in 18.733517s from www.ensembl.org (109.3 Kb/s); Redirect: 0s, DNS look up: 0.008016s, Connection: 0.02654s, Pretransfer: 0.02665s, First byte at: 0.113244s [2025-10-13 20:13:36] [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 18:13:18 GMT; Transfer-Encoding: chunked; Connection: Keep-Alive; X-Frame-Options: SAMEORIGIN [2025-10-13 20:13:36] [TRACE] [OmnipathR] Response headers: [Server=Apache,Content-Type=text/plain; charset=utf-8,Content-Security-Policy=frame-ancestors 'self',Date=Mon, 13 Oct 2025 18:13:18 GMT,Transfer-Encoding=chunked,Connection=Keep-Alive,X-Frame-Options=SAMEORIGIN] [2025-10-13 20:13:36] [TRACE] [OmnipathR] Calling reader callback on response. [2025-10-13 20:13:37] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2025-10-13 20:13:37] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2025-10-13 20:13:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:37] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2025-10-13 20:13:37] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 244093 records [2025-10-13 20:13:37] [TRACE] [OmnipathR] Translating complexes: 612 complexes in data. [2025-10-13 20:13:37] [TRACE] [OmnipathR] 451 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-10-13 20:13:38] [TRACE] [OmnipathR] Translated 451 complexes to 451. [2025-10-13 20:13:38] [TRACE] [OmnipathR] 71139 rows before translation, 4827 uniprot IDs in column `source`. [2025-10-13 20:13:38] [TRACE] [OmnipathR] 71220 rows after translation; translated 4827 `uniprot` IDs in column `source` to 4663 `genesymbol` IDs in column `genesymbol_source`. [2025-10-13 20:13:39] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2025-10-13 20:13:39] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2025-10-13 20:13:39] [TRACE] [OmnipathR] BioMart query: [2025-10-13 20:13:39] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:13:39] [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 20:13:39] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2025-10-13 20:13:39] [SUCCESS] [OmnipathR] www.ensembl.org: loaded 244093 records from cache [2025-10-13 20:13:39] [TRACE] [OmnipathR] Translating complexes: 381 complexes in data. [2025-10-13 20:13:39] [TRACE] [OmnipathR] 229 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-10-13 20:13:40] [TRACE] [OmnipathR] Translated 229 complexes to 229. [2025-10-13 20:13:40] [TRACE] [OmnipathR] 71220 rows before translation, 5240 uniprot IDs in column `target`. [2025-10-13 20:13:40] [TRACE] [OmnipathR] 72796 rows after translation; translated 5240 `uniprot` IDs in column `target` to 5086 `genesymbol` IDs in column `genesymbol_target`. [2025-10-13 20:13:40] [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 20:13:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:42] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:13:42] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:05:40 UTC; omnipath [2025-10-13 20:13:42] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:13:42] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:06:56 UTC; unix [2025-10-13 20:13:42] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-13 20:13:42] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:13:42] [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 20:13:42] [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 20:13:42] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.37.1(2025-08-03); 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 3.17.6(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 20:13:42] [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 20:13:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:13:42] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:13:42] [TRACE] [OmnipathR] Contains 8 files. [2025-10-13 20:13:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:13:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:13:42] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:13:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:13:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:43] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:13:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:43] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:13:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:43] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:13:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:43] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-13 20:13:43] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2025-10-13 20:13:43] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2025-10-13 20:13:43] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-13 20:13:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:43] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-13 20:13:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:43] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-13 20:13:43] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-13 20:13:43] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:13:43] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:13:43] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:13:43] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-13 20:13:43] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:13:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:13:43] [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 20:13:43] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:13:43] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:13:43] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:13:43] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:13:43] [TRACE] [OmnipathR] Downloaded 31.1 Kb in 0.195686s from www.ensembl.org (159.1 Kb/s); Redirect: 0s, DNS look up: 0.001511s, Connection: 0.019623s, Pretransfer: 0.074037s, First byte at: 0.177945s [2025-10-13 20:13:43] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:13:43 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31887; 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 18:13:43 GMT; Set-cookie: ENSEMBL_HINX_SESSION=ae7cbfbb264392f709333c28693c5b570d75fb36976eaa854ff24fa9; 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 18:13:43 GMT; Set-cookie: ENSEMBL_HINX_SESSION=ae7cbfbb264392f709333c28693c5b570d75fb36976eaa854ff24fa9; 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 20:13:43] [TRACE] [OmnipathR] Response headers: [Date=Mon, 13 Oct 2025 18:13:43 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31887,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 18:13:43 GMT,Set-cookie=ENSEMBL_HINX_SESSION=ae7cbfbb264392f709333c28693c5b570d75fb36976eaa854ff24fa9; 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 18:13:43 GMT,Set-cookie=ENSEMBL_HINX_SESSION=ae7cbfbb264392f709333c28693c5b570d75fb36976eaa854ff24fa9; 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 20:13:43] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-13 20:13:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:43] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-10-13 20:13:43] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:13:43] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:13:43] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:13:43] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:13:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:43] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-10-13 20:13:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:13:43] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:13:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:13:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:13:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:13:43] [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 20:13:43] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:13:43] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.058865s from omabrowser.org (147.6 Kb/s); Redirect: 0s, DNS look up: 0.001015s, Connection: 0.010496s, Pretransfer: 0.044537s, First byte at: 0.058711s [2025-10-13 20:13:43] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 13 Oct 2025 18:13:43 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 20:13:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:13:44] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-10-13 20:13:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:44] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-10-13 20:13:44] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:13:44] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-10-13 20:13:44] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:13:44] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-10-13 20:13:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:13:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:13:44] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2025-10-13 20:13:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-10-13 20:13:44] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:13:44] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:14:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-10-13 20:14:06] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2025-10-13 20:14:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:06] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2025-10-13 20:14:06] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-10-13 20:14:06] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2025-10-13 20:14:06] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:14:06] [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 20:14:06] [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 20:14:06] [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 20:14:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:06] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2025-10-13 20:14:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-10-13 20:14:06] [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 20:14:06] [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 20:14:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:14:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:14:06] [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 20:14:07] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:14:07] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.373589s from rest.uniprot.org (115 bytes/s); Redirect: 0s, DNS look up: 0.001034s, Connection: 0.019289s, Pretransfer: 0.072428s, First byte at: 0.373551s [2025-10-13 20:14:07] [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 18:14:07 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 20:14:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2025-10-13 20:14:16] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2025-10-13 20:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:16] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2025-10-13 20:14:16] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20420 records [2025-10-13 20:14:16] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2025-10-13 20:14:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:29] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:14:29] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:05:40 UTC; omnipath [2025-10-13 20:14:29] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:14:29] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:06:56 UTC; unix [2025-10-13 20:14:29] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-13 20:14:29] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:14:29] [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 20:14:29] [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 20:14:29] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.37.1(2025-08-03); 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 3.17.6(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 20:14:29] [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 20:14:29] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:14:29] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:14:29] [TRACE] [OmnipathR] Contains 10 files. [2025-10-13 20:14:29] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:14:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:14:29] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:14:29] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:14:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:29] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:14:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:29] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:14:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:29] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:14:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:29] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-13 