| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-27 11:58 -0500 (Fri, 27 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4891 |
| 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 1505/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.18.4 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| See other builds for OmnipathR in R Universe. | ||||||||||||||
|
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. |
| 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: 2026-02-27 02:13:16 -0500 (Fri, 27 Feb 2026) |
| EndedAt: 2026-02-27 02:53:17 -0500 (Fri, 27 Feb 2026) |
| EllapsedTime: 2400.6 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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
[2026-02-27 02:13:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:13:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:13:47] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-27 02:13:47] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-27 02:13:47] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26
[2026-02-27 02:13:47] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix
[2026-02-27 02:13:47] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-27 02:13:47] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-27 02:13:47] [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=2026-02-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-27 02:13:47] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/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]
[2026-02-27 02:13:48] [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(2026-02-26); 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)
[2026-02-27 02:13:48] [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
[2026-02-27 02:13:48] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-02-27 02:13:48] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-27 02:13:48] [TRACE] [OmnipathR] Contains 1 files.
[2026-02-27 02:13:48] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-02-27 02:13:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:13:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:13:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-27 02:13:48] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-27 02:13:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-27 02:13:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:13:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-27 02:13:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:13:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-27 02:13:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:13:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-27 02:13:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:13:48] [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
[2026-02-27 02:14:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:14:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:14:05] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-27 02:14:05] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-27 02:14:05] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26
[2026-02-27 02:14:05] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix
[2026-02-27 02:14:05] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-27 02:14:05] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-27 02:14:05] [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=2026-02-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-27 02:14:05] [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]
[2026-02-27 02:14:05] [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(2026-02-26); 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)
[2026-02-27 02:14:05] [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
[2026-02-27 02:14:05] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-02-27 02:14:05] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-27 02:14:05] [TRACE] [OmnipathR] Contains 1 files.
[2026-02-27 02:14:05] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-02-27 02:14:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:14:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:14:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-27 02:14:05] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-27 02:14:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-27 02:14:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:14:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-27 02:14:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:14:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-27 02:14:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:14:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-27 02:14:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:14:05] [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"))
[2026-02-27 02:29:22] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:29:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath]
[2026-02-27 02:29:22] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:29:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CA1,SIGNOR,SignaLink3],datasets=omnipath,query_type=interactions]
[2026-02-27 02:29:22] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:29:22] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:29:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-27 02:29:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:29:23] [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`
[2026-02-27 02:29:23] [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`
[2026-02-27 02:29:23] [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`
[2026-02-27 02:29:23] [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`
[2026-02-27 02:29:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CA1,SIGNOR,SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:29:23] [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`
[2026-02-27 02:29:23] [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`
[2026-02-27 02:29:23] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 02:29:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-27 02:29:23] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-27 02:29:28] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 02:29:28] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 5.204264s from omnipathdb.org (3 Kb/s); Redirect: 0s, DNS look up: 0.001802s, Connection: 0.002535s, Pretransfer: 0.194306s, First byte at: 5.20376s
[2026-02-27 02:29:28] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 07:29:28 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 08:29:28 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 02:29:32] [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`
[2026-02-27 02:29:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:29:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:29:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:29:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:29:32] [INFO] [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `unknown` to `started`.
[2026-02-27 02:29:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`.
[2026-02-27 02:29:33] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/029da7bc67579749c5723c06c82d60c331a10ad3-1.rds`.
[2026-02-27 02:29:33] [INFO] [OmnipathR] Download ready [key=029da7bc67579749c5723c06c82d60c331a10ad3, version=1]
[2026-02-27 02:29:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:29:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:29:33] [INFO] [OmnipathR] Cache item `029da7bc67579749c5723c06c82d60c331a10ad3` version 1: status changed from `started` to `ready`.
[2026-02-27 02:29:37] [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
+ )
[2026-02-27 02:29:37] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:29:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=SignaLink3,organisms=9606,query_type=interactions]
[2026-02-27 02:29:37] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:29:37] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:29:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-27 02:29:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:29:39] [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`
[2026-02-27 02:29:39] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2026-02-27 02:29:39] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:29:39] [SUCCESS] [OmnipathR] Loaded 1799 interactions from cache.
>
> pathways <- omnipath()
[2026-02-27 02:29:39] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:29:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2026-02-27 02:29:39] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:29:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2026-02-27 02:29:39] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:29:39] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:29:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:29:39] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a7b21d9d80a3837a50268df16d168128fc1c6ede-1.rds`.
