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This page was generated on 2026-03-05 11:57 -0500 (Thu, 05 Mar 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4894
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1505/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.18.4  (landing page)
Denes Turei
Snapshot Date: 2026-03-04 13:45 -0500 (Wed, 04 Mar 2026)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_22
git_last_commit: efaae39
git_last_commit_date: 2026-01-20 09:40:26 -0500 (Tue, 20 Jan 2026)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  
See other builds for OmnipathR in R Universe.

CHECK results for OmnipathR on nebbiolo2

To the developers/maintainers of the OmnipathR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: OmnipathR
Version: 3.18.4
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OmnipathR_3.18.4.tar.gz
StartedAt: 2026-03-05 02:21:22 -0500 (Thu, 05 Mar 2026)
EndedAt: 2026-03-05 02:55:29 -0500 (Thu, 05 Mar 2026)
EllapsedTime: 2046.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings OmnipathR_3.18.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.3 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 ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:21:52] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-05 02:21:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-05 02:21:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-03-04
[2026-03-05 02:21:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-03-04 20:09:49 UTC; unix
[2026-03-05 02:21:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-03-05 02:21:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-03-05 02:21:52] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-05; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-05 02:21:52] [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=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-05 02:21:52] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-03-04); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-05 02:21:52] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:21:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-05 02:21:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:21:52] [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
[2026-03-05 02:22:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:22:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:22:09] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-05 02:22:09] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-05 02:22:09] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-03-04
[2026-03-05 02:22:09] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-03-04 20:09:49 UTC; unix
[2026-03-05 02:22:09] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-03-05 02:22:09] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-03-05 02:22:09] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-05; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-05 02:22:09] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-05 02:22:10] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-03-04); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-05 02:22:10] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:22:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-05 02:22:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:22:10] [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 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: omnipath-interactions
> ### Title: Molecular interactions from OmniPath
> ### Aliases: omnipath-interactions omnipath_interactions
> ###   import_omnipath_interactions omnipath pathwayextra
> ###   import_pathwayextra_interactions kinaseextra
> ###   import_kinaseextra_interactions ligrecextra
> ###   import_ligrecextra_interactions post_translational
> ###   import_post_translational_interactions dorothea
> ###   import_dorothea_interactions tf_target import_tf_target_interactions
> ###   transcriptional import_transcriptional_interactions collectri
> ###   mirna_target import_mirnatarget_interactions tf_mirna
> ###   import_tf_mirna_interactions lncrna_mrna
> ###   import_lncrna_mrna_interactions small_molecule
> ###   import_small_molecule_protein_interactions all_interactions
> ###   import_all_interactions
> 
> ### ** Examples
> 
> op <- omnipath(resources = c("CA1", "SIGNOR", "SignaLink3"))
[2026-03-05 02:35:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:35:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath]
[2026-03-05 02:35:27] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:35:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath,query_type=interactions]
[2026-03-05 02:35:27] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:35:27] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:35:27] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-05 02:35:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:28] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:28] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:28] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:28] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:28] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-05 02:35:28] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-05 02:35:28] [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]
[2026-03-05 02:35:29] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-05 02:35:29] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.39399s from omnipathdb.org (39.8 Kb/s); Redirect: 0s, DNS look up: 0.011906s, Connection: 0.022109s, Pretransfer: 0.245621s, First byte at: 0.393537s
[2026-03-05 02:35:29] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 05 Mar 2026 07:35:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 05 Mar 2026 08:35:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-05 02:35:31] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:31] [INFO]    [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `unknown` to `started`.
[2026-03-05 02:35:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`.
[2026-03-05 02:35:32] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`.
[2026-03-05 02:35:32] [INFO]    [OmnipathR] Download ready [key=029da7bc67579749c5723c06c82d60c331a10ad3, version=1]
[2026-03-05 02:35:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:32] [INFO]    [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `started` to `ready`.
[2026-03-05 02:35:34] [SUCCESS] [OmnipathR] Downloaded 67035 interactions.
> op
# A tibble: 67,035 × 15
   source target source_genesymbol target_genesymbol is_directed is_stimulation
   <chr>  <chr>  <chr>             <chr>             <lgl>       <lgl>         
 1 Q13976 Q13507 PRKG1             TRPC3             TRUE        FALSE         
 2 P06241 Q9Y210 FYN               TRPC6             TRUE        TRUE          
 3 Q13976 Q9Y210 PRKG1             TRPC6             TRUE        FALSE         
 4 P12931 Q9Y210 SRC               TRPC6             TRUE        TRUE          
 5 Q13976 Q9HCX4 PRKG1             TRPC7             TRUE        TRUE          
 6 Q00535 Q8NER1 CDK5              TRPV1             TRUE        TRUE          
 7 Q13438 Q9HBA0 OS9               TRPV4             TRUE        TRUE          
 8 P18031 Q9H1D0 PTPN1             TRPV6             TRUE        FALSE         
 9 P63244 Q9BX84 RACK1             TRPM6             TRUE        FALSE         
10 Q9BX84 Q96QT4 TRPM6             TRPM7             TRUE        TRUE          
# ℹ 67,025 more rows
# ℹ 9 more variables: is_inhibition <lgl>, consensus_direction <lgl>,
#   consensus_stimulation <lgl>, consensus_inhibition <lgl>, sources <chr>,
#   references <chr>, curation_effort <dbl>, n_references <int>,
#   n_resources <int>
> 
> interactions = omnipath_interactions(
+     resources = "SignaLink3",
+     organism = 9606
+ )
[2026-03-05 02:35:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:35:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,organisms=9606,query_type=interactions]
[2026-03-05 02:35:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:35:34] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:35:34] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-05 02:35:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:35] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2026-03-05 02:35:35] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:35] [SUCCESS] [OmnipathR] Loaded 1799 interactions from cache.