20:14:30] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:14:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-10-13 20:14:30] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:14:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-10-13 20:14:30] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-13 20:14:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:30] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-13 20:14:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:30] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-13 20:14:30] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-13 20:14:30] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:14:30] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:14:30] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:14:30] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-13 20:14:30] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:14:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:14:30] [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 20:14:30] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:14:30] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:14:30] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:14:30] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:14:30] [TRACE] [OmnipathR] Downloaded 31.2 Kb in 0.188205s from www.ensembl.org (165.9 Kb/s); Redirect: 0s, DNS look up: 0.001576s, Connection: 0.019741s, Pretransfer: 0.075692s, First byte at: 0.170136s [2025-10-13 20:14:30] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:14:30 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31982; 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 18:14:30 GMT; Set-cookie: ENSEMBL_HINX_SESSION=ca498b6d0fcde27d0f8126b3693c5b860bc7ef0abf22bcba2b5f4337; 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 18:14:30 GMT; Set-cookie: ENSEMBL_HINX_SESSION=ca498b6d0fcde27d0f8126b3693c5b860bc7ef0abf22bcba2b5f4337; 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 20:14:30] [TRACE] [OmnipathR] Response headers: [Date=Mon, 13 Oct 2025 18:14:30 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31982,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 18:14:30 GMT,Set-cookie=ENSEMBL_HINX_SESSION=ca498b6d0fcde27d0f8126b3693c5b860bc7ef0abf22bcba2b5f4337; 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 18:14:30 GMT,Set-cookie=ENSEMBL_HINX_SESSION=ca498b6d0fcde27d0f8126b3693c5b860bc7ef0abf22bcba2b5f4337; 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 20:14:30] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-13 20:14:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:30] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-10-13 20:14:30] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:14:30] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:14:30] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:14:30] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:14:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:30] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-10-13 20:14:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:14:30] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:14:30] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:14:30] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:14:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:14:30] [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 20:14:31] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:14:31] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.063537s from omabrowser.org (136.8 Kb/s); Redirect: 0s, DNS look up: 0.001042s, Connection: 0.012371s, Pretransfer: 0.047371s, First byte at: 0.063357s [2025-10-13 20:14:31] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 13 Oct 2025 18:14:31 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 20:14:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:14:31] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-10-13 20:14:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:31] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-10-13 20:14:31] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:14:31] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-10-13 20:14:31] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:14:31] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-10-13 20:14:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:31] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2025-10-13 20:14:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-10-13 20:14:31] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:14:31] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:14:54] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-10-13 20:14:54] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2025-10-13 20:14:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:54] [WARN] [OmnipathR] Failed to update cache: key `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` does not exist. [2025-10-13 20:14:54] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-10-13 20:14:54] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:14:54] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:14:54] [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 20:14:54] [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 20:14:54] [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 20:14:54] [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 20:14:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:14:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:14:54] [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 20:14:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:14:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:14:54] [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 20:14:54] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:14:54] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.105883s from omnipathdb.org (148 Kb/s); Redirect: 0s, DNS look up: 0.010218s, Connection: 0.031311s, Pretransfer: 0.068095s, First byte at: 0.105609s [2025-10-13 20:14:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:14:54 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 19:14:54 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:14:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:14:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:55] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-10-13 20:14:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:14:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:14:55] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-10-13 20:14:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:14:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:14:55] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2025-10-13 20:14:58] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2025-10-13 20:15:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:02] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:15:02] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:05:40 UTC; omnipath [2025-10-13 20:15:02] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:15:02] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:06:56 UTC; unix [2025-10-13 20:15:02] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-13 20:15:02] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:15:02] [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 20:15:02] [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 20:15:03] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.37.1(2025-08-03); 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 3.17.6(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 20:15:03] [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 20:15:03] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Contains 9 files. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:03] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:03] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:03] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:03] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-13 20:15:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:15:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2025-10-13 20:15:03] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:03] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:03] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-13 20:15:03] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:15:03] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:15:03] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-13 20:15:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:15:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:15:03] [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 20:15:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:15:03] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:15:03] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:15:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Downloaded 31.3 Kb in 0.200771s from www.ensembl.org (156.1 Kb/s); Redirect: 0s, DNS look up: 0.001881s, Connection: 0.020048s, Pretransfer: 0.076787s, First byte at: 0.177773s [2025-10-13 20:15:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:15:03 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 32102; 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 18:15:03 GMT; Set-cookie: ENSEMBL_HINX_SESSION=6a6fa77e8eba983c0edb5921693c5ba70a9d9289e82b1c0a05f8b52b; 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 18:15:03 GMT; Set-cookie: ENSEMBL_HINX_SESSION=6a6fa77e8eba983c0edb5921693c5ba70a9d9289e82b1c0a05f8b52b; 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 20:15:03] [TRACE] [OmnipathR] Response headers: [Date=Mon, 13 Oct 2025 18:15:03 GMT,Content-Type=text/html; charset=utf-8,Content-Length=32102,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 18:15:03 GMT,Set-cookie=ENSEMBL_HINX_SESSION=6a6fa77e8eba983c0edb5921693c5ba70a9d9289e82b1c0a05f8b52b; 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 18:15:03 GMT,Set-cookie=ENSEMBL_HINX_SESSION=6a6fa77e8eba983c0edb5921693c5ba70a9d9289e82b1c0a05f8b52b; 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 20:15:03] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-13 20:15:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:03] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:15:03] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:15:03] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:03] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:15:03] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:15:03] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:15:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:15:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:15:03] [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 20:15:03] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:15:03] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.060996s from omabrowser.org (142.5 Kb/s); Redirect: 0s, DNS look up: 0.001134s, Connection: 0.011485s, Pretransfer: 0.045875s, First byte at: 0.060841s [2025-10-13 20:15:03] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 13 Oct 2025 18:15:03 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 20:15:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:15:04] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-10-13 20:15:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:04] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-10-13 20:15:04] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:15:04] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-10-13 20:15:04] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:15:04] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-10-13 20:15:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:04] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2025-10-13 20:15:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-10-13 20:15:04] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:15:04] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` Quitting from extra_attrs.Rmd:55-58 [load-interactions] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'extra_attrs.