[ Started: 2026-05-30 21:18:35 CEST ]
[ OmnipathR v3.18.4 for BioC-3.22 from https://git.bioconductor.org/packages/OmnipathR@RELEASE_3_22 (efaae39 2026-01-20 15:40:26) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.18.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2026-05-30 21:19:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:19:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:19:06] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:19:06] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-05-30 19:16:10 UTC; omnipath
[2026-05-30 21:19:06] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-05-30 21:19:06] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-30 19:18:37 UTC; unix
[2026-05-30 21:19:06] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-05-30 21:19:06] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-05-30 21:19:06] [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=2026-05-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-05-30 21:19:06] [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]
[2026-05-30 21:19:07] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.2(2026-05-29); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-30); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-30 21:19:07] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] Contains 1 files.
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:19:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:19:07] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2026-05-30 21:19:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:19:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:19:17] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:19:17] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-05-30 19:16:10 UTC; omnipath
[2026-05-30 21:19:17] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-05-30 21:19:17] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-30 19:18:37 UTC; unix
[2026-05-30 21:19:17] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-05-30 21:19:17] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-05-30 21:19:18] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-05-30 21:19:18] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-05-30 21:19:18] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.2(2026-05-29); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-30); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-30 21:19:18] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] Contains 1 files.
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:19:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:19:18] [TRACE]   [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
patch_httr2_keep_handle: no visible binding for global variable
  ‘handle’
patch_httr2_keep_handle: no visible global function definition for
  ‘ORIGINAL’
Undefined global functions or variables:
  ORIGINAL enzyme_genesymbol handle
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ensembl_id_mapping_table
> ### Title: Identifier translation table from Ensembl
> ### Aliases: ensembl_id_mapping_table
> 
> ### ** Examples
> 
> ensp_up <- ensembl_id_mapping_table("ensp")
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens
[2026-05-30 21:22:15] [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>
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:22:15] [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`.
[2026-05-30 21:22:15] [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`
[2026-05-30 21:22:15] [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`.
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:22:15] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2026-05-30 21:22:15] [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`
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-05-30 21:22:15] [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`
[2026-05-30 21:22:15] [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`.
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] Downloaded 1014 bytes in 0.066644s from www.ensembl.org (14.9 Kb/s); Redirect: 0s, DNS look up: 0.000818s, Connection: 0.029663s, Pretransfer: 0.029767s, First byte at: 0.066463s
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: D5EA:BF13D:3B5AAF:3E3A6F:6A0E4CF0; 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: 13ae7dcea3e4580ccca20fae179e9963c022b710; Content-Encoding: gzip; Date: Sat, 30 May 2026 19:22:15 GMT; Expires: 0; X-Served-By: cache-lcy-egml8630031-LCY; Pragma: no-cache; X-Timer: S1780168936.829105,VS0,VE0; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"68b6c2f9-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 516; Content-Length: 1014
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] Response headers: [X-GitHub-Request-Id=D5EA:BF13D:3B5AAF:3E3A6F:6A0E4CF0,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=13ae7dcea3e4580ccca20fae179e9963c022b710,Content-Encoding=gzip,Date=Sat, 30 May 2026 19:22:15 GMT,Expires=0,X-Served-By=cache-lcy-egml8630031-LCY,Pragma=no-cache,X-Timer=S1780168936.829105,VS0,VE0,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"68b6c2f9-8aa",Via=1.1 varnish,Connection=keep-alive,Age=516,Content-Length=1014]
[2026-05-30 21:22:15] [TRACE]   [OmnipathR] Calling reader callback on response.
[2026-05-30 21:22:16] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2026-05-30 21:22:16] [INFO]    [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1]
[2026-05-30 21:22:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:22:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:22:16] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`.
[2026-05-30 21:22:16] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <html>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <head>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <style>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] html,
[2026-05-30 21:22:16] [WARN]    [OmnipathR] body {
[2026-05-30 21:22:16] [WARN]    [OmnipathR] padding: 0;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] margin: 0;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] height: 100%;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] }
[2026-05-30 21:22:16] [WARN]    [OmnipathR] body {
[2026-05-30 21:22:16] [WARN]    [OmnipathR] display: grid;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] font-size: 90%;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] }
[2026-05-30 21:22:16] [WARN]    [OmnipathR] h1 {
[2026-05-30 21:22:16] [WARN]    [OmnipathR] font-size: 1.5rem;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] }
[2026-05-30 21:22:16] [WARN]    [OmnipathR] h2 {
[2026-05-30 21:22:16] [WARN]    [OmnipathR] font-size: 1.2rem;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] }
[2026-05-30 21:22:16] [WARN]    [OmnipathR] h3 {
[2026-05-30 21:22:16] [WARN]    [OmnipathR] font-size: 1.1rem;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] }
[2026-05-30 21:22:16] [WARN]    [OmnipathR] header {
[2026-05-30 21:22:16] [WARN]    [OmnipathR] grid-row: header;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] padding: 5px;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] height: 60px;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] background-color: #333366;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] }
[2026-05-30 21:22:16] [WARN]    [OmnipathR] header img {
[2026-05-30 21:22:16] [WARN]    [OmnipathR] width: 185px;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] height: 45px
[2026-05-30 21:22:16] [WARN]    [OmnipathR] }
[2026-05-30 21:22:16] [WARN]    [OmnipathR] main {
[2026-05-30 21:22:16] [WARN]    [OmnipathR] grid-row: main;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] padding: 20px;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] }
[2026-05-30 21:22:16] [WARN]    [OmnipathR] .mirrors {
[2026-05-30 21:22:16] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] margin-top: 20px;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] padding: 10px;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] }
[2026-05-30 21:22:16] [WARN]    [OmnipathR] footer {
[2026-05-30 21:22:16] [WARN]    [OmnipathR] grid-row: footer;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] padding: 0 20px;
[2026-05-30 21:22:16] [WARN]    [OmnipathR] }
[2026-05-30 21:22:16] [WARN]    [OmnipathR] </style>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] </head>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <body>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <header>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2026-05-30 21:22:16] [WARN]    [OmnipathR] </header>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <main>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <p>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2026-05-30 21:22:16] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2026-05-30 21:22:16] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2026-05-30 21:22:16] [WARN]    [OmnipathR] </p>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <div class="mirrors">
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <ul>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] </ul>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2026-05-30 21:22:16] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2026-05-30 21:22:16] [WARN]    [OmnipathR] data centre.
[2026-05-30 21:22:16] [WARN]    [OmnipathR] </div>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] </main>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <footer>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] <p>&copy; 2025 EMBL-EBI</p>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] </footer>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] </body>
[2026-05-30 21:22:16] [WARN]    [OmnipathR] </html>
[2026-05-30 21:22:16] [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
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
annotation_categories                68.896  0.039  69.055
curated_ligrec_stats                 29.156  1.337  39.172
all_uniprots                         17.772  1.018  28.818
curated_ligand_receptor_interactions  4.759  0.275   6.198
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
[2026-05-30 21:22:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:22:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:22:58] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:22:58] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-05-30 19:16:10 UTC; omnipath
[2026-05-30 21:22:58] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-05-30 21:22:58] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-30 19:18:37 UTC; unix
[2026-05-30 21:22:58] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-05-30 21:22:58] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-05-30 21:22:58] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-05-30 21:22:58] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-05-30 21:22:58] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.2(2026-05-29); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-30); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-30 21:22:58] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-05-30 21:22:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Contains 15 files.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:22:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2026-05-30 21:22:59] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:22:59] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:22:59] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-05-30 21:22:59] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:22:59] [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]
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.132939s from rescued.omnipathdb.org (299.8 Kb/s); Redirect: 0s, DNS look up: 0.001176s, Connection: 0.020597s, Pretransfer: 0.0735s, First byte at: 0.113186s
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:22:59 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 30 May 2026 20:22:59 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Sat, 30 May 2026 19:22:59 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 30 May 2026 20:22:59 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-05-30 21:22:59] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:22:59] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-30 21:22:59] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:22:59] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-30 21:22:59] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:22:59] [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]
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] Downloaded 5.3 Kb in 0.095255s from omabrowser.org (56 Kb/s); Redirect: 0s, DNS look up: 0.000594s, Connection: 0.011057s, Pretransfer: 0.043901s, First byte at: 0.09512s
[2026-05-30 21:22:59] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 30 May 2026 19:22:59 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=5%2FBiWv0Dx85Xa1vmSLOGCDo6e3M%2FFCwmzZlMTO9YL1GVnpzHSMIlmokAcc6ydcPWWJDOU6L%2BWBbEwUg1TBMg4Pou0gYPZ3z8VwkMC1vQyVThFKUdl1rDEKhpYRE7NDIb5g%3D%3D"}]}; cf-ray: a0401c5b6d90db12-FRA; alt-svc: h3=":443"; ma=86400
[2026-05-30 21:23:00] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-30 21:23:00] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-05-30 21:23:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:00] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-05-30 21:23:00] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:23:00] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-30 21:23:00] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:23:00] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-30 21:23:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:00] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:23:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-30 21:23:00] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:23:00] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:23:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-30 21:23:23] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-05-30 21:23:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:23] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-05-30 21:23:23] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-05-30 21:23:23] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:23:23] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:23:23] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:23:23] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:23:23] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:23:23] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:23:23] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:23:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:23:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:23:23] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:23:23] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:23:23] [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]
[2026-05-30 21:23:23] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:23:23] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.100818s from omnipathdb.org (155.7 Kb/s); Redirect: 0s, DNS look up: 0.000917s, Connection: 0.01934s, Pretransfer: 0.064027s, First byte at: 0.10043s
[2026-05-30 21:23:23] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:23:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:23:23 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:23:24] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:23:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:24] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:23:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2026-05-30 21:23:24] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8e1fed15bbe7704374f40d278e719e18b4a9d60f-1.rds`.
[2026-05-30 21:23:24] [INFO]    [OmnipathR] Download ready [key=8e1fed15bbe7704374f40d278e719e18b4a9d60f, version=1]
[2026-05-30 21:23:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:24] [INFO]    [OmnipathR] Cache item `8e1fed15bbe7704374f40d278e719e18b4a9d60f` version 1: status changed from `started` to `ready`.