> 
> pathways <- omnipath()
[2026-03-05 02:35:35] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:35:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-03-05 02:35:35] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:35:35] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-03-05 02:35:35] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:35:35] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:35:35] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:36] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-03-05 02:35:36] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:39] [SUCCESS] [OmnipathR] Loaded 85217 interactions from cache.
> pathways
# A tibble: 85,217 × 15
   source target source_genesymbol target_genesymbol is_directed is_stimulation
   <chr>  <chr>  <chr>             <chr>             <lgl>       <lgl>         
 1 P0DP25 P48995 CALM3             TRPC1             TRUE        FALSE         
 2 P0DP23 P48995 CALM1             TRPC1             TRUE        FALSE         
 3 P0DP24 P48995 CALM2             TRPC1             TRUE        FALSE         
 4 Q03135 P48995 CAV1              TRPC1             TRUE        TRUE          
 5 P14416 P48995 DRD2              TRPC1             TRUE        TRUE          
 6 Q99750 P48995 MDFI              TRPC1             TRUE        FALSE         
 7 Q14571 P48995 ITPR2             TRPC1             TRUE        TRUE          
 8 P29966 P48995 MARCKS            TRPC1             TRUE        FALSE         
 9 Q13255 P48995 GRM1              TRPC1             TRUE        TRUE          
10 Q13586 P48995 STIM1             TRPC1             TRUE        TRUE          
# ℹ 85,207 more rows
# ℹ 9 more variables: is_inhibition <lgl>, consensus_direction <lgl>,
#   consensus_stimulation <lgl>, consensus_inhibition <lgl>, sources <chr>,
#   references <chr>, curation_effort <dbl>, n_references <int>,
#   n_resources <int>
> 
> interactions <-
+     pathwayextra(
+         resources = c("BioGRID", "IntAct"),
+         organism = 9606
+     )
[2026-03-05 02:35:39] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:35:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra]
[2026-03-05 02:35:39] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:35:39] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra,query_type=interactions]
[2026-03-05 02:35:39] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:35:39] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:35:39] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-05 02:35:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:40] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:40] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:40] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:40] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:40] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-05 02:35:40] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-05 02:35:40] [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]
[2026-03-05 02:35:40] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-05 02:35:40] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.365425s from omnipathdb.org (43 Kb/s); Redirect: 0s, DNS look up: 0.001503s, Connection: 0.002363s, Pretransfer: 0.208032s, First byte at: 0.364659s
[2026-03-05 02:35:40] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 05 Mar 2026 07:35:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 05 Mar 2026 08:35:40 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-05 02:35:42] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:42] [INFO]    [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `unknown` to `started`.
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`.
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`.
[2026-03-05 02:35:42] [INFO]    [OmnipathR] Download ready [key=aa665c2ecdd9e913e13934eeb12c1fa7b0d21884, version=1]
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:42] [INFO]    [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `started` to `ready`.
[2026-03-05 02:35:42] [SUCCESS] [OmnipathR] Downloaded 2593 interactions.
> 
> kinase_substrate <-
+    kinaseextra(
+        resources = c('PhosphoPoint', 'PhosphoSite'),
+        organism = 9606
+    )
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra]
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra,query_type=interactions]
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:35:42] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-05 02:35:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:43] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:43] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:43] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:43] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:43] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:43] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:43] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-05 02:35:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-05 02:35:43] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-05 02:35:44] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-05 02:35:44] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.357467s from omnipathdb.org (43.9 Kb/s); Redirect: 0s, DNS look up: 0.001747s, Connection: 0.002508s, Pretransfer: 0.2s, First byte at: 0.356548s
[2026-03-05 02:35:44] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 05 Mar 2026 07:35:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 05 Mar 2026 08:35:43 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-05 02:35:45] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:45] [INFO]    [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `unknown` to `started`.
[2026-03-05 02:35:45] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`.
[2026-03-05 02:35:46] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`.