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error in `gzfile()`: ! cannot open the connection --- failed re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown [2025-10-13 20:15:30] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:15:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:30] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:15:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:05:40 UTC; omnipath [2025-10-13 20:15:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:15:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:06:56 UTC; unix [2025-10-13 20:15:30] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-13 20:15:30] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:15:31] [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 20:15:31] [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 20:15:31] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.37.1(2025-08-03); 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 3.17.6(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 20:15:31] [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 20:15:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:15:31] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:15:31] [TRACE] [OmnipathR] Contains 1 files. [2025-10-13 20:15:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:15:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:15:31] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:15:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:15:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:15:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:15:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:31] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:15:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:31] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-13 20:15:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:15:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:32] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:15:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2025-10-13 20:15:32] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:15:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2025-10-13 20:15:32] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-13 20:15:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:32] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-13 20:15:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:32] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-13 20:15:32] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-13 20:15:32] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:15:32] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:15:32] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:15:32] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-13 20:15:32] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:15:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:15:32] [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 20:15:32] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:15:32] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:15:32] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:15:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:15:32] [TRACE] [OmnipathR] Downloaded 31.2 Kb in 0.186753s from www.ensembl.org (167.2 Kb/s); Redirect: 0s, DNS look up: 0.001396s, Connection: 0.019521s, Pretransfer: 0.073574s, First byte at: 0.165644s [2025-10-13 20:15:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:15:32 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31979; 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 18:15:32 GMT; Set-cookie: ENSEMBL_HINX_SESSION=f89849e0f4f6fe330d6e14de693c5bc40928d97b6e5c9d9a40f3ca23; 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 18:15:32 GMT; Set-cookie: ENSEMBL_HINX_SESSION=f89849e0f4f6fe330d6e14de693c5bc40928d97b6e5c9d9a40f3ca23; 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 20:15:32] [TRACE] [OmnipathR] Response headers: [Date=Mon, 13 Oct 2025 18:15:32 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31979,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 18:15:32 GMT,Set-cookie=ENSEMBL_HINX_SESSION=f89849e0f4f6fe330d6e14de693c5bc40928d97b6e5c9d9a40f3ca23; 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 18:15:32 GMT,Set-cookie=ENSEMBL_HINX_SESSION=f89849e0f4f6fe330d6e14de693c5bc40928d97b6e5c9d9a40f3ca23; 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 20:15:32] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-13 20:15:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:32] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-10-13 20:15:33] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:15:33] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:15:33] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:15:33] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:15:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:33] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-10-13 20:15:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:15:33] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:15:33] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:15:33] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:15:33] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:15:33] [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 20:15:33] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:15:33] [TRACE] [OmnipathR] Downloaded 10 Kb in 0.068391s from omabrowser.org (145.5 Kb/s); Redirect: 0s, DNS look up: 0.001128s, Connection: 0.011549s, Pretransfer: 0.047156s, First byte at: 0.068164s [2025-10-13 20:15:33] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 13 Oct 2025 18:15:33 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 20:15:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:15:33] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-10-13 20:15:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:33] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-10-13 20:15:33] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:15:33] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-10-13 20:15:33] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:15:33] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-10-13 20:15:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:33] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2025-10-13 20:15:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-10-13 20:15:33] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:15:33] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:15:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-10-13 20:15:56] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2025-10-13 20:15:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:56] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2025-10-13 20:15:56] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-10-13 20:15:56] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:15:56] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:15:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:15:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:56] [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 20:15:56] [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 20:15:56] [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 20:15:56] [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 20:15:56] [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 20:15:56] [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 20:15:56] [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 20:15:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:15:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:15:56] [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 20:15:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:15:56] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.083962s from omnipathdb.org (186.6 Kb/s); Redirect: 0s, DNS look up: 0.000952s, Connection: 0.016722s, Pretransfer: 0.051659s, First byte at: 0.083669s [2025-10-13 20:15:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:15:56 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 19:15:56 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:15:57] [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 20:15:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:57] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2025-10-13 20:15:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2025-10-13 20:15:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2025-10-13 20:15:57] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2025-10-13 20:15:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:15:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:15:57] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2025-10-13 20:15:59] [SUCCESS] [OmnipathR] Downloaded 67773 interactions. [2025-10-13 20:16:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra] [2025-10-13 20:16:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions] [2025-10-13 20:16:02] [TRACE] [OmnipathR] Organism(s): 10090 [2025-10-13 20:16:02] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:16:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:02] [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 20:16:02] [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 20:16:02] [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 20:16:02] [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 20:16:02] [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 20:16:02] [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 20:16:02] [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 20:16:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:02] [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 20:16:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089097s from omnipathdb.org (175.8 Kb/s); Redirect: 0s, DNS look up: 0.000895s, Connection: 0.018348s, Pretransfer: 0.053331s, First byte at: 0.08884s [2025-10-13 20:16:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:02 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 19:16:02 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:16:02] [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 20:16:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:02] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2025-10-13 20:16:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2025-10-13 20:16:03] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1] [2025-10-13 20:16:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:03] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:04] [SUCCESS] [OmnipathR] Downloaded 41476 interactions. [2025-10-13 20:16:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra] [2025-10-13 20:16:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions] [2025-10-13 20:16:04] [TRACE] [OmnipathR] Organism(s): 10116 [2025-10-13 20:16:04] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:16:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:04] [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 20:16:04] [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 20:16:04] [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 20:16:04] [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 20:16:04] [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 20:16:04] [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 20:16:04] [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 20:16:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:04] [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 20:16:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:04] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.088607s from omnipathdb.org (176.8 Kb/s); Redirect: 0s, DNS look up: 0.000934s, Connection: 0.018151s, Pretransfer: 0.053503s, First byte at: 0.088352s [2025-10-13 20:16:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:04 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 19:16:04 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:16:05] [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 20:16:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:05] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2025-10-13 20:16:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2025-10-13 20:16:05] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2025-10-13 20:16:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:05] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:05] [SUCCESS] [OmnipathR] Downloaded 11083 interactions. [2025-10-13 20:16:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra] [2025-10-13 20:16:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions] [2025-10-13 20:16:05] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:16:05] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:16:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:05] [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 20:16:05] [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 20:16:05] [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 