[2026-05-30 21:23:28] [SUCCESS] [OmnipathR] Downloaded 131398 interactions.
[2026-05-30 21:23:31] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:23:31] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2026-05-30 21:23:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:23:31] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:23:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:31] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:31] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:31] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:31] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:31] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:31] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:23:31] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:23:31] [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]
[2026-05-30 21:23:31] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:23:31] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.084018s from omnipathdb.org (186.9 Kb/s); Redirect: 0s, DNS look up: 0.000954s, Connection: 0.017434s, Pretransfer: 0.051185s, First byte at: 0.083682s
[2026-05-30 21:23:31] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:23:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:23:31 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:23:32] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:32] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:23:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-05-30 21:23:32] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-05-30 21:23:32] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2026-05-30 21:23:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:32] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2026-05-30 21:23:33] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships.
[2026-05-30 21:23:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:23:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=interactions]
[2026-05-30 21:23:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:23:34] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:23:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:34] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:34] [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`
[2026-05-30 21:23:34] [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`
[2026-05-30 21:23:34] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:34] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:34] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:23:34] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:23:34] [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]
[2026-05-30 21:23:34] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:23:34] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.101565s from omnipathdb.org (154.6 Kb/s); Redirect: 0s, DNS look up: 0.001046s, Connection: 0.020285s, Pretransfer: 0.062523s, First byte at: 0.101256s
[2026-05-30 21:23:34] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:23:34 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:23:34 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:23:35] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:35] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:23:35] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-05-30 21:23:35] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-05-30 21:23:35] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2026-05-30 21:23:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:35] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2026-05-30 21:23:37] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=complexes]
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?license=academic`
[2026-05-30 21:23:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?license=academic`
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2026-05-30 21:23:38] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?license=academic`
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?license=academic`
[2026-05-30 21:23:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?license=academic`
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?license=academic`
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:23:38] [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]
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.095161s from omnipathdb.org (165 Kb/s); Redirect: 0s, DNS look up: 0.001142s, Connection: 0.020528s, Pretransfer: 0.055051s, First byte at: 0.09443s
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:23:38 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:23:38 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:23:38] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?license=academic`
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:39] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d562abda40303226daf98b436df9cb85eaeb2ef3-1.rds`.
[2026-05-30 21:23:39] [INFO]    [OmnipathR] Download ready [key=d562abda40303226daf98b436df9cb85eaeb2ef3, version=1]
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:39] [INFO]    [OmnipathR] Cache item `d562abda40303226daf98b436df9cb85eaeb2ef3` version 1: status changed from `started` to `ready`.
[2026-05-30 21:23:39] [SUCCESS] [OmnipathR] Downloaded 37629 protein complexes.
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:23:39] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:23:39] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:23:39] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:23:39] [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]
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.101137s from omnipathdb.org (155.2 Kb/s); Redirect: 0s, DNS look up: 0.001075s, Connection: 0.022482s, Pretransfer: 0.057789s, First byte at: 0.100754s
[2026-05-30 21:23:39] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:23:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:23:39 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:23:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:40] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-05-30 21:23:40] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:40] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2026-05-30 21:23:40] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records.
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=Uniprot_location,query_type=annotations]
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-05-30 21:23:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-05-30 21:23:40] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-05-30 21:23:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:23:40] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:23:40] [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]
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Downloaded 72 bytes in 0.086432s from omnipathdb.org (833 bytes/s); Redirect: 0s, DNS look up: 0.001082s, Connection: 0.021335s, Pretransfer: 0.066015s, First byte at: 0.086403s
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:23:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:23:41 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:23:41] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Uniprot_location&license=academic`
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:41] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1-1.rds`.
[2026-05-30 21:23:41] [INFO]    [OmnipathR] Download ready [key=07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1, version=1]
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:41] [INFO]    [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`.
[2026-05-30 21:23:41] [SUCCESS] [OmnipathR] Downloaded 0 annotation records.
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resuorces=UniProt_location,query_type=annotations]
[2026-05-30 21:23:41] [FATAL]   [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest.
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_location,query_type=annotations]
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-05-30 21:23:41] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:23:41] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV],wide=TRUE,resources=HPA_tissue,query_type=annotations]
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:23:41] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-05-30 21:23:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-05-30 21:23:42] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-05-30 21:23:42] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:23:42] [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]
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.103504s from omnipathdb.org (151.7 Kb/s); Redirect: 0s, DNS look up: 0.001035s, Connection: 0.019947s, Pretransfer: 0.064745s, First byte at: 0.102406s
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:23:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:23:42 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:23:42] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=HPA_tissue&proteins=DLL1,MEIS2,PHOX2A,BACH1,KLF11,FOXO3,MEFV&license=academic`
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:42] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/92ead83eb455386da8cefb938ee16521d1b5f02d-1.rds`.
[2026-05-30 21:23:42] [INFO]    [OmnipathR] Download ready [key=92ead83eb455386da8cefb938ee16521d1b5f02d, version=1]
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:42] [INFO]    [OmnipathR] Cache item `92ead83eb455386da8cefb938ee16521d1b5f02d` version 1: status changed from `started` to `ready`.
[2026-05-30 21:23:42] [SUCCESS] [OmnipathR] Downloaded 3752 annotation records.
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:23:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:23:42] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:23:42] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:23:42] [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]
[2026-05-30 21:23:42] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.098308s from omnipathdb.org (159.7 Kb/s); Redirect: 0s, DNS look up: 0.000966s, Connection: 0.021609s, Pretransfer: 0.055306s, First byte at: 0.097338s
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:23:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:23:42 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:23:43] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:43] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-05-30 21:23:43] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:43] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2026-05-30 21:23:43] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records.
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:43] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-05-30 21:23:43] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:23:46] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=SignaLink_pathway,query_type=annotations]
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-05-30 21:23:46] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:23:46] [SUCCESS] [OmnipathR] Loaded 2578 annotation records from cache.
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?license=academic`
[2026-05-30 21:23:46] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?license=academic`
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2026-05-30 21:23:46] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?license=academic`
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?license=academic`
[2026-05-30 21:23:46] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?license=academic`
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?license=academic`
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:23:46] [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]
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.08991s from omnipathdb.org (174.6 Kb/s); Redirect: 0s, DNS look up: 0.001016s, Connection: 0.019117s, Pretransfer: 0.052938s, First byte at: 0.089439s
[2026-05-30 21:23:46] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:23:46 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:23:46 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:23:48] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?license=academic`
[2026-05-30 21:23:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:48] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:23:48] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2026-05-30 21:23:50] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`.
[2026-05-30 21:23:50] [INFO]    [OmnipathR] Download ready [key=88868f24833199a6a4a8e27980fa32cd50c1c600, version=1]
[2026-05-30 21:23:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:50] [INFO]    [OmnipathR] Cache item `88868f24833199a6a4a8e27980fa32cd50c1c600` version 1: status changed from `started` to `ready`.
[2026-05-30 21:23:50] [SUCCESS] [OmnipathR] Downloaded 388239 intercellular communication role records.
[2026-05-30 21:23:51] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2026-05-30 21:23:51] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-05-30 21:23:51] [TRACE]   [OmnipathR] Bypassing call: `intercell_network()`.
[2026-05-30 21:23:51] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-05-30 21:23:51] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(icn, ligand_receptor = TRUE, consensus_percentile = 30, `.
[2026-05-30 21:23:51] [TRACE]   [OmnipathR] Bypassing call: `    loc_consensus_percentile = 50, simplify = TRUE)`.
[2026-05-30 21:23:51] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-05-30 21:23:51] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:23:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2026-05-30 21:23:52] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-05-30 21:23:52] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2026-05-30 21:23:52] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.091228s from omnipathdb.org (83.1 Kb/s); Redirect: 0s, DNS look up: 0.000993s, Connection: 0.021111s, Pretransfer: 0.069746s, First byte at: 0.091063s
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:23:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:23:52 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:23:52] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:52] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-05-30 21:23:52] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:52] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2026-05-30 21:23:52] [SUCCESS] [OmnipathR] Downloaded 1190 records.
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2026-05-30 21:23:52] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:23:52] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-05-30 21:23:52] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:23:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-30 21:23:53] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-05-30 21:23:53] [TRACE]   [OmnipathR] Downloaded 43 bytes in 0.451173s from rest.uniprot.org (95 bytes/s); Redirect: 0s, DNS look up: 0.00092s, Connection: 0.029981s, Pretransfer: 0.101197s, First byte at: 0.451097s
[2026-05-30 21:23:53] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 30-April-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 30 May 2026 19:23:53 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-05-30 21:24:02] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-05-30 21:24:02] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2026-05-30 21:24:02] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:02] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2026-05-30 21:24:02] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records
[2026-05-30 21:24:02] [TRACE]   [OmnipathR] Translating complexes: 0 complexes in data.
[2026-05-30 21:24:02] [TRACE]   [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-05-30 21:24:02] [TRACE]   [OmnipathR] Translated 0 complexes to 0.
[2026-05-30 21:24:02] [TRACE]   [OmnipathR] 4 rows before translation, 4 uniprot IDs in column `uniprot_id`.
[2026-05-30 21:24:02] [TRACE]   [OmnipathR] 4 rows after translation; translated 4 `uniprot` IDs in column `uniprot_id` to 4 `genesymbol` IDs in column `genesymbol`.
[2026-05-30 21:24:02] [TRACE]   [OmnipathR] Bypassing call: `go_ontology_download()`.
[2026-05-30 21:24:02] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-05-30 21:24:02] [TRACE]   [OmnipathR] Bypassing call: `relations_table_to_graph(go$rel_tbl_c2p)`.
[2026-05-30 21:24:02] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-05-30 21:24:02] [TRACE]   [OmnipathR] Bypassing call: `ontology_ensure_name("GO:0000022")`.
[2026-05-30 21:24:02] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘bioc_workshop.Rmd’

--- re-building ‘cosmos.Rmd’ using rmarkdown
[2026-05-30 21:24:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:04] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:24:04] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-05-30 19:16:10 UTC; omnipath
[2026-05-30 21:24:04] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-05-30 21:24:04] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-30 19:18:37 UTC; unix
[2026-05-30 21:24:04] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-05-30 21:24:04] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-05-30 21:24:04] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-05-30 21:24:04] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-05-30 21:24:04] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.2(2026-05-29); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-30); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-30 21:24:04] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-05-30 21:24:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-05-30 21:24:04] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:24:04] [TRACE]   [OmnipathR] Contains 15 files.