[2026-03-05 02:35:46] [INFO]    [OmnipathR] Download ready [key=7db24bdf2093c17feeea2eea249fad461c5a1d09, version=1]
[2026-03-05 02:35:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:46] [INFO]    [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `started` to `ready`.
[2026-03-05 02:35:46] [SUCCESS] [OmnipathR] Downloaded 11909 interactions.
> 
> ligand_receptor <- ligrecextra(
+     resources = c('HPRD', 'Guide2Pharma'),
+     organism = 9606
+ )
[2026-03-05 02:35:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:35:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra]
[2026-03-05 02:35:46] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:35:46] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2026-03-05 02:35:46] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:35:46] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:35:46] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-05 02:35:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:47] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:47] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:47] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:47] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:47] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:47] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:47] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-05 02:35:47] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-05 02:35:47] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-05 02:35:48] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-05 02:35:48] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.347691s from omnipathdb.org (45.2 Kb/s); Redirect: 0s, DNS look up: 0.001377s, Connection: 0.002228s, Pretransfer: 0.198532s, First byte at: 0.347286s
[2026-03-05 02:35:48] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 05 Mar 2026 07:35:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 05 Mar 2026 08:35:47 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-05 02:35:49] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:49] [INFO]    [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `unknown` to `started`.
[2026-03-05 02:35:49] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`.
[2026-03-05 02:35:49] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`.
[2026-03-05 02:35:49] [INFO]    [OmnipathR] Download ready [key=393dd95dc380ac2e0800d32dc3f2fbbc88166e57, version=1]
[2026-03-05 02:35:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:49] [INFO]    [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `started` to `ready`.
[2026-03-05 02:35:49] [SUCCESS] [OmnipathR] Downloaded 1864 interactions.
> 
> interactions <- post_translational(resources = "BioGRID")
[2026-03-05 02:35:49] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:35:49] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=BioGRID,query_type=interactions]
[2026-03-05 02:35:49] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:35:49] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:35:49] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-05 02:35:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:50] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:50] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:50] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:50] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:50] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:50] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:50] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-05 02:35:50] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-05 02:35:50] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-05 02:35:50] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-05 02:35:50] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.339981s from omnipathdb.org (46.2 Kb/s); Redirect: 0s, DNS look up: 0.001845s, Connection: 0.00246s, Pretransfer: 0.191263s, First byte at: 0.339081s
[2026-03-05 02:35:50] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 05 Mar 2026 07:35:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 05 Mar 2026 08:35:50 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-05 02:35:52] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:52] [INFO]    [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `unknown` to `started`.
[2026-03-05 02:35:52] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`.
[2026-03-05 02:35:52] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`.
[2026-03-05 02:35:52] [INFO]    [OmnipathR] Download ready [key=108f2cda262af403a026484add1c5a2c3d9c94fe, version=1]
[2026-03-05 02:35:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:52] [INFO]    [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `started` to `ready`.
[2026-03-05 02:35:52] [SUCCESS] [OmnipathR] Downloaded 2708 interactions.
> 
> dorothea_grn <- dorothea(
+     resources = c('DoRothEA', 'ARACNe-GTEx_DoRothEA'),
+     organism = 9606,
+     dorothea_levels = c('A', 'B', 'C')
+ )
[2026-03-05 02:35:52] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:35:52] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],resources=[DoRothEA,ARACNe-GTEx_DoRothEA],organisms=9606,query_type=interactions,datasets=dorothea]
[2026-03-05 02:35:52] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:35:52] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:35:52] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-05 02:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:53] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:35:53] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:35:53] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:35:53] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:35:53] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:35:53] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:35:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:35:53] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-05 02:35:53] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-05 02:35:53] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-05 02:35:54] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-05 02:35:54] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.382585s from omnipathdb.org (41 Kb/s); Redirect: 0s, DNS look up: 0.001504s, Connection: 0.002223s, Pretransfer: 0.203913s, First byte at: 0.382067s
[2026-03-05 02:35:54] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 05 Mar 2026 07:35:53 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 05 Mar 2026 08:35:53 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-05 02:35:55] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:35:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:55] [INFO]    [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `unknown` to `started`.
[2026-03-05 02:35:55] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`.
[2026-03-05 02:35:56] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`.
[2026-03-05 02:35:56] [INFO]    [OmnipathR] Download ready [key=ce66cb9846294c226acee9ccf50a608c089386dd, version=1]
[2026-03-05 02:35:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:35:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:56] [INFO]    [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `started` to `ready`.
[2026-03-05 02:35:57] [SUCCESS] [OmnipathR] Downloaded 32629 interactions.
