[ Started: 2026-03-19 06:03:16 CET ]
[ OmnipathR v3.19.8 for BioC-3.22 from https://github.com/saezlab/OmnipathR@devel (6e188b2 2026-03-17 17:46:36) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/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 ‘3.19.8’
* 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  6.9Mb
  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
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:03:47] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:03:47] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-03-19 05:01:21 UTC; omnipath
[2026-03-19 06:03:47] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-03-19 06:03:47] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-19 05:03:18 UTC; unix
[2026-03-19 06:03:47] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.8
[2026-03-19 06:03:47] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-03-19 06:03:47] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-19; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-03-19 06:03:47] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-19 06:03:47] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(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 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); 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 2.2.2(2026-02-12); 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 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.8(2026-03-19); 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 1.2.1(2026-01-09); 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(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); 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 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-19 06:03:47] [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
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:03:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-19 06:03:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:03:47] [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 ... WARNING
'::' or ':::' import not declared from: ‘SBMLR’
'loadNamespace' or 'requireNamespace' call not declared from: ‘SBMLR’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:03:58] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:03:58] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-03-19 05:01:21 UTC; omnipath
[2026-03-19 06:03:58] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-03-19 06:03:58] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-19 05:03:18 UTC; unix
[2026-03-19 06:03:58] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.8
[2026-03-19 06:03:58] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-03-19 06:03:58] [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=2026-03-19; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-03-19 06:03:58] [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]
[2026-03-19 06:03:58] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(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 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); 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 2.2.2(2026-02-12); 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 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.8(2026-03-19); 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 1.2.1(2026-01-09); 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(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); 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 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-19 06:03:58] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:03:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-19 06:03:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:03:59] [TRACE]   [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
get_pathway_participants: no visible binding for global variable
  ‘pathway_id’
get_pathway_participants: no visible binding for global variable
  ‘chebi_id’
get_pathway_participants: no visible binding for global variable
  ‘pathway_name’
get_pathway_participants: no visible binding for global variable
  ‘pathway_url’
get_reactome_pathway_relations: no visible binding for global variable
  ‘Parent’
get_reactome_pathway_relations: no visible binding for global variable
  ‘Child’
get_reactome_pathways: no visible binding for global variable
  ‘pathway_id’
get_reactome_pathways: no visible binding for global variable
  ‘pathway_name’
get_wikipathways: no visible binding for global variable ‘metabolites’
get_wikipathways_metabolites_sparql: no visible binding for global
  variable ‘met_xref_raw’
get_wikipathways_metabolites_sparql: no visible binding for global
  variable ‘met_id’
get_wikipathways_metabolites_sparql: no visible binding for global
  variable ‘pathway_url’
get_wikipathways_pathways: no visible binding for global variable
  ‘organism_species’
get_wikipathways_pathways: no visible binding for global variable
  ‘pathway_id’
get_wikipathways_pathways: no visible binding for global variable
  ‘pathway_name’
get_wikipathways_pathways: no visible binding for global variable
  ‘pathway_url’
metabolic_atlas_list_gems: no visible binding for global variable
  ‘git_repo’
metabolic_atlas_list_gems: no visible binding for global variable
  ‘git_host’
metabolic_atlas_list_gems: no visible binding for global variable
  ‘gem_info’
metabolic_atlas_list_gems: no visible binding for global variable
  ‘latest_version’
metabolic_atlas_model: no visible binding for global variable ‘path’
metabolic_atlas_model : silent_sbml: no visible binding for global
  variable ‘result’
metabolic_atlas_models: no visible binding for global variable ‘id’
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:
  Child ORIGINAL Parent chebi_id enzyme_genesymbol gem_info git_host
  git_repo handle id latest_version met_id met_xref_raw metabolites
  organism_species path pathway_id pathway_name pathway_url result
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> ### Name: ensembl_id_mapping_table
> ### Title: Identifier translation table from Ensembl
> ### Aliases: ensembl_id_mapping_table
> 
> ### ** Examples
> 
> ensp_up <- ensembl_id_mapping_table("ensp")
[2026-03-19 06:06:58] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens
[2026-03-19 06:06:58] [TRACE]   [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
    <Dataset name="hsapiens_gene_ensembl" interface="default" >
        <Attribute name="uniprotswissprot"/>
        <Attribute name="ensembl_peptide_id"/>
    </Dataset>
</Query>
[2026-03-19 06:06:58] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:06:58] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2026-03-19 06:06:58] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2026-03-19 06:06:58] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2026-03-19 06:06:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:06:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:06:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:06:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:06:58] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:06:58] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2026-03-19 06:06:58] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2026-03-19 06:06:58] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-03-19 06:06:58] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2026-03-19 06:06:58] [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=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2026-03-19 06:06:58] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:06:58] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:06:58] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:06:58] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:06:58] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-03-19 06:06:59] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-03-19 06:06:59] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:06:59] [TRACE]   [OmnipathR] Downloaded 346 bytes in 0.048225s from www.ensembl.org (7 Kb/s); Redirect: 0s, DNS look up: 0.000753s, Connection: 0.019177s, Pretransfer: 0.019312s, First byte at: 0.048202s
[2026-03-19 06:06:59] [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: Thu, 19 Mar 2026 05:06:59 GMT; Transfer-Encoding: chunked; Connection: Keep-Alive; X-Frame-Options: SAMEORIGIN
[2026-03-19 06:06:59] [TRACE]   [OmnipathR] Response headers: [Server=Apache,Content-Type=text/plain; charset=utf-8,Content-Security-Policy=frame-ancestors 'self',Date=Thu, 19 Mar 2026 05:06:59 GMT,Transfer-Encoding=chunked,Connection=Keep-Alive,X-Frame-Options=SAMEORIGIN]
[2026-03-19 06:06:59] [TRACE]   [OmnipathR] Calling reader callback on response.
[2026-03-19 06:06:59] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2026-03-19 06:06:59] [INFO]    [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1]
[2026-03-19 06:06:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:06:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:06:59] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`.
[2026-03-19 06:06:59] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2026-03-19 06:06:59] [WARN]    [OmnipathR] Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
[2026-03-19 06:06:59] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 1 records
Error in `set_names()`:
! The size of `nm` (2) must be compatible with the size of `x` (1).
Backtrace:
    ▆
 1. ├─OmnipathR::ensembl_id_mapping_table("ensp")
 2. │ └─... %>% trim_and_distinct
 3. ├─OmnipathR:::trim_and_distinct(.)
 4. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
 5. ├─dplyr::distinct(.)
 6. ├─dplyr::mutate(., across(everything(), str_trim))
 7. ├─rlang::set_names(., c("From", "To"))
 8. └─rlang::abort(message = message)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-03-19 05:01:21 UTC; omnipath
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-19 05:03:18 UTC; unix
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.8
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-19; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-03-19 06:07:42] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); 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 2.2.2(2026-02-12); 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 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.8(2026-03-19); 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 1.2.1(2026-01-09); 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(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); 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 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-19 06:07:42] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Contains 16 files.