[2026-05-30 21:24:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-05-30 21:24:04] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-05-30 21:24:05] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:05] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:05] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-05-30 21:24:05] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:24:05] [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]
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.118214s from rescued.omnipathdb.org (337.2 Kb/s); Redirect: 0s, DNS look up: 0.001154s, Connection: 0.021573s, Pretransfer: 0.056087s, First byte at: 0.097595s
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:24:05 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 30 May 2026 20:24:05 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Sat, 30 May 2026 19:24:05 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 30 May 2026 20:24:05 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-05-30 21:24:05] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:05] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-30 21:24:05] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:05] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-30 21:24:05] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:24:05] [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]
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] Downloaded 1.3 Kb in 0.077653s from omabrowser.org (17.1 Kb/s); Redirect: 0s, DNS look up: 0.000608s, Connection: 0.016567s, Pretransfer: 0.049552s, First byte at: 0.077527s
[2026-05-30 21:24:05] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 30 May 2026 19:24:05 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=jLp2%2FM1w5CtBcRD58pTiMUuZg6FXk152GDyzrKuWX3z%2BdofJgB9rdhV1zoMGlVdvHVO%2BUIMyWxWk3xbQPE7%2FeDj0tVVl5DwlctLrDf3CHF85LG2GIvQ6D7WCcZPkhTzYUw%3D%3D"}]}; cf-ray: a0401df82956d298-FRA; alt-svc: h3=":443"; ma=86400
[2026-05-30 21:24:06] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-30 21:24:06] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-05-30 21:24:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:06] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-05-30 21:24:06] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:24:06] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-30 21:24:06] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:24:06] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-30 21:24:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:06] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:06] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:24:06] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-30 21:24:06] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:24:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-30 21:24:27] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:27] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-05-30 21:24:27] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-05-30 21:24:27] [INFO]    [OmnipathR] OmniPath network for COSMOS PKN; datasets: omnipath; resources: all; interaction types: post-translational (PPI); organism: Human.
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions]
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:24:27] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:24:27] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:24:27] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:24:27] [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]
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.09717s from omnipathdb.org (161.6 Kb/s); Redirect: 0s, DNS look up: 0.001098s, Connection: 0.02187s, Pretransfer: 0.055223s, First byte at: 0.096845s
[2026-05-30 21:24:27] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:24:27 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:24:27 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:24:28] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:24:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:28] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:24:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-05-30 21:24:28] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-05-30 21:24:29] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2026-05-30 21:24:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:29] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2026-05-30 21:24:31] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using Ensembl BioMart.
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `external_gene_name`, for organism hsapiens
[2026-05-30 21:24:31] [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>
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2026-05-30 21:24:31] [INFO]    [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:31] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2026-05-30 21:24:31] [INFO]    [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] Preparing httr2 request to URL `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:24:31] [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]
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-05-30 21:24:31] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:24:32] [TRACE]   [OmnipathR] Downloaded 1014 bytes in 0.117456s from www.ensembl.org (8.4 Kb/s); Redirect: 0s, DNS look up: 0.008545s, Connection: 0.037492s, Pretransfer: 0.037571s, First byte at: 0.117309s
[2026-05-30 21:24:32] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; X-GitHub-Request-Id: D5EA:BF13D:3B5AAF:3E3A6F:6A0E4CF0; Server: GitHub.com; X-Cache-Hits: 11; 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: 939686f970be5061238bea3740196116728d9105; Content-Encoding: gzip; Date: Sat, 30 May 2026 19:24:31 GMT; Expires: 0; X-Served-By: cache-lcy-egml8630050-LCY; Pragma: no-cache; X-Timer: S1780169072.942856,VS0,VE0; Access-Control-Allow-Origin: *; Accept-Ranges: bytes; ETag: W/"68b6c2f9-8aa"; Via: 1.1 varnish; Connection: keep-alive; Age: 50; Content-Length: 1014
[2026-05-30 21:24:32] [TRACE]   [OmnipathR] Response headers: [X-GitHub-Request-Id=D5EA:BF13D:3B5AAF:3E3A6F:6A0E4CF0,Server=GitHub.com,X-Cache-Hits=11,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=939686f970be5061238bea3740196116728d9105,Content-Encoding=gzip,Date=Sat, 30 May 2026 19:24:31 GMT,Expires=0,X-Served-By=cache-lcy-egml8630050-LCY,Pragma=no-cache,X-Timer=S1780169072.942856,VS0,VE0,Access-Control-Allow-Origin=*,Accept-Ranges=bytes,ETag=W/"68b6c2f9-8aa",Via=1.1 varnish,Connection=keep-alive,Age=50,Content-Length=1014]
[2026-05-30 21:24:32] [TRACE]   [OmnipathR] Calling reader callback on response.
[2026-05-30 21:24:32] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d8282bd9b4260cbc5a0923f1eff00b1534d7f081-1.rds`.
[2026-05-30 21:24:32] [INFO]    [OmnipathR] Download ready [key=d8282bd9b4260cbc5a0923f1eff00b1534d7f081, version=1]
[2026-05-30 21:24:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:32] [INFO]    [OmnipathR] Cache item `d8282bd9b4260cbc5a0923f1eff00b1534d7f081` version 1: status changed from `started` to `ready`.
[2026-05-30 21:24:32] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <html>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <head>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <title>Service unavailable</title>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <meta name="robots" content="noindex">
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <base href="//status.ensembl.org">
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <style>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] html,
[2026-05-30 21:24:32] [WARN]    [OmnipathR] body {
[2026-05-30 21:24:32] [WARN]    [OmnipathR] padding: 0;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] margin: 0;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] height: 100%;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] }
[2026-05-30 21:24:32] [WARN]    [OmnipathR] body {
[2026-05-30 21:24:32] [WARN]    [OmnipathR] display: grid;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] grid-template-rows: [header] auto [main] 1fr [footer] auto;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] font-family: Luxi Sans, Helvetica, Arial, Geneva, sans-serif;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] font-size: 90%;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] }
[2026-05-30 21:24:32] [WARN]    [OmnipathR] h1 {
[2026-05-30 21:24:32] [WARN]    [OmnipathR] font-size: 1.5rem;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] }
[2026-05-30 21:24:32] [WARN]    [OmnipathR] h2 {
[2026-05-30 21:24:32] [WARN]    [OmnipathR] font-size: 1.2rem;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] }
[2026-05-30 21:24:32] [WARN]    [OmnipathR] h3 {
[2026-05-30 21:24:32] [WARN]    [OmnipathR] font-size: 1.1rem;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] }
[2026-05-30 21:24:32] [WARN]    [OmnipathR] header {
[2026-05-30 21:24:32] [WARN]    [OmnipathR] grid-row: header;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] padding: 5px;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] height: 60px;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] background-color: #333366;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] }
[2026-05-30 21:24:32] [WARN]    [OmnipathR] header img {
[2026-05-30 21:24:32] [WARN]    [OmnipathR] width: 185px;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] height: 45px
[2026-05-30 21:24:32] [WARN]    [OmnipathR] }
[2026-05-30 21:24:32] [WARN]    [OmnipathR] main {
[2026-05-30 21:24:32] [WARN]    [OmnipathR] grid-row: main;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] padding: 20px;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] }
[2026-05-30 21:24:32] [WARN]    [OmnipathR] .mirrors {
[2026-05-30 21:24:32] [WARN]    [OmnipathR] border: solid 1px #ccc;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] margin-top: 20px;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] padding: 10px;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] }
[2026-05-30 21:24:32] [WARN]    [OmnipathR] footer {
[2026-05-30 21:24:32] [WARN]    [OmnipathR] grid-row: footer;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] padding: 0 20px;
[2026-05-30 21:24:32] [WARN]    [OmnipathR] }
[2026-05-30 21:24:32] [WARN]    [OmnipathR] </style>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] </head>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <body>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <header>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <img src="/e-ensembl.png" alt="ensembl-logo" />
[2026-05-30 21:24:32] [WARN]    [OmnipathR] </header>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <main>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <h1>Server Status</h1>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <p>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <img src="/exclamation_alert.png" alt="[!]" style="float:left;padding:0 10px;width:100px;height:89px" />
[2026-05-30 21:24:32] [WARN]    [OmnipathR] The Ensembl web service you requested is temporarily unavailable.
[2026-05-30 21:24:32] [WARN]    [OmnipathR] We are working to restore the service as soon as possible, and apologise for any inconvenience caused.
[2026-05-30 21:24:32] [WARN]    [OmnipathR] </p>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <p>For all enquiries, please <a href="https://www.ensembl.info/contact-us/">contact our HelpDesk</a>.</p>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <div class="mirrors">
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <h3>Ensembl mirrors</h3>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] We now also manage two mirrors of the Ensembl website, hosted in different regions of the Amazon cloud:
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <ul>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <li><a href="https://useast.ensembl.org/index.html?redirect=no">useast.ensembl.org</a></li>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <li><a href="https://asia.ensembl.org/index.html?redirect=no">asia.ensembl.org</a></li>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] </ul>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] These will be available while the main service is unavailable, although please note that some of the
[2026-05-30 21:24:32] [WARN]    [OmnipathR] facilities on these mirror may not be fully functional as they rely on resources hosted at our main
[2026-05-30 21:24:32] [WARN]    [OmnipathR] data centre.
[2026-05-30 21:24:32] [WARN]    [OmnipathR] </div>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] </main>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <footer>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] <p>&copy; 2025 EMBL-EBI</p>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] </footer>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] </body>
[2026-05-30 21:24:32] [WARN]    [OmnipathR] </html>
[2026-05-30 21:24:32] [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
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-05-30 19:16:10 UTC; omnipath
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-30 19:18:37 UTC; unix
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-05-30 21:24:35] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.2(2026-05-29); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-30); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-30 21:24:35] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Contains 6 files.
