[ Started: 2026-02-09 03:28:34 CET ]
[ OmnipathR v3.19.6 for BioC-3.22 from https://github.com/saezlab/OmnipathR@devel (4c56371 2026-01-29 16:23:53) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/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 ‘3.19.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2026-02-09 03:29:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:29:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:29:05] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:29:05] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-02-09 02:27:15 UTC; omnipath
[2026-02-09 03:29:05] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-09 03:29:05] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-09 02:28:37 UTC; unix
[2026-02-09 03:29:05] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-09 03:29:05] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-09 03:29:06] [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=2026-02-09; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-09 03:29:06] [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]
[2026-02-09 03:29:06] [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 1.2.3(2024-06-02); 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 1.6.6(2025-04-12); 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 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); 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 3.19.6(2026-02-09); 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 2.1.6(2025-11-14); 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 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-09 03:29:06] [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
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] Contains 1 files.
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:29:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-09 03:29:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:29:06] [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
[2026-02-09 03:29:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:29:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:29:16] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:29:16] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-02-09 02:27:15 UTC; omnipath
[2026-02-09 03:29:16] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-09 03:29:16] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-09 02:28:37 UTC; unix
[2026-02-09 03:29:16] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-09 03:29:16] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-09 03:29:17] [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=2026-02-09; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-09 03:29:17] [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]
[2026-02-09 03:29:17] [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 1.2.3(2024-06-02); 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 1.6.6(2025-04-12); 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 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); 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 3.19.6(2026-02-09); 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 2.1.6(2025-11-14); 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 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-09 03:29:17] [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
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] Contains 1 files.
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:29:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:29:17] [TRACE]   [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
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:
  ORIGINAL enzyme_genesymbol gem_info git_host git_repo handle id
  latest_version path 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 ... WARNING
Codoc mismatches from Rd file 'load_db.Rd':
load_db
  Code: function(key, param = list(), reload = FALSE)
  Docs: function(key, param = list())
  Argument names in code not in docs:
    reload

* 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")
[2026-02-09 03:32:20] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens
[2026-02-09 03:32:20] [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>
[2026-02-09 03:32:20] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:32:20] [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`.
[2026-02-09 03:32:20] [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`
[2026-02-09 03:32:20] [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`.
[2026-02-09 03:32:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:32:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:32:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:32:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:32:20] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:32:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2026-02-09 03:32:20] [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`
[2026-02-09 03:32:20] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-09 03:32:20] [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`
[2026-02-09 03:32:20] [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`.
[2026-02-09 03:32:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:32:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:32:20] [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]
[2026-02-09 03:32:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:32:20] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-09 03:32:21] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-09 03:32:21] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:32:21] [TRACE]   [OmnipathR] Downloaded 1014 bytes in 0.040586s from www.ensembl.org (24.4 Kb/s); Redirect: 0s, DNS look up: 6.6e-05s, Connection: 0.018332s, Pretransfer: 0.018429s, First byte at: 0.040479s
[2026-02-09 03:32:21] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: 3118:11FA79:1AE112:1BCA44:697C5971; Server: GitHub.com; X-Cache-Hits: 22; Vary: Accept-Encoding; Cache-Control: no-cache, no-store, must-revalidate; x-proxy-cache: MISS; X-Cache: HIT; Content-Type: text/html; charset=utf-8; X-Fastly-Request-ID: b77e03444430f7735974d008b61e09b826acd3bd; Content-Encoding: gzip; Date: Mon, 09 Feb 2026 02:32:21 GMT; Expires: 0; X-Served-By: cache-lcy-egml8630067-LCY; Pragma: no-cache; X-Timer: S1770604341.014702,VS0,VE0; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"68b6c2f9-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 529; Content-Length: 1014
[2026-02-09 03:32:21] [TRACE]   [OmnipathR] Response headers: [X-GitHub-Request-Id=3118:11FA79:1AE112:1BCA44:697C5971,Server=GitHub.com,X-Cache-Hits=22,Vary=Accept-Encoding,Cache-Control=no-cache, no-store, must-revalidate,x-proxy-cache=MISS,X-Cache=HIT,Content-Type=text/html; charset=utf-8,X-Fastly-Request-ID=b77e03444430f7735974d008b61e09b826acd3bd,Content-Encoding=gzip,Date=Mon, 09 Feb 2026 02:32:21 GMT,Expires=0,X-Served-By=cache-lcy-egml8630067-LCY,Pragma=no-cache,X-Timer=S1770604341.014702,VS0,VE0,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"68b6c2f9-8aa",Via=1.1 varnish,Connection=keep-alive,Age=529,Content-Length=1014]
[2026-02-09 03:32:21] [TRACE]   [OmnipathR] Calling reader callback on response.
[2026-02-09 03:32:21] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2026-02-09 03:32:21] [INFO]    [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1]
[2026-02-09 03:32:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:32:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:32:21] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`.
[2026-02-09 03:32:21] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <html>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <head>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <style>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] html,
[2026-02-09 03:32:21] [WARN]    [OmnipathR] body {
[2026-02-09 03:32:21] [WARN]    [OmnipathR] padding: 0;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] margin: 0;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] height: 100%;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] }
[2026-02-09 03:32:21] [WARN]    [OmnipathR] body {
[2026-02-09 03:32:21] [WARN]    [OmnipathR] display: grid;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] font-size: 90%;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] }
[2026-02-09 03:32:21] [WARN]    [OmnipathR] h1 {
[2026-02-09 03:32:21] [WARN]    [OmnipathR] font-size: 1.5rem;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] }
[2026-02-09 03:32:21] [WARN]    [OmnipathR] h2 {
[2026-02-09 03:32:21] [WARN]    [OmnipathR] font-size: 1.2rem;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] }
[2026-02-09 03:32:21] [WARN]    [OmnipathR] h3 {
[2026-02-09 03:32:21] [WARN]    [OmnipathR] font-size: 1.1rem;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] }
[2026-02-09 03:32:21] [WARN]    [OmnipathR] header {
[2026-02-09 03:32:21] [WARN]    [OmnipathR] grid-row: header;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] padding: 5px;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] height: 60px;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] background-color: #333366;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] }
[2026-02-09 03:32:21] [WARN]    [OmnipathR] header img {
[2026-02-09 03:32:21] [WARN]    [OmnipathR] width: 185px;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] height: 45px
[2026-02-09 03:32:21] [WARN]    [OmnipathR] }
[2026-02-09 03:32:21] [WARN]    [OmnipathR] main {
[2026-02-09 03:32:21] [WARN]    [OmnipathR] grid-row: main;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] padding: 20px;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] }
[2026-02-09 03:32:21] [WARN]    [OmnipathR] .mirrors {
[2026-02-09 03:32:21] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] margin-top: 20px;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] padding: 10px;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] }
[2026-02-09 03:32:21] [WARN]    [OmnipathR] footer {
[2026-02-09 03:32:21] [WARN]    [OmnipathR] grid-row: footer;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] padding: 0 20px;
[2026-02-09 03:32:21] [WARN]    [OmnipathR] }
[2026-02-09 03:32:21] [WARN]    [OmnipathR] </style>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] </head>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <body>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <header>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2026-02-09 03:32:21] [WARN]    [OmnipathR] </header>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <main>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <p>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2026-02-09 03:32:21] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2026-02-09 03:32:21] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2026-02-09 03:32:21] [WARN]    [OmnipathR] </p>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <div class="mirrors">
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <ul>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] </ul>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2026-02-09 03:32:21] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2026-02-09 03:32:21] [WARN]    [OmnipathR] data centre.