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:07:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=[dorothea,tf_target,collectri],types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.131066s from rescued.omnipathdb.org (304.1 Kb/s); Redirect: 0s, DNS look up: 0.001316s, Connection: 0.019718s, Pretransfer: 0.075237s, First byte at: 0.112492s
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:07:42 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: Thu, 19 Mar 2026 06:07:42 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Thu, 19 Mar 2026 05:07:42 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=Thu, 19 Mar 2026 06:07:42 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:07:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:07:42] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-19 06:07:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:07:43] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-19 06:07:43] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.070683s from omabrowser.org (107 Kb/s); Redirect: 0s, DNS look up: 0.000585s, Connection: 0.004611s, Pretransfer: 0.037182s, First byte at: 0.070535s
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 19 Mar 2026 05:07:43 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=PI33p2GGpwUP7wbE1wwZKJEZpi1SJiD%2Fpn3juOLpL%2FezuGbYt9YnKW7YTbww0S%2FZbC%2F9r%2FqwPxJWOX1BmvN%2BH6FtgcZssFzhxm5%2Fr9X7"}]}; cf-ray: 9de9f48339c531bc-STR; alt-svc: h3=":443"; ma=86400
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-19 06:07:43] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:07:43] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-19 06:07:43] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:07:43] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-19 06:07:43] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:07:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:08:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-19 06:08:06] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-03-19 06:08:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:06] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-03-19 06:08:06] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-03-19 06:08:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:06] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:08:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-19 06:08:07] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:07] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-03-19 06:08:07] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=[dorothea,tf_target,collectri],types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort,dorothea_level],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=[A,B],qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-19 06:08:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-19 06:08:07] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-19 06:08:07] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.101132s from omnipathdb.org (155.2 Kb/s); Redirect: 0s, DNS look up: 0.000932s, Connection: 0.022837s, Pretransfer: 0.056134s, First byte at: 0.100688s
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:08:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:08:07 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:08:07] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-19 06:08:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:08] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:08:08] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2026-03-19 06:08:08] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2026-03-19 06:08:08] [INFO]    [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2026-03-19 06:08:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:08] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2026-03-19 06:08:12] [SUCCESS] [OmnipathR] Downloaded 131398 interactions.
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=enzyme-substrate relationships,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:15] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:15] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:15] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.099167s from omnipathdb.org (158.3 Kb/s); Redirect: 0s, DNS look up: 0.000966s, Connection: 0.021618s, Pretransfer: 0.055352s, First byte at: 0.09866s
[2026-03-19 06:08:15] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:08:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:08:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:08:16] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:16] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:08:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-03-19 06:08:16] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-03-19 06:08:16] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2026-03-19 06:08:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:16] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2026-03-19 06:08:17] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships.
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:18] [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`
[2026-03-19 06:08:18] [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`
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.101204s from omnipathdb.org (155.1 Kb/s); Redirect: 0s, DNS look up: 0.001085s, Connection: 0.023144s, Pretransfer: 0.056558s, First byte at: 0.100869s
[2026-03-19 06:08:18] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:08:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:08:18 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:08:19] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:19] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:08:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-19 06:08:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-19 06:08:19] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2026-03-19 06:08:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:19] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2026-03-19 06:08:21] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=complexes,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=complexes,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=protein complexes,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2026-03-19 06:08:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2026-03-19 06:08:22] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2026-03-19 06:08:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.0937s from omnipathdb.org (167.6 Kb/s); Redirect: 0s, DNS look up: 0.001059s, Connection: 0.019812s, Pretransfer: 0.055475s, First byte at: 0.093423s
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:08:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:08:22 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:08:22] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:22] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:08:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2026-03-19 06:08:23] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:23] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2026-03-19 06:08:23] [SUCCESS] [OmnipathR] Downloaded 37629 protein complexes.
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_location,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_location,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:08:23] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:08:23] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:08:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.088581s from omnipathdb.org (177.2 Kb/s); Redirect: 0s, DNS look up: 0.000946s, Connection: 0.018539s, Pretransfer: 0.052815s, First byte at: 0.088257s
[2026-03-19 06:08:23] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:08:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:08:23 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:08:24] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:24] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-03-19 06:08:24] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:24] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2026-03-19 06:08:24] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records.
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=Uniprot_location,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=Uniprot_location,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-03-19 06:08:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-03-19 06:08:24] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-03-19 06:08:24] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:08:24] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Downloaded 72 bytes in 0.079914s from omnipathdb.org (900 bytes/s); Redirect: 0s, DNS look up: 0.000998s, Connection: 0.02252s, Pretransfer: 0.056749s, First byte at: 0.079887s
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:08:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:08:25 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:08:25] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:25] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2026-03-19 06:08:25] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:25] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2026-03-19 06:08:25] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2026-03-19 06:08:25] [FATAL]   [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest.
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_location,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_location,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-03-19 06:08:25] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:08:25] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=HPA_tissue,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:08:25] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=HPA_tissue,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=[proteins1=DLL1,proteins2=MEIS2,proteins3=PHOX2A,proteins4=BACH1,proteins5=KLF11,proteins6=FOXO3,proteins7=MEFV],qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-19 06:08:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-19 06:08:26] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-19 06:08:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.102081s from omnipathdb.org (153.8 Kb/s); Redirect: 0s, DNS look up: 0.000966s, Connection: 0.019241s, Pretransfer: 0.063232s, First byte at: 0.100824s
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:08:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:08:26 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:08:26] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:26] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2026-03-19 06:08:26] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:26] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2026-03-19 06:08:26] [SUCCESS] [OmnipathR] Downloaded 3752 annotation records.
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:08:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:08:26] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:08:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:08:26] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.096231s from omnipathdb.org (163.2 Kb/s); Redirect: 0s, DNS look up: 0.001018s, Connection: 0.020832s, Pretransfer: 0.055141s, First byte at: 0.095172s
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:08:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:08:26 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:08:27] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:27] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-03-19 06:08:27] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:27] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2026-03-19 06:08:27] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records.
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:27] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-19 06:08:27] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:08:30] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-03-19 06:08:30] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:08:30] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache.
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2026-03-19 06:08:30] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2026-03-19 06:08:30] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2026-03-19 06:08:30] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.091644s from omnipathdb.org (171.3 Kb/s); Redirect: 0s, DNS look up: 0.001081s, Connection: 0.019045s, Pretransfer: 0.05466s, First byte at: 0.091211s
[2026-03-19 06:08:30] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:08:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:08:30 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:08:32] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2026-03-19 06:08:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:32] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:08:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2026-03-19 06:08:34] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2026-03-19 06:08:34] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2026-03-19 06:08:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:34] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2026-03-19 06:08:34] [SUCCESS] [OmnipathR] Downloaded 388239 intercellular communication role records.
[2026-03-19 06:08:35] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2026-03-19 06:08:35] [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.
[2026-03-19 06:08:35] [TRACE]   [OmnipathR] Bypassing call: `intercell_network()`.
[2026-03-19 06:08:35] [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.
[2026-03-19 06:08:35] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2026-03-19 06:08:35] [TRACE]   [OmnipathR] Bypassing call: `    loc_consensus_percentile = 50, simplify = TRUE)`.
[2026-03-19 06:08:35] [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.
[2026-03-19 06:08:35] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:08:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:35] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell_summary,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=NA,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:08:35] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:08:35] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:08:35] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell_summary,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=NA,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:08:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2026-03-19 06:08:36] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-03-19 06:08:36] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2026-03-19 06:08:36] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.080224s from omnipathdb.org (94.5 Kb/s); Redirect: 0s, DNS look up: 0.000976s, Connection: 0.020787s, Pretransfer: 0.056496s, First byte at: 0.080047s
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:08:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:08:36 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:08:36] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:36] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-03-19 06:08:36] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:36] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2026-03-19 06:08:36] [SUCCESS] [OmnipathR] Downloaded 1190 records.
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:08:36] [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`.
[2026-03-19 06:08:36] [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`
[2026-03-19 06:08:36] [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`.
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:36] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-03-19 06:08:36] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:08:36] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:08:37] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-19 06:08:37] [TRACE]   [OmnipathR] Downloaded 43 bytes in 0.349706s from rest.uniprot.org (122 bytes/s); Redirect: 0s, DNS look up: 0.001089s, Connection: 0.019642s, Pretransfer: 0.077621s, First byte at: 0.349655s
[2026-03-19 06:08:37] [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: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Thu, 19 Mar 2026 05:08:37 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
[2026-03-19 06:08:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-03-19 06:08:46] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2026-03-19 06:08:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:46] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2026-03-19 06:08:46] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records
[2026-03-19 06:08:46] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2026-03-19 06:08:46] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-03-19 06:08:46] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2026-03-19 06:08:46] [TRACE]   [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`.
