[ Started: 2026-05-23 21:17:16 CEST ] [ OmnipathR v3.18.4 for BioC-3.22 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_22 (efaae39 2026-01-20 15:40:26) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/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 ‘3.18.4’ * 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 [2026-05-23 21:17:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:17:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:17:47] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:17:47] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-23 19:15:52 UTC; omnipath [2026-05-23 21:17:47] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-23 21:17:47] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-23 19:17:18 UTC; unix [2026-05-23 21:17:47] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-23 21:17:47] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-23 21:17:47] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-23 21:17:47] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-05-23 21:17:48] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-23); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-05-23 21:17:48] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-05-23 21:17:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-23 21:17:48] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:17:48] [TRACE] [OmnipathR] Contains 1 files. [2026-05-23 21:17:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-23 21:17:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:17:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:17:48] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-23 21:17:48] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-23 21:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:17:48] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-23 21:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:17:48] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-23 21:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:17:48] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-23 21:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:17:48] [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 [2026-05-23 21:17:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:17:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:17:58] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:17:58] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-23 19:15:52 UTC; omnipath [2026-05-23 21:17:58] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-23 21:17:58] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-23 19:17:18 UTC; unix [2026-05-23 21:17:58] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-23 21:17:58] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-23 21:17:59] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-23 21:17:59] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-05-23 21:17:59] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-23); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-05-23 21:17:59] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-05-23 21:17:59] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-23 21:17:59] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:17:59] [TRACE] [OmnipathR] Contains 1 files. [2026-05-23 21:17:59] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-23 21:17:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:17:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:17:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:17:59] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-23 21:17:59] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-23 21:17:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:17:59] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-23 21:17:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:17:59] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-23 21:17:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:17:59] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-23 21:17:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:17:59] [TRACE] [OmnipathR] Cache locked: FALSE cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’ patch_httr2_keep_handle: no visible binding for global variable ‘handle’ patch_httr2_keep_handle: no visible global function definition for ‘ORIGINAL’ Undefined global functions or variables: ORIGINAL enzyme_genesymbol handle * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed annotation_categories 68.908 0.055 69.098 curated_ligrec_stats 28.767 1.249 38.710 omnipath-interactions 21.929 0.965 26.325 filter_extra_attrs 18.880 3.162 22.392 all_uniprots 17.822 0.830 29.477 uniprot_organisms 14.970 0.773 15.920 nichenet_gr_network_omnipath 13.026 0.635 14.262 nichenet_signaling_network_omnipath 12.786 0.390 13.839 extra_attr_values 9.617 1.035 10.929 extra_attrs_to_cols 9.718 0.885 10.972 with_extra_attrs 9.190 0.915 10.486 go_annot_download 8.316 0.566 8.414 pivot_annotations 7.460 0.697 8.775 giant_component 6.989 0.352 7.695 omnipath_for_cosmos 6.739 0.327 98.924 filter_by_resource 6.021 0.306 6.722 has_extra_attrs 5.387 0.660 6.095 extra_attrs 4.971 0.699 5.737 filter_intercell 4.923 0.477 5.305 translate_ids_multi 5.093 0.277 51.694 curated_ligand_receptor_interactions 4.731 0.298 6.168 print_interactions 4.345 0.238 5.027 ensembl_id_mapping_table 1.547 0.159 24.344 kegg_conv 1.016 0.119 11.951 uniprot_full_id_mapping_table 0.881 0.044 12.525 biomart_query 0.826 0.052 11.344 kinasephos 0.792 0.073 33.992 translate_ids 0.645 0.060 11.897 kegg_link 0.520 0.052 5.417 * 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 [2026-05-23 21:29:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:29:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:29:56] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:29:56] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-23 19:15:52 UTC; omnipath [2026-05-23 21:29:56] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-23 21:29:56] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-23 19:17:18 UTC; unix [2026-05-23 21:29:56] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-23 21:29:56] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-23 21:29:56] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-23 21:29:56] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-05-23 21:29:56] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-23); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); 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 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-05-23 21:29:56] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-05-23 21:29:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-23 21:29:56] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:29:56] [TRACE] [OmnipathR] Contains 15 files. [2026-05-23 21:29:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-23 21:29:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:29:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:29:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:29:56] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-23 21:29:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-23 21:29:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:29:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-23 21:29:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:29:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-23 21:29:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:29:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-23 21:29:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:29:56] [TRACE] [OmnipathR] Cache locked: FALSE [2026-05-23 21:29:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:29:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2026-05-23 21:29:56] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-05-23 21:29:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:29:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:29:56] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-05-23 21:29:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:29:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:29:56] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-05-23 21:29:56] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-05-23 21:29:56] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-23 21:29:56] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-23 21:29:56] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-23 21:29:56] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-05-23 21:29:56] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:29:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:29:56] [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] [2026-05-23 21:29:56] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:29:56] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-23 21:29:56] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-23 21:29:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:29:56] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.117914s from rescued.omnipathdb.org (338 Kb/s); Redirect: 0s, DNS look up: 0.001203s, Connection: 0.018175s, Pretransfer: 0.066007s, First byte at: 0.100684s [2026-05-23 21:29:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:29:56 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 23 May 2026 20:29:56 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-05-23 21:29:56] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 23 May 2026 19:29:56 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 23 May 2026 20:29:56 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-05-23 21:29:57] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-05-23 21:29:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:29:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:29:57] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-05-23 21:29:57] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:29:57] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-05-23 21:29:57] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:29:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-05-23 21:29:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:29:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:29:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:29:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:29:57] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-05-23 21:29:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-23 21:29:57] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:29:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:29:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:29:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:29:57] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:29:57] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-23 21:29:57] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.087801s from omabrowser.org (86.2 Kb/s); Redirect: 0s, DNS look up: 0.000595s, Connection: 0.006243s, Pretransfer: 0.039838s, First byte at: 0.087671s [2026-05-23 21:29:57] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 23 May 2026 19:29:57 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=0m16wmf0ztyhIC584smKKwnYse67NR8eoOipyTY%2BqOP8dHepw0RrmAZ6UGdFhwKvRn4cghvWf3dwwxJosFjNNS8gvIsVQsmIksCI4D0%2B5tqso5GQmc%2FGBZUstwEleO1RMw%3D%3D"}]}; cf-ray: a00678ed4ad2dc76-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-23 21:29:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-23 21:29:57] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-05-23 21:29:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:29:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:29:57] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-05-23 21:29:57] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:29:57] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-23 21:29:57] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:29:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-23 21:29:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:29:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:29:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:29:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:29:57] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-05-23 21:29:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-23 21:29:57] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:29:57] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:30:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-23 21:30:21] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-05-23 21:30:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:21] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-05-23 21:30:21] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-05-23 21:30:21] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:30:21] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:30:21] [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` [2026-05-23 21:30:21] [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` [2026-05-23 21:30:21] [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` [2026-05-23 21:30:21] [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` [2026-05-23 21:30:21] [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` [2026-05-23 21:30:21] [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` [2026-05-23 21:30:21] [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` [2026-05-23 21:30:21] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:30:21] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:30:21] [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] [2026-05-23 21:30:21] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:30:21] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094267s from omnipathdb.org (166.5 Kb/s); Redirect: 0s, DNS look up: 0.000973s, Connection: 0.017494s, Pretransfer: 0.061512s, First byte at: 0.093875s [2026-05-23 21:30:21] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:30:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:30:21 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:30:22] [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` [2026-05-23 21:30:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:22] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`. [2026-05-23 21:30:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2026-05-23 21:30:22] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`. [2026-05-23 21:30:22] [INFO] [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1] [2026-05-23 21:30:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:22] [INFO] [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`. [2026-05-23 21:30:26] [SUCCESS] [OmnipathR] Downloaded 131398 interactions. [2026-05-23 21:30:30] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:30:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2026-05-23 21:30:30] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:30:30] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:30:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:30] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:30] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:30] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:30] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:30] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:30] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:30] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:30:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:30:30] [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] [2026-05-23 21:30:30] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:30:30] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.106413s from omnipathdb.org (147.5 Kb/s); Redirect: 0s, DNS look up: 0.001105s, Connection: 0.019598s, Pretransfer: 0.068535s, First byte at: 0.106078s [2026-05-23 21:30:30] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:30:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:30:30 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:30:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:30] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2026-05-23 21:30:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-05-23 21:30:30] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-05-23 21:30:30] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2026-05-23 21:30:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:30] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2026-05-23 21:30:32] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships. [2026-05-23 21:30:32] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:30:32] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions] [2026-05-23 