[2026-02-09 03:32:21] [WARN]    [OmnipathR] </div>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] </main>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <footer>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] <p>&copy; 2025 EMBL-EBI</p>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] </footer>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] </body>
[2026-02-09 03:32:21] [WARN]    [OmnipathR] </html>
[2026-02-09 03:32:21] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 81 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
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:06] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:33:06] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-02-09 02:27:15 UTC; omnipath
[2026-02-09 03:33:06] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-09 03:33:06] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-09 02:28:37 UTC; unix
[2026-02-09 03:33:06] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-09 03:33:06] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-09 03:33:06] [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=2026-02-09; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-09 03:33:06] [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]
[2026-02-09 03:33:06] [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 1.2.3(2024-06-02); 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 1.6.6(2025-04-12); 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 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); 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 3.19.6(2026-02-09); 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 2.1.6(2025-11-14); 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 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-09 03:33:06] [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
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Contains 16 files.
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2026-02-09 03:33:06] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-02-09 03:33:06] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:06] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:06] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-09 03:33:06] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:33:06] [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]
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:33:06] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.124459s from rescued.omnipathdb.org (320.3 Kb/s); Redirect: 0s, DNS look up: 0.001174s, Connection: 0.018425s, Pretransfer: 0.072584s, First byte at: 0.106904s
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:33:07 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: Mon, 09 Feb 2026 03:33:07 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Mon, 09 Feb 2026 02:33:07 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=Mon, 09 Feb 2026 03:33:07 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-09 03:33:07] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:07] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-09 03:33:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:07] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-09 03:33:07] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:33:07] [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]
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.089092s from omabrowser.org (84.9 Kb/s); Redirect: 0s, DNS look up: 0.00058s, Connection: 0.006541s, Pretransfer: 0.03925s, First byte at: 0.088912s
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 09 Feb 2026 02:33:07 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=wTUUK%2BPVjIJ2MeKBdsySNq53lD5ZPBTPSdC3zVVm1JfSZTWINUtwNce2l0EilNCr8%2Bnbpk50tOsUstPIxac%2BWNGuwvWUDnw2gZoZlYnX"}]}; cf-ray: 9caff5cdab164d25-FRA; alt-svc: h3=":443"; ma=86400
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-09 03:33:07] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:07] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-09 03:33:07] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:07] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-09 03:33:07] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:33:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-09 03:33:30] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:30] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:30] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-09 03:33:30] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:30] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-02-09 03:33:30] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:33:30] [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`
[2026-02-09 03:33:30] [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`
[2026-02-09 03:33:30] [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`
[2026-02-09 03:33:30] [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`
[2026-02-09 03:33:30] [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`
[2026-02-09 03:33:30] [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`
[2026-02-09 03:33:30] [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`
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:33:30] [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]
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.113997s from omnipathdb.org (137.4 Kb/s); Redirect: 0s, DNS look up: 0.000991s, Connection: 0.020254s, Pretransfer: 0.064007s, First byte at: 0.113529s
[2026-02-09 03:33:30] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:33:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:33:30 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:33:31] [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`
[2026-02-09 03:33:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:31] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:33:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2026-02-09 03:33:32] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2026-02-09 03:33:32] [INFO]    [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2026-02-09 03:33:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:32] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2026-02-09 03:33:35] [SUCCESS] [OmnipathR] Downloaded 131398 interactions.
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:39] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:33:39] [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]
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.100739s from omnipathdb.org (155.5 Kb/s); Redirect: 0s, DNS look up: 0.00093s, Connection: 0.022758s, Pretransfer: 0.055875s, First byte at: 0.100355s
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:33:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:33:39 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:33:39] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:39] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:33:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-02-09 03:33:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-02-09 03:33:40] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2026-02-09 03:33:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:40] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2026-02-09 03:33:41] [SUCCESS] [OmnipathR] Downloaded 47840 enzyme-substrate relationships.
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:42] [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`
[2026-02-09 03:33:42] [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`
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:42] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:33:42] [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]
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.109062s from omnipathdb.org (143.7 Kb/s); Redirect: 0s, DNS look up: 0.000894s, Connection: 0.021327s, Pretransfer: 0.066783s, First byte at: 0.108299s
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:33:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:33:42 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:33:42] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:42] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:33:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-02-09 03:33:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-02-09 03:33:43] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2026-02-09 03:33:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:43] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2026-02-09 03:33:45] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2026-02-09 03:33:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2026-02-09 03:33:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2026-02-09 03:33:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:33:46] [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]
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.093654s from omnipathdb.org (167.3 Kb/s); Redirect: 0s, DNS look up: 0.000881s, Connection: 0.020444s, Pretransfer: 0.054033s, First byte at: 0.093318s
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:33:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:33:46 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:33:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:46] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:33:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2026-02-09 03:33:47] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:47] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2026-02-09 03:33:47] [SUCCESS] [OmnipathR] Downloaded 52085 protein complexes.
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:33:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:33:47] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:33:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:33:47] [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]
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.091296s from omnipathdb.org (171.6 Kb/s); Redirect: 0s, DNS look up: 0.000909s, Connection: 0.019771s, Pretransfer: 0.05315s, First byte at: 0.090468s
[2026-02-09 03:33:47] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:33:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:33:47 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:33:47] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:48] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-02-09 03:33:48] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:48] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2026-02-09 03:33:48] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records.
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-02-09 03:33:48] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-02-09 03:33:48] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-02-09 03:33:48] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:33:48] [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]
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] Downloaded 60 bytes in 0.085423s from omnipathdb.org (702 bytes/s); Redirect: 0s, DNS look up: 0.000896s, Connection: 0.018802s, Pretransfer: 0.067177s, First byte at: 0.085406s
[2026-02-09 03:33:48] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:33:48 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 60; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:33:48 GMT; Cache-Control: public; X-Frame-Options: DENY
[2026-02-09 03:33:49] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:49] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2026-02-09 03:33:49] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:49] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2026-02-09 03:33:49] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2026-02-09 03:33:49] [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.
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-02-09 03:33:49] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:33:49] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-02-09 03:33:49] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-02-09 03:33:49] [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`
[2026-02-09 03:33:49] [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`
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-02-09 03:33:49] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:33:49] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:33:49] [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]
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.108299s from omnipathdb.org (144.7 Kb/s); Redirect: 0s, DNS look up: 0.000915s, Connection: 0.020368s, Pretransfer: 0.068975s, First byte at: 0.107921s
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:33:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:33:50 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:33:50] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:50] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2026-02-09 03:33:50] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:50] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2026-02-09 03:33:50] [SUCCESS] [OmnipathR] Downloaded 3752 annotation records.
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:33:50] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:33:50] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:33:50] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:33:50] [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]
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.095274s from omnipathdb.org (164.4 Kb/s); Redirect: 0s, DNS look up: 0.000964s, Connection: 0.021167s, Pretransfer: 0.054732s, First byte at: 0.094928s
[2026-02-09 03:33:50] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:33:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:33:50 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:33:51] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:51] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-02-09 03:33:51] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:51] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2026-02-09 03:33:51] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records.
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:51] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-02-09 03:33:51] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:33:53] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2026-02-09 03:33:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:33:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2026-02-09 03:33:53] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:33:53] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:33:53] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:33:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:33:54] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-02-09 03:33:54] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:33:54] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache.
[2026-02-09 03:33:54] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:33:54] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:33:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2026-02-09 03:33:54] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2026-02-09 03:33:54] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2026-02-09 03:33:54] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2026-02-09 03:33:54] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2026-02-09 03:33:54] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2026-02-09 03:33:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2026-02-09 03:33:54] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:33:54] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:33:54] [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]
[2026-02-09 03:33:54] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:33:54] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.090896s from omnipathdb.org (172.4 Kb/s); Redirect: 0s, DNS look up: 0.000917s, Connection: 0.019286s, Pretransfer: 0.052949s, First byte at: 0.089733s
[2026-02-09 03:33:54] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:33:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:33:54 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:33:55] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2026-02-09 03:33:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:55] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:55] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:33:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2026-02-09 03:33:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2026-02-09 03:33:57] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2026-02-09 03:33:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:57] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2026-02-09 03:33:58] [SUCCESS] [OmnipathR] Downloaded 388239 intercellular communication role records.
[2026-02-09 03:33:58] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2026-02-09 03:33:58] [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.
[2026-02-09 03:33:58] [TRACE]   [OmnipathR] Bypassing call: `intercell_network()`.