[2026-03-19 06:08:46] [TRACE]   [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`.
[2026-03-19 06:08:46] [TRACE]   [OmnipathR] Bypassing call: `go_ontology_download()`.
[2026-03-19 06:08:46] [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.
[2026-03-19 06:08:46] [TRACE]   [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2026-03-19 06:08:46] [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.
[2026-03-19 06:08:46] [TRACE]   [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2026-03-19 06:08:46] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘bioc_workshop.Rmd’

--- re-building ‘cosmos.Rmd’ using rmarkdown
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:49] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:08:49] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-03-19 05:01:21 UTC; omnipath
[2026-03-19 06:08:49] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-03-19 06:08:49] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-19 05:03:18 UTC; unix
[2026-03-19 06:08:49] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.8
[2026-03-19 06:08:49] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-03-19 06:08:49] [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=2026-03-19; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-03-19 06:08:49] [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]
[2026-03-19 06:08:49] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); 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 2.2.2(2026-02-12); 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 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.8(2026-03-19); 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 1.2.1(2026-01-09); 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(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); 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 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-19 06:08:49] [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
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Contains 16 files.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2026-03-19 06:08:49] [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.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2026-03-19 06:08:49] [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.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2026-03-19 06:08:49] [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.
[2026-03-19 06:08:49] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-03-19 06:08:49] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:49] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:49] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-03-19 06:08:49] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.116877s from rescued.omnipathdb.org (341 Kb/s); Redirect: 0s, DNS look up: 0.001094s, Connection: 0.020852s, Pretransfer: 0.055583s, First byte at: 0.09686s
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:08:49 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: Thu, 19 Mar 2026 06:08:49 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-03-19 06:08:49] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Thu, 19 Mar 2026 05:08:49 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=Thu, 19 Mar 2026 06:08:49 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-03-19 06:08:50] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:50] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-19 06:08:50] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:50] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-19 06:08:50] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.079307s from omabrowser.org (95.4 Kb/s); Redirect: 0s, DNS look up: 0.000558s, Connection: 0.00456s, Pretransfer: 0.046225s, First byte at: 0.079176s
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 19 Mar 2026 05:08:50 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=5xyquDULwVCeQ8XifnGb8vapNHkMDCOUGuTEZ%2F4%2FvyRMUM03Ni3mlyY%2BxiCbGKUrUIkVx3P6ZIjqK06FnJ5BDtmBAjJJIWV%2BfA6iv2GF"}]}; cf-ray: 9de9f6265c5731bc-STR; alt-svc: h3=":443"; ma=86400
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-19 06:08:50] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:50] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-19 06:08:50] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:08:50] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-19 06:08:50] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:08:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:09:11] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-19 06:09:11] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-03-19 06:09:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:11] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:12] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-19 06:09:12] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:12] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-03-19 06:09:12] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-03-19 06:09:12] [INFO]    [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:09:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:09:12] [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`
[2026-03-19 06:09:12] [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`
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:09:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.085592s from omnipathdb.org (183.4 Kb/s); Redirect: 0s, DNS look up: 0.00119s, Connection: 0.017764s, Pretransfer: 0.051861s, First byte at: 0.085223s
[2026-03-19 06:09:12] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:09:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:09:12 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:09:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:09:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:13] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:09:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-19 06:09:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-19 06:09:14] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2026-03-19 06:09:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:14] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2026-03-19 06:09:16] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
    <Dataset name="hsapiens_gene_ensembl" interface="default" >
        <Attribute name="uniprotswissprot"/>
        <Attribute name="external_gene_name"/>
    </Dataset>
</Query>
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:09:16] [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`.
[2026-03-19 06:09:16] [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`
[2026-03-19 06:09:16] [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`.
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:16] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2026-03-19 06:09:16] [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`
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-03-19 06:09:16] [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`
[2026-03-19 06:09:16] [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`.
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-03-19 06:09:16] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:09:17] [TRACE]   [OmnipathR] Downloaded 346 bytes in 0.066306s from www.ensembl.org (5.1 Kb/s); Redirect: 0s, DNS look up: 0.018412s, Connection: 0.036895s, Pretransfer: 0.036952s, First byte at: 0.066269s
[2026-03-19 06:09:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: Apache; Content-Type: text/plain; charset=utf-8; Content-Security-Policy: frame-ancestors 'self'; Date: Thu, 19 Mar 2026 05:09:16 GMT; Transfer-Encoding: chunked; Connection: Keep-Alive; X-Frame-Options: SAMEORIGIN
[2026-03-19 06:09:17] [TRACE]   [OmnipathR] Response headers: [Server=Apache,Content-Type=text/plain; charset=utf-8,Content-Security-Policy=frame-ancestors 'self',Date=Thu, 19 Mar 2026 05:09:16 GMT,Transfer-Encoding=chunked,Connection=Keep-Alive,X-Frame-Options=SAMEORIGIN]
[2026-03-19 06:09:17] [TRACE]   [OmnipathR] Calling reader callback on response.
[2026-03-19 06:09:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2026-03-19 06:09:17] [INFO]    [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2026-03-19 06:09:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:17] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2026-03-19 06:09:17] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2026-03-19 06:09:17] [WARN]    [OmnipathR] Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_115: DBI connect('database=ensembl_mart_115;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_115/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
[2026-03-19 06:09:17] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 1 records

Quitting from cosmos.Rmd:175-179 [omnipath]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `set_names()`:
! The size of `nm` (2) must be compatible with the size of `x` (1).
---
Backtrace:
     ▆
  1. ├─OmnipathR::omnipath_for_cosmos()
  2. │ └─... %T>% ...
  3. ├─dplyr::bind_rows(...)
  4. │ └─rlang::list2(...)
  5. ├─OmnipathR::translate_ids_multi(...)
  6. │ └─source_cols %>% seq_along %>% ...
  7. ├─purrr::reduce(...)
  8. │ └─purrr:::reduce_impl(.x, .f, ..., .init = .init, .dir = .dir)
  9. │   └─OmnipathR (local) fn(out, elt, ...)
 10. │     └─OmnipathR::translate_ids(...)
 11. │       └─... %>% ...
 12. ├─purrr::reduce2(...)
 13. │ └─purrr:::reduce2_impl(.x, .y, .f, ..., .init = .init, .left = TRUE)
 14. │   └─OmnipathR (local) .f(out, .x[[x_i]], .y[[y_i]], ...)
 15. │     ├─... %>% ...
 16. │     └─OmnipathR:::id_translation_table(...)
 17. │       └─OmnipathR::ensembl_id_mapping_table(...)
 18. │         └─... %>% trim_and_distinct
 19. ├─OmnipathR:::ensure_character(., From, To)
 20. │ └─d %>% mutate(across(c(!!!cols), as.character))
 21. ├─dplyr::mutate(., across(c(!!!cols), as.character))
 22. ├─OmnipathR:::trim_and_distinct(.)
 23. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
 24. ├─dplyr::distinct(.)
 25. ├─dplyr::mutate(., across(everything(), str_trim))
 26. ├─rlang::set_names(., c("From", "To"))
 27. └─rlang::abort(message = message)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'cosmos.Rmd' failed with diagnostics:
The size of `nm` (2) must be compatible with the size of `x` (1).
--- failed re-building ‘cosmos.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-03-19 05:01:21 UTC; omnipath
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-19 05:03:18 UTC; unix
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.8
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-03-19 06:09:20] [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=2026-03-19; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-03-19 06:09:20] [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]
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); 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 2.2.2(2026-02-12); 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 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.8(2026-03-19); 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 1.2.1(2026-01-09); 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(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); 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 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-19 06:09:20] [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
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Contains 7 files.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Checking on-disk cache for database `up_gs`.
