[ Started: 2026-05-16 20:50:43 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-3.22/2026-05-16_2038/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 [2026-05-16 20:51:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 20:51:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 20:51:15] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-16 20:51:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-16 18:49:18 UTC; omnipath [2026-05-16 20:51:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-16 20:51:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-16 18:50:46 UTC; unix [2026-05-16 20:51:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-16 20:51:15] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-16 20:51:15] [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=2026-05-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-16 20:51:15] [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] [2026-05-16 20:51:15] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); 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(2026-05-16); 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 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.52.0(2026-05-10); 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) [2026-05-16 20:51:15] [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 [2026-05-16 20:51:15] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-16 20:51:15] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-16 20:51:15] [TRACE] [OmnipathR] Contains 1 files. [2026-05-16 20:51:15] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-16 20:51:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 20:51:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 20:51:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-16 20:51:15] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-16 20:51:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-16 20:51:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 20:51:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-16 20:51:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 20:51:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-16 20:51:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 20:51:15] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-16 20:51:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 20:51:15] [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 [2026-05-16 20:51:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 20:51:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 20:51:26] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-16 20:51:26] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-16 18:49:18 UTC; omnipath [2026-05-16 20:51:26] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-16 20:51:26] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-16 18:50:46 UTC; unix [2026-05-16 20:51:26] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-16 20:51:26] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-16 20:51:26] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-16 20:51:26] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-05-16 20:51:26] [INFO] [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.0(2026-04-21); 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(2026-05-16); 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 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.52.0(2026-05-10); 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) [2026-05-16 20:51:26] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-05-16 20:51:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-16 20:51:26] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-16 20:51:26] [TRACE] [OmnipathR] Contains 1 files. [2026-05-16 20:51:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-16 20:51:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 20:51:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 20:51:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-16 20:51:26] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-16 20:51:26] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-16 20:51:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 20:51:26] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-16 20:51:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 20:51:26] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-16 20:51:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 20:51:26] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-16 20:51:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 20:51:26] [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 69.160 0.024 69.304 curated_ligrec_stats 29.349 1.438 39.740 omnipath-interactions 22.338 1.016 26.359 filter_extra_attrs 18.916 3.244 22.441 all_uniprots 17.748 0.820 28.047 uniprot_organisms 15.241 0.754 16.164 nichenet_gr_network_omnipath 13.283 0.570 14.505 nichenet_signaling_network_omnipath 12.695 0.515 14.052 extra_attrs_to_cols 9.738 0.872 11.006 extra_attr_values 9.534 0.986 10.836 with_extra_attrs 9.091 1.051 10.508 go_annot_download 8.089 0.595 8.261 pivot_annotations 7.522 0.750 8.912 giant_component 7.247 0.386 7.996 omnipath_for_cosmos 6.867 0.357 23.946 filter_by_resource 6.079 0.294 6.859 has_extra_attrs 5.531 0.697 6.269 extra_attrs 5.135 0.615 5.823 translate_ids_multi 5.225 0.247 23.756 filter_intercell 4.920 0.443 5.296 curated_ligand_receptor_interactions 4.844 0.370 6.373 print_interactions 4.479 0.191 5.170 ensembl_id_mapping_table 1.496 0.203 20.241 kegg_conv 1.018 0.073 11.992 kinasephos 0.795 0.110 29.117 translate_ids 0.868 0.029 9.601 uniprot_full_id_mapping_table 0.731 0.028 11.525 kegg_link 0.557 0.044 5.669 * 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 [2026-05-16 21:01:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:01:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:01:27] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:01:27] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-16 18:49:18 UTC; omnipath [2026-05-16 21:01:27] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-16 21:01:27] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-16 18:50:46 UTC; unix [2026-05-16 21:01:27] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-16 21:01:27] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-16 21:01:27] [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=2026-05-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-16 21:01:27] [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] [2026-05-16 21:01:27] [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 4.8.0(2026-04-21); 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(2026-05-16); 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 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.52.0(2026-05-10); 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) [2026-05-16 21:01:27] [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 [2026-05-16 21:01:27] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-16 21:01:27] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:01:27] [TRACE] [OmnipathR] Contains 15 files. [2026-05-16 21:01:27] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-16 21:01:27] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:01:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:01:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:01:28] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-16 21:01:28] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-16 21:01:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:01:28] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-16 21:01:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:01:28] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-16 21:01:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:01:28] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-16 21:01:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:01:28] [TRACE] [OmnipathR] Cache locked: FALSE [2026-05-16 21:01:28] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:01:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions] [2026-05-16 21:01:28] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-05-16 21:01:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:01:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:01:28] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-05-16 21:01:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:01:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:01:28] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-05-16 21:01:28] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-05-16 21:01:28] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-16 21:01:28] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-16 21:01:28] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-16 21:01:28] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-05-16 21:01:28] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:01:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:01:28] [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] [2026-05-16 21:01:28] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:01:28] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-16 21:01:28] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-16 21:01:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:01:28] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.136347s from rescued.omnipathdb.org (292.3 Kb/s); Redirect: 0s, DNS look up: 0.001131s, Connection: 0.023118s, Pretransfer: 0.069565s, First byte at: 0.11416s [2026-05-16 21:01:28] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:01:28 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, 16 May 2026 20:01:28 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-05-16 21:01:28] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 16 May 2026 19:01:28 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, 16 May 2026 20:01:28 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-05-16 21:01:28] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-05-16 21:01:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:01:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:01:28] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-05-16 21:01:28] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:01:28] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-05-16 21:01:28] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:01:28] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-05-16 21:01:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:01:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:01:28] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:01:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:01:28] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-05-16 21:01:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-16 21:01:28] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:01:28] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:01:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:01:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:01:28] [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] [2026-05-16 21:01:28] [TRACE] [OmnipathR] HTTP v2 GET: status 503. [2026-05-16 21:01:28] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.076983s from omabrowser.org (0 bytes/s); Redirect: 0s, DNS look up: 0.000623s, Connection: 0.007682s, Pretransfer: 0.047735s, First byte at: 0.076948s [2026-05-16 21:01:28] [TRACE] [OmnipathR] HTTP headers: HTTP/2 503 ; date: Sat, 16 May 2026 19:01:28 GMT; content-type: text/html; charset=UTF-8; content-length: 7105; retry-after: 60; cache-control: private, max-age=0, no-store, no-cache, must-revalidate, post-check=0, pre-check=0; expires: Thu, 01 Jan 1970 00:00:01 GMT; referrer-policy: same-origin; x-frame-options: SAMEORIGIN; server: cloudflare; cf-ray: 9fcca1969cde9174-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:01:28] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 503 [2026-05-16 21:01:28] [WARN] [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 1/3); error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 503 [2026-05-16 21:01:33] [TRACE] [OmnipathR] Attempt 2/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:01:33] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:01:33] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:01:33] [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] [2026-05-16 21:01:33] [TRACE] [OmnipathR] HTTP v2 GET: status 503. [2026-05-16 21:01:33] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.062497s from omabrowser.org (0 bytes/s); Redirect: 0s, DNS look up: 0.000598s, Connection: 0.006212s, Pretransfer: 0.040966s, First byte at: 0.062482s [2026-05-16 21:01:33] [TRACE] [OmnipathR] HTTP headers: HTTP/2 503 ; date: Sat, 16 May 2026 19:01:33 GMT; content-type: text/html; charset=UTF-8; content-length: 7105; retry-after: 60; cache-control: private, max-age=0, no-store, no-cache, must-revalidate, post-check=0, pre-check=0; expires: Thu, 01 Jan 1970 00:00:01 GMT; referrer-policy: same-origin; x-frame-options: SAMEORIGIN; server: cloudflare; cf-ray: 9fcca1b6bf989290-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:01:33] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 503 [2026-05-16 21:01:33] [WARN] [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 2/3); error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 503 [2026-05-16 21:01:38] [TRACE] [OmnipathR] Attempt 3/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:01:38] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:01:38] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:01:38] [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] [2026-05-16 21:01:58] [TRACE] [OmnipathR] HTTP v2 GET: status 522. [2026-05-16 21:01:58] [TRACE] [OmnipathR] Downloaded 0 bytes in 19.783824s from omabrowser.org (0 bytes/s); Redirect: 0s, DNS look up: 0.001112s, Connection: 0.006606s, Pretransfer: 0.065379s, First byte at: 19.783787s [2026-05-16 21:01:58] [TRACE] [OmnipathR] HTTP headers: HTTP/2 522 ; date: Sat, 16 May 2026 19:01:58 GMT; content-type: text/html; charset=UTF-8; content-length: 7241; retry-after: 120; cache-control: private, max-age=0, no-store, no-cache, must-revalidate, post-check=0, pre-check=0; expires: Thu, 01 Jan 1970 00:00:01 GMT; referrer-policy: same-origin; x-frame-options: SAMEORIGIN; server: cloudflare; cf-ray: 9fcca1d6de553603-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:01:58] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:01:58] [ERROR] [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 3/3); error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:01:58] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-16 18:49:18 UTC; omnipath [2026-05-16 21:01:58] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-16 21:01:58] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-16 18:50:46 UTC; unix [2026-05-16 21:01:58] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-16 21:01:58] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-16 21:01:58] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-16 21:01:58] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-05-16 21:01:59] [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 4.8.0(2026-04-21); 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(2026-05-16); 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 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.52.0(2026-05-10); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); selectr 0.5-1(2025-12-17); 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); vroom 1.7.1(2026-03-31); 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) [2026-05-16 21:01:59] [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 Quitting from bioc_workshop.Rmd:215-218 [network] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `map_int()`: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error: ! Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 --- Backtrace: ▆ 1. ├─OmnipathR::transcriptional() 2. │ ├─rlang::exec(omnipath_query, !!!args) 3. │ └─OmnipathR (local) ``(...) 4. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 5. ├─OmnipathR:::omnipath_check_param(.) 6. │ └─param$organisms %<>% map_int(ncbi_taxid) 7. ├─purrr::map_int(., ncbi_taxid) 8. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 9. │ ├─purrr:::with_indexed_errors(...) 10. │ │ └─base::withCallingHandlers(...) 11. │ ├─purrr:::call_with_cleanup(...) 12. │ └─OmnipathR (local) .f(.x[[i]], ...) 13. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 14. ├─purrr::map_int(., taxon_name, "ncbi") 15. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 16. │ ├─purrr:::with_indexed_errors(...) 17. │ │ └─base::withCallingHandlers(...) 18. │ ├─purrr:::call_with_cleanup(...) 19. │ └─OmnipathR (local) .f(.x[[i]], ...) 20. │ ├─... %>% if_null_len0(NA) 21. │ └─OmnipathR::get_db("organisms") 22. │ └─OmnipathR::load_db(key, param = param) 23. │ ├─rlang::exec(loader, !!!param) 24. │ └─OmnipathR (local) ``() 25. │ └─... %>% ... 26. ├─OmnipathR:::if_null_len0(., NA) 27. │ └─value1 %>% is_empty_2 %>% if (value2) value1 28. ├─OmnipathR:::is_empty_2(.) 29. │ └─value %>% ... 30. ├─dplyr::pull(., name_type) 31. ├─dplyr::filter(...) 32. ├─dplyr::mutate(...) 33. ├─dplyr::full_join(...) 34. ├─dplyr::full_join(...) 35. ├─dplyr:::full_join.data.frame(...) 36. │ └─dplyr::auto_copy(x, y, copy = copy) 37. │ ├─dplyr::same_src(x, y) 38. │ └─dplyr:::same_src.data.frame(x, y) 39. │ └─base::is.data.frame(y) 40. ├─oma_organisms() %>% select(-genome_source, -oma_version) 41. ├─dplyr::select(., -genome_source, -oma_version) 42. ├─OmnipathR::oma_organisms() 43. │ └─"oma_species" %>% ... 44. ├─OmnipathR:::generic_downloader(...) 45. │ ├─... %>% omnipath_cache_save(url = url, post = post) 46. │ ├─rlang::exec(...) 47. │ └─OmnipathR (local) ``(...) 48. │ └─base::stop(result) 49. └─OmnipathR::omnipath_cache_save(., url = url, post = post) 50. └─base::saveRDS(data, target_path) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error: ! Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 --- failed re-building ‘bioc_workshop.Rmd’ --- re-building ‘cosmos.Rmd’ using rmarkdown [2026-05-16 21:02:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:01] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:02:01] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-16 18:49:18 UTC; omnipath [2026-05-16 21:02:01] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-16 21:02:01] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-16 18:50:46 UTC; unix [2026-05-16 21:02:01] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-16 21:02:01] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-16 21:02:01] [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=2026-05-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-16 21:02:01] [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] [2026-05-16 21:02:01] [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 4.8.0(2026-04-21); 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(2026-05-16); 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 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.52.0(2026-05-10); 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) [2026-05-16 21:02:01] [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 [2026-05-16 21:02:01] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-16 21:02:01] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:02:01] [TRACE] [OmnipathR] Contains 2 files. [2026-05-16 21:02:01] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-16 21:02:01] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:02:01] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-16 21:02:01] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-16 21:02:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:01] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-16 21:02:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:01] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-16 21:02:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:01] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-16 21:02:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:01] [TRACE] [OmnipathR] Cache locked: FALSE [2026-05-16 21:02:01] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_raw()`. [2026-05-16 21:02:01] [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. [2026-05-16 21:02:01] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem()`. [2026-05-16 21:02:01] [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. [2026-05-16 21:02:01] [TRACE] [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`. [2026-05-16 21:02:01] [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. [2026-05-16 21:02:02] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-05-16 21:02:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:02] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-05-16 21:02:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:02] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-05-16 21:02:02] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-05-16 21:02:02] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-16 21:02:02] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-16 21:02:02] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-16 21:02:02] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-05-16 21:02:02] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:02:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:02:02] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:02:02] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:02:02] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-16 21:02:02] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-16 21:02:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:02:02] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.128544s from rescued.omnipathdb.org (310.1 Kb/s); Redirect: 0s, DNS look up: 0.010282s, Connection: 0.030984s, Pretransfer: 0.065513s, First byte at: 0.107419s [2026-05-16 21:02:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:02:02 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, 16 May 2026 20:02:02 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-05-16 21:02:02] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 16 May 2026 19:02:02 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, 16 May 2026 20:02:02 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-05-16 21:02:02] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-05-16 21:02:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:02] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-05-16 21:02:02] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:02:02] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-05-16 21:02:02] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:02:02] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-05-16 21:02:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:02] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-05-16 21:02:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-16 21:02:02] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:02:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:02:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:02:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:02:02] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:02:02] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-16 21:02:02] [TRACE] [OmnipathR] Downloaded 12.6 Kb in 0.102314s from omabrowser.org (123.2 Kb/s); Redirect: 0s, DNS look up: 0.000582s, Connection: 0.0072s, Pretransfer: 0.040037s, First byte at: 0.101703s [2026-05-16 21:02:02] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 16 May 2026 19:02:02 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=zpEctjBCK0wqDpmSHztaYphWTxK5WkXQCZe0Ljg0%2BeNR%2BVyRH%2Fg6LvsJWYSJBL6zn3ZSr4DQfHGhPC0sN671DIl8XK1YZlJ1UBGOi%2F%2F5TCjwdcnhvq%2B6cS%2BGu7350IfPdg%3D%3D"}]}; cf-ray: 9fcca26aae4dd2c2-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:02:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-16 21:02:03] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-05-16 21:02:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:03] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-05-16 21:02:03] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:02:03] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-16 21:02:03] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:02:03] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-16 21:02:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:03] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-05-16 21:02:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-16 21:02:03] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:02:03] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:02:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-16 21:02:24] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-05-16 21:02:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:24] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-05-16 21:02:24] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-05-16 21:02:25] [INFO] [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human. [2026-05-16 21:02:25] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:02:25] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions] [2026-05-16 21:02:25] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:02:25] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:02:25] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:02:25] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:02:25] [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` [2026-05-16 21:02:25] [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` [2026-05-16 21:02:25] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:02:25] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:02:25] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:02:25] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:02:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:02:25] [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] [2026-05-16 21:02:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:02:25] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.124651s from omnipathdb.org (126 Kb/s); Redirect: 0s, DNS look up: 0.007659s, Connection: 0.028264s, Pretransfer: 0.083413s, First byte at: 0.124347s [2026-05-16 21:02:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:02:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:02:25 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:02:25] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:02:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:25] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-05-16 21:02:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-16 21:02:26] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-16 21:02:26] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-05-16 21:02:26] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:26] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-05-16 21:02:28] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-05-16 21:02:28] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2026-05-16 21:02:28] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2026-05-16 21:02:29] [TRACE] [OmnipathR] BioMart query: [2026-05-16 21:02:29] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:02:29] [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`. [2026-05-16 21:02:29] [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` [2026-05-16 21:02:29] [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`. [2026-05-16 21:02:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:29] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:29] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`. [2026-05-16 21:02:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-05-16 21:02:29] [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` [2026-05-16 21:02:29] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-16 21:02:29] [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` [2026-05-16 21:02:29] [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`. [2026-05-16 21:02:29] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:02:29] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:02:29] [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] [2026-05-16 21:02:29] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:02:29] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-16 21:02:48] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-16 21:02:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:02:48] [TRACE] [OmnipathR] Downloaded 2 Mb in 18.794164s from www.ensembl.org (108.9 Kb/s); Redirect: 0s, DNS look up: 0.001211s, Connection: 0.019449s, Pretransfer: 0.0195s, First byte at: 0.118635s [2026-05-16 21:02:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: Apache; Content-Type: text/plain; charset=utf-8; Content-Security-Policy: frame-ancestors 'self'; Date: Sat, 16 May 2026 19:02:29 GMT; Transfer-Encoding: chunked; Connection: Keep-Alive; X-Frame-Options: SAMEORIGIN [2026-05-16 21:02:48] [TRACE] [OmnipathR] Response headers: [Server=Apache,Content-Type=text/plain; charset=utf-8,Content-Security-Policy=frame-ancestors 'self',Date=Sat, 16 May 2026 19:02:29 GMT,Transfer-Encoding=chunked,Connection=Keep-Alive,X-Frame-Options=SAMEORIGIN] [2026-05-16 21:02:48] [TRACE] [OmnipathR] Calling reader callback on response. [2026-05-16 21:02:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-05-16 21:02:48] [INFO] [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1] [2026-05-16 21:02:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:48] [INFO] [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`. [2026-05-16 21:02:48] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 244093 records [2026-05-16 21:02:48] [TRACE] [OmnipathR] Translating complexes: 612 complexes in data. [2026-05-16 21:02:48] [TRACE] [OmnipathR] 451 complexes after removing the ones mapping to more than 1 items in target identifier space. [2026-05-16 21:02:50] [TRACE] [OmnipathR] Translated 451 complexes to 451. [2026-05-16 21:02:50] [TRACE] [OmnipathR] 71139 rows before translation, 4827 uniprot IDs in column `source`. [2026-05-16 21:02:50] [TRACE] [OmnipathR] 71220 rows after translation; translated 4827 `uniprot` IDs in column `source` to 4663 `genesymbol` IDs in column `genesymbol_source`. [2026-05-16 21:02:50] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart. [2026-05-16 21:02:50] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens [2026-05-16 21:02:50] [TRACE] [OmnipathR] BioMart query: [2026-05-16 21:02:50] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:02:50] [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`. [2026-05-16 21:02:50] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`. [2026-05-16 21:02:50] [SUCCESS] [OmnipathR] www.ensembl.org: loaded 244093 records from cache [2026-05-16 21:02:50] [TRACE] [OmnipathR] Translating complexes: 381 complexes in data. [2026-05-16 21:02:50] [TRACE] [OmnipathR] 229 complexes after removing the ones mapping to more than 1 items in target identifier space. [2026-05-16 21:02:51] [TRACE] [OmnipathR] Translated 229 complexes to 229. [2026-05-16 21:02:51] [TRACE] [OmnipathR] 71220 rows before translation, 5240 uniprot IDs in column `target`. [2026-05-16 21:02:51] [TRACE] [OmnipathR] 72796 rows after translation; translated 5240 `uniprot` IDs in column `target` to 5086 `genesymbol` IDs in column `genesymbol_target`. [2026-05-16 21:02:51] [INFO] [OmnipathR] OmniPath PPI for COSMOS PKN ready: 145749 interactions. --- finished re-building ‘cosmos.Rmd’ --- re-building ‘db_manager.Rmd’ using rmarkdown [2026-05-16 21:02:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:53] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:02:53] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-16 18:49:18 UTC; omnipath [2026-05-16 21:02:53] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-16 21:02:53] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-16 18:50:46 UTC; unix [2026-05-16 21:02:53] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-16 21:02:53] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-16 21:02:53] [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=2026-05-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-16 21:02:53] [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] [2026-05-16 21:02:54] [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 4.8.0(2026-04-21); 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(2026-05-16); 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 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.52.0(2026-05-10); 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) [2026-05-16 21:02:54] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-05-16 21:02:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Contains 6 files. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-16 21:02:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:54] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-16 21:02:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:54] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-16 21:02:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:54] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-16 21:02:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:54] [TRACE] [OmnipathR] Cache locked: FALSE [2026-05-16 21:02:54] [INFO] [OmnipathR] Loading database `UniProt-GeneSymbol table`. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE) [2026-05-16 21:02:54] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:54] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:54] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-05-16 21:02:54] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-16 21:02:54] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-16 21:02:54] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-05-16 21:02:54] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:02:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:02:54] [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] [2026-05-16 21:02:54] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:02:54] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-16 21:02:54] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-16 21:02:54] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.113976s from rescued.omnipathdb.org (349.7 Kb/s); Redirect: 0s, DNS look up: 0.001463s, Connection: 0.020617s, Pretransfer: 0.056784s, First byte at: 0.094932s [2026-05-16 21:02:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:02:54 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, 16 May 2026 20:02:54 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-05-16 21:02:54] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 16 May 2026 19:02:54 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, 16 May 2026 20:02:54 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-05-16 21:02:54] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-05-16 21:02:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:54] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-05-16 21:02:54] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:02:54] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:54] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:02:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:02:54] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-16 21:02:54] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:02:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:02:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:02:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:02:54] [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] [2026-05-16 21:02:54] [TRACE] [OmnipathR] HTTP v2 GET: status 503. [2026-05-16 21:02:54] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.06715s from omabrowser.org (0 bytes/s); Redirect: 0s, DNS look up: 0.000711s, Connection: 0.007284s, Pretransfer: 0.042541s, First byte at: 0.067134s [2026-05-16 21:02:54] [TRACE] [OmnipathR] HTTP headers: HTTP/2 503 ; date: Sat, 16 May 2026 19:02:54 GMT; content-type: text/html; charset=UTF-8; content-length: 7105; retry-after: 60; cache-control: private, max-age=0, no-store, no-cache, must-revalidate, post-check=0, pre-check=0; expires: Thu, 01 Jan 1970 00:00:01 GMT; referrer-policy: same-origin; x-frame-options: SAMEORIGIN; server: cloudflare; cf-ray: 9fcca3b0ce4137c8-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:02:54] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 503 [2026-05-16 21:02:54] [WARN] [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 1/3); error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 503 [2026-05-16 21:02:59] [TRACE] [OmnipathR] Attempt 2/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:02:59] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:02:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:02:59] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:02:59] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-16 21:02:59] [TRACE] [OmnipathR] Downloaded 12.6 Kb in 0.07064s from omabrowser.org (178.5 Kb/s); Redirect: 0s, DNS look up: 0.000623s, Connection: 0.009137s, Pretransfer: 0.044281s, First byte at: 0.070383s [2026-05-16 21:02:59] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 16 May 2026 19:02:59 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=AsCUId2%2BBGWUAr1CydOeLBcddoJI5E4MZ2SpQ55cPABEgGpg4%2FRr3xkWhdsH0kVw2oFJoSSKqe9O%2FtAJMw04ZubMLMe4rKZMn5tMpR0yveOhANrvgaL002v6DVcsUyG%2Fyw%3D%3D"}]}; cf-ray: 9fcca3d0cca53eba-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:03:00] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-16 21:03:00] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-05-16 21:03:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:03:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:00] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-05-16 21:03:00] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:03:00] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-16 21:03:00] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:03:00] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-16 21:03:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:03:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:00] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:03:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:00] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-05-16 21:03:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-16 21:03:00] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:03:00] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:03:24] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-16 21:03:24] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-05-16 21:03:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:03:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:24] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-05-16 21:03:24] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-05-16 21:03:24] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary [2026-05-16 21:03:24] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:03:24] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2026-05-16 21:03:24] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-05-16 21:03:24] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`. [2026-05-16 21:03:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:03:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:03:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:24] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`. [2026-05-16 21:03:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-05-16 21:03:24] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-05-16 21:03:24] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true` [2026-05-16 21:03:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:03:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:03:24] [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] [2026-05-16 21:03:25] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-16 21:03:25] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.342789s from rest.uniprot.org (125 bytes/s); Redirect: 0s, DNS look up: 0.007754s, Connection: 0.026343s, Pretransfer: 0.079639s, First byte at: 0.342673s [2026-05-16 21:03:25] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 30-April-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 16 May 2026 19:03:25 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 [2026-05-16 21:03:33] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`. [2026-05-16 21:03:33] [INFO] [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1] [2026-05-16 21:03:33] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:03:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:33] [INFO] [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`. [2026-05-16 21:03:33] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records [2026-05-16 21:03:33] [INFO] [OmnipathR] Loaded database `UniProt-GeneSymbol table`. --- finished re-building ‘db_manager.Rmd’ --- re-building ‘drug_targets.Rmd’ using rmarkdown [2026-05-16 21:03:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:03:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:46] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:03:46] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-16 18:49:18 UTC; omnipath [2026-05-16 21:03:46] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-16 21:03:46] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-16 18:50:46 UTC; unix [2026-05-16 21:03:46] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-16 21:03:46] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-16 21:03:46] [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=2026-05-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-16 21:03:46] [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] [2026-05-16 21:03:46] [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 4.8.0(2026-04-21); 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(2026-05-16); 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 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.52.0(2026-05-10); 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) [2026-05-16 21:03:46] [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 [2026-05-16 21:03:46] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-16 21:03:46] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:03:46] [TRACE] [OmnipathR] Contains 5 files. [2026-05-16 21:03:46] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-16 21:03:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:03:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:03:46] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-16 21:03:46] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-16 21:03:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:46] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-16 21:03:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:46] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-16 21:03:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:46] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-16 21:03:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:46] [TRACE] [OmnipathR] Cache locked: FALSE [2026-05-16 21:03:47] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:03:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-05-16 21:03:47] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:03:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-05-16 21:03:47] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-05-16 21:03:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:03:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:47] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-05-16 21:03:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:03:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:47] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-05-16 21:03:47] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-05-16 21:03:47] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-16 21:03:47] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-16 21:03:47] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-16 21:03:47] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-05-16 21:03:47] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:03:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:03:47] [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] [2026-05-16 21:03:47] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:03:47] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-16 21:03:47] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-16 21:03:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:03:47] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.118469s from rescued.omnipathdb.org (336.5 Kb/s); Redirect: 0s, DNS look up: 0.001256s, Connection: 0.019507s, Pretransfer: 0.064179s, First byte at: 0.100318s [2026-05-16 21:03:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:03:47 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, 16 May 2026 20:03:47 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-05-16 21:03:47] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 16 May 2026 19:03:47 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, 16 May 2026 20:03:47 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-05-16 21:03:47] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-05-16 21:03:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:03:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:47] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-05-16 21:03:47] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:03:47] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-05-16 21:03:47] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:03:47] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-05-16 21:03:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:03:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:03:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:03:47] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-05-16 21:03:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-16 21:03:47] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:03:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:03:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:03:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:03:47] [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] [2026-05-16 21:04:07] [TRACE] [OmnipathR] HTTP v2 GET: status 522. [2026-05-16 21:04:07] [TRACE] [OmnipathR] Downloaded 0 bytes in 19.446135s from omabrowser.org (0 bytes/s); Redirect: 0s, DNS look up: 0.000572s, Connection: 0.005052s, Pretransfer: 0.038373s, First byte at: 19.446099s [2026-05-16 21:04:07] [TRACE] [OmnipathR] HTTP