> dorothea_grn
# A tibble: 32,629 × 16
   source target source_genesymbol target_genesymbol is_directed is_stimulation
   <chr>  <chr>  <chr>             <chr>             <lgl>       <lgl>         
 1 P01106 O14746 MYC               TERT              TRUE        TRUE          
 2 P84022 P05412 SMAD3             JUN               TRUE        TRUE          
 3 Q13485 P05412 SMAD4             JUN               TRUE        TRUE          
 4 P08047 P04075 SP1               ALDOA             TRUE        TRUE          
 5 P04637 P08069 TP53              IGF1R             TRUE        FALSE         
 6 Q05516 P20248 ZBTB16            CCNA2             TRUE        FALSE         
 7 Q01196 P08700 RUNX1             IL3               TRUE        FALSE         
 8 P42224 P38936 STAT1             CDKN1A            TRUE        TRUE          
 9 P40763 P38936 STAT3             CDKN1A            TRUE        TRUE          
10 Q04206 P08183 RELA              ABCB1             TRUE        TRUE          
# ℹ 32,619 more rows
# ℹ 10 more variables: is_inhibition <lgl>, consensus_direction <lgl>,
#   consensus_stimulation <lgl>, consensus_inhibition <lgl>, sources <chr>,
#   references <chr>, dorothea_level <chr>, curation_effort <dbl>,
#   n_references <dbl>, n_resources <int>
> 
> interactions <- tf_target(resources = c("DoRothEA", "SIGNOR"))
[2026-03-05 02:35:57] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:35:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[DoRothEA,SIGNOR],query_type=interactions,datasets=tf_target]
[2026-03-05 02:35:57] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:35:57] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:35:57] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-05 02:35:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:35:58] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:58] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:58] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:58] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:58] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:58] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:58] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:35:58] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-05 02:35:58] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-05 02:35:58] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-05 02:35:58] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-05 02:35:58] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.360713s from omnipathdb.org (43.5 Kb/s); Redirect: 0s, DNS look up: 0.002476s, Connection: 0.003309s, Pretransfer: 0.20418s, First byte at: 0.36033s
[2026-03-05 02:35:58] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 05 Mar 2026 07:35:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 05 Mar 2026 08:35:58 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-05 02:36:00] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:00] [INFO]    [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `unknown` to `started`.
[2026-03-05 02:36:00] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`.
[2026-03-05 02:36:00] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`.
[2026-03-05 02:36:00] [INFO]    [OmnipathR] Download ready [key=8276e09e9336e7886c5a256f51a7e3d7d28f62ca, version=1]
[2026-03-05 02:36:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:00] [INFO]    [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `started` to `ready`.
[2026-03-05 02:36:01] [SUCCESS] [OmnipathR] Downloaded 21911 interactions.
> 
> grn <- transcriptional(resources = c("PAZAR", "ORegAnno", "DoRothEA"))
[2026-03-05 02:36:01] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:36:01] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],resources=[PAZAR,ORegAnno,DoRothEA],query_type=interactions]
[2026-03-05 02:36:01] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:36:01] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:36:01] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-05 02:36:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:02] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:36:02] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:36:02] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:36:02] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:36:02] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:36:02] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:36:02] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:36:02] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-05 02:36:02] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-05 02:36:02] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-05 02:36:03] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-05 02:36:03] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.360236s from omnipathdb.org (43.6 Kb/s); Redirect: 0s, DNS look up: 0.001782s, Connection: 0.002533s, Pretransfer: 0.203149s, First byte at: 0.359298s
[2026-03-05 02:36:03] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 05 Mar 2026 07:36:03 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 05 Mar 2026 08:36:03 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-05 02:36:05] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PAZAR,ORegAnno,DoRothEA&datasets=dorothea,tf_target,collectri&organisms=9606&dorothea_levels=A,B&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-03-05 02:36:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:05] [INFO]    [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `unknown` to `started`.
[2026-03-05 02:36:05] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`.
[2026-03-05 02:36:05] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`.
[2026-03-05 02:36:05] [INFO]    [OmnipathR] Download ready [key=fed61c7ea10ed87b5184e4f70ee57689f412965a, version=1]
[2026-03-05 02:36:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:05] [INFO]    [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `started` to `ready`.
[2026-03-05 02:36:06] [SUCCESS] [OmnipathR] Downloaded 34695 interactions.