[2026-02-27 02:29:39] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:29:45] [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
+ )
[2026-02-27 02:29:45] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:29:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra]
[2026-02-27 02:29:45] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:29:45] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[BioGRID,IntAct],organisms=9606,datasets=pathwayextra,query_type=interactions]
[2026-02-27 02:29:45] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:29:45] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:29:45] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-27 02:29:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:29:46] [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`
[2026-02-27 02:29:46] [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`
[2026-02-27 02:29:46] [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`
[2026-02-27 02:29:46] [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`
[2026-02-27 02:29:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:29:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:29:46] [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`
[2026-02-27 02:29:46] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 02:29:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-27 02:29:46] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-27 02:29:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 02:29:48] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 1.315815s from omnipathdb.org (11.9 Kb/s); Redirect: 0s, DNS look up: 0.001245s, Connection: 0.001944s, Pretransfer: 0.202109s, First byte at: 1.315343s
[2026-02-27 02:29:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 07:29:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 08:29:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 02:29:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=BioGRID,IntAct&datasets=pathwayextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:29:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:29:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:29:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:29:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:29:51] [INFO] [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `unknown` to `started`.
[2026-02-27 02:29:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`.
[2026-02-27 02:29:52] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/aa665c2ecdd9e913e13934eeb12c1fa7b0d21884-1.rds`.
[2026-02-27 02:29:52] [INFO] [OmnipathR] Download ready [key=aa665c2ecdd9e913e13934eeb12c1fa7b0d21884, version=1]
[2026-02-27 02:29:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:29:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:29:52] [INFO] [OmnipathR] Cache item `aa665c2ecdd9e913e13934eeb12c1fa7b0d21884` version 1: status changed from `started` to `ready`.
[2026-02-27 02:29:53] [SUCCESS] [OmnipathR] Downloaded 2593 interactions.
>
> kinase_substrate <-
+ kinaseextra(
+ resources = c('PhosphoPoint', 'PhosphoSite'),
+ organism = 9606
+ )
[2026-02-27 02:29:53] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:29:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra]
[2026-02-27 02:29:53] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:29:53] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[PhosphoPoint,PhosphoSite],organisms=9606,datasets=kinaseextra,query_type=interactions]
[2026-02-27 02:29:53] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:29:53] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:29:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-27 02:29:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:29:54] [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`
[2026-02-27 02:29:54] [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`
[2026-02-27 02:29:54] [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`
[2026-02-27 02:29:54] [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`
[2026-02-27 02:29:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:29:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:29:54] [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`
[2026-02-27 02:29:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 02:29:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-27 02:29:55] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-27 02:29:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 02:29:57] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 2.078218s from omnipathdb.org (7.5 Kb/s); Redirect: 0s, DNS look up: 0.004368s, Connection: 0.005406s, Pretransfer: 0.332951s, First byte at: 2.077751s
[2026-02-27 02:29:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 07:29:56 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 08:29:56 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 02:29:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=PhosphoPoint,PhosphoSite&datasets=kinaseextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:29:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:29:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:29:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:29:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:29:58] [INFO] [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `unknown` to `started`.
[2026-02-27 02:29:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`.
[2026-02-27 02:29:59] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/7db24bdf2093c17feeea2eea249fad461c5a1d09-1.rds`.
[2026-02-27 02:29:59] [INFO] [OmnipathR] Download ready [key=7db24bdf2093c17feeea2eea249fad461c5a1d09, version=1]
[2026-02-27 02:29:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:29:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:29:59] [INFO] [OmnipathR] Cache item `7db24bdf2093c17feeea2eea249fad461c5a1d09` version 1: status changed from `started` to `ready`.
[2026-02-27 02:29:59] [SUCCESS] [OmnipathR] Downloaded 11909 interactions.
>
> ligand_receptor <- ligrecextra(
+ resources = c('HPRD', 'Guide2Pharma'),
+ organism = 9606
+ )
[2026-02-27 02:29:59] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:29:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra]
[2026-02-27 02:29:59] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:29:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[HPRD,Guide2Pharma],organisms=9606,datasets=ligrecextra,query_type=interactions]
[2026-02-27 02:29:59] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:29:59] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:29:59] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-27 02:30:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:00] [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`
[2026-02-27 02:30:00] [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`
[2026-02-27 02:30:00] [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`
[2026-02-27 02:30:00] [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`
[2026-02-27 02:30:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:01] [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`
[2026-02-27 02:30:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 02:30:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-27 02:30:01] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-27 02:30:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 02:30:02] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 1.744206s from omnipathdb.org (9 Kb/s); Redirect: 0s, DNS look up: 0.005774s, Connection: 0.006563s, Pretransfer: 0.30966s, First byte at: 1.743703s
[2026-02-27 02:30:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 07:30:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 08:30:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 02:30:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=HPRD,Guide2Pharma&datasets=ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:05] [INFO] [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `unknown` to `started`.
[2026-02-27 02:30:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`.
[2026-02-27 02:30:05] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/393dd95dc380ac2e0800d32dc3f2fbbc88166e57-1.rds`.
[2026-02-27 02:30:05] [INFO] [OmnipathR] Download ready [key=393dd95dc380ac2e0800d32dc3f2fbbc88166e57, version=1]
[2026-02-27 02:30:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:05] [INFO] [OmnipathR] Cache item `393dd95dc380ac2e0800d32dc3f2fbbc88166e57` version 1: status changed from `started` to `ready`.
[2026-02-27 02:30:06] [SUCCESS] [OmnipathR] Downloaded 1864 interactions.