21:30:32] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:30:32] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:30:32] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:32] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:32] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:32] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:32] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:32] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:30:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:30:32] [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] [2026-05-23 21:30:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:30:32] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.094702s from omnipathdb.org (165.8 Kb/s); Redirect: 0s, DNS look up: 0.000935s, Connection: 0.020192s, Pretransfer: 0.05407s, First byte at: 0.093825s [2026-05-23 21:30:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:30:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:30:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:30:33] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:33] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-05-23 21:30:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-23 21:30:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-23 21:30:33] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-05-23 21:30:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:33] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-05-23 21:30:36] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-05-23 21:30:36] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:30:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=complexes] [2026-05-23 21:30:36] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:30:36] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:30:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic` [2026-05-23 21:30:36] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic` [2026-05-23 21:30:36] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic` [2026-05-23 21:30:36] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic` [2026-05-23 21:30:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic` [2026-05-23 21:30:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic` [2026-05-23 21:30:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic` [2026-05-23 21:30:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:30:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:30:36] [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] [2026-05-23 21:30:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:30:36] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093671s from omnipathdb.org (167.6 Kb/s); Redirect: 0s, DNS look up: 0.000869s, Connection: 0.020481s, Pretransfer: 0.054184s, First byte at: 0.093382s [2026-05-23 21:30:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:30:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:30:36 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:30:37] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic` [2026-05-23 21:30:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:37] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`. [2026-05-23 21:30:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2026-05-23 21:30:37] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`. [2026-05-23 21:30:37] [INFO] [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1] [2026-05-23 21:30:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:37] [INFO] [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`. [2026-05-23 21:30:37] [SUCCESS] [OmnipathR] Downloaded 37629 protein complexes. [2026-05-23 21:30:37] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:30:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2026-05-23 21:30:37] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:30:37] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:30:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:30:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:38] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:30:38] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:30:38] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:30:38] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:30:38] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:30:38] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:30:38] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:30:38] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:30:38] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:30:38] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:30:38] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:30:38] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097713s from omnipathdb.org (160.7 Kb/s); Redirect: 0s, DNS look up: 0.00091s, Connection: 0.021536s, Pretransfer: 0.055583s, First byte at: 0.097331s [2026-05-23 21:30:38] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:30:38 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:30:38 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:30:38] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:30:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:38] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2026-05-23 21:30:38] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-05-23 21:30:39] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-05-23 21:30:39] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2026-05-23 21:30:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:39] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2026-05-23 21:30:39] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2026-05-23 21:30:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:30:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations] [2026-05-23 21:30:39] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:30:39] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:30:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:30:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-05-23 21:30:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-05-23 21:30:39] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-05-23 21:30:39] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-05-23 21:30:39] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-05-23 21:30:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-05-23 21:30:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-05-23 21:30:39] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:30:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:30:39] [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] [2026-05-23 21:30:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:30:39] [TRACE] [OmnipathR] Downloaded 72 bytes in 0.09081s from omnipathdb.org (792 bytes/s); Redirect: 0s, DNS look up: 0.001016s, Connection: 0.021595s, Pretransfer: 0.070092s, First byte at: 0.090782s [2026-05-23 21:30:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:30:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:30:39 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:30:39] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic` [2026-05-23 21:30:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:39] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`. [2026-05-23 21:30:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2026-05-23 21:30:39] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`. [2026-05-23 21:30:39] [INFO] [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1] [2026-05-23 21:30:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:39] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2026-05-23 21:30:39] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. [2026-05-23 21:30:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:30:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations] [2026-05-23 21:30:39] [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. [2026-05-23 21:30:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:30:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations] [2026-05-23 21:30:39] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:30:39] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:30:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:30:40] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-05-23 21:30:40] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:30:40] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2026-05-23 21:30:40] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:30:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations] [2026-05-23 21:30:40] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:30:40] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:30:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:40] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-05-23 21:30:40] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-05-23 21:30:40] [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` [2026-05-23 21:30:40] [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` [2026-05-23 21:30:40] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-05-23 21:30:40] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-05-23 21:30:40] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-05-23 21:30:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:30:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:30:40] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:30:40] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:30:40] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.104615s from omnipathdb.org (150.1 Kb/s); Redirect: 0s, DNS look up: 0.00102s, Connection: 0.019061s, Pretransfer: 0.06819s, First byte at: 0.104266s [2026-05-23 21:30:40] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:30:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:30:40 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:30:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic` [2026-05-23 21:30:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:41] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`. [2026-05-23 21:30:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2026-05-23 21:30:41] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`. [2026-05-23 21:30:41] [INFO] [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1] [2026-05-23 21:30:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:41] [INFO] [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`. [2026-05-23 21:30:41] [SUCCESS] [OmnipathR] Downloaded 3752 annotation records. [2026-05-23 21:30:41] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:30:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2026-05-23 21:30:41] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:30:41] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:30:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:30:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:30:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:30:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:30:41] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:30:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:30:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:30:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:30:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:30:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:30:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:30:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:30:41] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095733s from omnipathdb.org (164 Kb/s); Redirect: 0s, DNS look up: 0.000882s, Connection: 0.021142s, Pretransfer: 0.054423s, First byte at: 0.095323s [2026-05-23 21:30:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:30:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:30:41 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:30:41] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:30:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:41] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2026-05-23 21:30:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-05-23 21:30:41] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-05-23 21:30:41] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2026-05-23 21:30:41] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:41] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2026-05-23 21:30:41] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2026-05-23 21:30:41] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:30:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-05-23 21:30:41] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:30:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-05-23 21:30:41] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:30:41] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:30:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:42] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-23 21:30:42] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:30:44] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. [2026-05-23 21:30:44] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:30:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations] [2026-05-23 21:30:44] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:30:44] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:30:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:30:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:30:44] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-05-23 21:30:44] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:30:44] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache. [2026-05-23 21:30:44] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:30:44] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:30:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic` [2026-05-23 21:30:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic` [2026-05-23 21:30:44] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic` [2026-05-23 21:30:44] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic` [2026-05-23 21:30:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic` [2026-05-23 21:30:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic` [2026-05-23 21:30:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic` [2026-05-23 21:30:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:30:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:30:45] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:30:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:30:45] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.101508s from omnipathdb.org (154.7 Kb/s); Redirect: 0s, DNS look up: 0.000947s, Connection: 0.022796s, Pretransfer: 0.057246s, First byte at: 0.100993s [2026-05-23 21:30:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:30:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:30:45 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:30:46] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic` [2026-05-23 21:30:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:47] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`. [2026-05-23 21:30:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2026-05-23 21:30:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2026-05-23 21:30:49] [INFO] [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1] [2026-05-23 21:30:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:49] [INFO] [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`. [2026-05-23 21:30:49] [SUCCESS] [OmnipathR] Downloaded 388239 intercellular communication role records. [2026-05-23 21:30:50] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2026-05-23 21:30:50] [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. [2026-05-23 21:30:50] [TRACE] [OmnipathR] Bypassing call: `intercell_network()`. [2026-05-23 21:30:50] [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. [2026-05-23 21:30:50] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `. [2026-05-23 21:30:50] [TRACE] [OmnipathR] Bypassing call: ` loc_consensus_percentile = 50, simplify = TRUE)`. [2026-05-23 21:30:50] [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. [2026-05-23 21:30:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:30:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:30:50] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:30:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2026-05-23 21:30:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2026-05-23 21:30:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2026-05-23 21:30:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2026-05-23 21:30:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2026-05-23 21:30:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2026-05-23 21:30:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2026-05-23 21:30:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:30:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:30:50] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:30:50] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:30:50] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.092341s from omnipathdb.org (82.1 Kb/s); Redirect: 0s, DNS look up: 0.000974s, Connection: 0.022585s, Pretransfer: 0.068421s, First byte at: 0.091887s [2026-05-23 21:30:50] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:30:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:30:50 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:30:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2026-05-23 21:30:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:50] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2026-05-23 21:30:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-05-23 21:30:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-05-23 21:30:50] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2026-05-23 21:30:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:50] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2026-05-23 21:30:50] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2026-05-23 21:30:50] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`. [2026-05-23 21:30:50] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-05-23 21:30:50] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2026-05-23 21:30:50] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:30:50] [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`. [2026-05-23 21:30:50] [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` [2026-05-23 21:30:50] [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`. [2026-05-23 21:30:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:30:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:30:50] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2026-05-23 21:30:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-05-23 21:30:50] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-05-23 21:30:50] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-05-23 21:30:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:30:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:30:50] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:30:51] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-23 21:30:51] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.439439s from rest.uniprot.org (97 bytes/s); Redirect: 0s, DNS look up: 0.007728s, Connection: 0.037231s, Pretransfer: 0.127816s, First byte at: 0.439373s [2026-05-23 21:30:51] [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: 30-April-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 23 May 2026 19:30:51 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; 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: 28-January-2026 [2026-05-23 21:31:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-05-23 21:31:00] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2026-05-23 21:31:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:00] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2026-05-23 21:31:00] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records [2026-05-23 21:31:01] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2026-05-23 21:31:01] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2026-05-23 21:31:01] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2026-05-23 21:31:01] [TRACE] [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`. [2026-05-23 21:31:01] [TRACE] [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`. [2026-05-23 21:31:01] [TRACE] [OmnipathR] Bypassing call: `go_ontology_download()`. [2026-05-23 21:31:01] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-05-23 21:31:01] [TRACE] [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`. [2026-05-23 21:31:01] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-05-23 21:31:01] [TRACE] [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`. [2026-05-23 21:31:01] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. --- finished re-building ‘bioc_workshop.Rmd’ --- re-building ‘cosmos.Rmd’ using rmarkdown [2026-05-23 21:31:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:03] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:31:03] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-23 19:15:52 UTC; omnipath [2026-05-23 21:31:03] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-23 21:31:03] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-23 19:17:18 UTC; unix [2026-05-23 21:31:03] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-23 21:31:03] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-23 21:31:03] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-23 21:31:03] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-05-23 21:31:03] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-23); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); 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 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-05-23 21:31:03] [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 [2026-05-23 21:31:03] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-23 21:31:03] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:31:03] [TRACE] [OmnipathR] Contains 15 files. [2026-05-23 21:31:03] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-23 21:31:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:31:03] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-23 21:31:03] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-23 21:31:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:03] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-23 21:31:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:03] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-23 21:31:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:03] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-23 21:31:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:03] [TRACE] [OmnipathR] Cache locked: FALSE [2026-05-23 21:31:03] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2026-05-23 21:31:03] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-05-23 21:31:03] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2026-05-23 21:31:03] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-05-23 21:31:03] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2026-05-23 21:31:03] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-05-23 21:31:03] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-05-23 21:31:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:03] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-05-23 21:31:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:03] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-05-23 21:31:03] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-05-23 21:31:03] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-23 21:31:03] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-23 21:31:03] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-23 21:31:03] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-05-23 21:31:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:31:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:31:03] [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] [2026-05-23 21:31:04] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:31:04] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-23 21:31:04] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-23 21:31:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:31:04] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.128377s from rescued.omnipathdb.org (310.5 Kb/s); Redirect: 0s, DNS look up: 0.001154s, Connection: 0.02153s, Pretransfer: 0.066965s, First byte at: 0.107751s [2026-05-23 21:31:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:31:04 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 23 May 2026 20:31:04 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-05-23 21:31:04] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 23 May 2026 19:31:04 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 23 May 2026 20:31:04 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-05-23 21:31:04] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-05-23 21:31:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:04] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-05-23 21:31:04] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:31:04] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-05-23 21:31:04] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:31:04] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-05-23 21:31:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:04] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-05-23 21:31:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-23 21:31:04] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:31:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:31:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:31:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:31:04] [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] [2026-05-23 21:31:04] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-23 21:31:04] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.09615s from omabrowser.org (78.7 Kb/s); Redirect: 0s, DNS look up: 0.000624s, Connection: 0.007426s, Pretransfer: 0.040234s, First byte at: 0.09597s [2026-05-23 21:31:04] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 23 May 2026 19:31:04 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=xx5%2BJr%2FrQtAuOEGXNyX3b%2BuU4wmy5fZF1pim3PRe6ZYSZZDccL%2F3j6%2BCoxeS5TDxWheCd9dWDokvvq3H2EuvhKE%2BncR3iGzr6Fo5HSW6Xqdk%2FY7MNHtK8cga%2BKIrh6BFrg%3D%3D"}]}; cf-ray: a0067a91693239ca-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-23 21:31:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-23 21:31:04] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-05-23 21:31:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:04] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-05-23 21:31:04] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:31:04] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-23 21:31:04] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:31:04] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-23 21:31:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:04] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-05-23 21:31:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-23 21:31:04] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:31:04] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:31:26] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-23 21:31:26] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-05-23 21:31:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:26] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-05-23 21:31:26] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-05-23 21:31:26] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2026-05-23 21:31:26] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:31:26] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2026-05-23 21:31:26] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:31:26] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:31:26] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:31:26] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:31:26] [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` [2026-05-23 21:31:26] [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` [2026-05-23 21:31:26] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:31:26] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:31:26] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:31:26] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:31:26] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:31:26] [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] [2026-05-23 21:31:26] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:31:26] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093992s from omnipathdb.org (167 Kb/s); Redirect: 0s, DNS look up: 0.000933s, Connection: 0.020491s, Pretransfer: 0.054189s, First byte at: 0.093626s [2026-05-23 21:31:27] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:31:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:31:26 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:31:27] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:31:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:27] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-05-23 21:31:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-23 21:31:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-23 21:31:28] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-05-23 21:31:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:28] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-05-23 21:31:30] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-05-23 21:31:30] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2026-05-23 21:31:30] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2026-05-23 21:31:30] [TRACE] [OmnipathR] BioMart query: [2026-05-23 21:31:30] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:31:30] [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`. [2026-05-23 21:31:30] [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` [2026-05-23 21:31:30] [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`. [2026-05-23 21:31:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:30] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2026-05-23 21:31:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-05-23 21:31:30] [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` [2026-05-23 21:31:30] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-23 21:31:30] [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` [2026-05-23 21:31:30] [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`. [2026-05-23 21:31:30] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:31:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:31:30] [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] [2026-05-23 21:31:30] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:31:30] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-23 21:31:31] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-23 21:31:31] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:31:31] [TRACE] [OmnipathR] Downloaded 1014 bytes in 0.076486s from www.ensembl.org (12.9 Kb/s); Redirect: 0s, DNS look up: 0.010134s, Connection: 0.03903s, Pretransfer: 0.039086s, First byte at: 0.076357s [2026-05-23 21:31:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: D5EA:BF13D:3B5AAF:3E3A6F:6A0E4CF0; Server: GitHub.com; X-Cache-Hits: 27; Vary: Accept-Encoding; Cache-Control: no-cache, no-store, must-revalidate; x-proxy-cache: MISS; X-Cache: HIT; Content-Type: text/html; charset=utf-8; X-Fastly-Request-ID: f7c4ed3f4d7dbe58d7c7712ab7f20d8c7469252e; Content-Encoding: gzip; Date: Sat, 23 May 2026 19:31:31 GMT; Expires: 0; X-Served-By: cache-lcy-egml8630071-LCY; Pragma: no-cache; X-Timer: S1779564691.050939,VS0,VE1; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"68b6c2f9-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 278; Content-Length: 1014 [2026-05-23 21:31:31] [TRACE] [OmnipathR] Response headers: [X-GitHub-Request-Id=D5EA:BF13D:3B5AAF:3E3A6F:6A0E4CF0,Server=GitHub.com,X-Cache-Hits=27,Vary=Accept-Encoding,Cache-Control=no-cache, no-store, must-revalidate,x-proxy-cache=MISS,X-Cache=HIT,Content-Type=text/html; charset=utf-8,X-Fastly-Request-ID=f7c4ed3f4d7dbe58d7c7712ab7f20d8c7469252e,Content-Encoding=gzip,Date=Sat, 23 May 2026 19:31:31 GMT,Expires=0,X-Served-By=cache-lcy-egml8630071-LCY,Pragma=no-cache,X-Timer=S1779564691.050939,VS0,VE1,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"68b6c2f9-8aa",Via=1.1 varnish,Connection=keep-alive,Age=278,Content-Length=1014] [2026-05-23 21:31:31] [TRACE] [OmnipathR] Calling reader callback on response. [2026-05-23 21:31:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-05-23 21:31:31] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2026-05-23 21:31:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:31] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2026-05-23 21:31:31] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message! [2026-05-23 21:31:31] [WARN] [OmnipathR] [2026-05-23 21:31:31] [WARN] [OmnipathR] [2026-05-23 21:31:31] [WARN] [OmnipathR] Service unavailable [2026-05-23 21:31:31] [WARN] [OmnipathR] [2026-05-23 21:31:31] [WARN] [OmnipathR] [2026-05-23 21:31:31] [WARN] [OmnipathR] [2026-05-23 21:31:31] [WARN] [OmnipathR] [2026-05-23 21:31:31] [WARN] [OmnipathR] [2026-05-23 21:31:31] [WARN] [OmnipathR]
[2026-05-23 21:31:31] [WARN] [OmnipathR] ensembl-logo [2026-05-23 21:31:31] [WARN] [OmnipathR]
[2026-05-23 21:31:31] [WARN] [OmnipathR]
[2026-05-23 21:31:31] [WARN] [OmnipathR]

Server Status

[2026-05-23 21:31:31] [WARN] [OmnipathR]

[2026-05-23 21:31:31] [WARN] [OmnipathR] [!] [2026-05-23 21:31:31] [WARN] [OmnipathR] The Ensembl web service you requested is temporarily unavailable. [2026-05-23 21:31:31] [WARN] [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused. [2026-05-23 21:31:31] [WARN] [OmnipathR]

[2026-05-23 21:31:31] [WARN] [OmnipathR]

For all enquiries, please contact our HelpDesk.