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.132258s from rescued.omnipathdb.org (301.4 Kb/s); Redirect: 0s, DNS look up: 0.001288s, Connection: 0.021038s, Pretransfer: 0.072511s, First byte at: 0.112286s
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:24:35 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 30 May 2026 20:24:35 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Sat, 30 May 2026 19:24:35 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 30 May 2026 20:24:35 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:35] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-30 21:24:36] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:36] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-30 21:24:36] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Downloaded 2.7 Kb in 0.119856s from omabrowser.org (22.2 Kb/s); Redirect: 0s, DNS look up: 0.000601s, Connection: 0.017146s, Pretransfer: 0.0512s, First byte at: 0.119737s
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 30 May 2026 19:24:36 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=CUzQTzMwTS8hFFiYXJP7zI3YkafhHCHTVfeO%2FTfN0gTKMfyCYx3Qg7mlUCPAHLhb4Zdoy5TO43WwHblZZaYAAUVSqGnW54gcVzX4JiBICW8eTLkVVSExP03k6kaZC%2F90qA%3D%3D"}]}; cf-ray: a0401eb6cf8adbb9-FRA; alt-svc: h3=":443"; ma=86400
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-30 21:24:36] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:36] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-30 21:24:36] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:24:36] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-30 21:24:36] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:24:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:25:00] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-30 21:25:00] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-05-30 21:25:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:00] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-05-30 21:25:01] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: accession,gene_primary
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2026-05-30 21:25:01] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`.
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:01] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-05-30 21:25:01] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:9606%20AND%20reviewed:true`
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:25:01] [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]
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] Downloaded 43 bytes in 0.416841s from rest.uniprot.org (103 bytes/s); Redirect: 0s, DNS look up: 0.001065s, Connection: 0.030242s, Pretransfer: 0.106586s, First byte at: 0.416803s
[2026-05-30 21:25:01] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 30-April-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 30 May 2026 19:25:01 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-05-30 21:25:10] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5edbb7050189a96382506b82b49b51a411621af7-1.rds`.
[2026-05-30 21:25:10] [INFO]    [OmnipathR] Download ready [key=5edbb7050189a96382506b82b49b51a411621af7, version=1]
[2026-05-30 21:25:10] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:10] [INFO]    [OmnipathR] Cache item `5edbb7050189a96382506b82b49b51a411621af7` version 1: status changed from `started` to `ready`.
[2026-05-30 21:25:10] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records
[2026-05-30 21:25:10] [INFO]    [OmnipathR] Loaded database `UniProt-GeneSymbol table`.
--- finished re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:23] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:25:23] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-05-30 19:16:10 UTC; omnipath
[2026-05-30 21:25:23] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-05-30 21:25:23] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-30 19:18:37 UTC; unix
[2026-05-30 21:25:23] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-05-30 21:25:23] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-05-30 21:25:23] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-05-30 21:25:23] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-05-30 21:25:23] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); ggplot2 4.0.3(2026-04-22); glue 1.8.1(2026-04-17); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.2(2026-05-29); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-30); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); S7 0.2.2(2026-04-22); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-30 21:25:23] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Contains 5 files.
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-05-30 21:25:23] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:23] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:23] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-05-30 21:25:23] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:25:23] [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]
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:25:23] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.120837s from rescued.omnipathdb.org (329.9 Kb/s); Redirect: 0s, DNS look up: 0.001344s, Connection: 0.022276s, Pretransfer: 0.057258s, First byte at: 0.099473s
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:25:23 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 30 May 2026 20:25:23 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Sat, 30 May 2026 19:25:23 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 30 May 2026 20:25:23 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-05-30 21:25:24] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:24] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-30 21:25:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:24] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-30 21:25:24] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:25:24] [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]
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] Downloaded 2.7 Kb in 0.131656s from omabrowser.org (20.2 Kb/s); Redirect: 0s, DNS look up: 0.007363s, Connection: 0.022397s, Pretransfer: 0.066543s, First byte at: 0.131482s
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 30 May 2026 19:25:24 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=raOxITXDZ6zJNs7nquOZcLPH9tonw2TJgSJFCJ8w6oci0VP%2BmjFyJKivLr%2BJsh1BsSG6uMCpivpDzJS6M%2BKqvkGLI2SzGrj%2B%2BPsy2mXYCtGPC0dziH2BLQwz74EupMw2EA%3D%3D"}]}; cf-ray: a0401fe44a684da1-FRA; alt-svc: h3=":443"; ma=86400
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-30 21:25:24] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:24] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-05-30 21:25:24] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:25:25] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-30 21:25:25] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:25:25] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-30 21:25:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:25] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:25:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-30 21:25:25] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:25:25] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:25:48] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-30 21:25:48] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-05-30 21:25:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:48] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-05-30 21:25:48] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-05-30 21:25:48] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:25:48] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:25:48] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:25:48] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:25:48] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:25:48] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:25:48] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:25:48] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:25:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:25:48] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:25:48] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:25:48] [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]
[2026-05-30 21:25:48] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:25:48] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.093722s from omnipathdb.org (167.5 Kb/s); Redirect: 0s, DNS look up: 0.000988s, Connection: 0.020958s, Pretransfer: 0.054201s, First byte at: 0.093366s
[2026-05-30 21:25:48] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:25:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:25:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:25:49] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:25:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:49] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:25:49] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-05-30 21:25:49] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-05-30 21:25:49] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2026-05-30 21:25:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:49] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2026-05-30 21:25:52] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
--- finished re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-05-30 19:16:10 UTC; omnipath
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-30 19:18:37 UTC; unix
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-05-30 21:25:56] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.2(2026-05-29); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-30); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-30 21:25:56] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Contains 5 files.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:25:56] [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]
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.114064s from rescued.omnipathdb.org (349.4 Kb/s); Redirect: 0s, DNS look up: 0.001169s, Connection: 0.01739s, Pretransfer: 0.064815s, First byte at: 0.097578s
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:25:56 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 30 May 2026 20:25:56 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Sat, 30 May 2026 19:25:56 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 30 May 2026 20:25:56 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:25:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-30 21:25:56] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:25:57] [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]
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] Downloaded 11.6 Kb in 0.09925s from omabrowser.org (116.5 Kb/s); Redirect: 0s, DNS look up: 0.00065s, Connection: 0.008285s, Pretransfer: 0.044408s, First byte at: 0.098913s
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 30 May 2026 19:25:57 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=cK89tQC3IJcU08HZcEYpmNJSboMJY8Mff1d2l15q%2Fy94PdWhQ%2Bxrhuch44Kr%2F7%2Fo4csxZBjaN%2BFBwJru4J%2FBQIlcuDWXImfRRBtJRQe59nRX2zN3MPNAWXH39fkIOUP9hQ%3D%3D"}]}; cf-ray: a04020afab5bf4f1-FRA; alt-svc: h3=":443"; ma=86400
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-30 21:25:57] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:57] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-30 21:25:57] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:25:57] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-30 21:25:57] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:25:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:26:20] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-30 21:26:20] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-05-30 21:26:20] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:26:20] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-05-30 21:26:20] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-05-30 21:26:20] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:26:20] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:26:20] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-05-30 21:26:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-05-30 21:26:20] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-05-30 21:26:20] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-05-30 21:26:20] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-05-30 21:26:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-05-30 21:26:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-05-30 21:26:20] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:26:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:26:20] [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]
[2026-05-30 21:26:20] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:26:20] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.098882s from omnipathdb.org (158.8 Kb/s); Redirect: 0s, DNS look up: 0.00112s, Connection: 0.021731s, Pretransfer: 0.056759s, First byte at: 0.09848s
[2026-05-30 21:26:20] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:26:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:26:20 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:26:21] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2026-05-30 21:26:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:26:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:26:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:26:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:26:21] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:26:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2026-05-30 21:26:22] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e9af339ce8e80bcec1a654822637ae3b71e035e2-1.rds`.
[2026-05-30 21:26:22] [INFO]    [OmnipathR] Download ready [key=e9af339ce8e80bcec1a654822637ae3b71e035e2, version=1]
[2026-05-30 21:26:22] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:26:22] [INFO]    [OmnipathR] Cache item `e9af339ce8e80bcec1a654822637ae3b71e035e2` version 1: status changed from `started` to `ready`.
[2026-05-30 21:26:22] [TRACE]   [OmnipathR] Converting JSON column `extra_attrs` to list.
[2026-05-30 21:26:31] [SUCCESS] [OmnipathR] Downloaded 139054 interactions.
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=UniProt_keyword,entity_types=protein,query_type=annotations]
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-05-30 21:32:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-05-30 21:32:43] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-05-30 21:32:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:32:43] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.092303s from omnipathdb.org (170.1 Kb/s); Redirect: 0s, DNS look up: 0.001054s, Connection: 0.019643s, Pretransfer: 0.053334s, First byte at: 0.091343s
[2026-05-30 21:32:44] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:32:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:32:43 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:32:44] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_keyword&entity_types=protein&license=academic`
[2026-05-30 21:32:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:44] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:32:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2026-05-30 21:32:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/0e2cc6ec8db9efe88661b213cfb09be72a32df7d-1.rds`.
[2026-05-30 21:32:45] [INFO]    [OmnipathR] Download ready [key=0e2cc6ec8db9efe88661b213cfb09be72a32df7d, version=1]
[2026-05-30 21:32:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:45] [INFO]    [OmnipathR] Cache item `0e2cc6ec8db9efe88661b213cfb09be72a32df7d` version 1: status changed from `started` to `ready`.
[2026-05-30 21:32:45] [SUCCESS] [OmnipathR] Downloaded 229780 annotation records.
[2026-05-30 21:32:45] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:32:45] [TRACE]   [OmnipathR] Arguments for OmniPath query: [types=ubiquitination,query_type=enzsub]
[2026-05-30 21:32:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:32:45] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:32:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-05-30 21:32:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-05-30 21:32:45] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-05-30 21:32:45] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-05-30 21:32:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-05-30 21:32:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-05-30 21:32:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-05-30 21:32:45] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:32:45] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:32:45] [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]
[2026-05-30 21:32:45] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:32:46] [TRACE]   [OmnipathR] Downloaded 1.3 Kb in 0.138973s from omnipathdb.org (9.1 Kb/s); Redirect: 0s, DNS look up: 0.039691s, Connection: 0.058885s, Pretransfer: 0.119202s, First byte at: 0.13889s
[2026-05-30 21:32:46] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:32:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:32:45 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:32:46] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic&types=ubiquitination`
[2026-05-30 21:32:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:46] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:32:46] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2026-05-30 21:32:46] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4525739875a94da1bbc48b8fada15795d234adcc-1.rds`.