>
> interactions <- post_translational(resources = "BioGRID")
[2026-02-27 02:30:06] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:30:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=BioGRID,query_type=interactions]
[2026-02-27 02:30:06] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:30:06] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:30:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-27 02:30:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:07] [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`
[2026-02-27 02:30:07] [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`
[2026-02-27 02:30:07] [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`
[2026-02-27 02:30:07] [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`
[2026-02-27 02:30:07] [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`
[2026-02-27 02:30:07] [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`
[2026-02-27 02:30:07] [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`
[2026-02-27 02:30:07] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 02:30:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-27 02:30:07] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-27 02:30:09] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 02:30:09] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 1.66045s from omnipathdb.org (9.4 Kb/s); Redirect: 0s, DNS look up: 0.009946s, Connection: 0.01089s, Pretransfer: 0.339435s, First byte at: 1.659872s
[2026-02-27 02:30:09] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 07:30:09 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 08:30:09 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 02:30:11] [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`
[2026-02-27 02:30:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:12] [INFO] [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `unknown` to `started`.
[2026-02-27 02:30:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`.
[2026-02-27 02:30:12] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/108f2cda262af403a026484add1c5a2c3d9c94fe-1.rds`.
[2026-02-27 02:30:12] [INFO] [OmnipathR] Download ready [key=108f2cda262af403a026484add1c5a2c3d9c94fe, version=1]
[2026-02-27 02:30:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:12] [INFO] [OmnipathR] Cache item `108f2cda262af403a026484add1c5a2c3d9c94fe` version 1: status changed from `started` to `ready`.
[2026-02-27 02:30:12] [SUCCESS] [OmnipathR] Downloaded 2708 interactions.
>
> dorothea_grn <- dorothea(
+ resources = c('DoRothEA', 'ARACNe-GTEx_DoRothEA'),
+ organism = 9606,
+ dorothea_levels = c('A', 'B', 'C')
+ )
[2026-02-27 02:30:12] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:30:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C],resources=[DoRothEA,ARACNe-GTEx_DoRothEA],organisms=9606,query_type=interactions,datasets=dorothea]
[2026-02-27 02:30:12] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:30:12] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:30:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-27 02:30:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:13] [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`
[2026-02-27 02:30:13] [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`
[2026-02-27 02:30:13] [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`
[2026-02-27 02:30:13] [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`
[2026-02-27 02:30:13] [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`
[2026-02-27 02:30:13] [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`
[2026-02-27 02:30:13] [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`
[2026-02-27 02:30:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 02:30:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-27 02:30:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-27 02:30:17] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 02:30:17] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 3.606038s from omnipathdb.org (4.3 Kb/s); Redirect: 0s, DNS look up: 0.001494s, Connection: 0.00216s, Pretransfer: 0.199654s, First byte at: 3.605683s
[2026-02-27 02:30:17] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 07:30:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 08:30:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 02:30:19] [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`
[2026-02-27 02:30:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:19] [INFO] [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `unknown` to `started`.
[2026-02-27 02:30:19] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`.
[2026-02-27 02:30:19] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ce66cb9846294c226acee9ccf50a608c089386dd-1.rds`.
[2026-02-27 02:30:19] [INFO] [OmnipathR] Download ready [key=ce66cb9846294c226acee9ccf50a608c089386dd, version=1]
[2026-02-27 02:30:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:19] [INFO] [OmnipathR] Cache item `ce66cb9846294c226acee9ccf50a608c089386dd` version 1: status changed from `started` to `ready`.
[2026-02-27 02:30:21] [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"))
[2026-02-27 02:30:21] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:30:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[DoRothEA,SIGNOR],query_type=interactions,datasets=tf_target]
[2026-02-27 02:30:21] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:30:21] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:30:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-27 02:30:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:22] [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`
[2026-02-27 02:30:22] [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`
[2026-02-27 02:30:22] [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`
[2026-02-27 02:30:22] [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`
[2026-02-27 02:30:22] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,SIGNOR&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:22] [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`
[2026-02-27 02:30:22] [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`
[2026-02-27 02:30:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 02:30:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-27 02:30:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-27 02:30:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 02:30:25] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 2.714016s from omnipathdb.org (5.8 Kb/s); Redirect: 0s, DNS look up: 0.001493s, Connection: 0.002099s, Pretransfer: 0.19698s, First byte at: 2.713627s
[2026-02-27 02:30:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 07:30:24 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 08:30:24 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 02:30:26] [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`
[2026-02-27 02:30:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:26] [INFO] [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `unknown` to `started`.
[2026-02-27 02:30:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`.
[2026-02-27 02:30:27] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8276e09e9336e7886c5a256f51a7e3d7d28f62ca-1.rds`.
[2026-02-27 02:30:27] [INFO] [OmnipathR] Download ready [key=8276e09e9336e7886c5a256f51a7e3d7d28f62ca, version=1]
[2026-02-27 02:30:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:27] [INFO] [OmnipathR] Cache item `8276e09e9336e7886c5a256f51a7e3d7d28f62ca` version 1: status changed from `started` to `ready`.