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Cache record does not exist: `db://up_gs`
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Loading database `up_gs` from source.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.117339s from rescued.omnipathdb.org (339.7 Kb/s); Redirect: 0s, DNS look up: 0.001224s, Connection: 0.021628s, Pretransfer: 0.056026s, First byte at: 0.096767s
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:09:20 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: Thu, 19 Mar 2026 06:09:20 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Thu, 19 Mar 2026 05:09:20 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=Thu, 19 Mar 2026 06:09:20 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:20] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-19 06:09:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:21] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-19 06:09:21] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.080705s from omabrowser.org (93.7 Kb/s); Redirect: 0s, DNS look up: 0.000561s, Connection: 0.005733s, Pretransfer: 0.046146s, First byte at: 0.080573s
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 19 Mar 2026 05:09:21 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=T2Cfo6irgqD41LrbFkDDTp3n0oExZonsOOidmn7YfOuF8io9asNmTtBHxO26SOCVRbGm6eK%2FdyjY3Wf%2Bx%2Fdarq%2BZ4TbVV9NOba1tIj7Y"}]}; cf-ray: 9de9f6e7df4ae859-STR; alt-svc: h3=":443"; ma=86400
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-19 06:09:21] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:21] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-19 06:09:21] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:21] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-19 06:09:21] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:09:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:09:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-19 06:09:45] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-03-19 06:09:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:45] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-03-19 06:09:45] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-03-19 06:09:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:45] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:09:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-19 06:09:46] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:46] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-03-19 06:09:46] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:09:46] [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`.
[2026-03-19 06:09:46] [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`
[2026-03-19 06:09:46] [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`.
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:46] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-03-19 06:09:46] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-19 06:09:46] [TRACE]   [OmnipathR] Downloaded 43 bytes in 0.370534s from rest.uniprot.org (116 bytes/s); Redirect: 0s, DNS look up: 0.000986s, Connection: 0.019546s, Pretransfer: 0.083369s, First byte at: 0.370427s
[2026-03-19 06:09:46] [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: 12-March-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Thu, 19 Mar 2026 05:09:46 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
[2026-03-19 06:09:56] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-03-19 06:09:56] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2026-03-19 06:09:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:56] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2026-03-19 06:09:56] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records
[2026-03-19 06:09:56] [TRACE]   [OmnipathR] Saving database `up_gs` to on-disk cache.
[2026-03-19 06:09:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:56] [INFO]    [OmnipathR] Cache item `7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:09:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f-1.rds`.
[2026-03-19 06:09:56] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f-1.rds`.
[2026-03-19 06:09:56] [INFO]    [OmnipathR] Download ready [key=7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f, version=1]
[2026-03-19 06:09:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:09:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:09:56] [INFO]    [OmnipathR] Cache item `7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f` version 1: status changed from `started` to `ready`.
[2026-03-19 06:09:56] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:09] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:10:09] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-03-19 05:01:21 UTC; omnipath
[2026-03-19 06:10:09] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-03-19 06:10:09] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-19 05:03:18 UTC; unix
[2026-03-19 06:10:09] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.8
[2026-03-19 06:10:09] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-03-19 06:10:09] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-19; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-03-19 06:10:09] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-19 06:10:09] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); glue 1.8.0(2024-09-30); 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 2.2.2(2026-02-12); 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 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.8(2026-03-19); 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 1.2.1(2026-01-09); 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(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-19 06:10:09] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] Contains 7 files.
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-03-19 06:10:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:10:10] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-03-19 06:10:10] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:10] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:10] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-03-19 06:10:10] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.108694s from rescued.omnipathdb.org (366.7 Kb/s); Redirect: 0s, DNS look up: 0.00116s, Connection: 0.018978s, Pretransfer: 0.054814s, First byte at: 0.090831s
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:10:10 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: Thu, 19 Mar 2026 06:10:10 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Thu, 19 Mar 2026 05:10:10 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=Thu, 19 Mar 2026 06:10:10 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-03-19 06:10:10] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:10] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-19 06:10:10] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:10] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-19 06:10:10] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.078455s from omabrowser.org (96.4 Kb/s); Redirect: 0s, DNS look up: 0.007017s, Connection: 0.010967s, Pretransfer: 0.0458s, First byte at: 0.078295s
[2026-03-19 06:10:10] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 19 Mar 2026 05:10:10 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=RiT354N70asKDEIZCLHFzgsiocTWyu2P6hmd21UXXe5kReAN%2BikDxmdG86QOaZbV6E8vYjo%2FQ14bgEB3ZeOf37jaOlHxJvmAJkH7hA32"}]}; cf-ray: 9de9f81cdd0631bc-STR; alt-svc: h3=":443"; ma=86400
[2026-03-19 06:10:11] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-19 06:10:11] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-03-19 06:10:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:11] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-03-19 06:10:11] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:10:11] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-19 06:10:11] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:10:11] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-19 06:10:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:11] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:10:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-19 06:10:11] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:10:11] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:10:34] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-19 06:10:34] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-03-19 06:10:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:34] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-03-19 06:10:34] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-03-19 06:10:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:34] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:10:34] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-19 06:10:35] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:35] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-03-19 06:10:35] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:10:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:10:35] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:10:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.085927s from omnipathdb.org (182.7 Kb/s); Redirect: 0s, DNS look up: 0.000993s, Connection: 0.017301s, Pretransfer: 0.052786s, First byte at: 0.085584s
[2026-03-19 06:10:35] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:10:35 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:10:35 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:10:35] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:10:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:36] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:10:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-19 06:10:36] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-19 06:10:36] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2026-03-19 06:10:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:36] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2026-03-19 06:10:38] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
--- finished re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2026-03-19 06:10:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:42] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:10:42] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-03-19 05:01:21 UTC; omnipath
[2026-03-19 06:10:42] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-03-19 06:10:42] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-19 05:03:18 UTC; unix
[2026-03-19 06:10:42] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.8
[2026-03-19 06:10:42] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-03-19 06:10:42] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-19; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-03-19 06:10:42] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-19 06:10:42] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); 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 2.2.2(2026-02-12); 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 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.8(2026-03-19); 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 1.2.1(2026-01-09); 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(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); 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 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-19 06:10:42] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-19 06:10:42] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-19 06:10:42] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:10:42] [TRACE]   [OmnipathR] Contains 6 files.
[2026-03-19 06:10:42] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-19 06:10:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:10:42] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-03-19 06:10:42] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-19 06:10:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:42] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-19 06:10:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=extra_attrs,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:10:43] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-03-19 06:10:43] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:43] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:43] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-03-19 06:10:43] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.123893s from rescued.omnipathdb.org (321.7 Kb/s); Redirect: 0s, DNS look up: 0.001217s, Connection: 0.023043s, Pretransfer: 0.057866s, First byte at: 0.101894s
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:10:43 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: Thu, 19 Mar 2026 06:10:43 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Thu, 19 Mar 2026 05:10:43 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=Thu, 19 Mar 2026 06:10:43 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-03-19 06:10:43] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:43] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-19 06:10:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:43] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-19 06:10:43] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.076951s from omabrowser.org (98.3 Kb/s); Redirect: 0s, DNS look up: 0.000666s, Connection: 0.003818s, Pretransfer: 0.045375s, First byte at: 0.07682s
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 19 Mar 2026 05:10:43 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=Vri6RSH8w3lFu69mEWaNao55p%2FO7ftCS0DBsPwcE5NxQWUZgLHdAIRC55ySECRv1f%2B6JmUANaNtGyvDCo3wu4nfjOUyXDoN7%2FOagvo0%2B"}]}; cf-ray: 9de9f8eadd2d2bb7-STR; alt-svc: h3=":443"; ma=86400
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-19 06:10:43] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:43] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-19 06:10:43] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-19 06:10:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:10:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:10:44] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:10:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-19 06:10:44] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:10:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:11:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-19 06:11:06] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-03-19 06:11:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:11:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:11:06] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:11:07] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-19 06:11:07] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:11:07] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-03-19 06:11:07] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=[omnipath,pathwayextra,kinaseextra,ligrecextra],types=<NULL>,genesymbols=yes,fields=[extra_attrs,sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:11:07] [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`
[2026-03-19 06:11:07] [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`
[2026-03-19 06:11:07] [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`
[2026-03-19 06:11:07] [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`
[2026-03-19 06:11:07] [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`
[2026-03-19 06:11:07] [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`
[2026-03-19 06:11:07] [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`
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.097441s from omnipathdb.org (161.1 Kb/s); Redirect: 0s, DNS look up: 0.001158s, Connection: 0.019028s, Pretransfer: 0.060787s, First byte at: 0.097114s
[2026-03-19 06:11:07] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:11:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:11:07 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:11:08] [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`
[2026-03-19 06:11:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:11:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:11:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:11:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:11:08] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:11:08] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2026-03-19 06:11:09] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2026-03-19 06:11:09] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2026-03-19 06:11:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:11:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:11:09] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2026-03-19 06:11:09] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2026-03-19 06:11:18] [SUCCESS] [OmnipathR] Downloaded 139054 interactions.