[2026-05-30 21:32:46] [INFO]    [OmnipathR] Download ready [key=4525739875a94da1bbc48b8fada15795d234adcc, version=1]
[2026-05-30 21:32:46] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:46] [INFO]    [OmnipathR] Cache item `4525739875a94da1bbc48b8fada15795d234adcc` version 1: status changed from `started` to `ready`.
[2026-05-30 21:32:46] [SUCCESS] [OmnipathR] Downloaded 68 enzyme-substrate relationships.
--- finished re-building ‘extra_attrs.Rmd’

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

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:49] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:32:49] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-05-30 19:16:10 UTC; omnipath
[2026-05-30 21:32:49] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-05-30 21:32:49] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-30 19:18:37 UTC; unix
[2026-05-30 21:32:49] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-05-30 21:32:49] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-05-30 21:32:49] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2026-05-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-05-30 21:32:49] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-05-30 21:32:49] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.2(2026-05-29); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-30); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-9(2026-03-15); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-30 21:32:49] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] Contains 7 files.
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:49] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2026-05-30 21:32:50] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:50] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:50] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-05-30 21:32:50] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:32:50] [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]
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:32:50] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.128321s from rescued.omnipathdb.org (310.6 Kb/s); Redirect: 0s, DNS look up: 0.00782s, Connection: 0.029246s, Pretransfer: 0.063888s, First byte at: 0.1068s
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:32:50 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 30 May 2026 20:32:50 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Sat, 30 May 2026 19:32:50 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 30 May 2026 20:32:50 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-05-30 21:32:51] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:51] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-30 21:32:51] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:51] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-30 21:32:51] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:32:51] [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]
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Downloaded 1.3 Kb in 0.103499s from omabrowser.org (12.8 Kb/s); Redirect: 0s, DNS look up: 0.007216s, Connection: 0.019304s, Pretransfer: 0.053107s, First byte at: 0.103425s
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 30 May 2026 19:32:51 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=lhFMaV7UOj42oSUF2vYHsQPoi%2FX9y1ifrIrMTpxXQZzAGcUViJdH4qQZdea%2FFFcDZ553z0C8j4w9binDvLYrDapRL15KZ8IuDDiIjDP6JsS5rt%2FCGVR8vxzXDLmxrJe3AQ%3D%3D"}]}; cf-ray: a0402acdaa7edbbd-FRA; alt-svc: h3=":443"; ma=86400
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-30 21:32:51] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:51] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-30 21:32:51] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:32:51] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-30 21:32:51] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:32:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-30 21:33:15] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:15] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:15] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:15] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:15] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:15] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.099891s from omnipathdb.org (157.2 Kb/s); Redirect: 0s, DNS look up: 0.001068s, Connection: 0.017867s, Pretransfer: 0.066048s, First byte at: 0.099564s
[2026-05-30 21:33:15] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:15 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:16] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3,PhosphoSite,SIGNOR&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:16] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2026-05-30 21:33:16] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5fc92405e5592146693f05f443dd80aec58163a5-1.rds`.
[2026-05-30 21:33:16] [INFO]    [OmnipathR] Download ready [key=5fc92405e5592146693f05f443dd80aec58163a5, version=1]
[2026-05-30 21:33:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:16] [INFO]    [OmnipathR] Cache item `5fc92405e5592146693f05f443dd80aec58163a5` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:18] [SUCCESS] [OmnipathR] Downloaded 67773 interactions.
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra]
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[Wang,Lit-BM-17],organisms=10090,datasets=pathwayextra,query_type=interactions]
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] Organism(s): 10090
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:20] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:20] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:20] [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]
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.089323s from omnipathdb.org (175.8 Kb/s); Redirect: 0s, DNS look up: 0.001083s, Connection: 0.019146s, Pretransfer: 0.052815s, First byte at: 0.08901s
[2026-05-30 21:33:20] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:20 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:21] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Wang,Lit-BM-17&datasets=pathwayextra&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:21] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2026-05-30 21:33:21] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3bebb563f03426a03a2bbe2548cea1de114c32e2-1.rds`.
[2026-05-30 21:33:21] [INFO]    [OmnipathR] Download ready [key=3bebb563f03426a03a2bbe2548cea1de114c32e2, version=1]
[2026-05-30 21:33:21] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:21] [INFO]    [OmnipathR] Cache item `3bebb563f03426a03a2bbe2548cea1de114c32e2` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:22] [SUCCESS] [OmnipathR] Downloaded 41476 interactions.
[2026-05-30 21:33:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra]
[2026-05-30 21:33:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:22] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=10116,datasets=kinaseextra,query_type=interactions]
[2026-05-30 21:33:22] [TRACE]   [OmnipathR] Organism(s): 10116
[2026-05-30 21:33:22] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:22] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:23] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:23] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:23] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:23] [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]
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.111066s from omnipathdb.org (141.4 Kb/s); Redirect: 0s, DNS look up: 0.000923s, Connection: 0.021819s, Pretransfer: 0.067524s, First byte at: 0.110171s
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:23 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:23] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=10116&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:23] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5cd314c4201dd53ec320a9f10d9b55c017d6143d-1.rds`.
[2026-05-30 21:33:23] [INFO]    [OmnipathR] Download ready [key=5cd314c4201dd53ec320a9f10d9b55c017d6143d, version=1]
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:23] [INFO]    [OmnipathR] Cache item `5cd314c4201dd53ec320a9f10d9b55c017d6143d` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:24] [SUCCESS] [OmnipathR] Downloaded 11083 interactions.
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra]
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[iTALK,Baccin2019],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:24] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:24] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:24] [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]
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.101023s from omnipathdb.org (155.4 Kb/s); Redirect: 0s, DNS look up: 0.00101s, Connection: 0.02294s, Pretransfer: 0.056457s, First byte at: 0.100634s
[2026-05-30 21:33:24] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:24 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:24 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:25] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=iTALK,Baccin2019&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:25] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/76b8ee6c20a073a1d42974b1a19964fdd2720dc5-1.rds`.
[2026-05-30 21:33:25] [INFO]    [OmnipathR] Download ready [key=76b8ee6c20a073a1d42974b1a19964fdd2720dc5, version=1]
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:25] [INFO]    [OmnipathR] Cache item `76b8ee6c20a073a1d42974b1a19964fdd2720dc5` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:25] [SUCCESS] [OmnipathR] Downloaded 2840 interactions.
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:25] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:25] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:25] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:25] [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]
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.097711s from omnipathdb.org (160.7 Kb/s); Redirect: 0s, DNS look up: 0.001109s, Connection: 0.022024s, Pretransfer: 0.055799s, First byte at: 0.097377s
[2026-05-30 21:33:25] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:25 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:26] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:26] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-05-30 21:33:26] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-05-30 21:33:26] [INFO]    [OmnipathR] Download ready [key=a7b21d9d80a3837a50268df16d168128fc1c6ede, version=1]
[2026-05-30 21:33:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:26] [INFO]    [OmnipathR] Cache item `a7b21d9d80a3837a50268df16d168128fc1c6ede` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:29] [SUCCESS] [OmnipathR] Downloaded 85217 interactions.
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=A,organisms=9606,query_type=interactions,datasets=dorothea]
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:33:30] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:33:30] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:33:30] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:30] [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]
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.098872s from omnipathdb.org (158.8 Kb/s); Redirect: 0s, DNS look up: 0.001184s, Connection: 0.022234s, Pretransfer: 0.056201s, First byte at: 0.098556s
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:30 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:30] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:30] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff-1.rds`.
[2026-05-30 21:33:30] [INFO]    [OmnipathR] Download ready [key=64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff, version=1]
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:30] [INFO]    [OmnipathR] Cache item `64f0eaeec4b695e11e6f2abe93eff9d2b0dc8bff` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:31] [SUCCESS] [OmnipathR] Downloaded 6128 interactions.
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[miR2Disease,miRDeathDB],query_type=interactions,datasets=mirnatarget]
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:31] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:31] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:31] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:31] [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]
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.099283s from omnipathdb.org (158.1 Kb/s); Redirect: 0s, DNS look up: 0.000915s, Connection: 0.021664s, Pretransfer: 0.055795s, First byte at: 0.098361s
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:31 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:31] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miR2Disease,miRDeathDB&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:31] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6fb27ffb4d0e53df1451b4f323099eab4e7b60ae-1.rds`.
[2026-05-30 21:33:31] [INFO]    [OmnipathR] Download ready [key=6fb27ffb4d0e53df1451b4f323099eab4e7b60ae, version=1]
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:31] [INFO]    [OmnipathR] Cache item `6fb27ffb4d0e53df1451b4f323099eab4e7b60ae` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:31] [SUCCESS] [OmnipathR] Downloaded 648 interactions.
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Arguments for OmniPath query: [sources=TRAMETINIB,query_type=interactions,datasets=small_molecule]
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-05-30 21:33:32] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-05-30 21:33:32] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-05-30 21:33:32] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:32] [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]
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Downloaded 112 bytes in 0.086679s from omnipathdb.org (1.3 Kb/s); Redirect: 0s, DNS look up: 0.000958s, Connection: 0.021138s, Pretransfer: 0.066484s, First byte at: 0.086649s
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:32] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=TRAMETINIB&license=academic`
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:32] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c8829fb056a995e6935c4c5f23770852f8035247-1.rds`.
[2026-05-30 21:33:32] [INFO]    [OmnipathR] Download ready [key=c8829fb056a995e6935c4c5f23770852f8035247, version=1]
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:32] [INFO]    [OmnipathR] Cache item `c8829fb056a995e6935c4c5f23770852f8035247` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:32] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=enzsub]
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:32] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:32] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:32] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:32] [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]
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.091869s from omnipathdb.org (170.9 Kb/s); Redirect: 0s, DNS look up: 0.001018s, Connection: 0.019769s, Pretransfer: 0.053864s, First byte at: 0.091491s
[2026-05-30 21:33:32] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:33] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:33] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-05-30 21:33:33] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a6f560033dff45b503a8016c14c974c4c04b5967-1.rds`.