20:16:05] [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 20:16:05] [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 20:16:05] [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 20:16:06] [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 20:16:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:06] [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 20:16:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:06] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097239s from omnipathdb.org (161.1 Kb/s); Redirect: 0s, DNS look up: 0.00102s, Connection: 0.020973s, Pretransfer: 0.056423s, First byte at: 0.096965s [2025-10-13 20:16:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:06 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 19:16:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:16:06] [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 20:16:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:06] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2025-10-13 20:16:06] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2025-10-13 20:16:06] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2025-10-13 20:16:06] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:06] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:06] [SUCCESS] [OmnipathR] Downloaded 2840 interactions. [2025-10-13 20:16:06] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-10-13 20:16:06] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-10-13 20:16:06] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:16:06] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:06] [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 20:16:06] [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 20:16:06] [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 20:16:06] [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 20:16:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:16:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:16:06] [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 20:16:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:06] [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 20:16:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:06] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099686s from omnipathdb.org (157.2 Kb/s); Redirect: 0s, DNS look up: 0.000968s, Connection: 0.022033s, Pretransfer: 0.056948s, First byte at: 0.09943s [2025-10-13 20:16:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:06 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 19:16:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:16:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:16:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:07] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:16:07] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:16:07] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-10-13 20:16:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:07] [WARN] [OmnipathR] Failed to update cache: key `a7b21d9d80a3837a50268df16d168128fc1c6ede` does not exist. [2025-10-13 20:16:10] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2025-10-13 20:16:12] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea] [2025-10-13 20:16:12] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:16:12] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:12] [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 20:16:12] [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 20:16:12] [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 20:16:12] [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 20:16:12] [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 20:16:12] [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 20:16:12] [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 20:16:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:12] [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 20:16:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:12] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.098257s from omnipathdb.org (159.4 Kb/s); Redirect: 0s, DNS look up: 0.001035s, Connection: 0.021313s, Pretransfer: 0.056854s, First byte at: 0.097998s [2025-10-13 20:16:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:12 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 19:16:12 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:16:12] [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 20:16:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:12] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2025-10-13 20:16:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2025-10-13 20:16:12] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1] [2025-10-13 20:16:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:12] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:12] [SUCCESS] [OmnipathR] Downloaded 6128 interactions. [2025-10-13 20:16:13] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget] [2025-10-13 20:16:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:16:13] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:16:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:13] [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 20:16:13] [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 20:16:13] [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 20:16:13] [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 20:16:13] [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 20:16:13] [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 20:16:13] [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 20:16:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:13] [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 20:16:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:13] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097715s from omnipathdb.org (160.3 Kb/s); Redirect: 0s, DNS look up: 0.001005s, Connection: 0.021298s, Pretransfer: 0.056881s, First byte at: 0.097397s [2025-10-13 20:16:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:13 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 19:16:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:16:13] [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 20:16:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:13] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2025-10-13 20:16:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2025-10-13 20:16:13] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1] [2025-10-13 20:16:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:13] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:13] [SUCCESS] [OmnipathR] Downloaded 648 interactions. [2025-10-13 20:16:13] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule] [2025-10-13 20:16:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:16:13] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:13] [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 20:16:13] [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 20:16:13] [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 20:16:13] [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 20:16:13] [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 20:16:13] [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 20:16:13] [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 20:16:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:13] [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 20:16:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:14] [TRACE] [OmnipathR] Downloaded 189 bytes in 0.078357s from omnipathdb.org (2.4 Kb/s); Redirect: 0s, DNS look up: 0.00103s, Connection: 0.021441s, Pretransfer: 0.056864s, First byte at: 0.078339s [2025-10-13 20:16:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:14 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 19:16:14 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-10-13 20:16:14] [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 20:16:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:14] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2025-10-13 20:16:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2025-10-13 20:16:14] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1] [2025-10-13 20:16:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:14] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:14] [SUCCESS] [OmnipathR] Downloaded 0 interactions. [2025-10-13 20:16:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:16:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2025-10-13 20:16:14] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:16:14] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:14] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:16:14] [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 20:16:14] [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 20:16:14] [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 20:16:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:16:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:16:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:16:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:14] [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 20:16:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:14] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09447s from omnipathdb.org (165.8 Kb/s); Redirect: 0s, DNS look up: 0.000869s, Connection: 0.020014s, Pretransfer: 0.055828s, First byte at: 0.094151s [2025-10-13 20:16:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:14 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 19:16:14 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:16:15] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:16:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:15] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-10-13 20:16:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2025-10-13 20:16:15] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2025-10-13 20:16:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:15] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:17] [SUCCESS] [OmnipathR] Downloaded 47840 enzyme-substrate relationships. [2025-10-13 20:16:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2025-10-13 20:16:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2025-10-13 20:16:17] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:16:17] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:17] [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 20:16:17] [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 20:16:17] [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 20:16:17] [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 20:16:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:16:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:16:17] [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 20:16:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:17] [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 20:16:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:17] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097826s from omnipathdb.org (160.2 Kb/s); Redirect: 0s, DNS look up: 0.001014s, Connection: 0.021279s, Pretransfer: 0.056643s, First byte at: 0.097573s [2025-10-13 20:16:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:17 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 19:16:17 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:16:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:16:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:17] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:16:18] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2025-10-13 20:16:18] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2025-10-13 20:16:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:18] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:21] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2025-10-13 20:16:21] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub] [2025-10-13 20:16:22] [TRACE] [OmnipathR] Organism(s): 10090 [2025-10-13 20:16:22] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:16:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:22] [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 20:16:22] [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 20:16:22] [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 20:16:22] [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 20:16:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2025-10-13 20:16:22] [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 20:16:22] [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 