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_keyword,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_keyword,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-19 06:17:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-19 06:17:20] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-19 06:17:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.090152s from omnipathdb.org (174.2 Kb/s); Redirect: 0s, DNS look up: 0.001091s, Connection: 0.019121s, Pretransfer: 0.052681s, First byte at: 0.089173s
[2026-03-19 06:17:20] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:17:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:17:20 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:17:21] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-03-19 06:17:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:21] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:17:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2026-03-19 06:17:22] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:22] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2026-03-19 06:17:22] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records.
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=<NULL>,datasets=<NULL>,types=ubiquitination,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,resources=<NULL>,datasets=<NULL>,types=ubiquitination,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=enzyme-substrate relationships,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-03-19 06:17:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-03-19 06:17:22] [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`
[2026-03-19 06:17:22] [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`
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-03-19 06:17:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Downloaded 1.3 Kb in 0.069379s from omnipathdb.org (18.2 Kb/s); Redirect: 0s, DNS look up: 0.000902s, Connection: 0.017889s, Pretransfer: 0.051765s, First byte at: 0.069332s
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:17:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:17:22 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:17:22] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:22] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2026-03-19 06:17:22] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:22] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2026-03-19 06:17:22] [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
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:26] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:17:26] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-03-19 05:01:21 UTC; omnipath
[2026-03-19 06:17:26] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-03-19 06:17:26] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-19 05:03:18 UTC; unix
[2026-03-19 06:17:26] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.8
[2026-03-19 06:17:26] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-03-19 06:17:26] [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=2026-03-19; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-03-19 06:17:26] [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]
[2026-03-19 06:17:26] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); 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 2.2.2(2026-02-12); 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 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.8(2026-03-19); 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 1.2.1(2026-01-09); 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(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); 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 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-19 06:17:26] [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
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] Contains 8 files.
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:26] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:17:27] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-03-19 06:17:27] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:27] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:27] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-03-19 06:17:27] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.119058s from rescued.omnipathdb.org (334.8 Kb/s); Redirect: 0s, DNS look up: 0.008954s, Connection: 0.027974s, Pretransfer: 0.061924s, First byte at: 0.099966s
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:17:27 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: Thu, 19 Mar 2026 06:17:27 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Thu, 19 Mar 2026 05:17:27 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=Thu, 19 Mar 2026 06:17:27 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-03-19 06:17:27] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:27] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-19 06:17:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:27] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-19 06:17:27] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:17:27] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.100129s from omabrowser.org (75.5 Kb/s); Redirect: 0s, DNS look up: 0.025705s, Connection: 0.030146s, Pretransfer: 0.063625s, First byte at: 0.099941s
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 19 Mar 2026 05:17:28 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=43BwCyjC%2FRg0EIXWgdIHB72zNWB%2FGE%2F%2FKq3q9RZu4cS%2FmwFL1Rz1MRi2%2FFxzv7xroVrcswe3jYQvvCW6H%2FwqHOxEwy5dKlRChD6kqn0B"}]}; cf-ray: 9dea02c9edaf2c10-STR; alt-svc: h3=":443"; ma=86400
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-19 06:17:28] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:28] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-19 06:17:28] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:28] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-19 06:17:28] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:17:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:17:51] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-19 06:17:51] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-03-19 06:17:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:51] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-03-19 06:17:51] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-03-19 06:17:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:51] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:17:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-19 06:17:52] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:52] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-03-19 06:17:52] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:17:52] [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`
[2026-03-19 06:17:52] [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`
[2026-03-19 06:17:52] [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`
[2026-03-19 06:17:52] [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`
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:17:52] [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`
[2026-03-19 06:17:52] [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`
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.106114s from omnipathdb.org (148 Kb/s); Redirect: 0s, DNS look up: 0.001075s, Connection: 0.019889s, Pretransfer: 0.068525s, First byte at: 0.105812s
[2026-03-19 06:17:52] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:17:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:17:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:17:53] [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`
[2026-03-19 06:17:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:53] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:17:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2026-03-19 06:17:53] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2026-03-19 06:17:53] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2026-03-19 06:17:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:53] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2026-03-19 06:17:55] [SUCCESS] [OmnipathR] Downloaded 67773 interactions.
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[Wang,Lit-BM-17],datasets=pathwayextra,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] Organism(s): 10090
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[Wang,Lit-BM-17],datasets=pathwayextra,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=10090,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:17:57] [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`
[2026-03-19 06:17:57] [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`
[2026-03-19 06:17:57] [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`
[2026-03-19 06:17:57] [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`
[2026-03-19 06:17:57] [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`
[2026-03-19 06:17:57] [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`
[2026-03-19 06:17:57] [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`
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.092179s from omnipathdb.org (170.3 Kb/s); Redirect: 0s, DNS look up: 0.001031s, Connection: 0.019072s, Pretransfer: 0.055932s, First byte at: 0.091817s
[2026-03-19 06:17:57] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:17:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:17:57 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:17:58] [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`
[2026-03-19 06:17:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:58] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:17:58] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2026-03-19 06:17:58] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2026-03-19 06:17:58] [INFO]    [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2026-03-19 06:17:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:17:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:58] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2026-03-19 06:17:59] [SUCCESS] [OmnipathR] Downloaded 41476 interactions.
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[PhosphoPoint,PhosphoSite],datasets=kinaseextra,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] Organism(s): 10116
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[PhosphoPoint,PhosphoSite],datasets=kinaseextra,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=10116,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:17:59] [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`
[2026-03-19 06:17:59] [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`
[2026-03-19 06:17:59] [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`
[2026-03-19 06:17:59] [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`
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:17:59] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:17:59] [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`
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.10544s from omnipathdb.org (148.9 Kb/s); Redirect: 0s, DNS look up: 0.001053s, Connection: 0.019167s, Pretransfer: 0.068212s, First byte at: 0.105077s
[2026-03-19 06:17:59] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:17:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:17:59 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:00] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:00] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2026-03-19 06:18:00] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:00] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:00] [SUCCESS] [OmnipathR] Downloaded 11083 interactions.
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[iTALK,Baccin2019],datasets=ligrecextra,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:00] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[iTALK,Baccin2019],datasets=ligrecextra,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:01] [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`
[2026-03-19 06:18:01] [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`
[2026-03-19 06:18:01] [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`
[2026-03-19 06:18:01] [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`
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:01] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:01] [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`
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.10848s from omnipathdb.org (144.7 Kb/s); Redirect: 0s, DNS look up: 0.001058s, Connection: 0.019794s, Pretransfer: 0.070531s, First byte at: 0.10817s
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:01 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:01] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:01] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2026-03-19 06:18:01] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:01] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:01] [SUCCESS] [OmnipathR] Downloaded 2840 interactions.