[2026-05-30 21:33:33] [INFO]    [OmnipathR] Download ready [key=a6f560033dff45b503a8016c14c974c4c04b5967, version=1]
[2026-05-30 21:33:33] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:33] [INFO]    [OmnipathR] Cache item `a6f560033dff45b503a8016c14c974c4c04b5967` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:34] [SUCCESS] [OmnipathR] Downloaded 41506 enzyme-substrate relationships.
[2026-05-30 21:33:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-05-30 21:33:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-05-30 21:33:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:34] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:34] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:34] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-05-30 21:33:34] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:37] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoSite,SIGNOR],organisms=10090,query_type=enzsub]
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] Organism(s): 10090
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:38] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:38] [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]
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.092143s from omnipathdb.org (170.4 Kb/s); Redirect: 0s, DNS look up: 0.001134s, Connection: 0.019542s, Pretransfer: 0.05363s, First byte at: 0.091074s
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:38 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:38 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:38] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/enzsub?genesymbols=yes&resources=PhosphoSite,SIGNOR&organisms=10090&fields=sources,references,curation_effort&license=academic`
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:39] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2026-05-30 21:33:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bce37a583e5f0da0390efc677c66c09007c26b09-1.rds`.
[2026-05-30 21:33:39] [INFO]    [OmnipathR] Download ready [key=bce37a583e5f0da0390efc677c66c09007c26b09, version=1]
[2026-05-30 21:33:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:39] [INFO]    [OmnipathR] Cache item `bce37a583e5f0da0390efc677c66c09007c26b09` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:39] [SUCCESS] [OmnipathR] Downloaded 16895 enzyme-substrate relationships.
[2026-05-30 21:33:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:33:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:39] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2026-05-30 21:33:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:39] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-05-30 21:33:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-05-30 21:33:40] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-05-30 21:33:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:40] [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]
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.108912s from omnipathdb.org (144.2 Kb/s); Redirect: 0s, DNS look up: 0.001185s, Connection: 0.019313s, Pretransfer: 0.071885s, First byte at: 0.108635s
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:40 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:40] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
[2026-05-30 21:33:40] [INFO]    [OmnipathR] Download ready [key=d9d7d22ab08109542a41373aee9f37f4a6e4f1a5, version=1]
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:40] [INFO]    [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:40] [SUCCESS] [OmnipathR] Downloaded 7233 protein complexes.
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,...],wide=FALSE,query_type=annotations]
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-05-30 21:33:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-05-30 21:33:42] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-05-30 21:33:42] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:42] [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]
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] Downloaded 11.6 Kb in 0.1135s from omnipathdb.org (102.5 Kb/s); Redirect: 0s, DNS look up: 0.001091s, Connection: 0.021173s, Pretransfer: 0.072826s, First byte at: 0.113203s
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:42 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:42 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:42] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?proteins=COMPLEX:NCAPD2_NCAPG_NCAPH_PARP1_SMC2_SMC4_XRCC1,COMPLEX:CCNA2_CDK2_LIG1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:CCNA2_CCNB1_CDK1_PARP1_POLA1_POLD1_POLE_RFC1_RFC2_RPA1_RPA2_RPA3_TOP1,COMPLEX:MRE11_PARP1_RAD50_TERF2_TERF2IP_XRCC5_XRCC6,COMPLEX:TERF2_WRN,COMPLEX:CALR_DHX30_H2AX_H2BC26_HSPA5_NPM1_PARP1,COMPLEX:CTCF_H2AC18_H2AZ1_KPNA1_KPNA3_LMNA_NPM1_PARP1_TOP2A,COMPLEX:ACTB_HSPA4_MYH10_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CDK8_MED6_PARP1,COMPLEX:HSPA4_NCL_NONO_NPM1_PARP1_RAD50_TLE1_TOP2B,COMPLEX:CREBBP_H3C11_H4C4_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:CAMK2D_CREBBP_HES1_KAT2B_NONO_PARP1_POLR2A_SRC,COMPLEX:WRN_XRCC5_XRCC6,COMPLEX:NCOA6_PARP1_PRKDC_XRCC5_XRCC6,COMPLEX:PARP1_WRN_XRCC5_XRCC6,COMPLEX:FEN1_WRN,COMPLEX:LIG3_PARP1,COMPLEX:ATE1_BANF1_PARP1,COMPLEX:PAXX_WRN_XRCC6,COMPLEX:PAXX_PRKDC_WRN_XRCC6,COMPLEX:KIAA0930_KLHL11_PEF1_WRN&license=academic`
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:43] [INFO]    [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`.
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a-1.rds`.
[2026-05-30 21:33:43] [INFO]    [OmnipathR] Download ready [key=cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a, version=1]
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:43] [INFO]    [OmnipathR] Cache item `cfb446cb3624b3ce7ea0de4f3be03e78f7b3182a` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:43] [SUCCESS] [OmnipathR] Downloaded 1234 annotation records.
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=NetPath,query_type=annotations]
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Downloaded 1.2 Kb in 0.075653s from omnipathdb.org (15.9 Kb/s); Redirect: 0s, DNS look up: 0.000996s, Connection: 0.020942s, Pretransfer: 0.054857s, First byte at: 0.075606s
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:43 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:43] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=NetPath&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:43] [INFO]    [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`.
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/3a9416f4b370e6979e4f7ad87feb5846267c0876-1.rds`.
[2026-05-30 21:33:43] [INFO]    [OmnipathR] Download ready [key=3a9416f4b370e6979e4f7ad87feb5846267c0876, version=1]
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:43] [INFO]    [OmnipathR] Cache item `3a9416f4b370e6979e4f7ad87feb5846267c0876` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:43] [SUCCESS] [OmnipathR] Downloaded 86 annotation records.
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Arguments for OmniPath query: [proteins=[NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,...],wide=FALSE,resources=ComPPI,query_type=annotations]
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:44] [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]
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Downloaded 2.7 Kb in 0.080122s from omnipathdb.org (34.1 Kb/s); Redirect: 0s, DNS look up: 0.000942s, Connection: 0.022803s, Pretransfer: 0.057391s, First byte at: 0.080043s
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:44 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:44] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=ComPPI&proteins=NCAPD2,NCAPG,NCAPH,PARP1,SMC2,SMC4,XRCC1,CCNA2,CDK2,LIG1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,CCNA2,CCNB1,CDK1,PARP1,POLA1,POLD1,POLE,RFC1,RFC2,RPA1,RPA2,RPA3,TOP1,MRE11,PARP1,RAD50,TERF2,TERF2IP,XRCC5,XRCC6,TERF2,WRN,CALR,DHX30,H2AX,H2BC26,HSPA5,NPM1,PARP1,CTCF,H2AC18,H2AZ1,KPNA1,KPNA3,LMNA,NPM1,PARP1,TOP2A,ACTB,HSPA4,MYH10,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CDK8,MED6,PARP1,HSPA4,NCL,NONO,NPM1,PARP1,RAD50,TLE1,TOP2B,CREBBP,H3C11,H4C4,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,CAMK2D,CREBBP,HES1,KAT2B,NONO,PARP1,POLR2A,SRC,WRN,XRCC5,XRCC6,NCOA6,PARP1,PRKDC,XRCC5,XRCC6,PARP1,WRN,XRCC5,XRCC6,FEN1,WRN,LIG3,PARP1,ATE1,BANF1,PARP1,PAXX,WRN,XRCC6,PAXX,PRKDC,WRN,XRCC6,KIAA0930,KLHL11,PEF1,WRN&license=academic`
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:44] [INFO]    [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`.
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/e41a9c717d93f0d64ff8b63412074cfad2a271ec-1.rds`.
[2026-05-30 21:33:44] [INFO]    [OmnipathR] Download ready [key=e41a9c717d93f0d64ff8b63412074cfad2a271ec, version=1]
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:44] [INFO]    [OmnipathR] Cache item `e41a9c717d93f0d64ff8b63412074cfad2a271ec` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:44] [SUCCESS] [OmnipathR] Downloaded 366 annotation records.
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,query_type=annotations]
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:33:44] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:33:44] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:33:44] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:44] [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]
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.09356s from omnipathdb.org (167.8 Kb/s); Redirect: 0s, DNS look up: 0.000927s, Connection: 0.019694s, Pretransfer: 0.054542s, First byte at: 0.092571s
[2026-05-30 21:33:44] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:44 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:45] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&license=academic`
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:45] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/48f6d1c796292ce438ca19de4baf3e99ff368b61-1.rds`.
[2026-05-30 21:33:45] [INFO]    [OmnipathR] Download ready [key=48f6d1c796292ce438ca19de4baf3e99ff368b61, version=1]
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:45] [INFO]    [OmnipathR] Cache item `48f6d1c796292ce438ca19de4baf3e99ff368b61` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:45] [SUCCESS] [OmnipathR] Downloaded 2578 annotation records.
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell_summary`
[2026-05-30 21:33:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell_summary`
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-05-30 21:33:45] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell_summary`
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell_summary`
[2026-05-30 21:33:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell_summary`
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell_summary`
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:45] [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]
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.070008s from omnipathdb.org (108.2 Kb/s); Redirect: 0s, DNS look up: 0.000925s, Connection: 0.017297s, Pretransfer: 0.051495s, First byte at: 0.069558s
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:45 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:45] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell_summary`
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:45] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4609206529e6ae997a8de976fe1277b3b74cc032-1.rds`.
[2026-05-30 21:33:45] [INFO]    [OmnipathR] Download ready [key=4609206529e6ae997a8de976fe1277b3b74cc032, version=1]
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:45] [INFO]    [OmnipathR] Cache item `4609206529e6ae997a8de976fe1277b3b74cc032` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:45] [SUCCESS] [OmnipathR] Downloaded 1190 records.