[2026-05-23 21:31:31] [WARN] [OmnipathR]
[2026-05-23 21:31:31] [WARN] [OmnipathR]

Ensembl mirrors

[2026-05-23 21:31:31] [WARN] [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud: [2026-05-23 21:31:31] [WARN] [OmnipathR] [2026-05-23 21:31:31] [WARN] [OmnipathR] These will be available while the main service is unavailable, although please note that some of the [2026-05-23 21:31:31] [WARN] [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main [2026-05-23 21:31:31] [WARN] [OmnipathR] data centre. [2026-05-23 21:31:31] [WARN] [OmnipathR]
[2026-05-23 21:31:31] [WARN] [OmnipathR]
[2026-05-23 21:31:31] [WARN] [OmnipathR]
[2026-05-23 21:31:31] [WARN] [OmnipathR]

© 2025 EMBL-EBI

[2026-05-23 21:31:31] [WARN] [OmnipathR]
[2026-05-23 21:31:31] [WARN] [OmnipathR] [2026-05-23 21:31:31] [WARN] [OmnipathR] [2026-05-23 21:31:31] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 81 records Quitting from cosmos.Rmd:175-179 [omnipath] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `set_names()`: ! The size of `nm` (2) must be compatible with the size of `x` (1). --- Backtrace: ▆ 1. ├─OmnipathR::omnipath_for_cosmos() 2. │ └─... %T>% ... 3. ├─dplyr::bind_rows(...) 4. │ └─rlang::list2(...) 5. ├─OmnipathR::translate_ids_multi(...) 6. │ └─source_cols %>% seq_along %>% ... 7. ├─purrr::reduce(...) 8. │ └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir) 9. │ └─OmnipathR (local) fn(out, elt, ...) 10. │ └─OmnipathR::translate_ids(...) 11. │ └─... %>% ... 12. ├─purrr::reduce2(...) 13. │ └─purrr:::reduce2_impl(.x, .y, .f, ..., .init = .init, .left = TRUE) 14. │ └─OmnipathR (local) .f(out, .x[[x_i]], .y[[y_i]], ...) 15. │ ├─... %>% ... 16. │ └─OmnipathR:::id_translation_table(...) 17. │ └─OmnipathR::ensembl_id_mapping_table(...) 18. │ └─... %>% trim_and_distinct 19. ├─OmnipathR:::ensure_character(., From, To) 20. │ └─d %>% mutate(across(c(!!!cols), as.character)) 21. ├─dplyr::mutate(., across(c(!!!cols), as.character)) 22. ├─OmnipathR:::trim_and_distinct(.) 23. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct 24. ├─dplyr::distinct(.) 25. ├─dplyr::mutate(., across(everything(), str_trim)) 26. ├─rlang::set_names(., c("From", "To")) 27. └─rlang::abort(message = message) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'cosmos.Rmd' failed with diagnostics: The size of `nm` (2) must be compatible with the size of `x` (1). --- failed re-building ‘cosmos.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2026-05-23 21:31:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:34] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:31:34] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-23 19:15:52 UTC; omnipath [2026-05-23 21:31:34] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-23 21:31:34] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-23 19:17:18 UTC; unix [2026-05-23 21:31:34] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-23 21:31:34] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-23 21:31:34] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-23 21:31:34] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-05-23 21:31:34] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-23); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); 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 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-05-23 21:31:34] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-05-23 21:31:34] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-23 21:31:34] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:31:34] [TRACE] [OmnipathR] Contains 6 files. [2026-05-23 21:31:34] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-23 21:31:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:31:34] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-23 21:31:34] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-23 21:31:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:34] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-23 21:31:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:34] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-23 21:31:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:34] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-23 21:31:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:34] [TRACE] [OmnipathR] Cache locked: FALSE [2026-05-23 21:31:34] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2026-05-23 21:31:34] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-05-23 21:31:34] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-05-23 21:31:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:34] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-05-23 21:31:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:34] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-05-23 21:31:34] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-05-23 21:31:34] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-23 21:31:34] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-23 21:31:34] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-23 21:31:34] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-05-23 21:31:34] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:31:34] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:31:34] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:31:34] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:31:34] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-23 21:31:34] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-23 21:31:34] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:31:35] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.128326s from rescued.omnipathdb.org (310.6 Kb/s); Redirect: 0s, DNS look up: 0.000969s, Connection: 0.021317s, Pretransfer: 0.067034s, First byte at: 0.107636s [2026-05-23 21:31:35] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:31:34 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 23 May 2026 20:31:34 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-05-23 21:31:35] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 23 May 2026 19:31:34 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 23 May 2026 20:31:34 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-05-23 21:31:35] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-05-23 21:31:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:35] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-05-23 21:31:35] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:31:35] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-05-23 21:31:35] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:31:35] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-05-23 21:31:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:35] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-05-23 21:31:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-23 21:31:35] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:31:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:31:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:31:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:31:35] [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] [2026-05-23 21:31:35] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-23 21:31:35] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.097373s from omabrowser.org (77.7 Kb/s); Redirect: 0s, DNS look up: 0.000602s, Connection: 0.008725s, Pretransfer: 0.047917s, First byte at: 0.097156s [2026-05-23 21:31:35] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 23 May 2026 19:31:35 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=EWFo%2Fekp7gou5AdemXQPTiNADbPR6KB4OEV%2BXYkMGbbZmrVOYY0Wx4IHFAuSdxi9DlrcKclzJYsFgxkJwRFc5UF0k8mR%2F92fxV66fKJQXuN5x97EEJ4r5wab7Qbd32I22w%3D%3D"}]}; cf-ray: a0067b526ca6dc8a-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-23 21:31:35] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-23 21:31:35] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-05-23 21:31:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:35] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-05-23 21:31:35] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:31:35] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-23 21:31:35] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:31:35] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-23 21:31:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:31:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:31:35] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-05-23 21:31:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-23 21:31:35] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:31:35] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:31:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-23 21:31:59] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-05-23 21:31:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:00] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-05-23 21:32:00] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-05-23 21:32:00] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2026-05-23 21:32:00] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:32:00] [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`. [2026-05-23 21:32:00] [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` [2026-05-23 21:32:00] [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`. [2026-05-23 21:32:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:00] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2026-05-23 21:32:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-05-23 21:32:00] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-05-23 21:32:00] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-05-23 21:32:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:32:00] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:32:00] [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] [2026-05-23 21:32:00] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-23 21:32:00] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.472969s from rest.uniprot.org (90 bytes/s); Redirect: 0s, DNS look up: 0.000906s, Connection: 0.029972s, Pretransfer: 0.102963s, First byte at: 0.47287s [2026-05-23 21:32:00] [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: 30-April-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 23 May 2026 19:32:00 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; 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: 28-January-2026 [2026-05-23 21:32:09] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-05-23 21:32:09] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2026-05-23 21:32:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:09] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2026-05-23 21:32:09] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records [2026-05-23 21:32:10] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2026-05-23 21:32:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:22] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:32:23] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-23 19:15:52 UTC; omnipath [2026-05-23 21:32:23] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-23 21:32:23] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-23 19:17:18 UTC; unix [2026-05-23 21:32:23] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-23 21:32:23] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-23 21:32:23] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-23 21:32:23] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-05-23 21:32:23] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); ggplot2 4.0.3(2026-04-22); glue 1.8.1(2026-04-17); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-23); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); S7 0.2.2(2026-04-22); 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 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-05-23 21:32:23] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-05-23 21:32:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-23 21:32:23] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:32:23] [TRACE] [OmnipathR] Contains 5 files. [2026-05-23 21:32:23] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-23 21:32:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:32:23] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-23 21:32:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-23 21:32:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-23 21:32:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-23 21:32:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-23 21:32:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:23] [TRACE] [OmnipathR] Cache locked: FALSE [2026-05-23 21:32:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:32:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-05-23 21:32:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:32:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-05-23 21:32:23] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-05-23 21:32:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:23] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-05-23 21:32:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:23] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-05-23 21:32:23] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-05-23 21:32:23] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-23 21:32:23] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-23 21:32:23] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-23 21:32:23] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-05-23 21:32:23] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:32:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:32:23] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:32:23] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:32:23] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-23 21:32:23] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-23 21:32:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:32:23] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.170162s from rescued.omnipathdb.org (234.2 Kb/s); Redirect: 0s, DNS look up: 0.039435s, Connection: 0.057451s, Pretransfer: 0.116071s, First byte at: 0.152146s [2026-05-23 21:32:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:32:23 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 23 May 2026 20:32:23 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-05-23 21:32:23] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 23 May 2026 19:32:23 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 23 May 2026 20:32:23 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-05-23 21:32:24] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-05-23 21:32:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:24] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-05-23 21:32:24] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:32:24] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-05-23 21:32:24] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:32:24] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-05-23 21:32:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:24] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-05-23 21:32:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-23 21:32:24] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:32:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:32:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:32:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:32:24] [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] [2026-05-23 21:32:24] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-23 21:32:24] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.112218s from omabrowser.org (67.4 Kb/s); Redirect: 0s, DNS look up: 0.000558s, Connection: 0.008429s, Pretransfer: 0.061382s, First byte at: 0.111997s [2026-05-23 21:32:24] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 23 May 2026 19:32:24 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=oHVByM86ZLl2s2hqDsky5I%2BaK8xybJgGMDeafkrnea%2B%2BNRgDw14XrTT5tYYSeVjjT9H5wpYT07cDUvwM4VQaWGW1mYBSyDAHIh0GtnwaeVEVsLqkqw1UgLZ0rHIZb%2BRrCw%3D%3D"}]}; cf-ray: a0067c842b55d282-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-23 21:32:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-23 21:32:24] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-05-23 21:32:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:24] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-05-23 21:32:24] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:32:24] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-23 21:32:24] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:32:24] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-23 21:32:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:24] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-05-23 21:32:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-23 21:32:24] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:32:24] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:32:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-23 21:32:48] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-05-23 21:32:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:48] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-05-23 21:32:48] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-05-23 21:32:48] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:32:48] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:32:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:32:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:32:48] [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` [2026-05-23 21:32:48] [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` [2026-05-23 21:32:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:32:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:32:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:32:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:32:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:32:48] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:32:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:32:48] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097049s from omnipathdb.org (161.8 Kb/s); Redirect: 0s, DNS look up: 0.000988s, Connection: 0.021735s, Pretransfer: 0.05419s, First byte at: 0.096125s [2026-05-23 21:32:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:32:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:32:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:32:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:32:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:49] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-05-23 21:32:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-23 21:32:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-23 21:32:49] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-05-23 21:32:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:49] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-05-23 21:32:52] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2026-05-23 21:32:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:56] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:32:56] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-23 19:15:52 UTC; omnipath [2026-05-23 21:32:56] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-23 21:32:56] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-23 19:17:18 UTC; unix [2026-05-23 21:32:56] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-23 21:32:56] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-23 21:32:56] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-23 21:32:56] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-05-23 21:32:56] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-23); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); 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 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-05-23 21:32:56] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-05-23 21:32:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-23 21:32:56] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:32:56] [TRACE] [OmnipathR] Contains 5 files. [2026-05-23 21:32:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-23 21:32:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:32:56] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-23 21:32:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-23 21:32:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-23 21:32:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-23 21:32:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-23 21:32:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:56] [TRACE] [OmnipathR] Cache locked: FALSE [2026-05-23 