headers: HTTP/2 522 ; date: Sat, 16 May 2026 19:04:07 GMT; content-type: text/html; charset=UTF-8; content-length: 7241; retry-after: 120; cache-control: private, max-age=0, no-store, no-cache, must-revalidate, post-check=0, pre-check=0; expires: Thu, 01 Jan 1970 00:00:01 GMT; referrer-policy: same-origin; x-frame-options: SAMEORIGIN; server: cloudflare; cf-ray: 9fcca4fc095403f0-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:04:07] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:04:07] [WARN] [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 1/3); error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:04:12] [TRACE] [OmnipathR] Attempt 2/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:04:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:04:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:04:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:04:12] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-16 21:04:12] [TRACE] [OmnipathR] Downloaded 11.3 Kb in 0.099424s from omabrowser.org (114.1 Kb/s); Redirect: 0s, DNS look up: 0.000863s, Connection: 0.007098s, Pretransfer: 0.050303s, First byte at: 0.098701s [2026-05-16 21:04:12] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 16 May 2026 19:04:12 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=YiHn1UuTIKQEprtKWmSIs2KdgASWzIKqVyxNNm1%2BP%2BXcV94U3iYEYrVsdCf%2Ff3xHArlAbfNb%2FznA%2BHH1Wt%2FgKOmvnJ7eCBj9wUPwsZjIx7tyaNyf22vY0Cbsf89aETCxpw%3D%3D"}]}; cf-ray: 9fcca5959ff0d36a-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:04:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-16 21:04:12] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-05-16 21:04:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:04:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:12] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-05-16 21:04:12] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:04:12] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-16 21:04:12] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:04:12] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-16 21:04:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:04:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:04:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:12] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-05-16 21:04:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-16 21:04:12] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:04:12] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:04:36] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-16 21:04:36] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-05-16 21:04:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:04:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:36] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-05-16 21:04:37] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-05-16 21:04:37] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:04:37] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:04:37] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:04:37] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:04:37] [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` [2026-05-16 21:04:37] [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` [2026-05-16 21:04:37] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:04:37] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:04:37] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:04:37] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:04:37] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:04:37] [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] [2026-05-16 21:04:37] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:04:37] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.090677s from omnipathdb.org (173.1 Kb/s); Redirect: 0s, DNS look up: 0.001046s, Connection: 0.019359s, Pretransfer: 0.053983s, First byte at: 0.090368s [2026-05-16 21:04:37] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:04:37 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:04:37 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:04:37] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:04:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:04:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:37] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:04:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:37] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-05-16 21:04:37] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-16 21:04:38] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-16 21:04:38] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-05-16 21:04:38] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:04:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:38] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-05-16 21:04:40] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. --- finished re-building ‘drug_targets.Rmd’ --- re-building ‘extra_attrs.Rmd’ using rmarkdown [2026-05-16 21:04:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:04:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:44] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:04:44] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-16 18:49:18 UTC; omnipath [2026-05-16 21:04:44] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-16 21:04:44] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-16 18:50:46 UTC; unix [2026-05-16 21:04:44] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-16 21:04:44] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-16 21:04:44] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-16 21:04:44] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-05-16 21:04:44] [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 4.8.0(2026-04-21); 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(2026-05-16); 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 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.52.0(2026-05-10); 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) [2026-05-16 21:04:44] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-05-16 21:04:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-16 21:04:44] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:04:44] [TRACE] [OmnipathR] Contains 5 files. [2026-05-16 21:04:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-16 21:04:44] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:04:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:04:44] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-16 21:04:44] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-16 21:04:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:44] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-16 21:04:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:44] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-16 21:04:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:44] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-16 21:04:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:44] [TRACE] [OmnipathR] Cache locked: FALSE [2026-05-16 21:04:45] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:04:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions] [2026-05-16 21:04:45] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-05-16 21:04:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:45] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-05-16 21:04:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:45] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-05-16 21:04:45] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-05-16 21:04:45] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-16 21:04:45] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-16 21:04:45] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-16 21:04:45] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-05-16 21:04:45] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:04:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:04:45] [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] [2026-05-16 21:04:45] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:04:45] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-16 21:04:45] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-16 21:04:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:04:45] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.121339s from rescued.omnipathdb.org (328.5 Kb/s); Redirect: 0s, DNS look up: 0.001249s, Connection: 0.022553s, Pretransfer: 0.056871s, First byte at: 0.099926s [2026-05-16 21:04:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:04:45 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, 16 May 2026 20:04:45 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-05-16 21:04:45] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 16 May 2026 19:04:45 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, 16 May 2026 20:04:45 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-05-16 21:04:45] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-05-16 21:04:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:45] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-05-16 21:04:45] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:04:45] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-05-16 21:04:45] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:04:45] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-05-16 21:04:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:04:45] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-05-16 21:04:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-16 21:04:45] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:04:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:04:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:04:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:04:45] [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] [2026-05-16 21:05:04] [TRACE] [OmnipathR] HTTP v2 GET: status 522. [2026-05-16 21:05:04] [TRACE] [OmnipathR] Downloaded 0 bytes in 19.363087s from omabrowser.org (0 bytes/s); Redirect: 0s, DNS look up: 0.000591s, Connection: 0.005349s, Pretransfer: 0.045644s, First byte at: 19.363055s [2026-05-16 21:05:04] [TRACE] [OmnipathR] HTTP headers: HTTP/2 522 ; date: Sat, 16 May 2026 19:05:04 GMT; content-type: text/html; charset=UTF-8; content-length: 7241; retry-after: 120; cache-control: private, max-age=0, no-store, no-cache, must-revalidate, post-check=0, pre-check=0; expires: Thu, 01 Jan 1970 00:00:01 GMT; referrer-policy: same-origin; x-frame-options: SAMEORIGIN; server: cloudflare; cf-ray: 9fcca6652fac37f2-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:05:04] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:05:04] [WARN] [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 1/3); error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:05:09] [TRACE] [OmnipathR] Attempt 2/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:05:09] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:05:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:05:10] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:05:54] [TRACE] [OmnipathR] HTTP v2 GET: status 522. [2026-05-16 21:05:54] [TRACE] [OmnipathR] Downloaded 0 bytes in 44.306738s from omabrowser.org (0 bytes/s); Redirect: 0s, DNS look up: 0.000635s, Connection: 0.005169s, Pretransfer: 0.039032s, First byte at: 44.306702s [2026-05-16 21:05:54] [TRACE] [OmnipathR] HTTP headers: HTTP/2 522 ; date: Sat, 16 May 2026 19:05:54 GMT; content-type: text/html; charset=UTF-8; content-length: 7241; retry-after: 120; cache-control: private, max-age=0, no-store, no-cache, must-revalidate, post-check=0, pre-check=0; expires: Thu, 01 Jan 1970 00:00:01 GMT; referrer-policy: same-origin; x-frame-options: SAMEORIGIN; server: cloudflare; cf-ray: 9fcca6fddefc9f25-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:05:54] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:05:54] [WARN] [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 2/3); error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:05:59] [TRACE] [OmnipathR] Attempt 3/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:05:59] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:05:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:05:59] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:05:59] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-16 21:05:59] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.12832s from omabrowser.org (58.9 Kb/s); Redirect: 0s, DNS look up: 0.02668s, Connection: 0.03486s, Pretransfer: 0.093518s, First byte at: 0.127856s [2026-05-16 21:05:59] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 16 May 2026 19:05:59 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=6RRHKQ8rgdUlTEQj7MTRLxo%2B4VB2HASpxFRJJNp0W%2FCrIp8KYEyyOriHHmupiltcL3NaR9dU3liRSpJO6L1a00Qj%2B%2BCr2Dvg3XBKOrKhYJbzh3MRhL2ZfVETLxhwYvfrxw%3D%3D"}]}; cf-ray: 9fcca832fd2be570-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:05:59] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-16 21:05:59] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-05-16 21:05:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:05:59] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-05-16 21:05:59] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:05:59] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-16 21:05:59] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:05:59] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-16 21:05:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:05:59] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:05:59] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-05-16 21:05:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-16 21:05:59] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:05:59] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:06:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-16 21:06:23] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-05-16 21:06:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:06:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:06:23] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-05-16 21:06:23] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-05-16 21:06:23] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:06:23] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:06:23] [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` [2026-05-16 21:06:23] [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` [2026-05-16 21:06:23] [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` [2026-05-16 21:06:23] [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` [2026-05-16 21:06:23] [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` [2026-05-16 21:06:23] [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` [2026-05-16 21:06:23] [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` [2026-05-16 21:06:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:06:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:06:23] [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] [2026-05-16 21:06:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:06:23] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.120456s from omnipathdb.org (130.3 Kb/s); Redirect: 0s, DNS look up: 0.000803s, Connection: 0.021104s, Pretransfer: 0.079871s, First byte at: 0.120088s [2026-05-16 21:06:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:06:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:06:23 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:06:24] [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` [2026-05-16 