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-05-30 21:33:45] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-05-30 21:33:45] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-05-30 21:33:45] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:45] [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]
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.090517s from omnipathdb.org (173.5 Kb/s); Redirect: 0s, DNS look up: 0.001108s, Connection: 0.019331s, Pretransfer: 0.053307s, First byte at: 0.090134s
[2026-05-30 21:33:45] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:33:45 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:33:47] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?scope=generic&aspect=locational&license=academic`
[2026-05-30 21:33:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:47] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:47] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2026-05-30 21:33:48] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a-1.rds`.
[2026-05-30 21:33:48] [INFO]    [OmnipathR] Download ready [key=f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a, version=1]
[2026-05-30 21:33:48] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:48] [INFO]    [OmnipathR] Cache item `f3016033f2ec7b4f644fc95cf98c28c15a2e1b8a` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:49] [SUCCESS] [OmnipathR] Downloaded 274444 intercellular communication role records.
[2026-05-30 21:33:49] [TRACE]   [OmnipathR] Bypassing call: `intercell_network(high_confidence = TRUE)`.
[2026-05-30 21:33:49] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-05-30 21:33:49] [TRACE]   [OmnipathR] Bypassing call: `filter_intercell_network(., min_curation_effort = 1, consensus_percentile = 33)`.
[2026-05-30 21:33:49] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
--- finished re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:52] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:33:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: 2026-05-30 19:16:10 UTC; omnipath
[2026-05-30 21:33:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: NA
[2026-05-30 21:33:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2026-05-30 19:18:37 UTC; unix
[2026-05-30 21:33:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-05-30 21:33:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: NA
[2026-05-30 21:33:52] [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=2026-05-30; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA]
[2026-05-30 21:33:52] [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]
[2026-05-30 21:33:52] [INFO]    [OmnipathR] Loaded packages: backports 1.5.1(2026-04-03); BiocManager 1.30.26(2025-06-05); BiocStyle 2.38.0(2025-10-29); bit 4.6.0(2025-03-06); bit64 4.8.2(2026-05-19); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.11.0(2026-05-16); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.6(2026-04-09); crayon 1.5.3(2024-06-20); curl 7.1.0(2026-04-22); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.1(2026-04-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.1(2026-04-17); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.3.2(2026-05-29); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lifecycle 1.0.5(2026-01-08); logger 0.4.2(2026-05-10); lubridate 1.9.5(2026-02-04); magrittr 2.0.5(2026-04-04); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-05-30); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.2(2026-04-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1-1.1(2026-04-24); readr 2.2.0(2026-02-19); readxl 1.5.0(2026-05-16); rlang 1.2.0(2026-04-06); rmarkdown 2.31(2026-03-26); RSQLite 3.53.1(2026-05-23); rvest 1.0.5(2025-08-29); sass 0.4.10(2025-04-11); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.3(2026-04-11); withr 3.0.2(2024-10-28); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-05-30 21:33:52] [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
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Contains 21 files.
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Cache locked: FALSE
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2026-05-30 21:33:52] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:52] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:52] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Cache file path: /home/omnipath/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-05-30 21:33:52] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.13425s from rescued.omnipathdb.org (296.9 Kb/s); Redirect: 0s, DNS look up: 0.001158s, Connection: 0.021469s, Pretransfer: 0.072803s, First byte at: 0.113678s
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:33:52 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 30 May 2026 20:33:52 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-05-30 21:33:52] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Sat, 30 May 2026 19:33:52 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 30 May 2026 20:33:52 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-05-30 21:33:53] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:53] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-30 21:33:53] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:53] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-30 21:33:53] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:33:53] [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]
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Downloaded 7.6 Kb in 0.099434s from omabrowser.org (76.1 Kb/s); Redirect: 0s, DNS look up: 0.000632s, Connection: 0.008182s, Pretransfer: 0.040927s, First byte at: 0.0976s
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 30 May 2026 19:33:53 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=yddgQwPId82HGgW4Liow6q9zNpZqbDYr9Cd8izAND6Zl2w5w9TBO76pVuGbdWlA1z0T1LWJp1RyJ0s2R6wUEcyPFjtWWW0qiXjC3ULQeRt4BBIze7N2aWHdaJT0bNKkp8g%3D%3D"}]}; cf-ray: a0402c501e0b1e10-FRA; alt-svc: h3=":443"; ma=86400
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-05-30 21:33:53] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:53] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-30 21:33:53] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:33:53] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-30 21:33:53] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:33:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-05-30 21:34:17] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:17] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:17] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-05-30 21:34:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-05-30 21:34:17] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-05-30 21:34:17] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:17] [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]
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.113346s from omnipathdb.org (138.5 Kb/s); Redirect: 0s, DNS look up: 0.00103s, Connection: 0.020593s, Pretransfer: 0.073644s, First byte at: 0.112975s
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:34:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:34:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:34:17] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&entity_types=protein&license=academic`
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:17] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/20f47c37df19181b9818be11b36773e366a53732-1.rds`.
[2026-05-30 21:34:17] [INFO]    [OmnipathR] Download ready [key=20f47c37df19181b9818be11b36773e366a53732, version=1]
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:17] [INFO]    [OmnipathR] Cache item `20f47c37df19181b9818be11b36773e366a53732` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:17] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Looking up in cache: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2026-05-30 21:34:17] [INFO]    [OmnipathR] Cache record does not exist: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`.
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:17] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2026-05-30 21:34:17] [INFO]    [OmnipathR] Retrieving URL: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://static-content.springer.com/esm/art%3A10.1038%2Fnrg2538/MediaObjects/41576_2009_BFnrg2538_MOESM6_ESM.txt`
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:17] [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]
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] Downloaded 14.8 Kb in 0.04657s from static-content.springer.com (317.7 Kb/s); Redirect: 0s, DNS look up: 0.001446s, Connection: 0.005789s, Pretransfer: 0.03826s, First byte at: 0.046388s
[2026-05-30 21:34:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; content-type: application/octet-stream; x-guploader-uploadid: AAVLpEipVVCSiGZEWWRT13O9073QAWQYVmKZvF9RyRmcsz7OWvabd9UBD8SHFjYtXPATJRoppMC5bWlCs3n_; 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: 89423; date: Sat, 30 May 2026 19:34:17 GMT; via: 1.1 varnish; x-served-by: cache-fra-eddf8230122-FRA; x-cache: HIT; x-cache-hits: 0; x-timer: S1780169658.934547,VS0,VE3; vary: Origin; alt-svc: h3=":443";ma=86400,h3-29=":443";ma=86400,h3-27=":443";ma=86400; content-length: 160972
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8-1.rds`.
[2026-05-30 21:34:18] [INFO]    [OmnipathR] Download ready [key=c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8, version=1]
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:18] [INFO]    [OmnipathR] Cache item `c36e2a3cf4ebcaf5e345791be4cbd2eeb374ddf8` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:18] [SUCCESS] [OmnipathR] TF census (static-content.springer.com): downloaded 1987 records
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],entity_types=protein,query_type=interactions]
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-05-30 21:34:18] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-05-30 21:34:18] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-05-30 21:34:18] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.100579s from omnipathdb.org (156.1 Kb/s); Redirect: 0s, DNS look up: 0.000929s, Connection: 0.019185s, Pretransfer: 0.063892s, First byte at: 0.100218s
[2026-05-30 21:34:18] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:34:18 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:34:18 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:34:19] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&entity_types=protein&license=academic`
[2026-05-30 21:34:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:19] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2026-05-30 21:34:19] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6a345040ad2eaef2ab94e12a1b14630e991963ba-1.rds`.
[2026-05-30 21:34:19] [INFO]    [OmnipathR] Download ready [key=6a345040ad2eaef2ab94e12a1b14630e991963ba, version=1]
[2026-05-30 21:34:19] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:19] [INFO]    [OmnipathR] Cache item `6a345040ad2eaef2ab94e12a1b14630e991963ba` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:24] [SUCCESS] [OmnipathR] Downloaded 147217 interactions.
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=[Ramilowski_location,UniProt_location,HPA_subcellular],entity_types=protein,query_type=annotations]
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-05-30 21:34:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-05-30 21:34:24] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-05-30 21:34:24] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:24] [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]
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.094378s from omnipathdb.org (166.4 Kb/s); Redirect: 0s, DNS look up: 0.001083s, Connection: 0.021002s, Pretransfer: 0.054385s, First byte at: 0.093997s
[2026-05-30 21:34:24] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:34:24 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:34:24 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:34:26] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=Ramilowski_location,UniProt_location,HPA_subcellular&entity_types=protein&license=academic`
[2026-05-30 21:34:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:26] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2026-05-30 21:34:27] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/d22e19552744752ac693b8572b5e500433b4f65b-1.rds`.
[2026-05-30 21:34:27] [INFO]    [OmnipathR] Download ready [key=d22e19552744752ac693b8572b5e500433b4f65b, version=1]
[2026-05-30 21:34:27] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:27] [INFO]    [OmnipathR] Cache item `d22e19552744752ac693b8572b5e500433b4f65b` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:27] [SUCCESS] [OmnipathR] Downloaded 601862 annotation records.
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-05-30 21:34:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-05-30 21:34:28] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-05-30 21:34:28] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:28] [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]
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.097583s from omnipathdb.org (160.9 Kb/s); Redirect: 0s, DNS look up: 0.001043s, Connection: 0.021749s, Pretransfer: 0.055497s, First byte at: 0.097161s
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:34:28 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:34:28 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:34:28] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=ligand&topology=secreted&license=academic`
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:28] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/8b4df10feeee656d8460263705d94f8a1d129497-1.rds`.
[2026-05-30 21:34:28] [INFO]    [OmnipathR] Download ready [key=8b4df10feeee656d8460263705d94f8a1d129497, version=1]
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:28] [INFO]    [OmnipathR] Cache item `8b4df10feeee656d8460263705d94f8a1d129497` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:28] [SUCCESS] [OmnipathR] Downloaded 10881 intercellular communication role records.