21:32:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:32:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2026-05-23 21:32:56] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-05-23 21:32:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:56] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-05-23 21:32:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:56] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-05-23 21:32:56] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-05-23 21:32:56] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-23 21:32:56] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-23 21:32:56] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-23 21:32:56] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-05-23 21:32:56] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:32:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:32:56] [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] [2026-05-23 21:32:56] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:32:56] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-23 21:32:56] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-23 21:32:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:32:56] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.132542s from rescued.omnipathdb.org (300.7 Kb/s); Redirect: 0s, DNS look up: 0.001108s, Connection: 0.020945s, Pretransfer: 0.072953s, First byte at: 0.112701s [2026-05-23 21:32:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:32:56 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 23 May 2026 20:32:56 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-05-23 21:32:56] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 23 May 2026 19:32:56 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 23 May 2026 20:32:56 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-05-23 21:32:56] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-05-23 21:32:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:56] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-05-23 21:32:56] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:32:57] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-05-23 21:32:57] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:32:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-05-23 21:32:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:57] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-05-23 21:32:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-23 21:32:57] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:32:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:32:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:32:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:32:57] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:32:57] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-23 21:32:57] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.093077s from omabrowser.org (81.3 Kb/s); Redirect: 0s, DNS look up: 0.000583s, Connection: 0.006441s, Pretransfer: 0.039682s, First byte at: 0.092873s [2026-05-23 21:32:57] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 23 May 2026 19:32:57 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=VT0%2Bw0LosBgMNsUb0cK1%2FD3ETt8JtnvKpIN%2FivXvVPPrIhMn7HU4XSElh26beq2oB3kjZZt2gxub31K6ogrIEiTOvJfZpH%2BtzSZpzX%2F%2FngjqyCHEhLGppZKHb62e0m3M%2Bw%3D%3D"}]}; cf-ray: a0067d512b1ed34c-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-23 21:32:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-23 21:32:57] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-05-23 21:32:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:57] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-05-23 21:32:57] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:32:57] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-23 21:32:57] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:32:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-23 21:32:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:32:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:32:57] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-05-23 21:32:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-23 21:32:57] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:32:57] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:33:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-23 21:33:20] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-05-23 21:33:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:33:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:33:20] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-05-23 21:33:20] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-05-23 21:33:20] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:33:20] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:33:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-05-23 21:33:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-05-23 21:33:20] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-05-23 21:33:20] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-05-23 21:33:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-05-23 21:33:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-05-23 21:33:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-05-23 21:33:20] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:33:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:33:20] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:33:20] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:33:20] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.114422s from omnipathdb.org (137.2 Kb/s); Redirect: 0s, DNS look up: 0.001161s, Connection: 0.022067s, Pretransfer: 0.072126s, First byte at: 0.114112s [2026-05-23 21:33:21] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:33:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:33:20 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:33:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic` [2026-05-23 21:33:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:33:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:33:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:33:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:33:21] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2026-05-23 21:33:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-05-23 21:33:22] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-05-23 21:33:22] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2026-05-23 21:33:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:33:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:33:22] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2026-05-23 21:33:22] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-05-23 21:33:31] [SUCCESS] [OmnipathR] Downloaded 139054 interactions. [2026-05-23 21:39:47] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:39:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations] [2026-05-23 21:39:47] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:39:47] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:39:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:39:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-23 21:39:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-23 21:39:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-23 21:39:47] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-23 21:39:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-23 21:39:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-23 21:39:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-23 21:39:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:39:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:39:47] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:39:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:39:48] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096226s from omnipathdb.org (163.2 Kb/s); Redirect: 0s, DNS look up: 0.001061s, Connection: 0.021098s, Pretransfer: 0.054322s, First byte at: 0.095173s [2026-05-23 21:39:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:39:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:39:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:39:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-23 21:39:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:48] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2026-05-23 21:39:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-05-23 21:39:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-05-23 21:39:49] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2026-05-23 21:39:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:49] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2026-05-23 21:39:49] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records. [2026-05-23 21:39:49] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:39:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub] [2026-05-23 21:39:49] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:39:49] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:39:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-05-23 21:39:49] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-05-23 21:39:49] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-05-23 21:39:49] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-05-23 21:39:49] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-05-23 21:39:49] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-05-23 21:39:49] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-05-23 21:39:49] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:39:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:39:49] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:39:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:39:49] [TRACE] [OmnipathR] Downloaded 1.3 Kb in 0.070577s from omnipathdb.org (17.9 Kb/s); Redirect: 0s, DNS look up: 0.000945s, Connection: 0.018985s, Pretransfer: 0.052323s, First byte at: 0.07053s [2026-05-23 21:39:49] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:39:49 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:39:49 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:39:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-05-23 21:39:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:50] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2026-05-23 21:39:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-05-23 21:39:50] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-05-23 21:39:50] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2026-05-23 21:39:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:50] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2026-05-23 21:39:50] [SUCCESS] [OmnipathR] Downloaded 68 enzyme-substrate relationships. --- finished re-building ‘extra_attrs.Rmd’ --- re-building ‘nichenet.Rmd’ using rmarkdown --- finished re-building ‘nichenet.Rmd’ --- re-building ‘omnipath_intro.Rmd’ using rmarkdown [2026-05-23 21:39:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:53] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:39:53] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-23 19:15:52 UTC; omnipath [2026-05-23 21:39:53] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-23 21:39:53] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-23 19:17:18 UTC; unix [2026-05-23 21:39:53] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-23 21:39:53] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-23 21:39:53] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-23 21:39:53] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-05-23 21:39:53] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-23); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-9(2026-03-15); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); 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 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-05-23 21:39:53] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-05-23 21:39:53] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-23 21:39:53] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:39:53] [TRACE] [OmnipathR] Contains 7 files. [2026-05-23 21:39:53] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-23 21:39:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:39:53] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-23 21:39:53] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-23 21:39:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:53] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-23 21:39:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:53] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-23 21:39:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:53] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-23 21:39:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:53] [TRACE] [OmnipathR] Cache locked: FALSE [2026-05-23 21:39:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:39:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:39:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2026-05-23 21:39:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:39:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2026-05-23 21:39:54] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-05-23 21:39:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:54] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-05-23 21:39:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:54] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-05-23 21:39:54] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-05-23 21:39:54] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-23 21:39:54] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-23 21:39:54] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-23 21:39:54] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-05-23 21:39:54] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:39:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:39:54] [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] [2026-05-23 21:39:54] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:39:54] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-23 21:39:55] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-23 21:39:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:39:55] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.114551s from rescued.omnipathdb.org (348 Kb/s); Redirect: 0s, DNS look up: 0.006932s, Connection: 0.025044s, Pretransfer: 0.060813s, First byte at: 0.096825s [2026-05-23 21:39:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:39:54 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 23 May 2026 20:39:54 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-05-23 21:39:55] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 23 May 2026 19:39:54 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 23 May 2026 20:39:54 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-05-23 21:39:55] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-05-23 21:39:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:55] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-05-23 21:39:55] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:39:55] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-05-23 21:39:55] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:39:55] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-05-23 21:39:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:55] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-05-23 21:39:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-23 21:39:55] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:39:55] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:39:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:39:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:39:55] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:39:55] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-23 21:39:55] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.158371s from omabrowser.org (47.8 Kb/s); Redirect: 0s, DNS look up: 0.034578s, Connection: 0.039688s, Pretransfer: 0.096923s, First byte at: 0.15813s [2026-05-23 21:39:55] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 23 May 2026 19:39:55 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=6Jr7dS4czt44XWH85bklpDy9MWIXqvEjeCPq%2FFXbvAfOexeGOMn4s7t5Et2rszrXcGROJkTcowHZgQpYOhwcoNWdb9xyBluQyReRWNIuDCr9ew0HpQuVhc6vrGH1l40LIA%3D%3D"}]}; cf-ray: a0068787fe783a61-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-23 21:39:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-23 21:39:55] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-05-23 21:39:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:55] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-05-23 21:39:55] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:39:55] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-23 21:39:55] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:39:55] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-23 21:39:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:39:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:39:55] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-05-23 21:39:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-23 21:39:55] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:39:55] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:40:19] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-23 21:40:19] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-05-23 21:40:19] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:19] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:19] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-05-23 21:40:19] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:19] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:40:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:19] [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` [2026-05-23 21:40:19] [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` [2026-05-23 21:40:19] [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` [2026-05-23 21:40:19] [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` [2026-05-23 21:40:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:19] [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` [2026-05-23 21:40:19] [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` [2026-05-23 21:40:19] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:19] [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] [2026-05-23 21:40:20] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:20] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.083295s from omnipathdb.org (188.5 Kb/s); Redirect: 0s, DNS look up: 0.001064s, Connection: 0.017008s, Pretransfer: 0.0513s, First byte at: 0.083012s [2026-05-23 21:40:20] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:20 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:20] [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` [2026-05-23 21:40:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:20] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-05-23 21:40:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-05-23 21:40:20] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2026-05-23 21:40:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:21] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:22] [SUCCESS] [OmnipathR] Downloaded 67773 interactions. [2026-05-23 21:40:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra] [2026-05-23 21:40:24] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions] [2026-05-23 21:40:25] [TRACE] [OmnipathR] Organism(s): 10090 [2026-05-23 21:40:25] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:40:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:25] [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` [2026-05-23 21:40:25] [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` [2026-05-23 21:40:25] [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` [2026-05-23 21:40:25] [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` [2026-05-23 21:40:25] [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` [2026-05-23 21:40:25] [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` [2026-05-23 21:40:25] [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` [2026-05-23 21:40:25] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:25] [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] [2026-05-23 21:40:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:25] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097425s from omnipathdb.org (161.2 Kb/s); Redirect: 0s, DNS look up: 0.001079s, Connection: 0.02122s, Pretransfer: 0.056509s, First byte at: 0.09713s [2026-05-23 21:40:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:25 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:25] [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` [2026-05-23 