21:06:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:06:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:06:24] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`. [2026-05-16 21:06:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-05-16 21:06:25] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`. [2026-05-16 21:06:25] [INFO] [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1] [2026-05-16 21:06:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:06:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:06:25] [INFO] [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`. [2026-05-16 21:06:25] [TRACE] [OmnipathR] Converting JSON column `extra_attrs` to list. [2026-05-16 21:06:34] [SUCCESS] [OmnipathR] Downloaded 139054 interactions. [2026-05-16 21:12:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:12:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations] [2026-05-16 21:12:50] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:12:50] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:12:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:12:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:50] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-16 21:12:50] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-16 21:12:50] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-16 21:12:50] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-16 21:12:50] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-16 21:12:50] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-16 21:12:50] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-16 21:12:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:12:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:12:50] [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] [2026-05-16 21:12:51] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:12:51] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.119963s from omnipathdb.org (130.9 Kb/s); Redirect: 0s, DNS look up: 0.000966s, Connection: 0.021482s, Pretransfer: 0.078767s, First byte at: 0.119562s [2026-05-16 21:12:51] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:12:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:12:51 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:12:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic` [2026-05-16 21:12:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:12:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:12:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:51] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`. [2026-05-16 21:12:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-05-16 21:12:52] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`. [2026-05-16 21:12:52] [INFO] [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1] [2026-05-16 21:12:52] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:12:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:52] [INFO] [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`. [2026-05-16 21:12:52] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records. [2026-05-16 21:12:52] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:12:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub] [2026-05-16 21:12:52] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:12:52] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:12:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-05-16 21:12:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-05-16 21:12:52] [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` [2026-05-16 21:12:52] [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` [2026-05-16 21:12:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-05-16 21:12:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-05-16 21:12:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-05-16 21:12:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:12:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:12:52] [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] [2026-05-16 21:12:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:12:52] [TRACE] [OmnipathR] Downloaded 1.3 Kb in 0.076427s from omnipathdb.org (16.5 Kb/s); Redirect: 0s, DNS look up: 0.001087s, Connection: 0.021883s, Pretransfer: 0.055339s, First byte at: 0.07638s [2026-05-16 21:12:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:12:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:12:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:12:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination` [2026-05-16 21:12:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:12:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:12:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:53] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`. [2026-05-16 21:12:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-05-16 21:12:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`. [2026-05-16 21:12:53] [INFO] [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1] [2026-05-16 21:12:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:12:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:53] [INFO] [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`. [2026-05-16 21:12:53] [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 [2026-05-16 21:12:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:12:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:56] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:12:56] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-16 18:49:18 UTC; omnipath [2026-05-16 21:12:56] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-16 21:12:56] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-16 18:50:46 UTC; unix [2026-05-16 21:12:56] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-16 21:12:56] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-16 21:12:56] [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=2026-05-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-16 21:12:56] [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] [2026-05-16 21:12:56] [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 4.8.0(2026-04-21); 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(2026-05-16); 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 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.52.0(2026-05-10); 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) [2026-05-16 21:12:56] [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 [2026-05-16 21:12:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-16 21:12:56] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:12:56] [TRACE] [OmnipathR] Contains 7 files. [2026-05-16 21:12:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-16 21:12:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:12:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:12:56] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-16 21:12:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-16 21:12:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-16 21:12:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-16 21:12:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-16 21:12:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:56] [TRACE] [OmnipathR] Cache locked: FALSE [2026-05-16 21:12:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:12:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath] [2026-05-16 21:12:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:12:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions] [2026-05-16 21:12:57] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-05-16 21:12:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:57] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-05-16 21:12:57] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:12:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:57] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-05-16 21:12:57] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-05-16 21:12:57] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-16 21:12:57] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-16 21:12:57] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-16 21:12:57] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-05-16 21:12:57] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:12:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:12:57] [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] [2026-05-16 21:12:57] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:12:57] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-16 21:12:57] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-16 21:12:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:12:57] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.136368s from rescued.omnipathdb.org (292.3 Kb/s); Redirect: 0s, DNS look up: 0.009037s, Connection: 0.028811s, Pretransfer: 0.076694s, First byte at: 0.116679s [2026-05-16 21:12:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:12:57 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, 16 May 2026 20:12:57 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-05-16 21:12:57] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 16 May 2026 19:12:57 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, 16 May 2026 20:12:57 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-05-16 21:12:58] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-05-16 21:12:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:12:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:58] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-05-16 21:12:58] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:12:58] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-05-16 21:12:58] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:12:58] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-05-16 21:12:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:12:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:12:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:12:58] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-05-16 21:12:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-16 21:12:58] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:12:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:12:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:12:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:12:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:13:17] [TRACE] [OmnipathR] HTTP v2 GET: status 522. [2026-05-16 21:13:17] [TRACE] [OmnipathR] Downloaded 0 bytes in 19.318331s from omabrowser.org (0 bytes/s); Redirect: 0s, DNS look up: 0.00639s, Connection: 0.012506s, Pretransfer: 0.046368s, First byte at: 19.318295s [2026-05-16 21:13:17] [TRACE] [OmnipathR] HTTP headers: HTTP/2 522 ; date: Sat, 16 May 2026 19:13:17 GMT; content-type: text/html; charset=UTF-8; content-length: 7241; retry-after: 120; cache-control: private, max-age=0, no-store, no-cache, must-revalidate, post-check=0, pre-check=0; expires: Thu, 01 Jan 1970 00:00:01 GMT; referrer-policy: same-origin; x-frame-options: SAMEORIGIN; server: cloudflare; cf-ray: 9fccb26cf9e5a592-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:13:17] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:13:17] [WARN] [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 1/3); error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:13:22] [TRACE] [OmnipathR] Attempt 2/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:13:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:13:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:13:22] [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] [2026-05-16 21:13:22] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2026-05-16 21:13:22] [TRACE] [OmnipathR] Downloaded 11.3 Kb in 0.098017s from omabrowser.org (115.8 Kb/s); Redirect: 0s, DNS look up: 0.000853s, Connection: 0.005792s, Pretransfer: 0.051134s, First byte at: 0.097755s [2026-05-16 21:13:22] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 16 May 2026 19:13:22 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; 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=Rju8BqzGY%2BkPoBuvA87OyoxTJfvc9MH8hmz5RVSHEVoYwVRe3QJYuwHP2rEtNYhtH0IJTeRtStRUsVSQchWJlaLWgTulh9dr7lgdJ2gFwFrPAvJyVd3zO1B%2FVXjWNk1h1A%3D%3D"}]}; vary: accept-encoding; cf-cache-status: DYNAMIC; cf-ray: 9fccb305af3d9750-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:13:23] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-16 21:13:23] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2026-05-16 21:13:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:23] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2026-05-16 21:13:23] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:13:23] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-16 21:13:23] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:13:23] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2026-05-16 21:13:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:23] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2026-05-16 21:13:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-16 21:13:23] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:13:23] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2026-05-16 21:13:47] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2026-05-16 21:13:47] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2026-05-16 21:13:47] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:47] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2026-05-16 21:13:47] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2026-05-16 21:13:47] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:13:47] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:13:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:13:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:47] [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` [2026-05-16 21:13:47] [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` [2026-05-16 21:13:47] [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` [2026-05-16 21:13:47] [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` [2026-05-16 21:13:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:13:47] [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` [2026-05-16 21:13:47] [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` [2026-05-16 21:13:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:13:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:13:47] [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] [2026-05-16 21:13:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:13:47] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.106746s from omnipathdb.org (147.1 Kb/s); Redirect: 0s, DNS look up: 0.001071s, Connection: 0.021781s, Pretransfer: 0.068158s, First byte at: 0.10643s [2026-05-16 21:13:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:13:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:13:47 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:13:48] [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` [2026-05-16 21:13:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:48] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`. [2026-05-16 21:13:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-05-16 21:13:48] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`. [2026-05-16 21:13:48] [INFO] [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1] [2026-05-16 21:13:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:48] [INFO] [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`. [2026-05-16 21:13:50] [SUCCESS] [OmnipathR] Downloaded 67773 interactions. [2026-05-16 