20:16:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:22] [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 20:16:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:22] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.100208s from omnipathdb.org (156.3 Kb/s); Redirect: 0s, DNS look up: 0.000962s, Connection: 0.02201s, Pretransfer: 0.057541s, First byte at: 0.099923s [2025-10-13 20:16:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:22 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 19:16:22 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:16:22] [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 20:16:22] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:16:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:22] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:16:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:22] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2025-10-13 20:16:22] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2025-10-13 20:16:22] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1] [2025-10-13 20:16:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:22] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:23] [SUCCESS] [OmnipathR] Downloaded 19838 enzyme-substrate relationships. [2025-10-13 20:16:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:16:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes] [2025-10-13 20:16:24] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:16:24] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:16:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:16:24] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:16:24] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:16:24] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:16:24] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:16:24] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:16:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:16:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:24] [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 20:16:24] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:24] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093928s from omnipathdb.org (166.8 Kb/s); Redirect: 0s, DNS look up: 0.000884s, Connection: 0.019458s, Pretransfer: 0.055997s, First byte at: 0.093695s [2025-10-13 20:16:24] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:24 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 19:16:24 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:16:24] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2025-10-13 20:16:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:24] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2025-10-13 20:16:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2025-10-13 20:16:24] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1] [2025-10-13 20:16:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:24] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:24] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes. [2025-10-13 20:16:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:16:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:25] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:25] [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 20:16:25] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:16:25] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:25] [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 20:16:25] [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 20:16:25] [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 20:16:25] [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 20:16:25] [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 20:16:25] [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 20:16:25] [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 20:16:25] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:25] [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 20:16:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:25] [TRACE] [OmnipathR] Downloaded 15.2 Kb in 0.091558s from omnipathdb.org (166.2 Kb/s); Redirect: 0s, DNS look up: 0.000957s, Connection: 0.019092s, Pretransfer: 0.054917s, First byte at: 0.091248s [2025-10-13 20:16:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:25 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 19:16:25 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:16:26] [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 20:16:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:26] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2025-10-13 20:16:26] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2025-10-13 20:16:26] [INFO] [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1] [2025-10-13 20:16:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:26] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:26] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records. [2025-10-13 20:16:26] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:26] [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 20:16:26] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:16:26] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:26] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:16:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:26] [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 20:16:26] [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 20:16:26] [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 20:16:26] [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 20:16:26] [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 20:16:26] [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 20:16:26] [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 20:16:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:26] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:26] [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 20:16:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:26] [TRACE] [OmnipathR] Downloaded 5.8 Kb in 0.077582s from omnipathdb.org (74.9 Kb/s); Redirect: 0s, DNS look up: 0.000924s, Connection: 0.020406s, Pretransfer: 0.056537s, First byte at: 0.077564s [2025-10-13 20:16:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:26 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 19:16:26 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-10-13 20:16:26] [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 20:16:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:26] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2025-10-13 20:16:26] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2025-10-13 20:16:26] [INFO] [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1] [2025-10-13 20:16:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:26] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:26] [SUCCESS] [OmnipathR] Downloaded 86 annotation records. [2025-10-13 20:16:26] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:27] [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 20:16:27] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:16:27] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:16:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:27] [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 20:16:27] [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 20:16:27] [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 20:16:27] [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 20:16:27] [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 20:16:27] [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 20:16:27] [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 20:16:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:27] [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 20:16:27] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:27] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.085828s from omnipathdb.org (182.9 Kb/s); Redirect: 0s, DNS look up: 0.001089s, Connection: 0.01719s, Pretransfer: 0.053501s, First byte at: 0.085797s [2025-10-13 20:16:27] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:27 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 19:16:27 GMT; Cache-Control: public; X-Frame-Options: DENY [2025-10-13 20:16:27] [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 20:16:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:27] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2025-10-13 20:16:27] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2025-10-13 20:16:27] [INFO] [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1] [2025-10-13 20:16:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:27] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:27] [SUCCESS] [OmnipathR] Downloaded 366 annotation records. [2025-10-13 20:16:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2025-10-13 20:16:27] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:16:27] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:16:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:27] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:16:27] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:16:27] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:16:27] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:16:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:16:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:16:27] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:16:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:27] [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 20:16:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:28] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091561s from omnipathdb.org (171.1 Kb/s); Redirect: 0s, DNS look up: 0.000992s, Connection: 0.019041s, Pretransfer: 0.0548s, First byte at: 0.091272s [2025-10-13 20:16:28] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:28 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 19:16:28 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:16:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2025-10-13 20:16:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:28] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-10-13 20:16:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2025-10-13 20:16:28] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2025-10-13 20:16:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:28] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:28] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2025-10-13 20:16:28] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:16:28] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:28] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:16:28] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:16:28] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2025-10-13 20:16:28] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2025-10-13 20:16:28] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2025-10-13 20:16:28] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:16:28] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:16:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:28] [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 20:16:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:28] [TRACE] [OmnipathR] Downloaded 9.4 Kb in 0.080655s from omnipathdb.org (116.4 Kb/s); Redirect: 0s, DNS look up: 0.001004s, Connection: 0.02131s, Pretransfer: 0.056907s, First byte at: 0.080469s [2025-10-13 20:16:28] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:28 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 19:16:28 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:16:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2025-10-13 20:16:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:28] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2025-10-13 20:16:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2025-10-13 20:16:29] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2025-10-13 20:16:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:29] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:29] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2025-10-13 20:16:29] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:16:29] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:16:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:16:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:16:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:16:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:16:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:16:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:16:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:16:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:29] [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 