21:40:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:25] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-05-23 21:40:26] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-05-23 21:40:26] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1] [2026-05-23 21:40:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:26] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:27] [SUCCESS] [OmnipathR] Downloaded 41476 interactions. [2026-05-23 21:40:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra] [2026-05-23 21:40:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions] [2026-05-23 21:40:27] [TRACE] [OmnipathR] Organism(s): 10116 [2026-05-23 21:40:27] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:40:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:27] [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` [2026-05-23 21:40:27] [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` [2026-05-23 21:40:27] [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` [2026-05-23 21:40:27] [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` [2026-05-23 21:40:27] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:27] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:27] [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` [2026-05-23 21:40:27] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:27] [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] [2026-05-23 21:40:27] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:27] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089779s from omnipathdb.org (174.9 Kb/s); Redirect: 0s, DNS look up: 0.000815s, Connection: 0.019001s, Pretransfer: 0.052804s, First byte at: 0.089463s [2026-05-23 21:40:27] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:27 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:27 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:28] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:28] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-05-23 21:40:28] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-05-23 21:40:28] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2026-05-23 21:40:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:28] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:28] [SUCCESS] [OmnipathR] Downloaded 11083 interactions. [2026-05-23 21:40:28] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra] [2026-05-23 21:40:28] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions] [2026-05-23 21:40:28] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:28] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:40:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:29] [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` [2026-05-23 21:40:29] [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` [2026-05-23 21:40:29] [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` [2026-05-23 21:40:29] [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` [2026-05-23 21:40:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:29] [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` [2026-05-23 21:40:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:29] [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] [2026-05-23 21:40:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:29] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.120905s from omnipathdb.org (129.9 Kb/s); Redirect: 0s, DNS look up: 0.00106s, Connection: 0.023174s, Pretransfer: 0.075261s, First byte at: 0.120009s [2026-05-23 21:40:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:29] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:29] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-05-23 21:40:29] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-05-23 21:40:29] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2026-05-23 21:40:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:29] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:29] [SUCCESS] [OmnipathR] Downloaded 2840 interactions. [2026-05-23 21:40:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-05-23 21:40:29] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:29] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-05-23 21:40:29] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:29] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:29] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:29] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:29] [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` [2026-05-23 21:40:29] [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` [2026-05-23 21:40:29] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:29] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:29] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:29] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:29] [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] [2026-05-23 21:40:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:29] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090643s from omnipathdb.org (173.2 Kb/s); Redirect: 0s, DNS look up: 0.000896s, Connection: 0.019467s, Pretransfer: 0.052979s, First byte at: 0.090341s [2026-05-23 21:40:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:30] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:30] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:30] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-23 21:40:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-23 21:40:31] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-05-23 21:40:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:31] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:33] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-05-23 21:40:34] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea] [2026-05-23 21:40:34] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:34] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:34] [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` [2026-05-23 21:40:34] [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` [2026-05-23 21:40:34] [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` [2026-05-23 21:40:34] [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` [2026-05-23 21:40:34] [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` [2026-05-23 21:40:34] [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` [2026-05-23 21:40:34] [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` [2026-05-23 21:40:34] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:34] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:34] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:40:34] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:34] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.114182s from omnipathdb.org (137.5 Kb/s); Redirect: 0s, DNS look up: 0.000985s, Connection: 0.021551s, Pretransfer: 0.073166s, First byte at: 0.113827s [2026-05-23 21:40:34] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:34 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:34 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:35] [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` [2026-05-23 21:40:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:35] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-05-23 21:40:35] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-05-23 21:40:35] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1] [2026-05-23 21:40:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:35] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:35] [SUCCESS] [OmnipathR] Downloaded 6128 interactions. [2026-05-23 21:40:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget] [2026-05-23 21:40:35] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:35] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:40:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:35] [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` [2026-05-23 21:40:35] [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` [2026-05-23 21:40:35] [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` [2026-05-23 21:40:35] [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` [2026-05-23 21:40:35] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:35] [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` [2026-05-23 21:40:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:35] [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] [2026-05-23 21:40:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:36] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.103736s from omnipathdb.org (151.3 Kb/s); Redirect: 0s, DNS look up: 0.000955s, Connection: 0.02338s, Pretransfer: 0.057259s, First byte at: 0.102688s [2026-05-23 21:40:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:36 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:36] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:36] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-05-23 21:40:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-05-23 21:40:36] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1] [2026-05-23 21:40:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:36] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:36] [SUCCESS] [OmnipathR] Downloaded 648 interactions. [2026-05-23 21:40:36] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule] [2026-05-23 21:40:36] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:36] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:36] [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` [2026-05-23 21:40:36] [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` [2026-05-23 21:40:36] [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` [2026-05-23 21:40:36] [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` [2026-05-23 21:40:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-05-23 21:40:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-05-23 21:40:36] [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` [2026-05-23 21:40:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:36] [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] [2026-05-23 21:40:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:36] [TRACE] [OmnipathR] Downloaded 112 bytes in 0.081002s from omnipathdb.org (1.3 Kb/s); Redirect: 0s, DNS look up: 0.000937s, Connection: 0.023885s, Pretransfer: 0.057769s, First byte at: 0.080971s [2026-05-23 21:40:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:36 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:36] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-05-23 21:40:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:36] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-05-23 21:40:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-05-23 21:40:36] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1] [2026-05-23 21:40:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:36] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:37] [SUCCESS] [OmnipathR] Downloaded 0 interactions. [2026-05-23 21:40:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:40:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:37] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2026-05-23 21:40:37] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:37] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:37] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:37] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:37] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:37] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:37] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:37] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:37] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:37] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:37] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:40:37] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:37] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.106594s from omnipathdb.org (147.3 Kb/s); Redirect: 0s, DNS look up: 0.00707s, Connection: 0.028666s, Pretransfer: 0.062418s, First byte at: 0.106215s [2026-05-23 21:40:37] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:37 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:37 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:37] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:37] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-05-23 21:40:38] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-05-23 21:40:38] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2026-05-23 21:40:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:38] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:39] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships. [2026-05-23 21:40:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-05-23 21:40:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-05-23 21:40:39] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:39] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:39] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-23 21:40:39] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:42] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. [2026-05-23 21:40:42] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub] [2026-05-23 21:40:42] [TRACE] [OmnipathR] Organism(s): 10090 [2026-05-23 21:40:42] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:40:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:43] [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` [2026-05-23 21:40:43] [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` [2026-05-23 21:40:43] [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` [2026-05-23 21:40:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:43] [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] [2026-05-23 21:40:43] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:43] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092543s from omnipathdb.org (169.7 Kb/s); Redirect: 0s, DNS look up: 0.000988s, Connection: 0.020034s, Pretransfer: 0.053855s, First byte at: 0.092146s [2026-05-23 21:40:43] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:43 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:43] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-05-23 21:40:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:43] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-05-23 21:40:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-05-23 21:40:43] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1] [2026-05-23 21:40:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:43] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:44] [SUCCESS] [OmnipathR] Downloaded 16895 enzyme-substrate relationships. [2026-05-23 21:40:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:40:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:44] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes] [2026-05-23 21:40:44] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:44] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:40:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-23 21:40:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-23 21:40:44] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-23 21:40:44] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-23 21:40:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-23 21:40:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-23 21:40:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-23 21:40:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:44] [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] [2026-05-23 21:40:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:44] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097912s from omnipathdb.org (160.3 Kb/s); Redirect: 0s, DNS look up: 0.000865s, Connection: 0.019386s, Pretransfer: 0.060584s, First byte at: 0.097633s [2026-05-23 21:40:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:44 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-23 21:40:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:45] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-05-23 21:40:45] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-05-23 21:40:45] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1] [2026-05-23 21:40:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:45] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:45] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes. [2026-05-23 21:40:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:40:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:46] [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] [2026-05-23 21:40:46] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:46] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:46] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:40:46] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:46] [TRACE] [OmnipathR] Downloaded 11.6 Kb in 0.116153s from omnipathdb.org (100.2 Kb/s); Redirect: 0s, DNS look up: 0.000981s, Connection: 0.023018s, Pretransfer: 0.071951s, First byte at: 0.115861s [2026-05-23 21:40:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:46 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:46] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:46] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-05-23 21:40:46] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-05-23 21:40:46] [INFO] [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1] [2026-05-23 21:40:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:46] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:46] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records. [2026-05-23 21:40:46] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations] [2026-05-23 21:40:46] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:46] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:40:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [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` [2026-05-23 21:40:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:46] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:40:46] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:46] [TRACE] [OmnipathR] Downloaded 1.2 Kb in 0.067991s from omnipathdb.org (17.6 Kb/s); Redirect: 0s, DNS look up: 0.000989s, Connection: 0.017154s, Pretransfer: 0.051414s, First byte at: 0.067943s [2026-05-23 21:40:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:46 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:47] [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` [2026-05-23 21:40:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:47] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-05-23 21:40:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-05-23 21:40:47] [INFO] [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1] [2026-05-23 21:40:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:47] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:47] [SUCCESS] [OmnipathR] Downloaded 86 annotation records. [2026-05-23 21:40:47] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations] [2026-05-23 21:40:47] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:47] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:40:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:47] [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` [2026-05-23 21:40:47] [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` [2026-05-23 21:40:47] [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` [2026-05-23 21:40:47] [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` [2026-05-23 21:40:47] [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` [2026-05-23 21:40:47] [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` [2026-05-23 21:40:47] [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` [2026-05-23 21:40:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:47] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:40:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:47] [TRACE] [OmnipathR] Downloaded 2.7 Kb in 0.072878s from omnipathdb.org (37.4 Kb/s); Redirect: 0s, DNS look up: 0.000836s, Connection: 0.017403s, Pretransfer: 0.052538s, First byte at: 0.072799s [2026-05-23 21:40:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:47 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:47] [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` [2026-05-23 21:40:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:47] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-05-23 21:40:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-05-23 21:40:47] [INFO] [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1] [2026-05-23 21:40:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:47] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:47] [SUCCESS] [OmnipathR] Downloaded 366 