21:13:52] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:13:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra] [2026-05-16 21:13:52] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:13:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions] [2026-05-16 21:13:52] [TRACE] [OmnipathR] Organism(s): 10090 [2026-05-16 21:13:52] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:13:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:13:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:52] [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` [2026-05-16 21:13:52] [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` [2026-05-16 21:13:52] [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` [2026-05-16 21:13:52] [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` [2026-05-16 21:13:52] [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` [2026-05-16 21:13:52] [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` [2026-05-16 21:13:52] [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` [2026-05-16 21:13:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:13:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:13:52] [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] [2026-05-16 21:13:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:13:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.083992s from omnipathdb.org (186.9 Kb/s); Redirect: 0s, DNS look up: 0.000978s, Connection: 0.017188s, Pretransfer: 0.050973s, First byte at: 0.083674s [2026-05-16 21:13:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:13:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:13:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:13:53] [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` [2026-05-16 21:13:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:53] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`. [2026-05-16 21:13:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-05-16 21:13:53] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`. [2026-05-16 21:13:53] [INFO] [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1] [2026-05-16 21:13:53] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:53] [INFO] [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`. [2026-05-16 21:13:54] [SUCCESS] [OmnipathR] Downloaded 41476 interactions. [2026-05-16 21:13:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:13:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra] [2026-05-16 21:13:54] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:13:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions] [2026-05-16 21:13:54] [TRACE] [OmnipathR] Organism(s): 10116 [2026-05-16 21:13:54] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:13:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:13:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:55] [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` [2026-05-16 21:13:55] [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` [2026-05-16 21:13:55] [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` [2026-05-16 21:13:55] [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` [2026-05-16 21:13:55] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:13:55] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:13:55] [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` [2026-05-16 21:13:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:13:55] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:13:55] [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] [2026-05-16 21:13:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:13:55] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095165s from omnipathdb.org (165 Kb/s); Redirect: 0s, DNS look up: 0.000991s, Connection: 0.020514s, Pretransfer: 0.054481s, First byte at: 0.094183s [2026-05-16 21:13:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:13:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:13:55 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:13:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:13:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:55] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`. [2026-05-16 21:13:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-05-16 21:13:55] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`. [2026-05-16 21:13:55] [INFO] [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1] [2026-05-16 21:13:55] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:55] [INFO] [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`. [2026-05-16 21:13:56] [SUCCESS] [OmnipathR] Downloaded 11083 interactions. [2026-05-16 21:13:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:13:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra] [2026-05-16 21:13:56] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:13:56] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions] [2026-05-16 21:13:56] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:13:56] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:13:56] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:13:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:56] [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` [2026-05-16 21:13:56] [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` [2026-05-16 21:13:56] [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` [2026-05-16 21:13:56] [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` [2026-05-16 21:13:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:13:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:13:56] [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` [2026-05-16 21:13:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:13:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:13:56] [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] [2026-05-16 21:13:56] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:13:56] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.109773s from omnipathdb.org (143 Kb/s); Redirect: 0s, DNS look up: 0.001084s, Connection: 0.020641s, Pretransfer: 0.069682s, First byte at: 0.108951s [2026-05-16 21:13:56] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:13:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:13:56 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:13:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:13:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:56] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`. [2026-05-16 21:13:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-05-16 21:13:56] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`. [2026-05-16 21:13:56] [INFO] [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1] [2026-05-16 21:13:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:56] [INFO] [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`. [2026-05-16 21:13:57] [SUCCESS] [OmnipathR] Downloaded 2840 interactions. [2026-05-16 21:13:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:13:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-05-16 21:13:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:13:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-05-16 21:13:57] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:13:57] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:13:57] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:13:57] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:13:57] [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` [2026-05-16 21:13:57] [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` [2026-05-16 21:13:57] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:13:57] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:13:57] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:13:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:13:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:13:57] [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] [2026-05-16 21:13:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:13:57] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097177s from omnipathdb.org (161.6 Kb/s); Redirect: 0s, DNS look up: 0.001045s, Connection: 0.02139s, Pretransfer: 0.056243s, First byte at: 0.096824s [2026-05-16 21:13:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:13:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:13:57 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:13:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:13:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:58] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`. [2026-05-16 21:13:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-16 21:13:58] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-16 21:13:58] [INFO] [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1] [2026-05-16 21:13:58] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:13:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:13:58] [INFO] [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`. [2026-05-16 21:14:01] [SUCCESS] [OmnipathR] Downloaded 85217 interactions. [2026-05-16 21:14:02] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:14:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea] [2026-05-16 21:14:02] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:14:02] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:14:02] [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` [2026-05-16 21:14:02] [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` [2026-05-16 21:14:02] [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` [2026-05-16 21:14:02] [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` [2026-05-16 21:14:02] [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` [2026-05-16 21:14:02] [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` [2026-05-16 21:14:02] [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` [2026-05-16 21:14:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:14:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:02] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:14:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:14:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.085384s from omnipathdb.org (183.9 Kb/s); Redirect: 0s, DNS look up: 0.001069s, Connection: 0.017604s, Pretransfer: 0.051649s, First byte at: 0.085099s [2026-05-16 21:14:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:14:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:14:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:14:02] [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` [2026-05-16 21:14:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:02] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`. [2026-05-16 21:14:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-05-16 21:14:02] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`. [2026-05-16 21:14:02] [INFO] [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1] [2026-05-16 21:14:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:02] [INFO] [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`. [2026-05-16 21:14:03] [SUCCESS] [OmnipathR] Downloaded 6128 interactions. [2026-05-16 21:14:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:14:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget] [2026-05-16 21:14:03] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:14:03] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:14:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:14:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:03] [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` [2026-05-16 21:14:03] [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` [2026-05-16 21:14:03] [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` [2026-05-16 21:14:03] [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` [2026-05-16 21:14:03] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:03] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:03] [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` [2026-05-16 21:14:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:14:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:03] [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] [2026-05-16 21:14:03] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:14:03] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.09803s from omnipathdb.org (160.2 Kb/s); Redirect: 0s, DNS look up: 0.001019s, Connection: 0.021747s, Pretransfer: 0.056042s, First byte at: 0.097699s [2026-05-16 21:14:03] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:14:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:14:03 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:14:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:03] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`. [2026-05-16 21:14:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-05-16 21:14:03] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`. [2026-05-16 21:14:03] [INFO] [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1] [2026-05-16 21:14:03] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:03] [INFO] [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`. [2026-05-16 21:14:03] [SUCCESS] [OmnipathR] Downloaded 648 interactions. [2026-05-16 21:14:03] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:14:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule] [2026-05-16 21:14:04] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:14:04] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:14:04] [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` [2026-05-16 21:14:04] [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` [2026-05-16 21:14:04] [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` [2026-05-16 21:14:04] [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` [2026-05-16 21:14:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-05-16 21:14:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-05-16 21:14:04] [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` [2026-05-16 21:14:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:14:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:04] [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] [2026-05-16 21:14:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:14:04] [TRACE] [OmnipathR] Downloaded 112 bytes in 0.072882s from omnipathdb.org (1.5 Kb/s); Redirect: 0s, DNS look up: 0.001074s, Connection: 0.019558s, Pretransfer: 0.054256s, First byte at: 0.072851s [2026-05-16 21:14:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:14:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:14:04 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:14:04] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic` [2026-05-16 21:14:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:04] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`. [2026-05-16 21:14:04] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-05-16 21:14:04] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`. [2026-05-16 21:14:04] [INFO] [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1] [2026-05-16 21:14:04] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:04] [INFO] [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`. [2026-05-16 21:14:04] [SUCCESS] [OmnipathR] Downloaded 0 interactions. [2026-05-16 21:14:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:14:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:14:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=enzsub] [2026-05-16 21:14:04] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:14:04] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:14:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:14:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:04] [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] [2026-05-16 