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-05-30 21:34:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-05-30 21:34:28] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-05-30 21:34:28] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:28] [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]
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.107654s from omnipathdb.org (145.8 Kb/s); Redirect: 0s, DNS look up: 0.00106s, Connection: 0.021402s, Pretransfer: 0.065721s, First byte at: 0.106658s
[2026-05-30 21:34:28] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:34:28 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:34:28 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:34:29] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:29] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-05-30 21:34:29] [INFO]    [OmnipathR] Download ready [key=9ecbbba7b7129c316d69501f7af5c2aced05a498, version=1]
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:29] [INFO]    [OmnipathR] Cache item `9ecbbba7b7129c316d69501f7af5c2aced05a498` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:29] [SUCCESS] [OmnipathR] Downloaded 23947 intercellular communication role records.
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-05-30 21:34:29] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-05-30 21:34:29] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-05-30 21:34:29] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.102206s from omnipathdb.org (153.6 Kb/s); Redirect: 0s, DNS look up: 0.001244s, Connection: 0.01903s, Pretransfer: 0.066843s, First byte at: 0.101839s
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:34:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:34:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:34:29] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&parent=receptor&topology=plasma_membrane_transmembrane&license=academic`
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:29] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/958b54b673bc1257aa3dafe979574736ad7d4632-1.rds`.
[2026-05-30 21:34:29] [INFO]    [OmnipathR] Download ready [key=958b54b673bc1257aa3dafe979574736ad7d4632, version=1]
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:29] [INFO]    [OmnipathR] Cache item `958b54b673bc1257aa3dafe979574736ad7d4632` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:29] [SUCCESS] [OmnipathR] Downloaded 22442 intercellular communication role records.
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-05-30 21:34:30] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-05-30 21:34:30] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-05-30 21:34:30] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-05-30 21:34:30] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-05-30 21:34:30] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:30] [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]
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.095624s from omnipathdb.org (164.2 Kb/s); Redirect: 0s, DNS look up: 0.000976s, Connection: 0.021224s, Pretransfer: 0.054823s, First byte at: 0.095222s
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:34:30 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:34:30 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:34:30] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=secreted&causality=trans&license=academic`
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:30] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f7af75e239c9ffc6d21bad01972722f2f0180e87-1.rds`.
[2026-05-30 21:34:30] [INFO]    [OmnipathR] Download ready [key=f7af75e239c9ffc6d21bad01972722f2f0180e87, version=1]
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:30] [INFO]    [OmnipathR] Cache item `f7af75e239c9ffc6d21bad01972722f2f0180e87` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:30] [SUCCESS] [OmnipathR] Downloaded 17663 intercellular communication role records.
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-05-30 21:34:30] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-05-30 21:34:30] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-05-30 21:34:30] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-05-30 21:34:30] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-05-30 21:34:30] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:30] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:30] [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]
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.11338s from omnipathdb.org (138.5 Kb/s); Redirect: 0s, DNS look up: 0.001057s, Connection: 0.021993s, Pretransfer: 0.07085s, First byte at: 0.112394s
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:34:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:34:31 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:34:31] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/intercell?entity_types=protein&topology=plasma_membrane_transmembrane&causality=rec&license=academic`
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:31] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/72c58fa11451e57015edbfc8235d55d71f9d7362-1.rds`.
[2026-05-30 21:34:31] [INFO]    [OmnipathR] Download ready [key=72c58fa11451e57015edbfc8235d55d71f9d7362, version=1]
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:31] [INFO]    [OmnipathR] Cache item `72c58fa11451e57015edbfc8235d55d71f9d7362` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:31] [SUCCESS] [OmnipathR] Downloaded 27365 intercellular communication role records.
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`.
[2026-05-30 21:34:31] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic`
[2026-05-30 21:34:31] [SUCCESS] [OmnipathR] Loaded 23947 intercellular communication role records from cache.
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein]
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,entity_types=protein,query_type=interactions]
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:31] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:31] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:31] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:31] [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]
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.102394s from omnipathdb.org (153.3 Kb/s); Redirect: 0s, DNS look up: 0.001089s, Connection: 0.023653s, Pretransfer: 0.056827s, First byte at: 0.102049s
[2026-05-30 21:34:31] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:34:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:34:31 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:34:32] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:32] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:32] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2026-05-30 21:34:32] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/4531fff8a97521fefd85568643520d934e90659c-1.rds`.
[2026-05-30 21:34:32] [INFO]    [OmnipathR] Download ready [key=4531fff8a97521fefd85568643520d934e90659c, version=1]
[2026-05-30 21:34:32] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:32] [INFO]    [OmnipathR] Cache item `4531fff8a97521fefd85568643520d934e90659c` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:35] [SUCCESS] [OmnipathR] Downloaded 84507 interactions.
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_pathway,entity_types=protein,query_type=annotations]
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-05-30 21:34:35] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-05-30 21:34:35] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-05-30 21:34:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] Downloaded 11.4 Kb in 0.095831s from omnipathdb.org (119.3 Kb/s); Redirect: 0s, DNS look up: 0.001057s, Connection: 0.02111s, Pretransfer: 0.05463s, First byte at: 0.09508s
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:34:35 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:34:35 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:34:35] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_pathway&entity_types=protein&license=academic`
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:36] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8-1.rds`.
[2026-05-30 21:34:36] [INFO]    [OmnipathR] Download ready [key=6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8, version=1]
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:36] [INFO]    [OmnipathR] Cache item `6061f30dac10cc2b0f8bcf13f7d870c3d69a0df8` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:36] [SUCCESS] [OmnipathR] Downloaded 1146 annotation records.
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SignaLink_function,entity_types=protein,query_type=annotations]
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-05-30 21:34:36] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-05-30 21:34:36] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-05-30 21:34:36] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Downloaded 10.6 Kb in 0.080862s from omnipathdb.org (130.9 Kb/s); Redirect: 0s, DNS look up: 0.001125s, Connection: 0.022406s, Pretransfer: 0.055638s, First byte at: 0.080222s
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:34:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:34:36 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:34:36] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=SignaLink_function&entity_types=protein&license=academic`
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:36] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/ec1ffe714d7618308311e03ab5d91a72b6ab30a3-1.rds`.
[2026-05-30 21:34:36] [INFO]    [OmnipathR] Download ready [key=ec1ffe714d7618308311e03ab5d91a72b6ab30a3, version=1]
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:36] [INFO]    [OmnipathR] Cache item `ec1ffe714d7618308311e03ab5d91a72b6ab30a3` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:36] [SUCCESS] [OmnipathR] Downloaded 1083 annotation records.
[2026-05-30 21:34:37] [TRACE]   [OmnipathR] Bypassing call: `simplify_intercell_network(.)`.
[2026-05-30 21:34:37] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2026-05-30 21:34:37] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:34:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],datasets=tf_target,entity_types=protein,resources=[ORegAnno,PAZAR],query_type=interactions]
[2026-05-30 21:34:37] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:37] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:37] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:34:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:38] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:38] [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]
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.104402s from omnipathdb.org (150.4 Kb/s); Redirect: 0s, DNS look up: 0.001101s, Connection: 0.02052s, Pretransfer: 0.06525s, First byte at: 0.104081s
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:34:38 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:34:38 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:34:38] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ORegAnno,PAZAR&datasets=tf_target&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort&entity_types=protein&license=academic`
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:38] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/eb0c13fd817d7fa62717fa239f8a329e85dcac2e-1.rds`.
[2026-05-30 21:34:38] [INFO]    [OmnipathR] Download ready [key=eb0c13fd817d7fa62717fa239f8a329e85dcac2e, version=1]
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:38] [INFO]    [OmnipathR] Cache item `eb0c13fd817d7fa62717fa239f8a329e85dcac2e` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:38] [SUCCESS] [OmnipathR] Downloaded 4242 interactions.
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:34:38] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:34:38] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:34:38] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:38] [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]
[2026-05-30 21:34:39] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:34:39] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.094509s from omnipathdb.org (166.1 Kb/s); Redirect: 0s, DNS look up: 0.001106s, Connection: 0.020962s, Pretransfer: 0.054279s, First byte at: 0.093624s
[2026-05-30 21:34:39] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:34:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:34:39 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:34:39] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:34:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:39] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-05-30 21:34:39] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-05-30 21:34:39] [INFO]    [OmnipathR] Download ready [key=f2e7cc5e753cd4e22d458171359dea86781ebae8, version=1]
[2026-05-30 21:34:39] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:39] [INFO]    [OmnipathR] Cache item `f2e7cc5e753cd4e22d458171359dea86781ebae8` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:39] [SUCCESS] [OmnipathR] Downloaded 85595 annotation records.
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-05-30 21:34:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-05-30 21:34:40] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-05-30 21:34:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-05-30 21:34:40] [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]
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.095552s from omnipathdb.org (164.3 Kb/s); Redirect: 0s, DNS look up: 0.000966s, Connection: 0.020965s, Pretransfer: 0.055206s, First byte at: 0.095168s
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 30 May 2026 19:34:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 30 May 2026 20:34:40 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-05-30 21:34:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:40] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `unknown` to `started`.
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-05-30 21:34:40] [INFO]    [OmnipathR] Download ready [key=422914ef8903d8480f1b9fbb47096e275567851d, version=1]
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-05-30 21:34:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:40] [INFO]    [OmnipathR] Cache item `422914ef8903d8480f1b9fbb47096e275567851d` version 1: status changed from `started` to `ready`.
[2026-05-30 21:34:41] [SUCCESS] [OmnipathR] Downloaded 2102 annotation records.
[2026-05-30 21:34:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:34:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=UniProt_location,query_type=annotations]
[2026-05-30 21:34:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:46] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:34:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:34:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/f2e7cc5e753cd4e22d458171359dea86781ebae8-1.rds`.
[2026-05-30 21:34:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=UniProt_location&license=academic`
[2026-05-30 21:34:47] [SUCCESS] [OmnipathR] Loaded 85595 annotation records from cache.
[2026-05-30 21:34:47] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-05-30 21:34:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=kinase.com,query_type=annotations]
[2026-05-30 21:34:47] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-05-30 21:34:47] [TRACE]   [OmnipathR] Orthology targets: 
[2026-05-30 21:34:47] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-05-30 21:34:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-05-30 21:34:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-05-30 21:34:47] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/422914ef8903d8480f1b9fbb47096e275567851d-1.rds`.
[2026-05-30 21:34:47] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=kinase.com&license=academic`
[2026-05-30 21:34:47] [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 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.22/2026-05-30_2105/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2026-05-30 21:34:56 CEST ]