annotation records. [2026-05-23 21:40:48] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2026-05-23 21:40:48] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:48] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:40:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:40:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:40:48] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:40:48] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:40:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:40:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:40:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:40:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:48] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:40:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:48] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.104238s from omnipathdb.org (150.6 Kb/s); Redirect: 0s, DNS look up: 0.000886s, Connection: 0.023792s, Pretransfer: 0.057791s, First byte at: 0.103872s [2026-05-23 21:40:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-23 21:40:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:48] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-05-23 21:40:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-05-23 21:40:48] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2026-05-23 21:40:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:48] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:48] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2026-05-23 21:40:48] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:48] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2026-05-23 21:40:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2026-05-23 21:40:48] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2026-05-23 21:40:48] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2026-05-23 21:40:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2026-05-23 21:40:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2026-05-23 21:40:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2026-05-23 21:40:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:48] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:40:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:48] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.09672s from omnipathdb.org (78.4 Kb/s); Redirect: 0s, DNS look up: 0.000957s, Connection: 0.024595s, Pretransfer: 0.070751s, First byte at: 0.096557s [2026-05-23 21:40:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2026-05-23 21:40:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:49] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-05-23 21:40:49] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-05-23 21:40:49] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2026-05-23 21:40:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:49] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:49] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2026-05-23 21:40:49] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:40:49] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:40:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-23 21:40:49] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-23 21:40:49] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-23 21:40:49] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-23 21:40:49] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-23 21:40:49] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-23 21:40:49] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-23 21:40:49] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:49] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:40:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:49] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095812s from omnipathdb.org (163.9 Kb/s); Redirect: 0s, DNS look up: 0.000985s, Connection: 0.021113s, Pretransfer: 0.054837s, First byte at: 0.095392s [2026-05-23 21:40:49] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:49 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:40:49 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:40:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-23 21:40:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:51] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-05-23 21:40:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-05-23 21:40:52] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1] [2026-05-23 21:40:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:52] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:52] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records. [2026-05-23 21:40:53] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2026-05-23 21:40:53] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-05-23 21:40:53] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`. [2026-05-23 21:40:53] [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 [2026-05-23 21:40:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:55] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:40:55] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-23 19:15:52 UTC; omnipath [2026-05-23 21:40:55] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-23 21:40:55] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-23 19:17:18 UTC; unix [2026-05-23 21:40:55] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-23 21:40:55] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-23 21:40:56] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-23; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-23 21:40:56] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-05-23 21:40:56] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.1(2026-05-04); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-23); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); 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 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-05-23 21:40:56] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-05-23 21:40:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Contains 21 files. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-23 21:40:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-23 21:40:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-23 21:40:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-23 21:40:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:56] [TRACE] [OmnipathR] Cache locked: FALSE [2026-05-23 21:40:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:40:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2026-05-23 21:40:56] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:56] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:56] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-05-23 21:40:56] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-23 21:40:56] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-23 21:40:56] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-05-23 21:40:56] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:40:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:56] [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] [2026-05-23 21:40:56] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-23 21:40:56] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-23 21:40:56] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-23 21:40:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.134723s from rescued.omnipathdb.org (295.9 Kb/s); Redirect: 0s, DNS look up: 0.001104s, Connection: 0.022497s, Pretransfer: 0.069797s, First byte at: 0.113073s [2026-05-23 21:40:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:40:56 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 23 May 2026 20:40:56 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-05-23 21:40:56] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 23 May 2026 19:40:56 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 23 May 2026 20:40:56 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-05-23 21:40:56] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-05-23 21:40:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:56] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-05-23 21:40:56] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:40:56] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:56] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-23 21:40:56] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:40:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-23 21:40:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:40:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:40:56] [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] [2026-05-23 21:40:56] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-23 21:40:56] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.088717s from omabrowser.org (85.3 Kb/s); Redirect: 0s, DNS look up: 0.000575s, Connection: 0.006293s, Pretransfer: 0.039048s, First byte at: 0.088312s [2026-05-23 21:40:56] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 23 May 2026 19:40:56 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=GwrxVmrzttQs8wpbdBIAUdlsqqbUQ3d1qLdOnQz3p1zbnF5%2BNLGT3VQ%2FR5bWab4yV06n%2FA6AHtpN8lxlQQnidOvcZ2WDlbe3xoNLycc3VFLLJxnlk4SXmmFbBC3rV5cT0g%3D%3D"}]}; cf-ray: a00689077fe2bd24-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-23 21:40:57] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-23 21:40:57] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-05-23 21:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:57] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-05-23 21:40:57] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:40:57] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-23 21:40:57] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:40:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-23 21:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:40:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:40:57] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-05-23 21:40:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-23 21:40:57] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:40:57] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-23 21:41:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-23 21:41:20] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-05-23 21:41:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:20] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:20] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-05-23 21:41:20] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:20] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:41:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-05-23 21:41:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-05-23 21:41:21] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-05-23 21:41:21] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-05-23 21:41:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-05-23 21:41:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-05-23 21:41:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-05-23 21:41:21] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:21] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:21] [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] [2026-05-23 21:41:21] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:41:21] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.087231s from omnipathdb.org (180 Kb/s); Redirect: 0s, DNS look up: 0.001096s, Connection: 0.018843s, Pretransfer: 0.051866s, First byte at: 0.086893s [2026-05-23 21:41:21] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:41:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:41:21 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:41:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic` [2026-05-23 21:41:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:21] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2026-05-23 21:41:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`. [2026-05-23 21:41:21] [INFO] [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1] [2026-05-23 21:41:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:21] [INFO] [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:21] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records. [2026-05-23 21:41:21] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-23 21:41:21] [TRACE] [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`. [2026-05-23 21:41:21] [INFO] [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-05-23 21:41:21] [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`. [2026-05-23 21:41:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:21] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2026-05-23 21:41:21] [INFO] [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-05-23 21:41:21] [TRACE] [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt` [2026-05-23 21:41:21] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:21] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:21] [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] [2026-05-23 21:41:21] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-23 21:41:21] [TRACE] [OmnipathR] Downloaded 10.8 Kb in 0.059395s from static-content.springer.com (181.1 Kb/s); Redirect: 0s, DNS look up: 0.008542s, Connection: 0.015399s, Pretransfer: 0.047946s, First byte at: 0.059372s [2026-05-23 21:41:21] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; content-type: application/octet-stream; x-guploader-uploadid: AGQBYWxtdKnIv94FC4JqnQwVWO2HzPNiX2aL2czpMf09TMcKyAbkEILX_dKWWe7LQxHvgvj9; 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: 3624; date: Sat, 23 May 2026 19:41:21 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230045-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1779565282.694122,VS0,VE4; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972 [2026-05-23 21:41:21] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`. [2026-05-23 21:41:21] [INFO] [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1] [2026-05-23 21:41:21] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:21] [INFO] [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:21] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records [2026-05-23 21:41:21] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:41:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions] [2026-05-23 21:41:21] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:21] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:21] [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` [2026-05-23 21:41:21] [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` [2026-05-23 21:41:21] [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` [2026-05-23 21:41:21] [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` [2026-05-23 21:41:21] [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` [2026-05-23 21:41:22] [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` [2026-05-23 21:41:22] [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` [2026-05-23 21:41:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:22] [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] [2026-05-23 21:41:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:41:22] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.099329s from omnipathdb.org (158.1 Kb/s); Redirect: 0s, DNS look up: 0.001167s, Connection: 0.02208s, Pretransfer: 0.055697s, First byte at: 0.098225s [2026-05-23 21:41:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:41:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:41:22 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:41:22] [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` [2026-05-23 21:41:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:22] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:22] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:22] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2026-05-23 21:41:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`. [2026-05-23 21:41:23] [INFO] [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1] [2026-05-23 21:41:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:23] [INFO] [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:27] [SUCCESS] [OmnipathR] Downloaded 147217 interactions. [2026-05-23 21:41:27] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:41:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations] [2026-05-23 21:41:27] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:27] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:41:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:28] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-05-23 21:41:28] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-05-23 21:41:28] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-05-23 21:41:28] [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` [2026-05-23 21:41:28] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-05-23 21:41:28] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-05-23 21:41:28] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-05-23 21:41:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:28] [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] [2026-05-23 21:41:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:41:28] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.082154s from omnipathdb.org (191.1 Kb/s); Redirect: 0s, DNS look up: 0.000889s, Connection: 0.01699s, Pretransfer: 0.049776s, First byte at: 0.08182s [2026-05-23 21:41:28] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:41:28 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:41:28 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:41:29] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic` [2026-05-23 21:41:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:29] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2026-05-23 21:41:31] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`. [2026-05-23 21:41:31] [INFO] [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1] [2026-05-23 21:41:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:31] [INFO] [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:31] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records. [2026-05-23 21:41:31] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:31] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-05-23 21:41:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-05-23 21:41:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-05-23 21:41:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-05-23 21:41:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-05-23 21:41:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-05-23 21:41:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-05-23 21:41:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:31] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:41:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:41:32] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097202s from omnipathdb.org (161.5 Kb/s); Redirect: 0s, DNS look up: 0.000891s, Connection: 0.021622s, Pretransfer: 0.054565s, First byte at: 0.096229s [2026-05-23 21:41:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:41:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:41:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:41:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic` [2026-05-23 21:41:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:32] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2026-05-23 21:41:32] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`. [2026-05-23 21:41:32] [INFO] [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1] [2026-05-23 21:41:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:32] [INFO] [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:32] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records. [2026-05-23 21:41:32] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:32] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:32] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-05-23 21:41:32] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-05-23 21:41:32] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-05-23 21:41:32] [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` [2026-05-23 21:41:32] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-05-23 21:41:32] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-05-23 21:41:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-05-23 21:41:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:32] [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] [2026-05-23 21:41:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:41:32] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.118738s from omnipathdb.org (132.2 Kb/s); Redirect: 0s, DNS look up: 