[2026-02-09 03:33:58] [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.
[2026-02-09 03:33:58] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2026-02-09 03:33:58] [TRACE]   [OmnipathR] Bypassing call: `    loc_consensus_percentile = 50, simplify = TRUE)`.
[2026-02-09 03:33:58] [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.
[2026-02-09 03:33:58] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:33:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:58] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2026-02-09 03:33:59] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-02-09 03:33:59] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2026-02-09 03:33:59] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:33:59] [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]
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Downloaded 9.4 Kb in 0.081844s from omnipathdb.org (114.7 Kb/s); Redirect: 0s, DNS look up: 0.000945s, Connection: 0.017473s, Pretransfer: 0.064013s, First byte at: 0.081652s
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:33:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:33:59 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:33:59] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:59] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-02-09 03:33:59] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:59] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2026-02-09 03:33:59] [SUCCESS] [OmnipathR] Downloaded 1190 records.
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:33:59] [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`.
[2026-02-09 03:33:59] [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`
[2026-02-09 03:33:59] [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`.
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:33:59] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-02-09 03:33:59] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:33:59] [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]
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-09 03:33:59] [TRACE]   [OmnipathR] Downloaded 43 bytes in 0.321021s from rest.uniprot.org (133 bytes/s); Redirect: 0s, DNS look up: 0.001024s, Connection: 0.019466s, Pretransfer: 0.071629s, First byte at: 0.32095s
[2026-02-09 03:33:59] [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: 28-January-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Mon, 09 Feb 2026 02:33:59 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
[2026-02-09 03:34:08] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-02-09 03:34:08] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2026-02-09 03:34:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:08] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2026-02-09 03:34:08] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records
[2026-02-09 03:34:08] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2026-02-09 03:34:08] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-02-09 03:34:08] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2026-02-09 03:34:08] [TRACE]   [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`.
[2026-02-09 03:34:08] [TRACE]   [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`.
[2026-02-09 03:34:08] [TRACE]   [OmnipathR] Bypassing call: `go_ontology_download()`.
[2026-02-09 03:34:08] [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.
[2026-02-09 03:34:08] [TRACE]   [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2026-02-09 03:34:08] [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.
[2026-02-09 03:34:08] [TRACE]   [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2026-02-09 03:34:08] [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
[2026-02-09 03:34:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:10] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:34:10] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-02-09 02:27:15 UTC; omnipath
[2026-02-09 03:34:10] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-09 03:34:10] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-09 02:28:37 UTC; unix
[2026-02-09 03:34:10] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-09 03:34:10] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-09 03:34:11] [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=2026-02-09; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-09 03:34:11] [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]
[2026-02-09 03:34:11] [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 1.2.3(2024-06-02); 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 1.6.6(2025-04-12); 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 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); 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 3.19.6(2026-02-09); 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 2.1.6(2025-11-14); 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 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-09 03:34:11] [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
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Contains 16 files.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2026-02-09 03:34:11] [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.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2026-02-09 03:34:11] [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.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2026-02-09 03:34:11] [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.
[2026-02-09 03:34:11] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-02-09 03:34:11] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:11] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:11] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-09 03:34:11] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:34:11] [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]
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.107961s from rescued.omnipathdb.org (369.2 Kb/s); Redirect: 0s, DNS look up: 0.001192s, Connection: 0.019228s, Pretransfer: 0.053881s, First byte at: 0.089836s
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:34:11 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: Mon, 09 Feb 2026 03:34:11 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Mon, 09 Feb 2026 02:34:11 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=Mon, 09 Feb 2026 03:34:11 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-09 03:34:11] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:11] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-09 03:34:11] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:11] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-09 03:34:11] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:34:11] [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]
[2026-02-09 03:34:11] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-09 03:34:12] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.105399s from omabrowser.org (71.8 Kb/s); Redirect: 0s, DNS look up: 0.000538s, Connection: 0.00502s, Pretransfer: 0.056816s, First byte at: 0.105241s
[2026-02-09 03:34:12] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 09 Feb 2026 02:34:11 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=tONOTxSpS56D5hUVO0iyQ9jW%2FxW6lV29o1VUTpUI4ek4MH4y5T7LAHV4fZjSpbk85JDWnVZP1gTLKWwC24TxHy3pqFdLRyGAkvoZ7iSL"}]}; cf-ray: 9caff760b80465a6-FRA; alt-svc: h3=":443"; ma=86400
[2026-02-09 03:34:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-09 03:34:12] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-09 03:34:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:12] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-09 03:34:12] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:34:12] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-09 03:34:12] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:34:12] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-09 03:34:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:12] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:34:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-09 03:34:12] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:34:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:34:33] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-09 03:34:33] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-09 03:34:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:33] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-09 03:34:33] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-02-09 03:34:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:33] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:34:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-09 03:34:34] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:34] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-02-09 03:34:34] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-09 03:34:34] [INFO]    [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:34:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:34:34] [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`
[2026-02-09 03:34:34] [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`
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:34:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:34:34] [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]
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.095296s from omnipathdb.org (164.4 Kb/s); Redirect: 0s, DNS look up: 0.000884s, Connection: 0.020725s, Pretransfer: 0.054558s, First byte at: 0.094531s
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:34:34 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:34:34 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:34:34] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:34] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:34:34] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-02-09 03:34:35] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-02-09 03:34:35] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2026-02-09 03:34:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:35] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2026-02-09 03:34:37] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
[2026-02-09 03:34:37] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2026-02-09 03:34:37] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2026-02-09 03:34:37] [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>
[2026-02-09 03:34:37] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:34:37] [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`.
[2026-02-09 03:34:37] [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`
[2026-02-09 03:34:37] [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`.
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:38] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2026-02-09 03:34:38] [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`
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-09 03:34:38] [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`
[2026-02-09 03:34:38] [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`.
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:34:38] [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]
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] Downloaded 1014 bytes in 0.051035s from www.ensembl.org (19.4 Kb/s); Redirect: 0s, DNS look up: 0.010948s, Connection: 0.029312s, Pretransfer: 0.029362s, First byte at: 0.050971s
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: 3118:11FA79:1AE112:1BCA44:697C5971; Server: GitHub.com; X-Cache-Hits: 45; Vary: Accept-Encoding; Cache-Control: no-cache, no-store, must-revalidate; x-proxy-cache: MISS; X-Cache: HIT; Content-Type: text/html; charset=utf-8; X-Fastly-Request-ID: ac3ad2cae53fd7974737d37061a1f23773978328; Content-Encoding: gzip; Date: Mon, 09 Feb 2026 02:34:38 GMT; Expires: 0; X-Served-By: cache-lcy-egml8630062-LCY; Pragma: no-cache; X-Timer: S1770604478.110781,VS0,VE0; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"68b6c2f9-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 62; Content-Length: 1014
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] Response headers: [X-GitHub-Request-Id=3118:11FA79:1AE112:1BCA44:697C5971,Server=GitHub.com,X-Cache-Hits=45,Vary=Accept-Encoding,Cache-Control=no-cache, no-store, must-revalidate,x-proxy-cache=MISS,X-Cache=HIT,Content-Type=text/html; charset=utf-8,X-Fastly-Request-ID=ac3ad2cae53fd7974737d37061a1f23773978328,Content-Encoding=gzip,Date=Mon, 09 Feb 2026 02:34:38 GMT,Expires=0,X-Served-By=cache-lcy-egml8630062-LCY,Pragma=no-cache,X-Timer=S1770604478.110781,VS0,VE0,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"68b6c2f9-8aa",Via=1.1 varnish,Connection=keep-alive,Age=62,Content-Length=1014]
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] Calling reader callback on response.