20:16:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:29] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092904s from omnipathdb.org (168.6 Kb/s); Redirect: 0s, DNS look up: 0.001121s, Connection: 0.019475s, Pretransfer: 0.05557s, First byte at: 0.092556s [2025-10-13 20:16:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:16:29 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 19:16:29 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:16:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2025-10-13 20:16:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:30] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2025-10-13 20:16:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2025-10-13 20:16:32] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1] [2025-10-13 20:16:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:32] [WARN] [OmnipathR] Failed to update cache: key `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` does not exist. [2025-10-13 20:16:32] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records. [2025-10-13 20:16:32] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2025-10-13 20:16:32] [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 20:16:32] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`. [2025-10-13 20:16:32] [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 20:16:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:35] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:16:35] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-10-13 18:05:40 UTC; omnipath [2025-10-13 20:16:35] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-10-13 20:16:35] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-13 18:06:56 UTC; unix [2025-10-13 20:16:35] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.6 [2025-10-13 20:16:35] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-10-13 20:16:35] [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 20:16:35] [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 20:16:35] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.37.1(2025-08-03); 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 3.17.6(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 20:16:35] [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 20:16:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:16:35] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:16:35] [TRACE] [OmnipathR] Contains 3 files. [2025-10-13 20:16:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:16:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-10-13 20:16:35] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-10-13 20:16:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:16:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:16:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:16:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:35] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:16:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:35] [TRACE] [OmnipathR] Cache locked: FALSE [2025-10-13 20:16:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:16:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2025-10-13 20:16:35] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-10-13 20:16:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:35] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-10-13 20:16:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:35] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-10-13 20:16:35] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-10-13 20:16:35] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:16:35] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-10-13 20:16:35] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-10-13 20:16:35] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-10-13 20:16:35] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:16:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:35] [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 20:16:35] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-10-13 20:16:35] [TRACE] [OmnipathR] Sending HTTP request. [2025-10-13 20:16:36] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-10-13 20:16:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:16:36] [TRACE] [OmnipathR] Downloaded 31.4 Kb in 0.200799s from www.ensembl.org (156.4 Kb/s); Redirect: 0s, DNS look up: 0.001487s, Connection: 0.019646s, Pretransfer: 0.075164s, First byte at: 0.177938s [2025-10-13 20:16:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Mon, 13 Oct 2025 18:16:35 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 32166; 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 18:16:35 GMT; Set-cookie: ENSEMBL_HINX_SESSION=82130f2d8bbf936d0f941f7d693c5c030bd2ce6edf28e11c05f22a96; 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 18:16:35 GMT; Set-cookie: ENSEMBL_HINX_SESSION=82130f2d8bbf936d0f941f7d693c5c030bd2ce6edf28e11c05f22a96; 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 20:16:36] [TRACE] [OmnipathR] Response headers: [Date=Mon, 13 Oct 2025 18:16:35 GMT,Content-Type=text/html; charset=utf-8,Content-Length=32166,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 18:16:35 GMT,Set-cookie=ENSEMBL_HINX_SESSION=82130f2d8bbf936d0f941f7d693c5c030bd2ce6edf28e11c05f22a96; 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 18:16:35 GMT,Set-cookie=ENSEMBL_HINX_SESSION=82130f2d8bbf936d0f941f7d693c5c030bd2ce6edf28e11c05f22a96; 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 20:16:36] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-10-13 20:16:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:36] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-10-13 20:16:36] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:16:36] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:16:36] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:16:36] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-10-13 20:16:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:36] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:16:36] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:16:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-10-13 20:16:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:16:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:16:36] [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 20:16:36] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:16:36] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.060197s from omabrowser.org (144.3 Kb/s); Redirect: 0s, DNS look up: 0.000962s, Connection: 0.011276s, Pretransfer: 0.045319s, First byte at: 0.060034s [2025-10-13 20:16:36] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 13 Oct 2025 18:16:36 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 20:16:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-10-13 20:16:36] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-10-13 20:16:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:36] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-10-13 20:16:36] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:16:36] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-10-13 20:16:36] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:16:36] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-10-13 20:16:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:16:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:16:36] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2025-10-13 20:16:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-10-13 20:16:36] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:16:36] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-10-13 20:17:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-10-13 20:17:00] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2025-10-13 20:17:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:00] [WARN] [OmnipathR] Failed to update cache: key `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` does not exist. [2025-10-13 20:17:00] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-10-13 20:17:00] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:00] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:17:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:17:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:17:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:17:00] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:17:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:17:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:17:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:17:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:00] [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 20:17:00] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:00] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095511s from omnipathdb.org (164 Kb/s); Redirect: 0s, DNS look up: 0.000941s, Connection: 0.020622s, Pretransfer: 0.05519s, First byte at: 0.095143s [2025-10-13 20:17:00] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:00 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 19:17:00 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2025-10-13 20:17:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:01] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2025-10-13 20:17:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2025-10-13 20:17:01] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2025-10-13 20:17:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:01] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:01] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records. [2025-10-13 20:17:01] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-10-13 20:17:01] [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 20:17:01] [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 20:17:01] [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 20:17:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:01] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2025-10-13 20:17:01] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2025-10-13 20:17:01] [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 20:17:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:01] [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 20:17:01] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-10-13 20:17:01] [TRACE] [OmnipathR] Downloaded 16 Kb in 0.054561s from static-content.springer.com (293.1 Kb/s); Redirect: 0s, DNS look up: 0.006279s, Connection: 0.010523s, Pretransfer: 0.04425s, First byte at: 0.052565s [2025-10-13 20:17:01] [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: 46372; date: Mon, 13 Oct 2025 18:17:01 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230058-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1760379421.224307,VS0,VE3; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972 [2025-10-13 20:17:01] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2025-10-13 20:17:01] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2025-10-13 20:17:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:01] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:01] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2025-10-13 20:17:01] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:17:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions] [2025-10-13 20:17:01] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:01] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:01] [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 20:17:01] [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 20:17:01] [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 20:17:01] [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 20:17:01] [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 20:17:01] [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 20:17:01] [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 20:17:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:01] [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 20:17:01] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:01] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.106071s from omnipathdb.org (147.7 Kb/s); Redirect: 0s, DNS look up: 0.001051s, Connection: 0.023695s, Pretransfer: 0.058165s, First byte at: 0.105819s [2025-10-13 20:17:01] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:01 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 19:17:01 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:02] [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 