> grn
# A tibble: 34,695 × 16
   source target source_genesymbol target_genesymbol is_directed is_stimulation
   <chr>  <chr>  <chr>             <chr>             <lgl>       <lgl>         
 1 P01106 O14746 MYC               TERT              TRUE        TRUE          
 2 Q04206 P25445 RELA              FAS               TRUE        TRUE          
 3 P84022 P05412 SMAD3             JUN               TRUE        TRUE          
 4 Q13485 P05412 SMAD4             JUN               TRUE        TRUE          
 5 P08047 P04075 SP1               ALDOA             TRUE        TRUE          
 6 P04637 P08069 TP53              IGF1R             TRUE        FALSE         
 7 Q05516 P20248 ZBTB16            CCNA2             TRUE        FALSE         
 8 Q01196 P08700 RUNX1             IL3               TRUE        FALSE         
 9 P42224 P38936 STAT1             CDKN1A            TRUE        TRUE          
10 P40763 P38936 STAT3             CDKN1A            TRUE        TRUE          
# ℹ 34,685 more rows
# ℹ 10 more variables: is_inhibition <lgl>, consensus_direction <lgl>,
#   consensus_stimulation <lgl>, consensus_inhibition <lgl>, sources <chr>,
#   references <chr>, dorothea_level <chr>, curation_effort <dbl>,
#   n_references <dbl>, n_resources <int>
> 
> collectri_grn <- collectri()
[2026-03-05 02:36:06] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:36:06] [TRACE]   [OmnipathR] Arguments for OmniPath query: [query_type=interactions,datasets=collectri]
[2026-03-05 02:36:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:36:06] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:36:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:06] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:06] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:06] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:06] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-05 02:36:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-05 02:36:06] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-05 02:36:07] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-05 02:36:07] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.36364s from omnipathdb.org (43.2 Kb/s); Redirect: 0s, DNS look up: 0.001458s, Connection: 0.002197s, Pretransfer: 0.204595s, First byte at: 0.362793s
[2026-03-05 02:36:07] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 05 Mar 2026 07:36:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 05 Mar 2026 08:36:07 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-05 02:36:09] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:09] [INFO]    [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `unknown` to `started`.
[2026-03-05 02:36:09] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`.
[2026-03-05 02:36:10] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`.
[2026-03-05 02:36:10] [INFO]    [OmnipathR] Download ready [key=e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02, version=1]
[2026-03-05 02:36:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:10] [INFO]    [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `started` to `ready`.
[2026-03-05 02:36:12] [SUCCESS] [OmnipathR] Downloaded 64516 interactions.
> collectri_grn
# A tibble: 64,516 × 15
   source  target source_genesymbol target_genesymbol is_directed is_stimulation
   <chr>   <chr>  <chr>             <chr>             <lgl>       <lgl>         
 1 COMPLE… P03372 FOSL1_JUNB        ESR1              TRUE        TRUE          
 2 COMPLE… P03372 JUND              ESR1              TRUE        TRUE          
 3 COMPLE… P03372 JUN               ESR1              TRUE        TRUE          
 4 COMPLE… P03372 FOSL2_JUNB        ESR1              TRUE        TRUE          
 5 COMPLE… P03372 FOSL2_JUN         ESR1              TRUE        TRUE          
 6 COMPLE… P03372 FOSB_JUNB         ESR1              TRUE        TRUE          
 7 COMPLE… P03372 FOSL1_JUND        ESR1              TRUE        TRUE          
 8 COMPLE… P01375 RELA              TNF               TRUE        TRUE          
 9 COMPLE… P03372 FOSL2_JUND        ESR1              TRUE        TRUE          
10 COMPLE… P03372 FOSB_JUN          ESR1              TRUE        TRUE          
# ℹ 64,506 more rows
# ℹ 9 more variables: is_inhibition <lgl>, consensus_direction <lgl>,
#   consensus_stimulation <lgl>, consensus_inhibition <lgl>, sources <chr>,
#   references <chr>, curation_effort <dbl>, n_references <dbl>,
#   n_resources <int>
> 
> interactions <- mirna_target( resources = c("miRTarBase", "miRecords"))
[2026-03-05 02:36:12] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:36:12] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[miRTarBase,miRecords],query_type=interactions,datasets=mirnatarget]
[2026-03-05 02:36:12] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:36:12] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:36:12] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-05 02:36:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:13] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:13] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:13] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:13] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:13] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:13] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:13] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-05 02:36:13] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-05 02:36:13] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-05 02:36:14] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-05 02:36:14] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.349854s from omnipathdb.org (44.9 Kb/s); Redirect: 0s, DNS look up: 0.001903s, Connection: 0.002643s, Pretransfer: 0.202026s, First byte at: 0.349424s
[2026-03-05 02:36:14] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 05 Mar 2026 07:36:14 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 05 Mar 2026 08:36:14 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-05 02:36:15] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:15] [INFO]    [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `unknown` to `started`.
[2026-03-05 02:36:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`.
[2026-03-05 02:36:15] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`.
[2026-03-05 02:36:15] [INFO]    [OmnipathR] Download ready [key=fc18df7465bfc9f5b72d079bc3dc9408636597cc, version=1]
[2026-03-05 02:36:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:15] [INFO]    [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `started` to `ready`.
[2026-03-05 02:36:16] [SUCCESS] [OmnipathR] Downloaded 8982 interactions.
> 
> interactions <- tf_mirna(resources = "TransmiR")
[2026-03-05 02:36:16] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:36:16] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,query_type=interactions,datasets=tf_mirna]
[2026-03-05 02:36:16] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:36:16] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:36:16] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-05 02:36:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:17] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:17] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:17] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:17] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:17] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:17] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:17] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:17] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-05 02:36:17] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-05 02:36:17] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-05 02:36:17] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-05 02:36:17] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.363392s from omnipathdb.org (43.2 Kb/s); Redirect: 0s, DNS look up: 0.001695s, Connection: 0.002514s, Pretransfer: 0.206696s, First byte at: 0.362665s
[2026-03-05 02:36:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 05 Mar 2026 07:36:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 05 Mar 2026 08:36:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-05 02:36:18] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:18] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`.