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2026-02-09 03:34:38] [INFO]    [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:38] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2026-02-09 03:34:38] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <html>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <head>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <style>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] html,
[2026-02-09 03:34:38] [WARN]    [OmnipathR] body {
[2026-02-09 03:34:38] [WARN]    [OmnipathR] padding: 0;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] margin: 0;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] height: 100%;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] }
[2026-02-09 03:34:38] [WARN]    [OmnipathR] body {
[2026-02-09 03:34:38] [WARN]    [OmnipathR] display: grid;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] font-size: 90%;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] }
[2026-02-09 03:34:38] [WARN]    [OmnipathR] h1 {
[2026-02-09 03:34:38] [WARN]    [OmnipathR] font-size: 1.5rem;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] }
[2026-02-09 03:34:38] [WARN]    [OmnipathR] h2 {
[2026-02-09 03:34:38] [WARN]    [OmnipathR] font-size: 1.2rem;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] }
[2026-02-09 03:34:38] [WARN]    [OmnipathR] h3 {
[2026-02-09 03:34:38] [WARN]    [OmnipathR] font-size: 1.1rem;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] }
[2026-02-09 03:34:38] [WARN]    [OmnipathR] header {
[2026-02-09 03:34:38] [WARN]    [OmnipathR] grid-row: header;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] padding: 5px;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] height: 60px;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] background-color: #333366;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] }
[2026-02-09 03:34:38] [WARN]    [OmnipathR] header img {
[2026-02-09 03:34:38] [WARN]    [OmnipathR] width: 185px;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] height: 45px
[2026-02-09 03:34:38] [WARN]    [OmnipathR] }
[2026-02-09 03:34:38] [WARN]    [OmnipathR] main {
[2026-02-09 03:34:38] [WARN]    [OmnipathR] grid-row: main;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] padding: 20px;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] }
[2026-02-09 03:34:38] [WARN]    [OmnipathR] .mirrors {
[2026-02-09 03:34:38] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] margin-top: 20px;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] padding: 10px;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] }
[2026-02-09 03:34:38] [WARN]    [OmnipathR] footer {
[2026-02-09 03:34:38] [WARN]    [OmnipathR] grid-row: footer;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] padding: 0 20px;
[2026-02-09 03:34:38] [WARN]    [OmnipathR] }
[2026-02-09 03:34:38] [WARN]    [OmnipathR] </style>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] </head>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <body>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <header>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2026-02-09 03:34:38] [WARN]    [OmnipathR] </header>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <main>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <p>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2026-02-09 03:34:38] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2026-02-09 03:34:38] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2026-02-09 03:34:38] [WARN]    [OmnipathR] </p>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <div class="mirrors">
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <ul>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] </ul>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2026-02-09 03:34:38] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2026-02-09 03:34:38] [WARN]    [OmnipathR] data centre.
[2026-02-09 03:34:38] [WARN]    [OmnipathR] </div>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] </main>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <footer>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] <p>&copy; 2025 EMBL-EBI</p>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] </footer>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] </body>
[2026-02-09 03:34:38] [WARN]    [OmnipathR] </html>
[2026-02-09 03:34:38] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 81 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
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:41] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:34:41] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-02-09 02:27:15 UTC; omnipath
[2026-02-09 03:34:41] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-09 03:34:41] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-09 02:28:37 UTC; unix
[2026-02-09 03:34:41] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-09 03:34:41] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-09 03:34:41] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-02-09; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-09 03:34:41] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-09 03:34:41] [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 1.2.3(2024-06-02); 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 1.6.6(2025-04-12); 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 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); 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 3.19.6(2026-02-09); 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 2.1.6(2025-11-14); 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 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-09 03:34:41] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Contains 7 files.
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-02-09 03:34:41] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Checking on-disk cache for database `up_gs`.
[2026-02-09 03:34:41] [INFO]    [OmnipathR] Cache record does not exist: `db://up_gs`
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Loading database `up_gs` from source.
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2026-02-09 03:34:41] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-02-09 03:34:41] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:41] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:41] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-09 03:34:41] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:34:41] [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]
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:34:41] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.116161s from rescued.omnipathdb.org (343.1 Kb/s); Redirect: 0s, DNS look up: 0.001254s, Connection: 0.021275s, Pretransfer: 0.05607s, First byte at: 0.095916s
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:34:41 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: Mon, 09 Feb 2026 03:34:41 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Mon, 09 Feb 2026 02:34:41 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=Mon, 09 Feb 2026 03:34:41 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-09 03:34:42] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:42] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-09 03:34:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:42] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-09 03:34:42] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:34:42] [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]
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.097571s from omabrowser.org (77.5 Kb/s); Redirect: 0s, DNS look up: 0.000586s, Connection: 0.008486s, Pretransfer: 0.049073s, First byte at: 0.097402s
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 09 Feb 2026 02:34:42 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=3h5f4zzZDsppYPLq%2BWV4zWEKHLgZ0C%2Bga2KSOQeuvYdJ9yFdAAaC7m6KdRte0byYPpMdjKiWIfYEd1FzI9JMJ3mC7H59F9J0%2Bs%2Bl3eMV"}]}; cf-ray: 9caff81f5b70d9d0-FRA; alt-svc: h3=":443"; ma=86400
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-09 03:34:42] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:42] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-09 03:34:42] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:34:42] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-09 03:34:42] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:34:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-09 03:35:06] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:06] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:06] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-09 03:35:06] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:06] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-02-09 03:35:06] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2026-02-09 03:35:06] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:06] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-02-09 03:35:06] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:35:06] [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]
[2026-02-09 03:35:06] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-09 03:35:07] [TRACE]   [OmnipathR] Downloaded 15.4 Kb in 0.101901s from rest.uniprot.org (151.5 Kb/s); Redirect: 0s, DNS look up: 0.001017s, Connection: 0.019401s, Pretransfer: 0.073152s, First byte at: 0.101122s
[2026-02-09 03:35:07] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 28-January-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Mon, 09 Feb 2026 02:33:59 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; content-length: 129406
[2026-02-09 03:35:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-02-09 03:35:07] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2026-02-09 03:35:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:07] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2026-02-09 03:35:07] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records
[2026-02-09 03:35:07] [TRACE]   [OmnipathR] Saving database `up_gs` to on-disk cache.
[2026-02-09 03:35:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:07] [INFO]    [OmnipathR] Cache item `7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:35:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f-1.rds`.
[2026-02-09 03:35:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f-1.rds`.
[2026-02-09 03:35:07] [INFO]    [OmnipathR] Download ready [key=7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f, version=1]
[2026-02-09 03:35:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:07] [INFO]    [OmnipathR] Cache item `7c8278e6b01b64a18e9d24e1fb2620181f5f2e7f` version 1: status changed from `started` to `ready`.
[2026-02-09 03:35:07] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:20] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:35:20] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-02-09 02:27:15 UTC; omnipath
[2026-02-09 03:35:20] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-09 03:35:20] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-09 02:28:37 UTC; unix
[2026-02-09 03:35:20] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-09 03:35:20] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-09 03:35:20] [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=2026-02-09; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-09 03:35:20] [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]
[2026-02-09 03:35:20] [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 1.2.3(2024-06-02); 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 1.6.6(2025-04-12); 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 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); 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 3.19.6(2026-02-09); 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 2.1.6(2025-11-14); 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 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-09 03:35:20] [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
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Contains 7 files.