0.001056s, Connection: 0.023816s, Pretransfer: 0.07326s, First byte at: 0.118312s [2026-05-23 21:41:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:41:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:41:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:41:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-05-23 21:41:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:32] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:32] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-05-23 21:41:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-05-23 21:41:33] [INFO] [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1] [2026-05-23 21:41:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:33] [INFO] [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:33] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records. [2026-05-23 21:41:33] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:33] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-05-23 21:41:33] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-05-23 21:41:33] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-05-23 21:41:33] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-05-23 21:41:33] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-05-23 21:41:33] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-05-23 21:41:33] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-05-23 21:41:33] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:33] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:33] [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] [2026-05-23 21:41:33] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:41:33] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.103518s from omnipathdb.org (151.7 Kb/s); Redirect: 0s, DNS look up: 0.000983s, Connection: 0.020741s, Pretransfer: 0.063606s, First byte at: 0.103147s [2026-05-23 21:41:33] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:41:33 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:41:33 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:41:33] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic` [2026-05-23 21:41:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:33] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2026-05-23 21:41:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`. [2026-05-23 21:41:33] [INFO] [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1] [2026-05-23 21:41:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:33] [INFO] [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:33] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records. [2026-05-23 21:41:33] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:33] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-05-23 21:41:33] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-05-23 21:41:33] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-05-23 21:41:33] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-05-23 21:41:33] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:33] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-05-23 21:41:33] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-05-23 21:41:33] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-05-23 21:41:33] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-05-23 21:41:33] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-05-23 21:41:33] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-05-23 21:41:33] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-05-23 21:41:33] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:33] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:33] [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] [2026-05-23 21:41:34] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:41:34] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.096025s from omnipathdb.org (163.5 Kb/s); Redirect: 0s, DNS look up: 0.001048s, Connection: 0.021489s, Pretransfer: 0.054593s, First byte at: 0.095639s [2026-05-23 21:41:34] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:41:34 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:41:34 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:41:34] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic` [2026-05-23 21:41:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:34] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2026-05-23 21:41:34] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`. [2026-05-23 21:41:34] [INFO] [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1] [2026-05-23 21:41:34] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:34] [INFO] [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:34] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records. [2026-05-23 21:41:34] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:34] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:34] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-05-23 21:41:34] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-05-23 21:41:34] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-05-23 21:41:34] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-05-23 21:41:34] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:34] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:34] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-05-23 21:41:34] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-05-23 21:41:34] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-05-23 21:41:34] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-05-23 21:41:34] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-05-23 21:41:34] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-05-23 21:41:34] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-05-23 21:41:34] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:34] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:34] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:41:34] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:41:34] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.092392s from omnipathdb.org (169.9 Kb/s); Redirect: 0s, DNS look up: 0.00096s, Connection: 0.020272s, Pretransfer: 0.053204s, First byte at: 0.092039s [2026-05-23 21:41:34] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:41:34 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:41:34 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:41:35] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic` [2026-05-23 21:41:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:35] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2026-05-23 21:41:35] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`. [2026-05-23 21:41:35] [INFO] [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1] [2026-05-23 21:41:35] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:35] [INFO] [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:35] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records. [2026-05-23 21:41:35] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:35] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-05-23 21:41:35] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2026-05-23 21:41:35] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2026-05-23 21:41:35] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache. [2026-05-23 21:41:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:41:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein] [2026-05-23 21:41:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:41:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions] [2026-05-23 21:41:35] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:35] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:35] [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` [2026-05-23 21:41:35] [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` [2026-05-23 21:41:35] [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` [2026-05-23 21:41:35] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-05-23 21:41:35] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-05-23 21:41:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-05-23 21:41:35] [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` [2026-05-23 21:41:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:35] [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] [2026-05-23 21:41:35] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:41:35] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097617s from omnipathdb.org (160.8 Kb/s); Redirect: 0s, DNS look up: 0.001096s, Connection: 0.017452s, Pretransfer: 0.063222s, First byte at: 0.096813s [2026-05-23 21:41:35] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:41:35 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:41:35 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:41:36] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic` [2026-05-23 21:41:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:36] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2026-05-23 21:41:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`. [2026-05-23 21:41:36] [INFO] [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1] [2026-05-23 21:41:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:36] [INFO] [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:39] [SUCCESS] [OmnipathR] Downloaded 84507 interactions. [2026-05-23 21:41:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:41:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations] [2026-05-23 21:41:39] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:39] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:41:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-05-23 21:41:39] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-05-23 21:41:39] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-05-23 21:41:39] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-05-23 21:41:39] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-05-23 21:41:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-05-23 21:41:39] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-05-23 21:41:39] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:39] [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] [2026-05-23 21:41:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:41:39] [TRACE] [OmnipathR] Downloaded 11.4 Kb in 0.101193s from omnipathdb.org (112.9 Kb/s); Redirect: 0s, DNS look up: 0.000903s, Connection: 0.019633s, Pretransfer: 0.063698s, First byte at: 0.10095s [2026-05-23 21:41:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:41:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:41:39 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:41:39] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic` [2026-05-23 21:41:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:39] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:39] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2026-05-23 21:41:39] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`. [2026-05-23 21:41:39] [INFO] [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1] [2026-05-23 21:41:39] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:39] [INFO] [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:39] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records. [2026-05-23 21:41:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:41:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations] [2026-05-23 21:41:39] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:39] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:41:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-05-23 21:41:40] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-05-23 21:41:40] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-05-23 21:41:40] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-05-23 21:41:40] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-05-23 21:41:40] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-05-23 21:41:40] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-05-23 21:41:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:40] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:41:40] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:41:40] [TRACE] [OmnipathR] Downloaded 10.6 Kb in 0.095067s from omnipathdb.org (111.3 Kb/s); Redirect: 0s, DNS look up: 0.000955s, Connection: 0.021545s, Pretransfer: 0.054391s, First byte at: 0.094812s [2026-05-23 21:41:40] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:41:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:41:40 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:41:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic` [2026-05-23 21:41:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:40] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2026-05-23 21:41:40] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`. [2026-05-23 21:41:40] [INFO] [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1] [2026-05-23 21:41:40] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:40] [INFO] [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:40] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records. [2026-05-23 21:41:41] [TRACE] [OmnipathR] Bypassing call: `simplify_intercell_network(.)`. [2026-05-23 21:41:41] [TRACE] [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server. [2026-05-23 21:41:41] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:41:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions] [2026-05-23 21:41:41] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:41] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:41] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:41:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:41] [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` [2026-05-23 21:41:41] [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` [2026-05-23 21:41:41] [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` [2026-05-23 21:41:41] [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` [2026-05-23 21:41:41] [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` [2026-05-23 21:41:41] [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` [2026-05-23 21:41:41] [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` [2026-05-23 21:41:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:41:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:41:41] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.10058s from omnipathdb.org (156.1 Kb/s); Redirect: 0s, DNS look up: 0.000985s, Connection: 0.022414s, Pretransfer: 0.056649s, First byte at: 0.099697s [2026-05-23 21:41:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:41:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:41:41 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:41:42] [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` [2026-05-23 21:41:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:42] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2026-05-23 21:41:42] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`. [2026-05-23 21:41:42] [INFO] [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1] [2026-05-23 21:41:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:42] [INFO] [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:42] [SUCCESS] [OmnipathR] Downloaded 4242 interactions. [2026-05-23 21:41:42] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:41:42] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2026-05-23 21:41:42] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:42] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:42] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:41:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:42] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:41:42] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:41:42] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:41:42] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:41:42] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:41:42] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:41:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:41:42] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:42] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-23 21:41:42] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:41:42] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.10073s from omnipathdb.org (155.9 Kb/s); Redirect: 0s, DNS look up: 0.001076s, Connection: 0.02311s, Pretransfer: 0.056453s, First byte at: 0.100348s [2026-05-23 21:41:42] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:41:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:41:42 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:41:43] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:41:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:43] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:43] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-05-23 21:41:43] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-05-23 21:41:43] [INFO] [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1] [2026-05-23 21:41:43] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:43] [INFO] [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:43] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records. [2026-05-23 21:41:44] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:41:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2026-05-23 21:41:44] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:44] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:41:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:44] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-05-23 21:41:44] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-05-23 21:41:44] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-05-23 21:41:44] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-05-23 21:41:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-05-23 21:41:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-05-23 21:41:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-05-23 21:41:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-23 21:41:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-23 21:41:44] [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] [2026-05-23 21:41:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-23 21:41:44] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.108342s from omnipathdb.org (144.9 Kb/s); Redirect: 0s, DNS look up: 0.001082s, Connection: 0.020742s, Pretransfer: 0.069511s, First byte at: 0.107952s [2026-05-23 21:41:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 23 May 2026 19:41:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 23 May 2026 20:41:44 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-23 21:41:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-05-23 21:41:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:44] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`. [2026-05-23 21:41:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-05-23 21:41:44] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-05-23 21:41:44] [INFO] [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1] [2026-05-23 21:41:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-23 21:41:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:44] [INFO] [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`. [2026-05-23 21:41:44] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records. [2026-05-23 21:41:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:41:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations] [2026-05-23 21:41:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:50] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:41:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:41:50] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`. [2026-05-23 21:41:50] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic` [2026-05-23 21:41:50] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache. [2026-05-23 21:41:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-23 21:41:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations] [2026-05-23 21:41:51] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-23 21:41:51] [TRACE] [OmnipathR] Orthology targets: [2026-05-23 21:41:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-23 21:41:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-23 21:41:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-05-23 21:41:51] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`. [2026-05-23 21:41:51] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic` [2026-05-23 21:41:51] [SUCCESS] [OmnipathR] Loaded 2102 annotation records from cache. --- finished re-building ‘paths.Rmd’ SUMMARY: processing the following file failed: ‘cosmos.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-23_2105/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2026-05-23 21:42:00 CEST ]