[2026-02-27 02:30:27] [SUCCESS] [OmnipathR] Downloaded 21911 interactions.
>
> grn <- transcriptional(resources = c("PAZAR", "ORegAnno", "DoRothEA"))
[2026-02-27 02:30:27] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:30:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],resources=[PAZAR,ORegAnno,DoRothEA],query_type=interactions]
[2026-02-27 02:30:27] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:30:27] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:30:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-27 02:30:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:28] [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`
[2026-02-27 02:30:28] [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`
[2026-02-27 02:30:28] [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`
[2026-02-27 02:30:28] [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`
[2026-02-27 02:30:28] [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`
[2026-02-27 02:30:28] [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`
[2026-02-27 02:30:28] [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`
[2026-02-27 02:30:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 02:30:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-27 02:30:28] [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]
[2026-02-27 02:30:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 02:30:32] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 3.970575s from omnipathdb.org (3.9 Kb/s); Redirect: 0s, DNS look up: 0.001606s, Connection: 0.002218s, Pretransfer: 0.208078s, First byte at: 3.970073s
[2026-02-27 02:30:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 07:30:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 08:30:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 02:30:35] [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`
[2026-02-27 02:30:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:35] [INFO] [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `unknown` to `started`.
[2026-02-27 02:30:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`.
[2026-02-27 02:30:35] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/fed61c7ea10ed87b5184e4f70ee57689f412965a-1.rds`.
[2026-02-27 02:30:35] [INFO] [OmnipathR] Download ready [key=fed61c7ea10ed87b5184e4f70ee57689f412965a, version=1]
[2026-02-27 02:30:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:35] [INFO] [OmnipathR] Cache item `fed61c7ea10ed87b5184e4f70ee57689f412965a` version 1: status changed from `started` to `ready`.
[2026-02-27 02:30:36] [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()
[2026-02-27 02:30:36] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:30:36] [TRACE] [OmnipathR] Arguments for OmniPath query: [query_type=interactions,datasets=collectri]
[2026-02-27 02:30:36] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:30:36] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:30:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:36] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:36] [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`
[2026-02-27 02:30:36] [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`
[2026-02-27 02:30:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 02:30:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-27 02:30:36] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-27 02:30:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 02:30:42] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 5.033935s from omnipathdb.org (3.1 Kb/s); Redirect: 0s, DNS look up: 0.001482s, Connection: 0.002282s, Pretransfer: 0.202636s, First byte at: 5.033484s
[2026-02-27 02:30:42] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 07:30:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 08:30:41 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 02:30:44] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:44] [INFO] [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `unknown` to `started`.
[2026-02-27 02:30:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`.
[2026-02-27 02:30:45] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02-1.rds`.
[2026-02-27 02:30:45] [INFO] [OmnipathR] Download ready [key=e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02, version=1]
[2026-02-27 02:30:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:45] [INFO] [OmnipathR] Cache item `e48832a5c4cfc5e7d427a9e7ffb60fd5bc902b02` version 1: status changed from `started` to `ready`.
[2026-02-27 02:30:47] [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 P01106 O14746 MYC TERT TRUE TRUE
2 COMPLE… P10145 NFKB1_REL CXCL8 TRUE TRUE
3 P17947 P02818 SPI1 BGLAP TRUE TRUE
4 COMPLE… P05412 JUN_JUND JUN TRUE TRUE
5 COMPLE… P05412 FOS_JUND JUN TRUE TRUE
6 COMPLE… P05412 JUNB JUN TRUE TRUE
7 COMPLE… P05412 JUN_JUNB JUN TRUE TRUE
8 COMPLE… P10145 NFKB2 CXCL8 TRUE TRUE
9 COMPLE… P05412 FOSL1_JUN JUN TRUE TRUE
10 COMPLE… P05412 FOSL1_JUNB JUN 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"))
[2026-02-27 02:30:47] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:30:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[miRTarBase,miRecords],query_type=interactions,datasets=mirnatarget]
[2026-02-27 02:30:47] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:30:47] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:30:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-27 02:30:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:48] [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`
[2026-02-27 02:30:48] [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`
[2026-02-27 02:30:48] [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`
[2026-02-27 02:30:48] [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`
[2026-02-27 02:30:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:48] [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`
[2026-02-27 02:30:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 02:30:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-27 02:30:48] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-27 02:30:50] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 02:30:50] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 1.752566s from omnipathdb.org (8.9 Kb/s); Redirect: 0s, DNS look up: 0.002139s, Connection: 0.002942s, Pretransfer: 0.201898s, First byte at: 1.752192s
[2026-02-27 02:30:50] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 07:30:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 08:30:50 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 02:30:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=miRTarBase,miRecords&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:51] [INFO] [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `unknown` to `started`.
[2026-02-27 02:30:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`.
[2026-02-27 02:30:51] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/fc18df7465bfc9f5b72d079bc3dc9408636597cc-1.rds`.