20:17:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:02] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2025-10-13 20:17:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2025-10-13 20:17:02] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1] [2025-10-13 20:17:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:02] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:06] [SUCCESS] [OmnipathR] Downloaded 124225 interactions. [2025-10-13 20:17:06] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:17:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations] [2025-10-13 20:17:06] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:06] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:17:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:06] [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 20:17:06] [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 20:17:06] [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 20:17:06] [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 20:17:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-10-13 20:17:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-10-13 20:17:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-10-13 20:17:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:06] [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 20:17:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:06] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101549s from omnipathdb.org (154.3 Kb/s); Redirect: 0s, DNS look up: 0.001064s, Connection: 0.022255s, Pretransfer: 0.058499s, First byte at: 0.101185s [2025-10-13 20:17:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:06 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 19:17:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:08] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2025-10-13 20:17:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:08] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2025-10-13 20:17:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2025-10-13 20:17:09] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1] [2025-10-13 20:17:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:09] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:09] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records. [2025-10-13 20:17:10] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:10] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:17:10] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:17:10] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:17:10] [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 20:17:10] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:17:10] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:17:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:17:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:10] [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 20:17:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:10] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095028s from omnipathdb.org (164.9 Kb/s); Redirect: 0s, DNS look up: 0.001203s, Connection: 0.020607s, Pretransfer: 0.055328s, First byte at: 0.094641s [2025-10-13 20:17:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:10 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 19:17:10 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2025-10-13 20:17:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:10] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:10] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2025-10-13 20:17:10] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2025-10-13 20:17:10] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1] [2025-10-13 20:17:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:10] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:10] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records. [2025-10-13 20:17:10] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:10] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:10] [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 20:17:10] [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 20:17:10] [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 20:17:10] [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 20:17:10] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:17:10] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:17:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:17:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:10] [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 20:17:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:10] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09317s from omnipathdb.org (168.2 Kb/s); Redirect: 0s, DNS look up: 0.000935s, Connection: 0.019855s, Pretransfer: 0.054452s, First byte at: 0.092801s [2025-10-13 20:17:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:10 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 19:17:10 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:17:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:11] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-10-13 20:17:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-10-13 20:17:11] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2025-10-13 20:17:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:11] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:11] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records. [2025-10-13 20:17:11] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:11] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:11] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-10-13 20:17:11] [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 20:17:11] [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 20:17:11] [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 20:17:11] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-10-13 20:17:11] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-10-13 20:17:11] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-10-13 20:17:11] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:11] [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 20:17:11] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:11] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.091591s from omnipathdb.org (171.1 Kb/s); Redirect: 0s, DNS look up: 0.001091s, Connection: 0.019056s, Pretransfer: 0.054613s, First byte at: 0.091222s [2025-10-13 20:17:11] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:11 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 19:17:11 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2025-10-13 20:17:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:11] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2025-10-13 20:17:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2025-10-13 20:17:11] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1] [2025-10-13 20:17:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:11] [WARN] [OmnipathR] Failed to update cache: key `958b54b673bc1257aa3dafe979574736ad7d4632` does not exist. [2025-10-13 20:17:11] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records. [2025-10-13 20:17:12] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:12] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:12] [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 20:17:12] [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 20:17:12] [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 20:17:12] [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 20:17:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:17:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:17:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:17:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:12] [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 20:17:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:12] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.102642s from omnipathdb.org (152.6 Kb/s); Redirect: 0s, DNS look up: 0.001045s, Connection: 0.023017s, Pretransfer: 0.057566s, First byte at: 0.10229s [2025-10-13 20:17:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:12 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 19:17:12 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:17:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:12] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-10-13 20:17:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-10-13 20:17:12] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2025-10-13 20:17:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:12] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:12] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records. [2025-10-13 20:17:12] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:12] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:17:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:17:12] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:17:12] [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 20:17:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:17:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:17:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:17:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:12] [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 20:17:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:12] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.10318s from omnipathdb.org (151.8 Kb/s); Redirect: 0s, DNS look up: 0.000997s, Connection: 0.022968s, Pretransfer: 0.058622s, First byte at: 0.102841s [2025-10-13 20:17:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:12 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 19:17:12 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2025-10-13 20:17:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:13] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2025-10-13 20:17:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2025-10-13 20:17:13] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1] [2025-10-13 20:17:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:13] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:13] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records. [2025-10-13 20:17:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:13] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:13] [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 20:17:13] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-10-13 20:17:13] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:17:13] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2025-10-13 20:17:13] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:13] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-10-13 20:17:13] [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 20:17:13] [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 20:17:13] [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 20:17:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-10-13 20:17:13] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-10-13 20:17:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-10-13 20:17:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:13] [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 20:17:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:13] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099154s from omnipathdb.org (158 Kb/s); Redirect: 0s, DNS look up: 0.000943s, Connection: 0.021614s, Pretransfer: 0.057089s, First byte at: 0.098819s [2025-10-13 20:17:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:13 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 19:17:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:13] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2025-10-13 20:17:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:13] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:13] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2025-10-13 20:17:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2025-10-13 20:17:14] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1] [2025-10-13 20:17:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:14] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:14] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records. [2025-10-13 20:17:14] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:14] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:14] [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 20:17:14] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2025-10-13 20:17:14] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2025-10-13 20:17:14] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2025-10-13 