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-02-09 03:35:20] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-09 03:35:20] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-02-09 03:35:21] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:21] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:21] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-09 03:35:21] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:35:21] [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]
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.124056s from rescued.omnipathdb.org (321.3 Kb/s); Redirect: 0s, DNS look up: 0.001291s, Connection: 0.020372s, Pretransfer: 0.06613s, First byte at: 0.104691s
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:35:21 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: Mon, 09 Feb 2026 03:35:21 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Mon, 09 Feb 2026 02:35:21 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=Mon, 09 Feb 2026 03:35:21 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-09 03:35:21] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:21] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-09 03:35:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:21] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-09 03:35:21] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:35:21] [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]
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.11929s from omabrowser.org (63.4 Kb/s); Redirect: 0s, DNS look up: 0.026021s, Connection: 0.033073s, Pretransfer: 0.071864s, First byte at: 0.119101s
[2026-02-09 03:35:21] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 09 Feb 2026 02:35:21 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=5mfcizBy3XRF%2FWgORhmM3%2FP7IWMKKd644iIsfD3ZUz0ZRZbm%2FklFRzlYPF%2Bgdmy0M3nYE7dLXTVnOqYegq7z4DyTBSzu0lZZs2Bm0pO8"}]}; cf-ray: 9caff9149f74d2ca-FRA; alt-svc: h3=":443"; ma=86400
[2026-02-09 03:35:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-09 03:35:22] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-09 03:35:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:22] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-09 03:35:22] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:35:22] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-09 03:35:22] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:35:22] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-09 03:35:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:22] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:35:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-09 03:35:22] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:35:22] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:35:44] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-09 03:35:44] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-09 03:35:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:44] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-09 03:35:44] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-02-09 03:35:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:44] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:35:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-09 03:35:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-09 03:35:45] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-02-09 03:35:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:45] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-02-09 03:35:45] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-09 03:35:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:35:45] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:35:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:35:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:35:45] [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`
[2026-02-09 03:35:45] [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`
[2026-02-09 03:35:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:35:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:35:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:35:45] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:35:45] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:35:45] [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]
[2026-02-09 03:35:45] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:35:45] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.10467s from omnipathdb.org (149.7 Kb/s); Redirect: 0s, DNS look up: 0.000903s, Connection: 0.023601s, Pretransfer: 0.058265s, First byte at: 0.104338s
[2026-02-09 03:35:45] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:35:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:35:45 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:35:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:35:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:46] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:35:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-02-09 03:35:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-02-09 03:35:46] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2026-02-09 03:35:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:46] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2026-02-09 03:35:48] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
--- finished re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2026-02-09 03:35:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:52] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:35:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-02-09 02:27:15 UTC; omnipath
[2026-02-09 03:35:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-09 03:35:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-09 02:28:37 UTC; unix
[2026-02-09 03:35:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-09 03:35:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-09 03:35:52] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-02-09; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-09 03:35:52] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-09 03:35:52] [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 1.2.3(2024-06-02); 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 1.6.6(2025-04-12); 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 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); 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 3.19.6(2026-02-09); 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 2.1.6(2025-11-14); 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 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-09 03:35:52] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-09 03:35:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-09 03:35:52] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:35:52] [TRACE]   [OmnipathR] Contains 6 files.
[2026-02-09 03:35:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-09 03:35:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:35:52] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-02-09 03:35:52] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-09 03:35:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:52] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-09 03:35:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2026-02-09 03:35:53] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-02-09 03:35:53] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:53] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:53] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-09 03:35:53] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:35:53] [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]
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.110286s from rescued.omnipathdb.org (361.4 Kb/s); Redirect: 0s, DNS look up: 0.001201s, Connection: 0.01962s, Pretransfer: 0.054152s, First byte at: 0.091425s
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:35:53 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: Mon, 09 Feb 2026 03:35:53 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Mon, 09 Feb 2026 02:35:53 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=Mon, 09 Feb 2026 03:35:53 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-09 03:35:53] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:53] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-09 03:35:53] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:53] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-09 03:35:53] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:35:53] [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]
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.080275s from omabrowser.org (94.2 Kb/s); Redirect: 0s, DNS look up: 0.000617s, Connection: 0.005076s, Pretransfer: 0.037508s, First byte at: 0.080131s
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 09 Feb 2026 02:35:53 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=ykp3glYaYXV0DQGEwDCxmwxmJRoQOegNcTDZvYIULbgRA2%2FtzbKcmd9oJjWa7QiDtRfSIU7R0JeFi89mg7Yd1%2FaI4DtMGIIW2xsvFSx4"}]}; cf-ray: 9caff9dc38e9d372-FRA; alt-svc: h3=":443"; ma=86400
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-09 03:35:53] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:53] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-09 03:35:53] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:35:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:35:54] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:35:54] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-09 03:35:54] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:35:54] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:36:16] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-09 03:36:16] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-09 03:36:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:36:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:36:16] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-09 03:36:16] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-02-09 03:36:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:36:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:36:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:36:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:36:16] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:36:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-09 03:36:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-09 03:36:17] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-02-09 03:36:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:36:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:36:17] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-02-09 03:36:17] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-09 03:36:17] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:36:17] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:36:17] [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`
[2026-02-09 03:36:17] [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`
[2026-02-09 03:36:17] [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`
[2026-02-09 03:36:17] [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`
[2026-02-09 03:36:17] [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`
[2026-02-09 03:36:17] [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`
[2026-02-09 03:36:17] [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`
[2026-02-09 03:36:17] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:36:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:36:17] [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]
[2026-02-09 03:36:17] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:36:17] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.096834s from omnipathdb.org (161.8 Kb/s); Redirect: 0s, DNS look up: 0.000993s, Connection: 0.021766s, Pretransfer: 0.055494s, First byte at: 0.096487s
[2026-02-09 03:36:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:36:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:36:17 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:36:18] [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`
[2026-02-09 03:36:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:36:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:36:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:36:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:36:18] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:36:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2026-02-09 03:36:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2026-02-09 03:36:18] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2026-02-09 03:36:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:36:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:36:18] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2026-02-09 03:36:18] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2026-02-09 03:36:27] [SUCCESS] [OmnipathR] Downloaded 139054 interactions.
[2026-02-09 03:42:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:42:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2026-02-09 03:42:25] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:42:25] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:42:25] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-02-09 03:42:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-02-09 03:42:26] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-02-09 03:42:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:42:26] [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]
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.097035s from omnipathdb.org (161.5 Kb/s); Redirect: 0s, DNS look up: 0.000943s, Connection: 0.02188s, Pretransfer: 0.055097s, First byte at: 0.096689s
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:42:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:42:26 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:42:26] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:26] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:42:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2026-02-09 03:42:27] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:27] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2026-02-09 03:42:27] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records.
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-02-09 03:42:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-02-09 03:42:27] [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`
[2026-02-09 03:42:27] [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`
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-02-09 03:42:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:42:27] [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]
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] Downloaded 11.6 Kb in 0.090005s from omnipathdb.org (128.9 Kb/s); Redirect: 0s, DNS look up: 0.000984s, Connection: 0.01948s, Pretransfer: 0.052338s, First byte at: 0.089985s
[2026-02-09 03:42:27] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:42:27 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 11882; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:42:27 GMT; Cache-Control: public; X-Frame-Options: DENY
[2026-02-09 03:42:28] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-02-09 03:42:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:28] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:42:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2026-02-09 03:42:28] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2026-02-09 03:42:28] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2026-02-09 03:42:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:28] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2026-02-09 03:42:28] [SUCCESS] [OmnipathR] Downloaded 164 enzyme-substrate relationships.
--- finished re-building ‘extra_attrs.Rmd’

--- re-building ‘nichenet.Rmd’ using rmarkdown
--- finished re-building ‘nichenet.Rmd’

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:31] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:42:31] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-02-09 02:27:15 UTC; omnipath
[2026-02-09 03:42:31] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-09 03:42:31] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-09 02:28:37 UTC; unix
[2026-02-09 03:42:31] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-09 03:42:31] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-09 03:42:31] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-02-09; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-09 03:42:31] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-09 03:42:31] [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 1.2.3(2024-06-02); 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 1.6.6(2025-04-12); 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 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); 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 3.19.6(2026-02-09); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(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 2.1.6(2025-11-14); 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 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-09 03:42:31] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] Contains 8 files.