[2026-02-27 02:30:51] [INFO] [OmnipathR] Download ready [key=fc18df7465bfc9f5b72d079bc3dc9408636597cc, version=1]
[2026-02-27 02:30:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:52] [INFO] [OmnipathR] Cache item `fc18df7465bfc9f5b72d079bc3dc9408636597cc` version 1: status changed from `started` to `ready`.
[2026-02-27 02:30:52] [SUCCESS] [OmnipathR] Downloaded 8982 interactions.
>
> interactions <- tf_mirna(resources = "TransmiR")
[2026-02-27 02:30:52] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:30:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,query_type=interactions,datasets=tf_mirna]
[2026-02-27 02:30:52] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:30:52] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:30:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-27 02:30:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:53] [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`
[2026-02-27 02:30:53] [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`
[2026-02-27 02:30:53] [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`
[2026-02-27 02:30:53] [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`
[2026-02-27 02:30:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:53] [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`
[2026-02-27 02:30:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 02:30:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-27 02:30:53] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-27 02:30:54] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 02:30:54] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 1.268906s from omnipathdb.org (12.3 Kb/s); Redirect: 0s, DNS look up: 0.001689s, Connection: 0.00233s, Pretransfer: 0.192942s, First byte at: 1.267903s
[2026-02-27 02:30:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 07:30:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 08:30:54 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 02:30:55] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:55] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`.
[2026-02-27 02:30:55] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2026-02-27 02:30:55] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2026-02-27 02:30:55] [INFO] [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1]
[2026-02-27 02:30:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:55] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`.
[2026-02-27 02:30:55] [SUCCESS] [OmnipathR] Downloaded 3788 interactions.
>
> interactions <- lncrna_mrna(resources = c("ncRDeathDB"))
[2026-02-27 02:30:55] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:30:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=ncRDeathDB,query_type=interactions,datasets=lncrna_mrna]
[2026-02-27 02:30:55] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:30:55] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:30:55] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-27 02:30:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:56] [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`
[2026-02-27 02:30:56] [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`
[2026-02-27 02:30:56] [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`
[2026-02-27 02:30:56] [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`
[2026-02-27 02:30:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:56] [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`
[2026-02-27 02:30:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 02:30:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-27 02:30:56] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-27 02:30:57] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 02:30:57] [TRACE] [OmnipathR] Downloaded 2.6 Kb in 0.996145s from omnipathdb.org (2.6 Kb/s); Redirect: 0s, DNS look up: 0.001833s, Connection: 0.002528s, Pretransfer: 0.205024s, First byte at: 0.996004s
[2026-02-27 02:30:57] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 07:30:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 08:30:57 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 02:30:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=ncRDeathDB&datasets=lncrna_mrna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 02:30:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:58] [INFO] [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `unknown` to `started`.
[2026-02-27 02:30:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`.
[2026-02-27 02:30:58] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f327904e6e8d62e0cafeae1a4c3b8cc1af68503f-1.rds`.
[2026-02-27 02:30:58] [INFO] [OmnipathR] Download ready [key=f327904e6e8d62e0cafeae1a4c3b8cc1af68503f, version=1]
[2026-02-27 02:30:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:30:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:30:58] [INFO] [OmnipathR] Cache item `f327904e6e8d62e0cafeae1a4c3b8cc1af68503f` version 1: status changed from `started` to `ready`.
[2026-02-27 02:30:58] [SUCCESS] [OmnipathR] Downloaded 130 interactions.
>
> # What are the targets of aspirin?
> interactions <- small_molecule(sources = "ASPIRIN")
[2026-02-27 02:30:58] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 02:30:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [sources=ASPIRIN,query_type=interactions,datasets=small_molecule]
[2026-02-27 02:30:58] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:30:58] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:30:58] [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`
[2026-02-27 02:30:58] [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`
[2026-02-27 02:30:58] [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`
[2026-02-27 02:30:58] [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`
[2026-02-27 02:30:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2026-02-27 02:30:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2026-02-27 02:30:58] [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`
[2026-02-27 02:30:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 02:30:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-27 02:30:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-27 02:30:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 02:30:59] [TRACE] [OmnipathR] Downloaded 116 bytes in 1.005191s from omnipathdb.org (115 bytes/s); Redirect: 0s, DNS look up: 0.001693s, Connection: 0.002443s, Pretransfer: 0.204027s, First byte at: 1.005135s
[2026-02-27 02:30:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 07:30:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 08:30:59 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 02:31:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=small_molecule&organisms=9606&fields=sources,references,curation_effort&sources=ASPIRIN&license=academic`
[2026-02-27 02:31:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:31:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:31:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:31:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:31:00] [INFO] [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `unknown` to `started`.
[2026-02-27 02:31:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`.
[2026-02-27 02:31:00] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f9f812113b53ae5b9c2613603e0c3316aa921419-1.rds`.
[2026-02-27 02:31:00] [INFO] [OmnipathR] Download ready [key=f9f812113b53ae5b9c2613603e0c3316aa921419, version=1]
[2026-02-27 02:31:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:31:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:31:00] [INFO] [OmnipathR] Cache item `f9f812113b53ae5b9c2613603e0c3316aa921419` version 1: status changed from `started` to `ready`.