21:14:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:14:04] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.095107s from omnipathdb.org (165.1 Kb/s); Redirect: 0s, DNS look up: 0.000881s, Connection: 0.020528s, Pretransfer: 0.054773s, First byte at: 0.094716s [2026-05-16 21:14:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:14:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:14:04 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:14:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:05] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`. [2026-05-16 21:14:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-05-16 21:14:05] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`. [2026-05-16 21:14:05] [INFO] [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1] [2026-05-16 21:14:05] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:05] [INFO] [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`. [2026-05-16 21:14:06] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships. [2026-05-16 21:14:06] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:14:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath] [2026-05-16 21:14:06] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:14:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions] [2026-05-16 21:14:06] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:14:06] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:14:06] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:06] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`. [2026-05-16 21:14:06] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:09] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache. [2026-05-16 21:14:10] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:14:10] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub] [2026-05-16 21:14:10] [TRACE] [OmnipathR] Organism(s): 10090 [2026-05-16 21:14:10] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:14:10] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:14:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:10] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:10] [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` [2026-05-16 21:14:10] [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` [2026-05-16 21:14:10] [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` [2026-05-16 21:14:10] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:10] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:10] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:10] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:14:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:10] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:14:10] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:14:10] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.097021s from omnipathdb.org (161.8 Kb/s); Redirect: 0s, DNS look up: 0.001117s, Connection: 0.021537s, Pretransfer: 0.055858s, First byte at: 0.096636s [2026-05-16 21:14:10] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:14:10 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:14:10 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:14:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic` [2026-05-16 21:14:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:11] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`. [2026-05-16 21:14:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-05-16 21:14:11] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`. [2026-05-16 21:14:11] [INFO] [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1] [2026-05-16 21:14:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:11] [INFO] [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`. [2026-05-16 21:14:11] [SUCCESS] [OmnipathR] Downloaded 16895 enzyme-substrate relationships. [2026-05-16 21:14:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:14:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:14:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes] [2026-05-16 21:14:11] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:14:11] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:14:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:14:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-16 21:14:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-16 21:14:12] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-16 21:14:12] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-16 21:14:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-16 21:14:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-16 21:14:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-16 21:14:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:14:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:14:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:14:12] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.089023s from omnipathdb.org (176.4 Kb/s); Redirect: 0s, DNS look up: 0.001032s, Connection: 0.018931s, Pretransfer: 0.052826s, First byte at: 0.088756s [2026-05-16 21:14:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:14:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:14:12 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:14:12] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic` [2026-05-16 21:14:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:12] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`. [2026-05-16 21:14:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-05-16 21:14:12] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`. [2026-05-16 21:14:12] [INFO] [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1] [2026-05-16 21:14:12] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:12] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`. [2026-05-16 21:14:12] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes. [2026-05-16 21:14:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:14:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:13] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:14:13] [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] [2026-05-16 21:14:13] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:14:13] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:14:13] [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` [2026-05-16 21:14:13] [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` [2026-05-16 21:14:13] [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` [2026-05-16 21:14:13] [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` [2026-05-16 21:14:13] [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` [2026-05-16 21:14:13] [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` [2026-05-16 21:14:13] [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` [2026-05-16 21:14:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:14:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:14:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:14:13] [TRACE] [OmnipathR] Downloaded 11.6 Kb in 0.116917s from omnipathdb.org (99.5 Kb/s); Redirect: 0s, DNS look up: 0.000985s, Connection: 0.023175s, Pretransfer: 0.072536s, First byte at: 0.116589s [2026-05-16 21:14:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:14:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:14:13 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:14:14] [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` [2026-05-16 21:14:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:14] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`. [2026-05-16 21:14:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-05-16 21:14:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`. [2026-05-16 21:14:14] [INFO] [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1] [2026-05-16 21:14:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:14] [INFO] [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`. [2026-05-16 21:14:14] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records. [2026-05-16 21:14:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:14:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations] [2026-05-16 21:14:14] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:14:14] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:14:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:14:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:14] [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` [2026-05-16 21:14:14] [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` [2026-05-16 21:14:14] [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` [2026-05-16 21:14:14] [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` [2026-05-16 21:14:14] [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` [2026-05-16 21:14:14] [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` [2026-05-16 21:14:14] [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` [2026-05-16 21:14:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:14:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:14:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:14:14] [TRACE] [OmnipathR] Downloaded 1.2 Kb in 0.089472s from omnipathdb.org (13.4 Kb/s); Redirect: 0s, DNS look up: 0.000899s, Connection: 0.019792s, Pretransfer: 0.070549s, First byte at: 0.089424s [2026-05-16 21:14:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:14:14 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:14:14 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:14:14] [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` [2026-05-16 21:14:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:14] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`. [2026-05-16 21:14:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-05-16 21:14:14] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`. [2026-05-16 21:14:14] [INFO] [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1] [2026-05-16 21:14:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:14] [INFO] [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`. [2026-05-16 21:14:14] [SUCCESS] [OmnipathR] Downloaded 86 annotation records. [2026-05-16 21:14:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:14:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations] [2026-05-16 21:14:14] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:14:14] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:14:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:14:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:15] [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` [2026-05-16 21:14:15] [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` [2026-05-16 21:14:15] [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` [2026-05-16 21:14:15] [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` [2026-05-16 21:14:15] [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` [2026-05-16 21:14:15] [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` [2026-05-16 21:14:15] [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` [2026-05-16 21:14:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:14:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:15] [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] [2026-05-16 21:14:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:14:15] [TRACE] [OmnipathR] Downloaded 2.7 Kb in 0.078525s from omnipathdb.org (34.7 Kb/s); Redirect: 0s, DNS look up: 0.000996s, Connection: 0.02222s, Pretransfer: 0.056183s, First byte at: 0.078446s [2026-05-16 21:14:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:14:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:14:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:14:15] [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` [2026-05-16 21:14:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:15] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`. [2026-05-16 21:14:15] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-05-16 21:14:15] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`. [2026-05-16 21:14:15] [INFO] [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1] [2026-05-16 21:14:15] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:15] [INFO] [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`. [2026-05-16 21:14:15] [SUCCESS] [OmnipathR] Downloaded 366 annotation records. [2026-05-16 21:14:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:14:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations] [2026-05-16 21:14:15] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:14:15] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:14:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2026-05-16 21:14:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:15] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-16 21:14:15] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-16 21:14:15] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-16 21:14:15] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-16 21:14:15] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-16 21:14:15] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-16 21:14:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-16 21:14:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:14:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:15] [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] [2026-05-16 21:14:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:14:15] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.093825s from omnipathdb.org (167.3 Kb/s); Redirect: 0s, DNS look up: 0.000932s, Connection: 0.020261s, Pretransfer: 0.055355s, First byte at: 0.093518s [2026-05-16 21:14:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:14:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:14:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:14:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic` [2026-05-16 21:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:16] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`. [2026-05-16 21:14:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-05-16 21:14:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`. [2026-05-16 21:14:16] [INFO] [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1] [2026-05-16 21:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:16] [INFO] [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`. [2026-05-16 21:14:16] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records. [2026-05-16 21:14:16] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:14:16] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:14:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary` [2026-05-16 21:14:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary` [2026-05-16 21:14:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary` [2026-05-16 21:14:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary` [2026-05-16 21:14:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary` [2026-05-16 21:14:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary` [2026-05-16 21:14:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary` [2026-05-16 21:14:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:14:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:16] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:14:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:14:16] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.074823s from omnipathdb.org (101.3 Kb/s); Redirect: 0s, DNS look up: 0.001098s, Connection: 0.019369s, Pretransfer: 0.054542s, First byte at: 0.074657s [2026-05-16 