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:31] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2026-02-09 03:42:32] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-02-09 03:42:32] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:32] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:32] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-09 03:42:32] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:42:32] [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]
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.133607s from rescued.omnipathdb.org (298.3 Kb/s); Redirect: 0s, DNS look up: 0.00692s, Connection: 0.027647s, Pretransfer: 0.072079s, First byte at: 0.113092s
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:42:32 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: Mon, 09 Feb 2026 03:42:32 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:42:32] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Mon, 09 Feb 2026 02:42:32 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=Mon, 09 Feb 2026 03:42:32 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-09 03:42:33] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:33] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-09 03:42:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:33] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-09 03:42:33] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:42:33] [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]
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.101327s from omabrowser.org (74.7 Kb/s); Redirect: 0s, DNS look up: 0.010645s, Connection: 0.015954s, Pretransfer: 0.05648s, First byte at: 0.101112s
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 09 Feb 2026 02:42:33 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=UJjLqD95V52hYo58P4JE8aP%2FLomejkTSZhugsXzhBMFeSwuQ5wBf8LdyFcMdlx7marjYwf%2F1672VJbRwho9A%2BvklUhbWgerM8gW87L4B"}]}; cf-ray: 9cb0039e9e35d3b1-FRA; alt-svc: h3=":443"; ma=86400
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-09 03:42:33] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:33] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-09 03:42:33] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:33] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-09 03:42:33] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:42:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-09 03:42:56] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:56] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:56] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-09 03:42:56] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:56] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-02-09 03:42:56] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:42:56] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:42:57] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:42:57] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:42:57] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:42:57] [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]
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.109863s from omnipathdb.org (142.6 Kb/s); Redirect: 0s, DNS look up: 0.001035s, Connection: 0.020833s, Pretransfer: 0.069442s, First byte at: 0.109582s
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:42:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:42:57 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:42:57] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:57] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2026-02-09 03:42:57] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:42:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:42:58] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2026-02-09 03:42:59] [SUCCESS] [OmnipathR] Downloaded 67773 interactions.
[2026-02-09 03:43:01] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2026-02-09 03:43:01] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2026-02-09 03:43:01] [TRACE]   [OmnipathR] Organism(s): 10090
[2026-02-09 03:43:01] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:01] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:43:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:01] [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`
[2026-02-09 03:43:01] [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`
[2026-02-09 03:43:01] [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`
[2026-02-09 03:43:01] [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`
[2026-02-09 03:43:01] [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`
[2026-02-09 03:43:01] [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`
[2026-02-09 03:43:01] [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`
[2026-02-09 03:43:01] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:01] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:01] [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]
[2026-02-09 03:43:02] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:02] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.089824s from omnipathdb.org (174.4 Kb/s); Redirect: 0s, DNS look up: 0.001025s, Connection: 0.019258s, Pretransfer: 0.053011s, First byte at: 0.089543s
[2026-02-09 03:43:02] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:02 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:02] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:02] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:02] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2026-02-09 03:43:02] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2026-02-09 03:43:02] [INFO]    [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2026-02-09 03:43:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:02] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:03] [SUCCESS] [OmnipathR] Downloaded 41476 interactions.
[2026-02-09 03:43:03] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:03] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2026-02-09 03:43:03] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:03] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] Organism(s): 10116
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:04] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:04] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:04] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:04] [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]
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.108767s from omnipathdb.org (144 Kb/s); Redirect: 0s, DNS look up: 0.001015s, Connection: 0.01955s, Pretransfer: 0.070684s, First byte at: 0.107957s
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:04 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:04] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:04] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2026-02-09 03:43:04] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:04] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:05] [SUCCESS] [OmnipathR] Downloaded 11083 interactions.
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:05] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:05] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:05] [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`
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:05] [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]
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.095653s from omnipathdb.org (163.8 Kb/s); Redirect: 0s, DNS look up: 0.000948s, Connection: 0.021154s, Pretransfer: 0.055144s, First byte at: 0.094901s
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:05 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:05 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:05] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:05] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2026-02-09 03:43:05] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:05] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:06] [SUCCESS] [OmnipathR] Downloaded 2840 interactions.
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:06] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:06] [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]
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.088886s from omnipathdb.org (176.3 Kb/s); Redirect: 0s, DNS look up: 0.000931s, Connection: 0.018879s, Pretransfer: 0.052108s, First byte at: 0.088619s
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:06] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:06] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-02-09 03:43:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-02-09 03:43:07] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2026-02-09 03:43:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:07] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:09] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
[2026-02-09 03:43:10] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:11] [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`
[2026-02-09 03:43:11] [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`
[2026-02-09 03:43:11] [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`
[2026-02-09 03:43:11] [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`
[2026-02-09 03:43:11] [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`
[2026-02-09 03:43:11] [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`
[2026-02-09 03:43:11] [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`
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:11] [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]
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.10903s from omnipathdb.org (143.7 Kb/s); Redirect: 0s, DNS look up: 0.001055s, Connection: 0.021016s, Pretransfer: 0.069093s, First byte at: 0.108749s
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:11 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:11 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:11] [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`
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:11] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2026-02-09 03:43:11] [INFO]    [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:11] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:11] [SUCCESS] [OmnipathR] Downloaded 6128 interactions.
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:11] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:12] [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`
[2026-02-09 03:43:12] [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`
[2026-02-09 03:43:12] [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`
[2026-02-09 03:43:12] [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`
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:12] [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`
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:12] [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]
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.094892s from omnipathdb.org (165.1 Kb/s); Redirect: 0s, DNS look up: 0.001016s, Connection: 0.020923s, Pretransfer: 0.054554s, First byte at: 0.094598s
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:12 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:12] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:12] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2026-02-09 03:43:12] [INFO]    [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:12] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:12] [SUCCESS] [OmnipathR] Downloaded 648 interactions.
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:12] [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`
[2026-02-09 03:43:12] [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`
[2026-02-09 03:43:12] [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`
[2026-02-09 03:43:12] [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`
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-02-09 03:43:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-02-09 03:43:12] [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`
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:12] [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]
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] Downloaded 189 bytes in 0.089087s from omnipathdb.org (2.1 Kb/s); Redirect: 0s, DNS look up: 0.001072s, Connection: 0.022192s, Pretransfer: 0.066839s, First byte at: 0.089069s
[2026-02-09 03:43:12] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:12 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 189; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:12 GMT; Cache-Control: public; X-Frame-Options: DENY
[2026-02-09 03:43:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:13] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2026-02-09 03:43:13] [INFO]    [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:13] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:13] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:13] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:13] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:13] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:13] [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]
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.094821s from omnipathdb.org (165.2 Kb/s); Redirect: 0s, DNS look up: 0.001013s, Connection: 0.020915s, Pretransfer: 0.054645s, First byte at: 0.094474s
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:13] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:13] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:13] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-02-09 03:43:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-02-09 03:43:14] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2026-02-09 03:43:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:14] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:15] [SUCCESS] [OmnipathR] Downloaded 47840 enzyme-substrate relationships.
[2026-02-09 03:43:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-02-09 03:43:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-02-09 03:43:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:15] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:15] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-02-09 03:43:15] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:18] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub]
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] Organism(s): 10090
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:19] [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`
[2026-02-09 03:43:19] [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`
[2026-02-09 03:43:19] [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`
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:19] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:19] [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]
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.111731s from omnipathdb.org (140.2 Kb/s); Redirect: 0s, DNS look up: 0.000987s, Connection: 0.021284s, Pretransfer: 0.0714s, First byte at: 0.111419s
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:19 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:19 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:19] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:19] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2026-02-09 03:43:19] [INFO]    [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:19] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:20] [SUCCESS] [OmnipathR] Downloaded 19838 enzyme-substrate relationships.
[2026-02-09 03:43:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:43:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2026-02-09 03:43:20] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:20] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:43:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-02-09 03:43:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-02-09 03:43:21] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-02-09 03:43:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:21] [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]
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.100596s from omnipathdb.org (155.7 Kb/s); Redirect: 0s, DNS look up: 0.001013s, Connection: 0.017346s, Pretransfer: 0.0673s, First byte at: 0.100339s
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:21 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:21] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:21] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2026-02-09 03:43:21] [INFO]    [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:21] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:21] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes.
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:23] [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]
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:23] [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`
[2026-02-09 03:43:23] [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`
[2026-02-09 03:43:23] [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`
[2026-02-09 03:43:23] [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`
[2026-02-09 03:43:23] [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`
[2026-02-09 03:43:23] [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`
[2026-02-09 03:43:23] [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`
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:23] [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]
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] Downloaded 15.2 Kb in 0.11146s from omnipathdb.org (136.5 Kb/s); Redirect: 0s, DNS look up: 0.00088s, Connection: 0.021214s, Pretransfer: 0.069723s, First byte at: 0.11056s
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:23 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:23] [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`
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:23] [INFO]    [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`.