[2026-02-27 02:31:00] [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
+ )
[2026-02-27 02:31:00] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 02:31:00] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 02:31:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2026-02-27 02:31:00] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/d4a3f6fd0083bc974e7269e2ff6b02df9633e303-1.rds`.
[2026-02-27 02:31:00] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/queries/interactions?format=json&license=academic`
[2026-02-27 02:31:00] [SUCCESS] [OmnipathR] Downloaded 24 records.
[2026-02-27 02:31:00] [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 91.369 0.057 96.272
curated_ligrec_stats 50.749 4.276 166.623
filter_extra_attrs 39.897 6.774 53.902
all_uniprots 25.386 1.845 39.978
extra_attr_values 24.789 2.436 44.588
nichenet_signaling_network_omnipath 24.918 1.182 39.414
nichenet_gr_network_omnipath 20.801 1.322 35.501
extra_attrs_to_cols 19.296 1.775 24.005
has_extra_attrs 12.239 1.593 14.366
go_annot_download 12.889 0.789 13.627
filter_by_resource 12.608 0.577 23.285
find_all_paths 11.507 0.672 16.074
giant_component 11.197 0.694 24.432
filter_intercell 10.548 0.905 42.570
extra_attrs 7.504 1.202 9.666
curated_ligand_receptor_interactions 6.884 0.857 37.474
ensembl_id_mapping_table 4.668 0.245 25.218
enzsub_graph 3.857 0.183 8.077
kegg_conv 2.430 0.184 14.008
intercell_consensus_filter 2.441 0.149 9.605
database_summary 2.369 0.123 5.356
annotated_network 1.593 0.135 16.580
kegg_link 1.353 0.161 7.709
metalinksdb_sqlite 1.098 0.211 9.990
biomart_query 1.188 0.106 13.307
kegg_picture 1.244 0.027 5.846
kinasephos 1.114 0.115 17.703
annotations 0.832 0.075 12.291
kegg_rm_prefix 0.790 0.091 5.395
* 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 ...
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 [2026-02-26 15:08:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-26 15:08:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-26 15:08:36] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-02-26 15:08:36] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-02-26 15:08:36] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26 [2026-02-26 15:08:36] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix [2026-02-26 15:08:36] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-02-26 15:08:36] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2026-02-26 15:08:36] [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=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-02-26 15:08:36] [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] [2026-02-26 15:08:36] [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(2026-02-26); 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) [2026-02-26 15:08:36] [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 [2026-02-26 15:08:36] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-02-26 15:08:36] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-02-26 15:08:36] [TRACE] [OmnipathR] Contains 7 files. [2026-02-26 15:08:36] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-02-26 15:08:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-26 15:08:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-26 15:08:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-02-26 15:08:36] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2026-02-26 15:08:36] [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). [2026-02-26 15:08:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-26 15:08:37] [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). [2026-02-26 15:08:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-26 15:08:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-02-26 15:08:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-26 15:08:37] [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). [2026-02-26 15:08:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-26 15:08:37] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-02-26 15:08:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-26 15:08:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-26 15:08:39] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-02-26 15:08:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-02-26 15:08:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26 [2026-02-26 15:08:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix [2026-02-26 15:08:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4 [2026-02-26 15:08:39] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2026-02-26 15:08:39] [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=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-02-26 15:08:39] [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] [2026-02-26 15:08:39] [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(2026-02-26); 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) [2026-02-26 15:08:39] [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 [2026-02-26 15:08:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-02-26 15:08:39] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-02-26 15:08:39] [TRACE] [OmnipathR] Contains 1 files. [2026-02-26 15:08:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-02-26 15:08:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-26 15:08:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-26 15:08:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-02-26 15:08:39] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2026-02-26 15:08:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-02-26 15:08:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-26 15:08:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-02-26 15:08:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-26 15:08:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-02-26 15:08:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-26 15:08:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-02-26 15:08:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-26 15:08:39] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
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
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/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)
[2026-02-27 02:31:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:31:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:31:02] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-27 02:31:02] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-27 02:31:02] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26
[2026-02-27 02:31:02] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix
[2026-02-27 02:31:02] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-27 02:31:02] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-27 02:31:03] [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=2026-02-27; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-27 02:31:03] [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]
[2026-02-27 02:31:03] [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(2026-02-26); 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)
[2026-02-27 02:31:03] [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
[2026-02-27 02:31:03] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-02-27 02:31:03] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-27 02:31:03] [TRACE] [OmnipathR] Contains 75 files.