[2026-03-05 02:36:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2026-03-05 02:36:18] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2026-03-05 02:36:18] [INFO]    [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1]
[2026-03-05 02:36:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:18] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`.
[2026-03-05 02:36:18] [SUCCESS] [OmnipathR] Downloaded 3788 interactions.
> 
> interactions <- lncrna_mrna(resources = c("ncRDeathDB"))
[2026-03-05 02:36:18] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:36:18] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=ncRDeathDB,query_type=interactions,datasets=lncrna_mrna]
[2026-03-05 02:36:18] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:36:18] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:36:18] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-05 02:36:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:19] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:19] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:19] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:19] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:19] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:19] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-05 02:36:19] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-05 02:36:19] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-05 02:36:20] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-05 02:36:20] [TRACE]   [OmnipathR] Downloaded 2.3 Kb in 0.286591s from omnipathdb.org (8.2 Kb/s); Redirect: 0s, DNS look up: 0.001489s, Connection: 0.002255s, Pretransfer: 0.209226s, First byte at: 0.286484s
[2026-03-05 02:36:20] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 05 Mar 2026 07:36:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 05 Mar 2026 08:36:20 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-05 02:36:20] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-05 02:36:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:20] [INFO]    [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `unknown` to `started`.
[2026-03-05 02:36:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`.
[2026-03-05 02:36:20] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`.
[2026-03-05 02:36:20] [INFO]    [OmnipathR] Download ready [key=f327904e6e8d62e0cafeae1a4c3b8cc1af68503f, version=1]
[2026-03-05 02:36:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:20] [INFO]    [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `started` to `ready`.
[2026-03-05 02:36:20] [SUCCESS] [OmnipathR] Downloaded 130 interactions.
> 
> # What are the targets of aspirin?
> interactions <- small_molecule(sources = "ASPIRIN")
[2026-03-05 02:36:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-05 02:36:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [sources=ASPIRIN,query_type=interactions,datasets=small_molecule]
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2026-03-05 02:36:21] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2026-03-05 02:36:21] [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=ASPIRIN&license=academic`
[2026-03-05 02:36:21] [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=ASPIRIN&license=academic`
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2026-03-05 02:36:21] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] Downloaded 112 bytes in 0.28967s from omnipathdb.org (386 bytes/s); Redirect: 0s, DNS look up: 0.001309s, Connection: 0.001923s, Pretransfer: 0.213345s, First byte at: 0.289595s
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 05 Mar 2026 07:36:21 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Thu, 05 Mar 2026 08:36:21 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; X-Cache-Status: HIT; Content-Encoding: gzip
[2026-03-05 02:36:21] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:21] [INFO]    [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `unknown` to `started`.
[2026-03-05 02:36:22] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`.
[2026-03-05 02:36:22] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`.
[2026-03-05 02:36:22] [INFO]    [OmnipathR] Download ready [key=f9f812113b53ae5b9c2613603e0c3316aa921419, version=1]
[2026-03-05 02:36:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:22] [INFO]    [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `started` to `ready`.
[2026-03-05 02:36:22] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
> # The prostaglandin synthases:
> interactions
# A tibble: 0 × 14
# ℹ 14 variables: source <chr>, target <chr>, source_genesymbol <chr>,
#   target_genesymbol <chr>, is_directed <chr>, is_stimulation <chr>,
#   is_inhibition <chr>, consensus_direction <chr>,
#   consensus_stimulation <chr>, consensus_inhibition <chr>, sources <chr>,
#   references <chr>, curation_effort <chr>, n_references <lgl>
> 
> interactions <- all_interactions(
+     resources = c("HPRD", "BioGRID"),
+     organism = 9606
+ )
[2026-03-05 02:36:22] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-05 02:36:22] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-05 02:36:22] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2026-03-05 02:36:22] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/d4a3f6fd0083bc974e7269e2ff6b02df9633e303-1.rds`.
[2026-03-05 02:36:22] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2026-03-05 02:36:22] [SUCCESS] [OmnipathR] Downloaded 24 records.