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:01] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:01] [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`
[2026-03-19 06:18:01] [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`
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:01] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.111453s from omnipathdb.org (140.9 Kb/s); Redirect: 0s, DNS look up: 0.00109s, Connection: 0.023424s, Pretransfer: 0.056806s, First byte at: 0.111001s
[2026-03-19 06:18:01] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:01 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:02] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:02] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-19 06:18:03] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-19 06:18:03] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2026-03-19 06:18:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:03] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:05] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
[2026-03-19 06:18:06] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:06] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2026-03-19 06:18:06] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=dorothea,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:06] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:06] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=dorothea,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort,dorothea_level],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=A,organisms=9606,qt_message=interactions,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:06] [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`
[2026-03-19 06:18:06] [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`
[2026-03-19 06:18:06] [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`
[2026-03-19 06:18:06] [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`
[2026-03-19 06:18:06] [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`
[2026-03-19 06:18:06] [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`
[2026-03-19 06:18:06] [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`
[2026-03-19 06:18:06] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:06] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:06] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:06] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.10575s from omnipathdb.org (148.5 Kb/s); Redirect: 0s, DNS look up: 0.001118s, Connection: 0.019542s, Pretransfer: 0.0682s, First byte at: 0.105429s
[2026-03-19 06:18:06] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:06 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:07] [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`
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:07] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2026-03-19 06:18:07] [INFO]    [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:07] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:07] [SUCCESS] [OmnipathR] Downloaded 6128 interactions.
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[miR2Disease,miRDeathDB],datasets=mirnatarget,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=[miR2Disease,miRDeathDB],datasets=mirnatarget,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:07] [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`
[2026-03-19 06:18:07] [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`
[2026-03-19 06:18:07] [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`
[2026-03-19 06:18:07] [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`
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:07] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:07] [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`
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.090258s from omnipathdb.org (173.9 Kb/s); Redirect: 0s, DNS look up: 0.001001s, Connection: 0.019512s, Pretransfer: 0.052956s, First byte at: 0.089915s
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:07 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:08] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:08] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2026-03-19 06:18:08] [INFO]    [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:08] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:08] [SUCCESS] [OmnipathR] Downloaded 648 interactions.
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=small_molecule,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=small_molecule,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,sources=TRAMETINIB,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:08] [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`
[2026-03-19 06:18:08] [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`
[2026-03-19 06:18:08] [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`
[2026-03-19 06:18:08] [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`
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-03-19 06:18:08] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-03-19 06:18:08] [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`
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Downloaded 112 bytes in 0.080588s from omnipathdb.org (1.4 Kb/s); Redirect: 0s, DNS look up: 0.00089s, Connection: 0.020293s, Pretransfer: 0.060029s, First byte at: 0.080558s
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:08 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:08] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:08] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2026-03-19 06:18:08] [INFO]    [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:08] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:08] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
[2026-03-19 06:18:08] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=enzyme-substrate relationships,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:09] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:09] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.096242s from omnipathdb.org (163.1 Kb/s); Redirect: 0s, DNS look up: 0.001083s, Connection: 0.021376s, Pretransfer: 0.054908s, First byte at: 0.095867s
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:09 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:09 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:09] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-03-19 06:18:09] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:09] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:11] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships.
[2026-03-19 06:18:11] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-03-19 06:18:11] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-03-19 06:18:11] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:11] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:11] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:11] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:11] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-19 06:18:11] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:13] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2026-03-19 06:18:14] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:14] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub]
[2026-03-19 06:18:14] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=[PhosphoSite,SIGNOR],datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:14] [TRACE]   [OmnipathR] Organism(s): 10090
[2026-03-19 06:18:14] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:14] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=enzsub,organism=9606,resources=[PhosphoSite,SIGNOR],datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,organisms=10090,qt_message=enzyme-substrate relationships,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:15] [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`
[2026-03-19 06:18:15] [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`
[2026-03-19 06:18:15] [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`
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:15] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.092666s from omnipathdb.org (169.4 Kb/s); Redirect: 0s, DNS look up: 0.00103s, Connection: 0.020146s, Pretransfer: 0.054038s, First byte at: 0.092287s
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:15] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:15] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2026-03-19 06:18:15] [INFO]    [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:15] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:16] [SUCCESS] [OmnipathR] Downloaded 16895 enzyme-substrate relationships.
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=complexes,organism=9606,resources=[CORUM,hu.MAP],datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=complexes,resources=[CORUM,hu.MAP],datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=protein complexes,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-19 06:18:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-19 06:18:16] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-19 06:18:16] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.089061s from omnipathdb.org (176.3 Kb/s); Redirect: 0s, DNS look up: 0.001135s, Connection: 0.018677s, Pretransfer: 0.052532s, First byte at: 0.088787s
[2026-03-19 06:18:16] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:17] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-03-19 06:18:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:17] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2026-03-19 06:18:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2026-03-19 06:18:17] [INFO]    [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2026-03-19 06:18:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:17] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:17] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes.
[2026-03-19 06:18:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:18:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:19] [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]
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=[proteins1=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,proteins2=COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,proteins3=COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,proteins4=COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,proteins5=COMPLEX:TERF2_WRN,proteins6=COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,proteins7=COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,proteins8=COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,proteins9=COMPLEX:CDK8_MED6_PARP1,proteins10=COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,...],qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Downloaded 11.6 Kb in 0.115278s from omnipathdb.org (100.9 Kb/s); Redirect: 0s, DNS look up: 0.001109s, Connection: 0.023545s, Pretransfer: 0.070212s, First byte at: 0.114952s
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:19 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:19 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:19] [INFO]    [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`.
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`.
[2026-03-19 06:18:19] [INFO]    [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1]
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:19] [INFO]    [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:19] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records.
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations]
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=NetPath,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=NetPath,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=[proteins1=NCAPD2,proteins2=NCAPG,proteins3=NCAPH,proteins4=PARP1,proteins5=SMC2,proteins6=SMC4,proteins7=XRCC1,proteins8=CCNA2,proteins9=CDK2,proteins10=LIG1,...],qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [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`
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] Downloaded 1.2 Kb in 0.083894s from omnipathdb.org (14.3 Kb/s); Redirect: 0s, DNS look up: 0.001157s, Connection: 0.024108s, Pretransfer: 0.060634s, First byte at: 0.083844s
[2026-03-19 06:18:19] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:19 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:19 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:20] [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`
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:20] [INFO]    [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`.
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`.
[2026-03-19 06:18:20] [INFO]    [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1]
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:20] [INFO]    [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:20] [SUCCESS] [OmnipathR] Downloaded 86 annotation records.
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations]
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=ComPPI,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=ComPPI,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=[proteins1=NCAPD2,proteins2=NCAPG,proteins3=NCAPH,proteins4=PARP1,proteins5=SMC2,proteins6=SMC4,proteins7=XRCC1,proteins8=CCNA2,proteins9=CDK2,proteins10=LIG1,...],qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:20] [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`
[2026-03-19 06:18:20] [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`
[2026-03-19 06:18:20] [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`
[2026-03-19 06:18:20] [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`
[2026-03-19 06:18:20] [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`
[2026-03-19 06:18:20] [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`
[2026-03-19 06:18:20] [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`
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Downloaded 2.7 Kb in 0.096784s from omnipathdb.org (28.2 Kb/s); Redirect: 0s, DNS look up: 0.001091s, Connection: 0.017524s, Pretransfer: 0.078476s, First byte at: 0.096701s
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:20 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:20] [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`
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:20] [INFO]    [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`.
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`.
[2026-03-19 06:18:20] [INFO]    [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1]
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:20] [INFO]    [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:20] [SUCCESS] [OmnipathR] Downloaded 366 annotation records.
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:18:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:18:21] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:18:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.121125s from omnipathdb.org (129.6 Kb/s); Redirect: 0s, DNS look up: 0.001054s, Connection: 0.023214s, Pretransfer: 0.075251s, First byte at: 0.12019s
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:21 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:21] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:21] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-03-19 06:18:21] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:21] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:21] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records.