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`.
[2026-02-09 03:43:23] [INFO]    [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1]
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:23] [INFO]    [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:23] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records.
[2026-02-09 03:43:23] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations]
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:24] [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]
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Downloaded 5.8 Kb in 0.080763s from omnipathdb.org (71.9 Kb/s); Redirect: 0s, DNS look up: 0.001s, Connection: 0.023913s, Pretransfer: 0.057821s, First byte at: 0.080746s
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:24 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 5949; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:24 GMT; Cache-Control: public; X-Frame-Options: DENY
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:24] [INFO]    [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`.
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`.
[2026-02-09 03:43:24] [INFO]    [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1]
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:24] [INFO]    [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:24] [SUCCESS] [OmnipathR] Downloaded 86 annotation records.
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations]
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [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`
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:24] [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]
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Downloaded 17.9 Kb in 0.093842s from omnipathdb.org (190.8 Kb/s); Redirect: 0s, DNS look up: 0.000976s, Connection: 0.017143s, Pretransfer: 0.061876s, First byte at: 0.093811s
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:24 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 18335; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:24 GMT; Cache-Control: public; X-Frame-Options: DENY
[2026-02-09 03:43:25] [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`
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:25] [INFO]    [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`.
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`.
[2026-02-09 03:43:25] [INFO]    [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1]
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:25] [INFO]    [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:25] [SUCCESS] [OmnipathR] Downloaded 366 annotation records.
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:43:25] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:43:25] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:43:25] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:25] [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]
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.093649s from omnipathdb.org (167.3 Kb/s); Redirect: 0s, DNS look up: 0.000929s, Connection: 0.019381s, Pretransfer: 0.056429s, First byte at: 0.093305s
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:25 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:25] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:26] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-02-09 03:43:26] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:26] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:26] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records.
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2026-02-09 03:43:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-02-09 03:43:26] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2026-02-09 03:43:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:26] [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]
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Downloaded 9.4 Kb in 0.06864s from omnipathdb.org (136.8 Kb/s); Redirect: 0s, DNS look up: 0.001009s, Connection: 0.017571s, Pretransfer: 0.051152s, First byte at: 0.068464s
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:26 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:26] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:26] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-02-09 03:43:26] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:26] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:26] [SUCCESS] [OmnipathR] Downloaded 1190 records.
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-02-09 03:43:26] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-02-09 03:43:26] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-02-09 03:43:26] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:26] [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]
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.112386s from omnipathdb.org (139.4 Kb/s); Redirect: 0s, DNS look up: 0.001002s, Connection: 0.021425s, Pretransfer: 0.069946s, First byte at: 0.111385s
[2026-02-09 03:43:26] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:26 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:27] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-02-09 03:43:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:27] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:27] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2026-02-09 03:43:29] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2026-02-09 03:43:29] [INFO]    [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2026-02-09 03:43:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:29] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:29] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records.
[2026-02-09 03:43:29] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2026-02-09 03:43:29] [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.
[2026-02-09 03:43:29] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`.
[2026-02-09 03:43:29] [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
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:32] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:43:32] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-02-09 02:27:15 UTC; omnipath
[2026-02-09 03:43:32] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-02-09 03:43:32] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-02-09 02:28:37 UTC; unix
[2026-02-09 03:43:32] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-09 03:43:32] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-02-09 03:43:32] [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=2026-02-09; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-02-09 03:43:32] [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]
[2026-02-09 03:43:32] [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 1.2.3(2024-06-02); 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 1.6.6(2025-04-12); 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 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); 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 3.19.6(2026-02-09); 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 2.1.6(2025-11-14); 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 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-09 03:43:32] [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
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] Contains 22 files.
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:32] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2026-02-09 03:43:32] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-02-09 03:43:33] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:33] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:33] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-09 03:43:33] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:33] [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]
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.120034s from rescued.omnipathdb.org (332.1 Kb/s); Redirect: 0s, DNS look up: 0.001121s, Connection: 0.018432s, Pretransfer: 0.068242s, First byte at: 0.10305s
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:33 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: Mon, 09 Feb 2026 03:43:33 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Mon, 09 Feb 2026 02:43:33 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=Mon, 09 Feb 2026 03:43:33 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-09 03:43:33] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:33] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-09 03:43:33] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:33] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-09 03:43:33] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:33] [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]
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.098956s from omabrowser.org (76.4 Kb/s); Redirect: 0s, DNS look up: 0.000589s, Connection: 0.007429s, Pretransfer: 0.048115s, First byte at: 0.098591s
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 09 Feb 2026 02:43:33 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=eChkiTQQQCWz4co%2BtbuHlxFgmCgSfqPCR4q5B4JcnG5RKG%2BpAWipKLMVkRT7DssS%2BS1ae4C01W64QxSiBz3uRWtUR0NFnxrA9kKrAg%3D%3D"}]}; cf-ray: 9cb005170a975c9e-FRA; alt-svc: h3=":443"; ma=86400
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-09 03:43:33] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:33] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-09 03:43:33] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:33] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-09 03:43:33] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:43:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-09 03:43:56] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-09 03:43:56] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-09 03:43:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:56] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:56] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-02-09 03:43:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:56] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-09 03:43:57] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:57] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:57] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-02-09 03:43:57] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-02-09 03:43:57] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-02-09 03:43:57] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:57] [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]
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.10001s from omnipathdb.org (156.7 Kb/s); Redirect: 0s, DNS look up: 0.000834s, Connection: 0.018648s, Pretransfer: 0.063904s, First byte at: 0.099697s
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:57 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:57] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:57] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2026-02-09 03:43:57] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:57] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:57] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2026-02-09 03:43:57] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-02-09 03:43:57] [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`.
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:57] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2026-02-09 03:43:57] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:57] [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]
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] Downloaded 16 Kb in 0.052308s from static-content.springer.com (305.9 Kb/s); Redirect: 0s, DNS look up: 0.008552s, Connection: 0.013134s, Pretransfer: 0.046018s, First byte at: 0.052283s
[2026-02-09 03:43:57] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; content-type: application/octet-stream; x-guploader-uploadid: AJRbA5VkTYJAsyvA76Xuoc8zK9j8HylOnnsaksfpVoEU1z9rRHZ98dxmccvj5Ja-HfDuNBIPg7VUNL0; 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: 6160; date: Mon, 09 Feb 2026 02:43:57 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230087-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1770605038.974759,VS0,VE2; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2026-02-09 03:43:58] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:58] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2026-02-09 03:43:58] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:43:58] [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`
[2026-02-09 03:43:58] [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`
[2026-02-09 03:43:58] [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`
[2026-02-09 03:43:58] [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`
[2026-02-09 03:43:58] [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`
[2026-02-09 03:43:58] [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`
[2026-02-09 03:43:58] [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`
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:43:58] [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]
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.116187s from omnipathdb.org (134.8 Kb/s); Redirect: 0s, DNS look up: 0.001062s, Connection: 0.023015s, Pretransfer: 0.067367s, First byte at: 0.11588s
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:43:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:43:58 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:43:58] [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`
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:58] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:43:58] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2026-02-09 03:43:59] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2026-02-09 03:43:59] [INFO]    [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2026-02-09 03:43:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:43:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:43:59] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2026-02-09 03:44:02] [SUCCESS] [OmnipathR] Downloaded 124225 interactions.