[2026-02-27 02:31:03] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-02-27 02:31:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 02:31:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:31:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-27 02:31:03] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-27 02:31:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-27 02:31:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:31:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-27 02:31:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:31:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-27 02:31:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:31:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-27 02:31:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 02:31:03] [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
45.353 3.317 110.130
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.017 | 0.001 | 0.018 | |
| all_uniprots | 25.386 | 1.845 | 39.978 | |
| ancestors | 0.008 | 0.001 | 0.009 | |
| annotated_network | 1.593 | 0.135 | 16.580 | |
| annotation_categories | 91.369 | 0.057 | 96.272 | |
| annotation_resources | 0.192 | 0.035 | 0.989 | |
| annotations | 0.832 | 0.075 | 12.291 | |
| biomart_query | 1.188 | 0.106 | 13.307 | |
| bioplex1 | 0.005 | 0.003 | 0.008 | |
| bioplex2 | 0.006 | 0.002 | 0.008 | |
| bioplex3 | 0.005 | 0.003 | 0.007 | |
| bioplex_all | 0.008 | 0.000 | 0.008 | |
| bioplex_hct116_1 | 0.008 | 0.000 | 0.008 | |
| bma_motif_es | 0.687 | 0.069 | 2.862 | |
| bma_motif_vs | 0.245 | 0.016 | 1.100 | |
| chalmers_gem | 0.009 | 0.000 | 0.009 | |
| chalmers_gem_id_mapping_table | 0.009 | 0.000 | 0.008 | |
| chalmers_gem_id_type | 0.001 | 0.000 | 0.000 | |
| chalmers_gem_metabolites | 0.007 | 0.000 | 0.008 | |
| chalmers_gem_network | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_raw | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_reactions | 0.008 | 0.000 | 0.008 | |
| common_name | 0.141 | 0.000 | 0.140 | |
| complex_genes | 0.744 | 0.046 | 3.438 | |
| complex_resources | 0.156 | 0.015 | 1.063 | |
| complexes | 0.286 | 0.008 | 1.107 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.008 | 0.000 | 0.007 | |
| cosmos_pkn | 0.000 | 0.000 | 0.001 | |
| curated_ligand_receptor_interactions | 6.884 | 0.857 | 37.474 | |
| curated_ligrec_stats | 50.749 | 4.276 | 166.623 | |
| database_summary | 2.369 | 0.123 | 5.356 | |
| descendants | 0.015 | 0.000 | 0.016 | |
| ensembl_dataset | 0.072 | 0.001 | 0.073 | |
| ensembl_id_mapping_table | 4.668 | 0.245 | 25.218 | |
| ensembl_id_type | 0.002 | 0.000 | 0.001 | |
| ensembl_name | 0.562 | 0.010 | 0.575 | |
| ensembl_organisms | 0.237 | 0.022 | 0.260 | |
| ensembl_organisms_raw | 0.253 | 0.019 | 0.306 | |
| ensembl_orthology | 0.000 | 0.000 | 0.001 | |
| enzsub_graph | 3.857 | 0.183 | 8.077 | |
| enzsub_resources | 0.190 | 0.025 | 1.015 | |
| enzyme_substrate | 1.754 | 0.033 | 2.582 | |
| evex_download | 0.019 | 0.001 | 0.018 | |
| evidences | 0.000 | 0.000 | 0.001 | |
| extra_attr_values | 24.789 | 2.436 | 44.588 | |
| extra_attrs | 7.504 | 1.202 | 9.666 | |
| extra_attrs_to_cols | 19.296 | 1.775 | 24.005 | |
| filter_by_resource | 12.608 | 0.577 | 23.285 | |
| filter_extra_attrs | 39.897 | 6.774 | 53.902 | |
| filter_intercell | 10.548 | 0.905 | 42.570 | |
| filter_intercell_network | 0.032 | 0.002 | 0.033 | |
| find_all_paths | 11.507 | 0.672 | 16.074 | |
| from_evidences | 0.000 | 0.000 | 0.004 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.020 | 0.002 | 0.022 | |
| giant_component | 11.197 | 0.694 | 24.432 | |
| go_annot_download | 12.889 | 0.789 | 13.627 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.017 | 0.002 | 0.019 | |
| guide2pharma_download | 0.017 | 0.001 | 0.018 | |
| harmonizome_download | 0.017 | 0.001 | 0.018 | |
| has_extra_attrs | 12.239 | 1.593 | 14.366 | |
| hmdb_id_mapping_table | 0.009 | 0.000 | 0.009 | |
| hmdb_id_type | 0.001 | 0.000 | 0.001 | |
| hmdb_metabolite_fields | 0.001 | 0.000 | 0.001 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.008 | 0.000 | 0.008 | |
| homologene_download | 0.008 | 0.000 | 0.008 | |