[2026-03-05 02:36:22] [TRACE]   [OmnipathR] Processing args for OmniPath query
Error in `<current-expression>` : subscript out of bounds
Calls: all_interactions ... modifyList -> stopifnot -> modifyList -> stopifnot -> modifyList
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
annotation_categories                91.307  0.052  92.590
curated_ligrec_stats                 44.969  4.065 126.467
filter_extra_attrs                   35.810  5.815  48.410
extra_attrs_to_cols                  29.929  2.364  42.198
nichenet_signaling_network_omnipath  29.188  1.114  36.620
nichenet_gr_network_omnipath         27.582  1.462  32.281
all_uniprots                         24.077  2.068  47.812
extra_attr_values                    21.338  2.105  32.743
go_annot_download                    20.345  0.731  30.033
has_extra_attrs                      12.360  1.531  15.312
filter_by_resource                   12.514  0.854  15.680
filter_intercell                     12.558  0.526  20.098
giant_component                      12.228  0.590  15.548
find_all_paths                       11.365  0.412  13.467
extra_attrs                          10.223  1.408  13.760
curated_ligand_receptor_interactions  7.371  0.787  18.566
hpo_download                          4.600  0.330   7.168
kegg_conv                             2.629  0.243  13.487
ensembl_id_mapping_table              2.538  0.275  24.400
kegg_picture                          2.498  0.119   7.751
annotated_network                     1.612  0.192   5.111
metalinksdb_sqlite                    1.546  0.188  11.356
kegg_link                             1.511  0.109   8.431
kinasephos                            1.094  0.113  16.712
kegg_rm_prefix                        1.077  0.075   5.474
* 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.18.4’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2026-03-04 15:10:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-04 15:10:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-04 15:10:03] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-04 15:10:03] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-04 15:10:03] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-03-04
[2026-03-04 15:10:03] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-03-04 20:09:49 UTC; unix
[2026-03-04 15:10:03] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-03-04 15:10:03] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-03-04 15:10:04] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-04; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-04 15:10:04] [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=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-04 15:10:04] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-03-04); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-04 15:10:04] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] Contains 9 files.
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-04 15:10:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-04 15:10:04] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2026-03-04 15:10:06] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-04 15:10:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-04 15:10:06] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-04 15:10:06] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-04 15:10:06] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-03-04
[2026-03-04 15:10:06] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-03-04 20:09:49 UTC; unix
[2026-03-04 15:10:06] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-03-04 15:10:06] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-03-04 15:10:07] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-04; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-04 15:10:07] [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=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-04 15:10:07] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-03-04); 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); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-04 15:10:07] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-04 15:10:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-04 15:10:07] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

Tests output

OmnipathR.Rcheck/tests/testthat.Rout


R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2024
> #  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> #  File author(s): Alberto Valdeolivas
> #                  Dénes Türei (turei.denes@gmail.com)
> #                  Attila Gábor
> #
> #  Distributed under the MIT (Expat) License.
> #  See accompanying file `LICENSE` or find a copy at
> #      https://directory.fsf.org/wiki/License:Expat
> #
> #  Website: https://r.omnipathdb.org/
> #  Git repo: https://github.com/saezlab/OmnipathR
> #
> 
> 
> library(testthat)
> library(OmnipathR)
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:25] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-05 02:36:25] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-05 02:36:25] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-03-04
[2026-03-05 02:36:25] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-03-04 20:09:49 UTC; unix
[2026-03-05 02:36:25] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-03-05 02:36:25] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-03-05 02:36:25] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-05; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-05 02:36:25] [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=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-05 02:36:25] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-03-04); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); testthat 3.3.2(2026-01-11); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-05 02:36:25] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] Contains 75 files.