20:17:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:17:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein] [2025-10-13 20:17:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:17:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions] [2025-10-13 20:17:14] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:14] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:14] [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 20:17:14] [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 20:17:14] [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 20:17:14] [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 20:17:14] [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 20:17:14] [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 20:17:14] [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 20:17:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:14] [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 20:17:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:14] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095805s from omnipathdb.org (163.5 Kb/s); Redirect: 0s, DNS look up: 0.001039s, Connection: 0.020976s, Pretransfer: 0.05547s, First byte at: 0.095549s [2025-10-13 20:17:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:14 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 19:17:14 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:14] [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 20:17:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:15] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2025-10-13 20:17:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2025-10-13 20:17:15] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2025-10-13 20:17:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:15] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:16] [SUCCESS] [OmnipathR] Downloaded 32281 interactions. [2025-10-13 20:17:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:17:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations] [2025-10-13 20:17:16] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:16] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:17:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:17:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:17:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:17:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:17:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:17:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:17:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:17:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:16] [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 20:17:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:16] [TRACE] [OmnipathR] Downloaded 13.1 Kb in 0.095386s from omnipathdb.org (137.5 Kb/s); Redirect: 0s, DNS look up: 0.001113s, Connection: 0.020648s, Pretransfer: 0.055643s, First byte at: 0.095145s [2025-10-13 20:17:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:16 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 19:17:16 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2025-10-13 20:17:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:17] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2025-10-13 20:17:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2025-10-13 20:17:17] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2025-10-13 20:17:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:17] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:17] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records. [2025-10-13 20:17:17] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:17:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations] [2025-10-13 20:17:17] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:17] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:17] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:17:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:17:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:17:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:17:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:17:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:17:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:17:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:17:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:17] [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 20:17:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:17] [TRACE] [OmnipathR] Downloaded 12.2 Kb in 0.093541s from omnipathdb.org (130.1 Kb/s); Redirect: 0s, DNS look up: 0.000805s, Connection: 0.019615s, Pretransfer: 0.055367s, First byte at: 0.093305s [2025-10-13 20:17:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:17 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 19:17:17 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:17] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2025-10-13 20:17:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:17] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2025-10-13 20:17:17] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2025-10-13 20:17:17] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1] [2025-10-13 20:17:17] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:17] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:17] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records. [2025-10-13 20:17:18] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`. [2025-10-13 20:17:18] [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 20:17:18] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:17:18] [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 20:17:18] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:18] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:17:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:18] [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 20:17:18] [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 20:17:18] [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 20:17:18] [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 20:17:18] [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 20:17:18] [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 20:17:18] [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 20:17:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:18] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:18] [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 20:17:18] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:18] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.102632s from omnipathdb.org (152.7 Kb/s); Redirect: 0s, DNS look up: 0.000908s, Connection: 0.022643s, Pretransfer: 0.058526s, First byte at: 0.102381s [2025-10-13 20:17:18] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:18 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 19:17:18 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:19] [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 20:17:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:19] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2025-10-13 20:17:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2025-10-13 20:17:19] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1] [2025-10-13 20:17:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:19] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:19] [SUCCESS] [OmnipathR] Downloaded 4242 interactions. [2025-10-13 20:17:19] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:17:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2025-10-13 20:17:19] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:19] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:17:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:17:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:17:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:17:19] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:17:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:17:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:17:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:17:19] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:19] [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 20:17:19] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:19] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101173s from omnipathdb.org (154.9 Kb/s); Redirect: 0s, DNS look up: 0.000999s, Connection: 0.022558s, Pretransfer: 0.057346s, First byte at: 0.100883s [2025-10-13 20:17:19] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:19 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 19:17:19 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:20] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:17:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:20] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-10-13 20:17:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-10-13 20:17:20] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2025-10-13 20:17:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:20] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:20] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2025-10-13 20:17:21] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:17:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2025-10-13 20:17:21] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:21] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:17:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:17:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:17:21] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:17:21] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:17:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:17:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:17:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:17:21] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-10-13 20:17:21] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-10-13 20:17:21] [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 20:17:21] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-10-13 20:17:21] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089226s from omnipathdb.org (175.6 Kb/s); Redirect: 0s, DNS look up: 0.000976s, Connection: 0.018222s, Pretransfer: 0.053744s, First byte at: 0.08892s [2025-10-13 20:17:21] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 13 Oct 2025 18:17:21 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 19:17:21 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-10-13 20:17:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:17:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:21] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`. [2025-10-13 20:17:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-10-13 20:17:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-10-13 20:17:21] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1] [2025-10-13 20:17:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:17:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:21] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`. [2025-10-13 20:17:21] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records. [2025-10-13 20:17:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:17:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2025-10-13 20:17:23] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:23] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:17:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:17:24] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2025-10-13 20:17:24] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2025-10-13 20:17:24] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2025-10-13 20:17:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-10-13 20:17:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2025-10-13 20:17:24] [TRACE] [OmnipathR] Organism(s): 9606 [2025-10-13 20:17:24] [TRACE] [OmnipathR] Orthology targets: [2025-10-13 20:17:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-10-13 20:17:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:17:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:17:24] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2025-10-13 20:17:24] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2025-10-13 20:17:24] [SUCCESS] [OmnipathR] Loaded 2102 annotation records from cache. --- finished re-building ‘paths.Rmd’ SUMMARY: processing the following files failed: ‘bioc_workshop.Rmd’ ‘extra_attrs.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 2 WARNINGs, 2 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2025-10-13_1954/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2025-10-13 20:17:34 CEST ]