[2026-02-09 03:44:02] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:44:02] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2026-02-09 03:44:02] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:02] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:02] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:44:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-02-09 03:44:03] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-02-09 03:44:03] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-02-09 03:44:03] [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`
[2026-02-09 03:44:03] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-02-09 03:44:03] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-02-09 03:44:03] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-02-09 03:44:03] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:44:03] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:44:03] [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]
[2026-02-09 03:44:03] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:44:03] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.083921s from omnipathdb.org (186.7 Kb/s); Redirect: 0s, DNS look up: 0.000983s, Connection: 0.017101s, Pretransfer: 0.050558s, First byte at: 0.08352s
[2026-02-09 03:44:03] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:44:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:44:03 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:44:04] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-02-09 03:44:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:04] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:44:04] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2026-02-09 03:44:05] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2026-02-09 03:44:05] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2026-02-09 03:44:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:05] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2026-02-09 03:44:05] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records.
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-02-09 03:44:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-02-09 03:44:06] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-02-09 03:44:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:44:06] [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]
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.105412s from omnipathdb.org (148.6 Kb/s); Redirect: 0s, DNS look up: 0.000988s, Connection: 0.021152s, Pretransfer: 0.064769s, First byte at: 0.105057s
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:44:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:44:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:44:06] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:06] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2026-02-09 03:44:06] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:06] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2026-02-09 03:44:06] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records.
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-02-09 03:44:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-02-09 03:44:06] [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`
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-02-09 03:44:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:44:06] [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]
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.093241s from omnipathdb.org (168 Kb/s); Redirect: 0s, DNS look up: 0.001002s, Connection: 0.020483s, Pretransfer: 0.053939s, First byte at: 0.092825s
[2026-02-09 03:44:06] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:44:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:44:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:44:07] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:07] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-02-09 03:44:07] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:07] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2026-02-09 03:44:07] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records.
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-02-09 03:44:07] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-02-09 03:44:07] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-02-09 03:44:07] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:44:07] [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]
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.112682s from omnipathdb.org (139 Kb/s); Redirect: 0s, DNS look up: 0.001133s, Connection: 0.022819s, Pretransfer: 0.068811s, First byte at: 0.112312s
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:44:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:44:07 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:44:07] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:07] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2026-02-09 03:44:07] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:07] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2026-02-09 03:44:07] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records.
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:07] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-02-09 03:44:08] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-02-09 03:44:08] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-02-09 03:44:08] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-02-09 03:44:08] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-02-09 03:44:08] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:44:08] [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]
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.105094s from omnipathdb.org (149.1 Kb/s); Redirect: 0s, DNS look up: 0.001037s, Connection: 0.0209s, Pretransfer: 0.064831s, First byte at: 0.104717s
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:44:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:44:08 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:44:08] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:08] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2026-02-09 03:44:08] [INFO]    [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:08] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2026-02-09 03:44:08] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records.
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-02-09 03:44:08] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-02-09 03:44:08] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-02-09 03:44:08] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-02-09 03:44:08] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-02-09 03:44:08] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:44:08] [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]
[2026-02-09 03:44:08] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.100705s from omnipathdb.org (155.6 Kb/s); Redirect: 0s, DNS look up: 0.00088s, Connection: 0.019228s, Pretransfer: 0.063761s, First byte at: 0.100366s
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:44:08 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:44:08 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:44:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:09] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2026-02-09 03:44:09] [INFO]    [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:09] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2026-02-09 03:44:09] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records.
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-02-09 03:44:09] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-02-09 03:44:09] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:09] [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`
[2026-02-09 03:44:09] [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`
[2026-02-09 03:44:09] [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`
[2026-02-09 03:44:09] [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`
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-02-09 03:44:09] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-02-09 03:44:09] [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`
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:44:09] [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]
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.126532s from omnipathdb.org (123.8 Kb/s); Redirect: 0s, DNS look up: 0.001178s, Connection: 0.025649s, Pretransfer: 0.077526s, First byte at: 0.126216s
[2026-02-09 03:44:09] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:44:09 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:44:09 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:44:10] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-02-09 03:44:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:10] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:44:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2026-02-09 03:44:10] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2026-02-09 03:44:10] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2026-02-09 03:44:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:10] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2026-02-09 03:44:11] [SUCCESS] [OmnipathR] Downloaded 32281 interactions.
[2026-02-09 03:44:11] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:44:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2026-02-09 03:44:11] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:11] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:11] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:44:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:11] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-02-09 03:44:11] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-02-09 03:44:11] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-02-09 03:44:11] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-02-09 03:44:11] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-02-09 03:44:11] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-02-09 03:44:11] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-02-09 03:44:11] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:44:11] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:44:11] [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]
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Downloaded 13.1 Kb in 0.097873s from omnipathdb.org (134 Kb/s); Redirect: 0s, DNS look up: 0.000975s, Connection: 0.021725s, Pretransfer: 0.055797s, First byte at: 0.097592s
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:44:11 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:44:11 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:44:12] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:12] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2026-02-09 03:44:12] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:12] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2026-02-09 03:44:12] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records.
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-02-09 03:44:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-02-09 03:44:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-02-09 03:44:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:44:12] [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]
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Downloaded 12.2 Kb in 0.09016s from omnipathdb.org (135 Kb/s); Redirect: 0s, DNS look up: 0.000948s, Connection: 0.019125s, Pretransfer: 0.052616s, First byte at: 0.089479s
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:44:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:44:12 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:44:12] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:12] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2026-02-09 03:44:12] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:12] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2026-02-09 03:44:12] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records.
[2026-02-09 03:44:13] [TRACE]   [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2026-02-09 03:44:13] [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.
[2026-02-09 03:44:13] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:44:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2026-02-09 03:44:13] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:13] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:13] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:44:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:13] [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`
[2026-02-09 03:44:13] [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`
[2026-02-09 03:44:13] [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`
[2026-02-09 03:44:13] [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`
[2026-02-09 03:44:13] [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`
[2026-02-09 03:44:13] [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`
[2026-02-09 03:44:13] [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`
[2026-02-09 03:44:13] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:44:13] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:44:13] [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]
[2026-02-09 03:44:13] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:44:13] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.0905s from omnipathdb.org (173.1 Kb/s); Redirect: 0s, DNS look up: 0.001031s, Connection: 0.019323s, Pretransfer: 0.053388s, First byte at: 0.09023s
[2026-02-09 03:44:13] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:44:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:44:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:44:14] [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`
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:14] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2026-02-09 03:44:14] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:14] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2026-02-09 03:44:14] [SUCCESS] [OmnipathR] Downloaded 4242 interactions.
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:44:14] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:44:14] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:44:14] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:44:14] [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]
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.089871s from omnipathdb.org (174.3 Kb/s); Redirect: 0s, DNS look up: 0.000937s, Connection: 0.019117s, Pretransfer: 0.052986s, First byte at: 0.089552s
[2026-02-09 03:44:14] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:44:14 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:44:14 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:44:15] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:44:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:15] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:44:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-02-09 03:44:15] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-02-09 03:44:15] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2026-02-09 03:44:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:15] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2026-02-09 03:44:15] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records.
[2026-02-09 03:44:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:44:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2026-02-09 03:44:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:15] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:15] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-02-09 03:44:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-02-09 03:44:16] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-02-09 03:44:16] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-09 03:44:16] [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]
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.099529s from omnipathdb.org (157.4 Kb/s); Redirect: 0s, DNS look up: 0.000973s, Connection: 0.017475s, Pretransfer: 0.066356s, First byte at: 0.099227s
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 09 Feb 2026 02:44:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 09 Feb 2026 03:44:16 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-09 03:44:16] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:16] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-02-09 03:44:16] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-09 03:44:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:16] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2026-02-09 03:44:16] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records.
[2026-02-09 03:44:18] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:44:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2026-02-09 03:44:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:19] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:44:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:44:19] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-02-09 03:44:19] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-02-09 03:44:19] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2026-02-09 03:44:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-02-09 03:44:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2026-02-09 03:44:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-02-09 03:44:19] [TRACE]   [OmnipathR] Orthology targets: 
[2026-02-09 03:44:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-09 03:44:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-02-09 03:44:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-02-09 03:44:19] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-02-09 03:44:19] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-02-09 03:44:19] [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, 2 WARNINGs, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-02-09_0317/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2026-02-09 03:44:28 CET ]