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell_summary,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=NA,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell_summary,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=NA,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,qt_message=records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2026-03-19 06:18:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-03-19 06:18:21] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2026-03-19 06:18:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:21] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.081814s from omnipathdb.org (92.6 Kb/s); Redirect: 0s, DNS look up: 0.000938s, Connection: 0.022457s, Pretransfer: 0.057746s, First byte at: 0.081372s
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:21 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:22] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:22] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-03-19 06:18:22] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:22] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:22] [SUCCESS] [OmnipathR] Downloaded 1190 records.
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=<NULL>,scope=generic,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=<NULL>,scope=generic,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-19 06:18:22] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-19 06:18:22] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-19 06:18:22] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.097836s from omnipathdb.org (160.5 Kb/s); Redirect: 0s, DNS look up: 0.001035s, Connection: 0.021241s, Pretransfer: 0.055512s, First byte at: 0.096758s
[2026-03-19 06:18:22] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:22 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:24] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-03-19 06:18:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:24] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2026-03-19 06:18:25] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2026-03-19 06:18:25] [INFO]    [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2026-03-19 06:18:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:25] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:25] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records.
[2026-03-19 06:18:26] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2026-03-19 06:18:26] [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.
[2026-03-19 06:18:26] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`.
[2026-03-19 06:18:26] [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
[2026-03-19 06:18:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:28] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:18:28] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-03-19 05:01:21 UTC; omnipath
[2026-03-19 06:18:28] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-03-19 06:18:28] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-03-19 05:03:18 UTC; unix
[2026-03-19 06:18:28] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.8
[2026-03-19 06:18:28] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-03-19 06:18:29] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-03-19; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-03-19 06:18:29] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-19 06:18:29] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.7(2026-03-06); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); 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 2.2.2(2026-02-12); 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 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.8(2026-03-19); 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 1.2.1(2026-01-09); 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(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); 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 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-19 06:18:29] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Contains 22 files.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=TFcensus,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:29] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-03-19 06:18:29] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:29] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:29] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-03-19 06:18:29] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.130095s from rescued.omnipathdb.org (306.4 Kb/s); Redirect: 0s, DNS look up: 0.001278s, Connection: 0.021798s, Pretransfer: 0.068072s, First byte at: 0.109033s
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:29 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: Thu, 19 Mar 2026 06:18:29 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Thu, 19 Mar 2026 05:18:29 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=Thu, 19 Mar 2026 06:18:29 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-03-19 06:18:29] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:29] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-19 06:18:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:29] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-19 06:18:29] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.0705s from omabrowser.org (107.3 Kb/s); Redirect: 0s, DNS look up: 0.000583s, Connection: 0.003745s, Pretransfer: 0.036675s, First byte at: 0.07037s
[2026-03-19 06:18:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 19 Mar 2026 05:18:29 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=JZc3Ty6dEGFwiHMTfdqDMTS5LQuH%2BIp2YMEcwGoieFMEEJnvMmDBdlkV%2FzwtxUoIqx4KcTf%2B33k6iuRHqt2IuyZHPd3ki7W%2Bnha%2Ffuz6"}]}; cf-ray: 9dea044d099d2c10-STR; alt-svc: h3=":443"; ma=86400
[2026-03-19 06:18:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-19 06:18:30] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-03-19 06:18:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:30] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:30] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:18:30] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-19 06:18:30] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:18:30] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-19 06:18:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:30] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-19 06:18:30] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:18:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-19 06:18:53] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-19 06:18:53] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-03-19 06:18:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:53] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:53] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-03-19 06:18:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:53] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-19 06:18:54] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:54] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:54] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=TFcensus,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-19 06:18:54] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-19 06:18:54] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-19 06:18:54] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.083305s from omnipathdb.org (188.5 Kb/s); Redirect: 0s, DNS look up: 0.001169s, Connection: 0.016962s, Pretransfer: 0.050522s, First byte at: 0.082955s
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:54 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:54] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:55] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2026-03-19 06:18:55] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:55] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:55] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2026-03-19 06:18:55] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:55] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2026-03-19 06:18:55] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Downloaded 14.8 Kb in 0.06554s from static-content.springer.com (225.7 Kb/s); Redirect: 0s, DNS look up: 0.008683s, Connection: 0.01323s, Pretransfer: 0.057668s, First byte at: 0.064644s
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; content-type: application/octet-stream; x-guploader-uploadid: AGQBYWxtdKnIv94FC4JqnQwVWO2HzPNiX2aL2czpMf09TMcKyAbkEILX_dKWWe7LQxHvgvj9; cache-control: private, max-age=86400; last-modified: Thu, 16 Nov 2023 16:51:13 GMT; etag: "daa03c1eafd00cad9456b660ca85b849"; x-goog-generation: 1700153472991609; x-goog-metageneration: 1; x-goog-stored-content-encoding: identity; x-goog-stored-content-length: 160972; x-goog-hash: crc32c=v/3p0Q==; x-goog-hash: md5=2qA8Hq/QDK2UVrZgyoW4SQ==; x-goog-storage-class: MULTI_REGIONAL; server: UploadServer; x-cdn-origin: GCS, SNPaaS; accept-ranges: bytes; age: 1088; date: Thu, 19 Mar 2026 05:18:55 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230191-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1773897535.185275,VS0,VE2; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2026-03-19 06:18:55] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:55] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2026-03-19 06:18:55] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=[dorothea,tf_target,collectri],types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=[dorothea,tf_target,collectri],types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort,dorothea_level],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=[A,B,C],entity_types=protein,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-19 06:18:55] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-19 06:18:55] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-19 06:18:55] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.122714s from omnipathdb.org (127.9 Kb/s); Redirect: 0s, DNS look up: 0.001056s, Connection: 0.02374s, Pretransfer: 0.075679s, First byte at: 0.121619s
[2026-03-19 06:18:55] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:18:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:18:55 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:18:56] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-03-19 06:18:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:56] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:18:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2026-03-19 06:18:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2026-03-19 06:18:57] [INFO]    [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2026-03-19 06:18:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:18:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:18:57] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2026-03-19 06:19:01] [SUCCESS] [OmnipathR] Downloaded 147217 interactions.
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-19 06:19:01] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-19 06:19:01] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-19 06:19:01] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.111698s from omnipathdb.org (140.6 Kb/s); Redirect: 0s, DNS look up: 0.001136s, Connection: 0.021604s, Pretransfer: 0.067975s, First byte at: 0.110417s
[2026-03-19 06:19:01] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:19:01 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:19:01 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:19:03] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-03-19 06:19:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:03] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:03] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:19:03] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2026-03-19 06:19:04] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2026-03-19 06:19:04] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2026-03-19 06:19:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:04] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2026-03-19 06:19:04] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records.
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=ligand,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=secreted,causality=<NULL>,entity_types=protein,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=ligand,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=secreted,causality=<NULL>,entity_types=protein,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-19 06:19:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-19 06:19:05] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-19 06:19:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.104148s from omnipathdb.org (150.7 Kb/s); Redirect: 0s, DNS look up: 0.001074s, Connection: 0.018937s, Pretransfer: 0.068305s, First byte at: 0.103774s
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:19:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:19:05 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:19:05] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:05] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2026-03-19 06:19:05] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2026-03-19 06:19:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:06] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2026-03-19 06:19:06] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records.
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-19 06:19:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-19 06:19:06] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-19 06:19:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.094187s from omnipathdb.org (166.7 Kb/s); Redirect: 0s, DNS look up: 0.001136s, Connection: 0.020611s, Pretransfer: 0.054269s, First byte at: 0.093763s
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:19:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:19:06 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:19:06] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:06] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-03-19 06:19:06] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:06] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2026-03-19 06:19:06] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records.