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-05 02:36:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-05 02:36:26] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 66.000   5.008 109.835

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0160.0010.016
all_uniprots24.077 2.06847.812
ancestors0.0090.0000.009
annotated_network1.6120.1925.111
annotation_categories91.307 0.05292.590
annotation_resources0.1970.0410.996
annotations0.8350.0611.951
biomart_query1.1190.0803.695
bioplex10.0090.0000.010
bioplex20.0080.0000.008
bioplex30.0070.0010.008
bioplex_all0.0060.0010.008
bioplex_hct116_10.0070.0010.008
bma_motif_es0.8420.0741.979
bma_motif_vs0.2740.0101.136
chalmers_gem0.0090.0010.009
chalmers_gem_id_mapping_table0.0080.0000.008
chalmers_gem_id_type0.0000.0000.001
chalmers_gem_metabolites0.0080.0000.008
chalmers_gem_network0.0070.0010.008
chalmers_gem_raw0.0060.0010.008
chalmers_gem_reactions0.0080.0000.007
common_name0.1390.0030.142
complex_genes0.7930.0312.706
complex_resources0.1900.0201.005
complexes0.3200.0131.130
consensuspathdb_download0.0010.0000.000
consensuspathdb_raw_table0.0080.0000.008
cosmos_pkn000
curated_ligand_receptor_interactions 7.371 0.78718.566
curated_ligrec_stats 44.969 4.065126.467
database_summary1.5790.0993.025
descendants0.0090.0010.009
ensembl_dataset0.0500.0010.051
ensembl_id_mapping_table 2.538 0.27524.400
ensembl_id_type000
ensembl_name0.2870.0100.297
ensembl_organisms0.1120.0120.123
ensembl_organisms_raw0.1070.0210.125
ensembl_orthology000
enzsub_graph2.0990.1334.014
enzsub_resources0.1530.0200.976
enzyme_substrate0.9740.0571.823
evex_download0.0080.0010.008
evidences000
extra_attr_values21.338 2.10532.743
extra_attrs10.223 1.40813.760
extra_attrs_to_cols29.929 2.36442.198
filter_by_resource12.514 0.85415.680
filter_extra_attrs35.810 5.81548.410
filter_intercell12.558 0.52620.098
filter_intercell_network0.0370.0020.039
find_all_paths11.365 0.41213.467
from_evidences000
get_db000
get_ontology_db0.0140.0010.015
giant_component12.228 0.59015.548
go_annot_download20.345 0.73130.033
go_annot_slim000
go_ontology_download0.0100.0000.009
guide2pharma_download0.0080.0000.008
harmonizome_download0.0080.0010.009
has_extra_attrs12.360 1.53115.312
hmdb_id_mapping_table0.0180.0010.019
hmdb_id_type0.0020.0000.002
hmdb_metabolite_fields0.0010.0000.001
hmdb_protein_fields000
hmdb_table0.0160.0010.016
homologene_download0.0160.0000.017
homologene_raw0.0980.0000.097
homologene_uniprot_orthology0.0170.0000.018
hpo_download4.6000.3307.168
htridb_download0.0170.0010.018
id_translation_resources000
id_types0.0670.0070.074
inbiomap_download000
inbiomap_raw000
interaction_datasets1.8680.1732.679
interaction_graph0.8420.0712.008
interaction_resources0.2240.0271.233
interaction_types0.1590.0060.176
intercell1.8360.1112.915
intercell_categories0.9990.0511.322
intercell_consensus_filter2.3870.2464.231
intercell_generic_categories0.0870.0000.089
intercell_network0.0090.0000.009
intercell_resources0.1730.0100.995
intercell_summary0.1260.0090.134
is_ontology_id0.0010.0000.000
is_swissprot0.1620.0190.181
is_trembl0.0980.0050.101
is_uniprot0.0180.0000.018
kegg_api_templates0.0020.0010.003
kegg_conv 2.629 0.24313.487
kegg_databases000
kegg_ddi1.4250.0783.593
kegg_find1.3520.1353.501
kegg_info0.0220.0020.034
kegg_link1.5110.1098.431
kegg_list1.7590.0914.442
kegg_open0.0250.0000.053
kegg_operations0.0000.0000.001
kegg_organism_codes0.0230.0130.067
kegg_organisms0.0470.0050.103
kegg_pathway_annotations000
kegg_pathway_download0.0240.0000.048
kegg_pathway_list0.0200.0010.042
kegg_pathways_download000
kegg_picture2.4980.1197.751
kegg_process0.0300.0010.031
kegg_query0.0140.0010.015
kegg_request0.1370.0090.146
kegg_rm_prefix1.0770.0755.474
kinasephos 1.094 0.11316.712
latin_name0.2780.0050.282
load_db0.0700.0090.079
metalinksdb_sqlite 1.546 0.18811.356
metalinksdb_table0.4210.0640.752
metalinksdb_tables0.0380.0040.098
ncbi_taxid0.4380.0180.683
nichenet_build_model000
nichenet_expression_data0.0210.0010.043
nichenet_gr_network0.0610.0070.120
nichenet_gr_network_evex0.0210.0080.028
nichenet_gr_network_harmonizome0.0210.0010.020
nichenet_gr_network_htridb0.0160.0050.028
nichenet_gr_network_omnipath27.582 1.46232.281
nichenet_gr_network_pathwaycommons0.0120.0010.013
nichenet_gr_network_regnetwork0.0090.0020.010
nichenet_gr_network_remap0.0080.0030.011
nichenet_gr_network_trrust0.0120.0000.012
nichenet_ligand_activities000
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0300.0020.032
nichenet_lr_network_guide2pharma0.0070.0030.010
nichenet_lr_network_omnipath0.0300.0010.031
nichenet_lr_network_ramilowski0.0100.0010.010
nichenet_main0.0010.0000.000
nichenet_networks0.0510.0020.053
nichenet_optimization000
nichenet_remove_orphan_ligands0.0280.0010.029
nichenet_results_dir000
nichenet_signaling_network0.1250.0030.128
nichenet_signaling_network_cpdb0.0120.0000.013
nichenet_signaling_network_evex0.0110.0010.012
nichenet_signaling_network_harmonizome0.0100.0000.011
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath29.188 1.11436.620
nichenet_signaling_network_pathwaycommons0.0100.0010.011
nichenet_signaling_network_vinayagam0.0090.0010.010
nichenet_test000
nichenet_workarounds000
obo_parser0.2000.0110.354
oma_code0.1270.0010.129
oma_organisms0.1030.0060.110
oma_pairwise0.0080.0010.009
oma_pairwise_genesymbols0.0080.0010.008
oma_pairwise_translated0.0060.0020.008