21:14:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:14:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:14:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:14:16] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary` [2026-05-16 21:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:16] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`. [2026-05-16 21:14:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-05-16 21:14:16] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`. [2026-05-16 21:14:16] [INFO] [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1] [2026-05-16 21:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:16] [INFO] [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`. [2026-05-16 21:14:16] [SUCCESS] [OmnipathR] Downloaded 1190 records. [2026-05-16 21:14:16] [TRACE] [OmnipathR] Organism(s): 9606 [2026-05-16 21:14:16] [TRACE] [OmnipathR] Orthology targets: [2026-05-16 21:14:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-16 21:14:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-16 21:14:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-16 21:14:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-16 21:14:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-16 21:14:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-16 21:14:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-16 21:14:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:14:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:16] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:14:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:14:17] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.135017s from omnipathdb.org (116.3 Kb/s); Redirect: 0s, DNS look up: 0.001086s, Connection: 0.0261s, Pretransfer: 0.084974s, First byte at: 0.134524s [2026-05-16 21:14:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:14:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 16 May 2026 20:14:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip [2026-05-16 21:14:18] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic` [2026-05-16 21:14:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:18] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:18] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`. [2026-05-16 21:14:18] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-05-16 21:14:20] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`. [2026-05-16 21:14:20] [INFO] [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1] [2026-05-16 21:14:20] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:20] [INFO] [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`. [2026-05-16 21:14:20] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records. [2026-05-16 21:14:20] [TRACE] [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`. [2026-05-16 21:14:20] [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. [2026-05-16 21:14:20] [TRACE] [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`. [2026-05-16 21:14:20] [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 [2026-05-16 21:14:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:23] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:14:23] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-16 18:49:18 UTC; omnipath [2026-05-16 21:14:23] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-16 21:14:23] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-16 18:50:46 UTC; unix [2026-05-16 21:14:23] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-16 21:14:23] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-16 21:14:23] [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=2026-05-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-16 21:14:23] [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] [2026-05-16 21:14:23] [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 4.8.0(2026-04-21); 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(2026-05-16); 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 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.52.0(2026-05-10); 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) [2026-05-16 21:14:23] [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 [2026-05-16 21:14:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-05-16 21:14:23] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:14:23] [TRACE] [OmnipathR] Contains 21 files. [2026-05-16 21:14:23] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-05-16 21:14:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2026-05-16 21:14:23] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2026-05-16 21:14:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-05-16 21:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-05-16 21:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-05-16 21:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:23] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-05-16 21:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:23] [TRACE] [OmnipathR] Cache locked: FALSE [2026-05-16 21:14:23] [TRACE] [OmnipathR] Processing args for OmniPath query [2026-05-16 21:14:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations] [2026-05-16 21:14:23] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2026-05-16 21:14:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:23] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2026-05-16 21:14:23] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:23] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2026-05-16 21:14:23] [TRACE] [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2026-05-16 21:14:23] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-16 21:14:23] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2026-05-16 21:14:23] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2026-05-16 21:14:23] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2026-05-16 21:14:23] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:14:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:23] [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] [2026-05-16 21:14:23] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2026-05-16 21:14:23] [TRACE] [OmnipathR] Sending HTTP request. [2026-05-16 21:14:24] [TRACE] [OmnipathR] HTTP 200 (OK) [2026-05-16 21:14:24] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2026-05-16 21:14:24] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.100014s from rescued.omnipathdb.org (398.5 Kb/s); Redirect: 0s, DNS look up: 0.001179s, Connection: 0.017122s, Pretransfer: 0.052044s, First byte at: 0.084026s [2026-05-16 21:14:24] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 16 May 2026 19:14:23 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, 16 May 2026 20:14:23 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2026-05-16 21:14:24] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 16 May 2026 19:14:23 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, 16 May 2026 20:14:23 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip] [2026-05-16 21:14:24] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1] [2026-05-16 21:14:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:24] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`. [2026-05-16 21:14:24] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2026-05-16 21:14:24] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2026-05-16 21:14:24] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:14:24] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2026-05-16 21:14:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:24] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-05-16 21:14:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-05-16 21:14:24] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2026-05-16 21:14:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2026-05-16 21:14:24] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:14:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:14:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:14:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:24] [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] [2026-05-16 21:14:43] [TRACE] [OmnipathR] HTTP v2 GET: status 522. [2026-05-16 21:14:43] [TRACE] [OmnipathR] Downloaded 0 bytes in 19.308984s from omabrowser.org (0 bytes/s); Redirect: 0s, DNS look up: 0.000622s, Connection: 0.007471s, Pretransfer: 0.040325s, First byte at: 19.308945s [2026-05-16 21:14:43] [TRACE] [OmnipathR] HTTP headers: HTTP/2 522 ; date: Sat, 16 May 2026 19:14:43 GMT; content-type: text/html; charset=UTF-8; content-length: 7241; retry-after: 120; cache-control: private, max-age=0, no-store, no-cache, must-revalidate, post-check=0, pre-check=0; expires: Thu, 01 Jan 1970 00:00:01 GMT; referrer-policy: same-origin; x-frame-options: SAMEORIGIN; server: cloudflare; cf-ray: 9fccb486ea21db08-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:14:43] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:14:43] [WARN] [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 1/3); error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:14:48] [TRACE] [OmnipathR] Attempt 2/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:14:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:14:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:14:48] [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] [2026-05-16 21:15:08] [TRACE] [OmnipathR] HTTP v2 GET: status 522. [2026-05-16 21:15:08] [TRACE] [OmnipathR] Downloaded 0 bytes in 19.679186s from omabrowser.org (0 bytes/s); Redirect: 0s, DNS look up: 0.000971s, Connection: 0.008112s, Pretransfer: 0.055728s, First byte at: 19.67917s [2026-05-16 21:15:08] [TRACE] [OmnipathR] HTTP headers: HTTP/2 522 ; date: Sat, 16 May 2026 19:15:08 GMT; content-type: text/html; charset=UTF-8; content-length: 7241; retry-after: 120; cache-control: private, max-age=0, no-store, no-cache, must-revalidate, post-check=0, pre-check=0; expires: Thu, 01 Jan 1970 00:00:01 GMT; referrer-policy: same-origin; x-frame-options: SAMEORIGIN; server: cloudflare; cf-ray: 9fccb51fa84fd7d5-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:15:08] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:15:08] [WARN] [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 2/3); error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:15:13] [TRACE] [OmnipathR] Attempt 3/3: `https://omabrowser.org/All/oma-species.txt` [2026-05-16 21:15:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2026-05-16 21:15:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2026-05-16 21:15:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2026-05-16 21:15:32] [TRACE] [OmnipathR] HTTP v2 GET: status 522. [2026-05-16 21:15:32] [TRACE] [OmnipathR] Downloaded 0 bytes in 19.318914s from omabrowser.org (0 bytes/s); Redirect: 0s, DNS look up: 0.000728s, Connection: 0.009464s, Pretransfer: 0.043522s, First byte at: 19.318899s [2026-05-16 21:15:32] [TRACE] [OmnipathR] HTTP headers: HTTP/2 522 ; date: Sat, 16 May 2026 19:15:32 GMT; content-type: text/html; charset=UTF-8; content-length: 7241; retry-after: 120; cache-control: private, max-age=0, no-store, no-cache, must-revalidate, post-check=0, pre-check=0; expires: Thu, 01 Jan 1970 00:00:01 GMT; referrer-policy: same-origin; x-frame-options: SAMEORIGIN; server: cloudflare; cf-ray: 9fccb5ba0e92d26c-FRA; alt-svc: h3=":443"; ma=86400 [2026-05-16 21:15:32] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:15:32] [ERROR] [OmnipathR] Failed to download `https://omabrowser.org/All/oma-species.txt` (attempt 3/3); error: Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 [2026-05-16 21:15:32] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2026-05-16 18:49:18 UTC; omnipath [2026-05-16 21:15:32] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2026-05-16 21:15:32] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-16 18:50:46 UTC; unix [2026-05-16 21:15:32] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-05-16 21:15:32] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2026-05-16 21:15:33] [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=2026-05-16; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2026-05-16 21:15:33] [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] [2026-05-16 21:15:33] [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 4.8.0(2026-04-21); 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(2026-05-16); 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 1.4.5(2025-03-07); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.52.0(2026-05-10); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); selectr 0.5-1(2025-12-17); 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); vroom 1.7.1(2026-03-31); 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) [2026-05-16 21:15:33] [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 Quitting from paths.Rmd:55-67 [tfcensus-op] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `map_int()`: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error: ! Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 --- Backtrace: ▆ 1. ├─... %>% unique 2. ├─base::unique(.) 3. ├─dplyr::pull(., genesymbol) 4. ├─OmnipathR::annotations(resources = "TFcensus", entity_types = "protein") 5. │ ├─rlang::exec(omnipath_query, proteins = proteins, !!!args) 6. │ └─OmnipathR (local) ``(...) 7. │ └─environment() %>% as.list %>% c(list(...)) %>% ... 8. ├─OmnipathR:::omnipath_check_param(.) 9. │ └─param$organisms %<>% map_int(ncbi_taxid) 10. ├─purrr::map_int(., ncbi_taxid) 11. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 12. │ ├─purrr:::with_indexed_errors(...) 13. │ │ └─base::withCallingHandlers(...) 14. │ ├─purrr:::call_with_cleanup(...) 15. │ └─OmnipathR (local) .f(.x[[i]], ...) 16. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer 17. ├─purrr::map_int(., taxon_name, "ncbi") 18. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress) 19. │ ├─purrr:::with_indexed_errors(...) 20. │ │ └─base::withCallingHandlers(...) 21. │ ├─purrr:::call_with_cleanup(...) 22. │ └─OmnipathR (local) .f(.x[[i]], ...) 23. │ ├─... %>% if_null_len0(NA) 24. │ └─OmnipathR::get_db("organisms") 25. │ └─OmnipathR::load_db(key, param = param) 26. │ ├─rlang::exec(loader, !!!param) 27. │ └─OmnipathR (local) ``() 28. │ └─... %>% ... 29. ├─OmnipathR:::if_null_len0(., NA) 30. │ └─value1 %>% is_empty_2 %>% if (value2) value1 31. ├─OmnipathR:::is_empty_2(.) 32. │ └─value %>% ... 33. ├─dplyr::pull(., name_type) 34. ├─dplyr::filter(...) 35. ├─dplyr::mutate(...) 36. ├─dplyr::full_join(...) 37. ├─dplyr::full_join(...) 38. ├─dplyr:::full_join.data.frame(...) 39. │ └─dplyr::auto_copy(x, y, copy = copy) 40. │ ├─dplyr::same_src(x, y) 41. │ └─dplyr:::same_src.data.frame(x, y) 42. │ └─base::is.data.frame(y) 43. ├─oma_organisms() %>% select(-genome_source, -oma_version) 44. ├─dplyr::select(., -genome_source, -oma_version) 45. ├─OmnipathR::oma_organisms() 46. │ └─"oma_species" %>% ... 47. ├─OmnipathR:::generic_downloader(...) 48. │ ├─... %>% omnipath_cache_save(url = url, post = post) 49. │ ├─rlang::exec(...) 50. │ └─OmnipathR (local) ``(...) 51. │ └─base::stop(result) 52. └─OmnipathR::omnipath_cache_save(., url = url, post = post) 53. └─base::saveRDS(data, target_path) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'paths.Rmd' failed with diagnostics: ℹ In index: 1. Caused by error in `map_int()`: ℹ In index: 1. Caused by error: ! Failed to open 'https://omabrowser.org/All/oma-species.txt': The requested URL returned error: 522 --- failed re-building ‘paths.Rmd’ SUMMARY: processing the following files failed: ‘bioc_workshop.Rmd’ ‘paths.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-3.22/2026-05-16_2038/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2026-05-16 21:15:41 CEST ]