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=receptor,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=plasma_membrane_transmembrane,causality=<NULL>,entity_types=protein,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=receptor,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=plasma_membrane_transmembrane,causality=<NULL>,entity_types=protein,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-19 06:19:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-19 06:19:06] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-19 06:19:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.10149s from omnipathdb.org (154.7 Kb/s); Redirect: 0s, DNS look up: 0.000985s, Connection: 0.02285s, Pretransfer: 0.057017s, First byte at: 0.10109s
[2026-03-19 06:19:06] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:19:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:19:06 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:19:07] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:07] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2026-03-19 06:19:07] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:07] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2026-03-19 06:19:07] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records.
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-03-19 06:19:07] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-19 06:19:07] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=secreted,causality=trans,entity_types=protein,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=secreted,causality=trans,entity_types=protein,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-19 06:19:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-19 06:19:07] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-19 06:19:07] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.106472s from omnipathdb.org (147.5 Kb/s); Redirect: 0s, DNS look up: 0.001011s, Connection: 0.020602s, Pretransfer: 0.065914s, First byte at: 0.105503s
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:19:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:19:07 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:19:07] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:07] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2026-03-19 06:19:08] [INFO]    [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:08] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2026-03-19 06:19:08] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records.
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-03-19 06:19:08] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-19 06:19:08] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=plasma_membrane_transmembrane,causality=rec,entity_types=protein,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=<NULL>,scope=<NULL>,aspect=<NULL>,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=plasma_membrane_transmembrane,causality=rec,entity_types=protein,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-19 06:19:08] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-19 06:19:08] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-19 06:19:08] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.091892s from omnipathdb.org (170.9 Kb/s); Redirect: 0s, DNS look up: 0.001094s, Connection: 0.019616s, Pretransfer: 0.054195s, First byte at: 0.091547s
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:19:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:19:08 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:19:08] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:08] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2026-03-19 06:19:08] [INFO]    [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:08] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2026-03-19 06:19:08] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records.
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Args for `omnipath_query`: [categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,query_type=intercell,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane]]
[2026-03-19 06:19:08] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,organism=9606,resources=<NULL>,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=intercell,resources=<NULL>,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=[transmitter,receiver,secreted,plasma_membrane_peripheral,plasma_membrane_transmembrane],download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,categories=<NULL>,parent=[secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral],scope=<NULL>,aspect=locational,source=<NULL>,transmitter=<NULL>,receiver=<NULL>,secreted=<NULL>,plasma_membrane_peripheral=<NULL>,plasma_membrane_transmembrane=<NULL>,proteins=<NULL>,topology=<NULL>,causality=<NULL>,qt_message=intercellular communication role records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-03-19 06:19:09] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-03-19 06:19:09] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=<NULL>,datasets=omnipath,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,entity_types=protein,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:09] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:09] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.089713s from omnipathdb.org (175 Kb/s); Redirect: 0s, DNS look up: 0.001093s, Connection: 0.018842s, Pretransfer: 0.05348s, First byte at: 0.089394s
[2026-03-19 06:19:09] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:19:09 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:19:09 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:19:10] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:10] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:19:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2026-03-19 06:19:10] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2026-03-19 06:19:10] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2026-03-19 06:19:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:10] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2026-03-19 06:19:12] [SUCCESS] [OmnipathR] Downloaded 84507 interactions.
[2026-03-19 06:19:12] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:19:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2026-03-19 06:19:12] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:12] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:12] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_pathway,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Downloaded 11.4 Kb in 0.111934s from omnipathdb.org (102.1 Kb/s); Redirect: 0s, DNS look up: 0.001199s, Connection: 0.022211s, Pretransfer: 0.068052s, First byte at: 0.111264s
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:19:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:19:13 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:19:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:13] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2026-03-19 06:19:13] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:13] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2026-03-19 06:19:13] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records.
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=SignaLink_function,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=SignaLink_function,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,entity_types=protein,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:19:13] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:19:14] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:19:14] [TRACE]   [OmnipathR] Downloaded 10.6 Kb in 0.09s from omnipathdb.org (117.6 Kb/s); Redirect: 0s, DNS look up: 0.000989s, Connection: 0.021013s, Pretransfer: 0.065564s, First byte at: 0.089791s
[2026-03-19 06:19:14] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:19:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:19:13 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:19:14] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-03-19 06:19:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:14] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:19:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2026-03-19 06:19:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2026-03-19 06:19:14] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2026-03-19 06:19:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:14] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2026-03-19 06:19:14] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records.
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2026-03-19 06:19:15] [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.
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,organism=9606,resources=[ORegAnno,PAZAR],datasets=tf_target,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=interactions,resources=[ORegAnno,PAZAR],datasets=tf_target,types=<NULL>,genesymbols=yes,fields=[sources,references,curation_effort],default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,dorothea_levels=[A,B],entity_types=protein,qt_message=interactions,organisms=9606,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:15] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:15] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:15] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.126377s from omnipathdb.org (124.2 Kb/s); Redirect: 0s, DNS look up: 0.00101s, Connection: 0.023271s, Pretransfer: 0.07832s, First byte at: 0.126025s
[2026-03-19 06:19:15] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:19:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:19:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:19:16] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:16] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2026-03-19 06:19:16] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:16] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2026-03-19 06:19:16] [SUCCESS] [OmnipathR] Downloaded 4242 interactions.
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_location,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_location,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:19:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:19:16] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:19:16] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.099594s from omnipathdb.org (157.6 Kb/s); Redirect: 0s, DNS look up: 0.001004s, Connection: 0.019072s, Pretransfer: 0.063308s, First byte at: 0.099259s
[2026-03-19 06:19:16] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:19:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:19:16 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:19:17] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:19:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:17] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:19:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-03-19 06:19:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-03-19 06:19:17] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2026-03-19 06:19:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:17] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2026-03-19 06:19:17] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records.
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=kinase.com,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=kinase.com,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-19 06:19:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-19 06:19:18] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-19 06:19:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.102692s from omnipathdb.org (152.9 Kb/s); Redirect: 0s, DNS look up: 0.000876s, Connection: 0.022739s, Pretransfer: 0.057531s, First byte at: 0.101693s
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 19 Mar 2026 05:19:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 19 Mar 2026 06:19:18 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-19 06:19:18] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:18] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-03-19 06:19:18] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-19 06:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:18] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2026-03-19 06:19:18] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records.
[2026-03-19 06:19:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:19:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2026-03-19 06:19:24] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=UniProt_location,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:24] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:19:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:24] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=UniProt_location,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:19:24] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-03-19 06:19:24] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-03-19 06:19:24] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2026-03-19 06:19:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-19 06:19:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2026-03-19 06:19:24] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,organism=9606,resources=kinase.com,datasets=<NULL>,types=<NULL>,genesymbols=yes,fields=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],format=data.frame,references_by_resource=TRUE,add_counts=TRUE,license=<NULL>,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE]
[2026-03-19 06:19:25] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-19 06:19:25] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-19 06:19:25] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-19 06:19:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-19 06:19:25] [TRACE]   [OmnipathR] Param in `omnipath_query`: [query_type=annotations,resources=kinase.com,datasets=<NULL>,types=<NULL>,default_fields=TRUE,silent=FALSE,logicals=<NULL>,download_args=[],references_by_resource=TRUE,add_counts=TRUE,license=academic,password=<NULL>,exclude=<NULL>,json_param=[],strict_evidences=FALSE,genesymbol_resource=UniProt,cache=TRUE,proteins=<NULL>,qt_message=annotation records,keep_evidences=FALSE,orthology_targets=integer(0)]
[2026-03-19 06:19:25] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-19 06:19:25] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-03-19 06:19:25] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-03-19 06:19:25] [SUCCESS] [OmnipathR] Loaded 2102 annotation records from cache.
--- finished re-building ‘paths.Rmd’

SUMMARY: processing the following file failed:
  ‘cosmos.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-03-19_0551/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2026-03-19 06:19:34 CET ]