| homologene_raw | 0.053 | 0.002 | 0.055 | |
| homologene_uniprot_orthology | 0.008 | 0.000 | 0.009 | |
| hpo_download | 2.697 | 0.192 | 3.302 | |
| htridb_download | 0.008 | 0.000 | 0.009 | |
| id_translation_resources | 0.000 | 0.000 | 0.001 | |
| id_types | 0.039 | 0.002 | 0.041 | |
| inbiomap_download | 0.000 | 0.000 | 0.001 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.777 | 0.024 | 1.028 | |
| interaction_graph | 0.491 | 0.014 | 1.369 | |
| interaction_resources | 0.158 | 0.005 | 0.947 | |
| interaction_types | 0.111 | 0.002 | 0.113 | |
| intercell | 1.672 | 0.100 | 4.218 | |
| intercell_categories | 1.539 | 0.089 | 3.344 | |
| intercell_consensus_filter | 2.441 | 0.149 | 9.605 | |
| intercell_generic_categories | 0.076 | 0.003 | 0.078 | |
| intercell_network | 0.013 | 0.001 | 0.020 | |
| intercell_resources | 0.178 | 0.038 | 1.096 | |
| intercell_summary | 0.086 | 0.010 | 0.094 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.097 | 0.015 | 0.112 | |
| is_trembl | 0.057 | 0.004 | 0.061 | |
| is_uniprot | 0.007 | 0.002 | 0.010 | |
| kegg_api_templates | 0.000 | 0.001 | 0.001 | |
| kegg_conv | 2.430 | 0.184 | 14.008 | |
| kegg_databases | 0 | 0 | 0 | |
| kegg_ddi | 0.740 | 0.085 | 2.142 | |
| kegg_find | 1.223 | 0.097 | 4.211 | |
| kegg_info | 0.019 | 0.001 | 0.020 | |
| kegg_link | 1.353 | 0.161 | 7.709 | |
| kegg_list | 0.738 | 0.061 | 1.738 | |
| kegg_open | 0.009 | 0.000 | 0.008 | |
| kegg_operations | 0 | 0 | 0 | |
| kegg_organism_codes | 0.012 | 0.009 | 0.021 | |
| kegg_organisms | 0.020 | 0.002 | 0.022 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.009 | 0.001 | 0.010 | |
| kegg_pathway_list | 0.008 | 0.000 | 0.008 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 1.244 | 0.027 | 5.846 | |
| kegg_process | 0.014 | 0.002 | 0.016 | |
| kegg_query | 0.007 | 0.000 | 0.007 | |
| kegg_request | 0.068 | 0.016 | 0.085 | |
| kegg_rm_prefix | 0.790 | 0.091 | 5.395 | |
| kinasephos | 1.114 | 0.115 | 17.703 | |
| latin_name | 0.256 | 0.006 | 0.261 | |
| load_db | 0.076 | 0.010 | 0.085 | |
| metalinksdb_sqlite | 1.098 | 0.211 | 9.990 | |
| metalinksdb_table | 0.215 | 0.011 | 0.226 | |
| metalinksdb_tables | 0.017 | 0.001 | 0.018 | |
| ncbi_taxid | 0.253 | 0.008 | 0.261 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.008 | 0.002 | 0.009 | |
| nichenet_gr_network | 0.026 | 0.001 | 0.026 | |
| nichenet_gr_network_evex | 0.009 | 0.000 | 0.008 | |
| nichenet_gr_network_harmonizome | 0.008 | 0.000 | 0.009 | |
| nichenet_gr_network_htridb | 0.007 | 0.001 | 0.009 | |
| nichenet_gr_network_omnipath | 20.801 | 1.322 | 35.501 | |
| nichenet_gr_network_pathwaycommons | 0.018 | 0.001 | 0.018 | |
| nichenet_gr_network_regnetwork | 0.016 | 0.015 | 0.043 | |
| nichenet_gr_network_remap | 0.016 | 0.002 | 0.017 | |
| nichenet_gr_network_trrust | 0.015 | 0.002 | 0.017 | |
| nichenet_ligand_activities | 0.000 | 0.000 | 0.001 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.322 | 0.023 | 0.345 | |
| nichenet_lr_network_guide2pharma | 0.015 | 0.002 | 0.017 | |
| nichenet_lr_network_omnipath | 0.042 | 0.002 | 0.043 | |
| nichenet_lr_network_ramilowski | 0.014 | 0.001 | 0.015 | |
| nichenet_main | 0.001 | 0.000 | 0.001 | |
| nichenet_networks | 0.083 | 0.005 | 0.087 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.049 | 0.005 | 0.056 | |
| nichenet_results_dir | 0.000 | 0.000 | 0.001 | |
| nichenet_signaling_network | 0.050 | 0.001 | 0.051 | |
| nichenet_signaling_network_cpdb | 0.015 | 0.002 | 0.017 | |
| nichenet_signaling_network_evex | 0.016 | 0.002 | 0.018 | |
| nichenet_signaling_network_harmonizome | 0.018 | 0.001 | 0.019 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 24.918 | 1.182 | 39.414 | |
| nichenet_signaling_network_pathwaycommons | 0.01 | 0.00 | 0.01 | |
| nichenet_signaling_network_vinayagam | 0.008 | 0.000 | 0.008 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.204 | 0.011 | 0.663 | |
| oma_code | 0.126 | 0.000 | 0.126 | |
| oma_organisms | 0.055 | 0.004 | 0.059 | |
| oma_pairwise | 0.009 | 0.000 | 0.009 | |
| oma_pairwise_genesymbols | 0.005 | 0.003 | 0.008 | |
| oma_pairwise_translated | 0.008 | 0.000 | 0.008 | |