Denes Turei
| Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 3c7d7f1 |
| git_last_commit_date: 2024-10-29 10:41:00 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-20 12:07 -0400 (Thu, 20 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
| 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 1456/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.14.0 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
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: 3.14.0 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings OmnipathR_3.14.0.tar.gz |
| StartedAt: 2025-03-18 04:02:40 -0400 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 04:26:02 -0400 (Tue, 18 Mar 2025) |
| EllapsedTime: 1402.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings OmnipathR_3.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.3.0
GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OmnipathR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OmnipathR' version '3.14.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... 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 whether startup messages can be suppressed ... NOTE
[2025-03-18 04:03:13] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 04:03:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:03:13] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-18 04:03:13] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 04:03:13] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-18 04:03:13] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-18 04:03:13] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-18 04:03:13] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 04:03:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:03:13] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-18 04:03:13] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 04:03:13] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 04:03:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:03:13] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 04:03:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:03:13] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 04:03:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:03:13] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 04:03:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:03:13] [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
[2025-03-18 04:03:31] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 04:03:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:03:31] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-18 04:03:31] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 04:03:31] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-18 04:03:31] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-18 04:03:31] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-18 04:03:31] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 04:03:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:03:31] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-18 04:03:32] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 04:03:32] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 04:03:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:03:32] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 04:03:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:03:32] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 04:03:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:03:32] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 04:03:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:03:32] [TRACE] [OmnipathR] Cache locked: FALSE
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 58.17 0.06 58.97
curated_ligrec_stats 31.21 1.47 78.13
omnipath-interactions 28.50 1.07 43.00
filter_extra_attrs 24.81 0.19 26.03
go_annot_download 14.91 1.13 18.66
nichenet_gr_network_omnipath 13.48 1.17 15.14
extra_attr_values 14.20 0.14 16.69
extra_attrs_to_cols 13.01 0.08 13.41
giant_component 11.79 0.31 13.89
nichenet_signaling_network_omnipath 9.18 0.50 10.25
omnipath_for_cosmos 9.33 0.24 31.60
pivot_annotations 8.95 0.57 11.00
with_extra_attrs 9.08 0.22 9.74
translate_ids_multi 8.17 0.29 72.08
extra_attrs 8.19 0.07 8.47
filter_intercell 7.66 0.59 16.08
has_extra_attrs 8.04 0.06 8.48
find_all_paths 7.48 0.19 7.83
filter_by_resource 7.41 0.14 10.98
static_table 6.85 0.46 7.47
print_interactions 6.02 0.20 8.28
signed_ptms 5.95 0.01 6.39
curated_ligand_receptor_interactions 5.22 0.38 12.30
enzsub_graph 2.91 0.04 12.47
ensembl_id_mapping_table 1.82 0.07 29.11
translate_ids 1.19 0.24 260.31
uniprot_full_id_mapping_table 1.16 0.22 192.16
all_uniprots 0.77 0.19 157.50
intercell 0.56 0.03 6.18
kegg_picture 0.12 0.00 22.05
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'F:/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'OmnipathR' ... ** 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 [2025-03-17 15:53:15] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-03-17 15:53:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 15:53:15] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-03-17 15:53:15] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-17 15:53:15] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-03-17 15:53:15] [TRACE] [OmnipathR] Contains 1 files. [2025-03-17 15:53:15] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-17 15:53:15] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-03-17 15:53:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 15:53:15] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-03-17 15:53:15] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-17 15:53:15] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-17 15:53:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 15:53:15] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-17 15:53:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 15:53:15] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-17 15:53:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 15:53:15] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-17 15:53:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 15:53:15] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-03-17 15:53:17] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-03-17 15:53:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 15:53:17] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-03-17 15:53:18] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-17 15:53:18] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-03-17 15:53:18] [TRACE] [OmnipathR] Contains 1 files. [2025-03-17 15:53:18] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-17 15:53:18] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-03-17 15:53:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 15:53:18] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-03-17 15:53:18] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-17 15:53:18] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-17 15:53:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 15:53:18] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-17 15:53:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 15:53:18] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-17 15:53:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 15:53:18] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-17 15:53:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 15:53:18] [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 4.4.3 (2025-02-28 ucrt) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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)
[2025-03-18 04:25:07] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 04:25:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:25:07] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-18 04:25:07] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 04:25:07] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-18 04:25:07] [TRACE] [OmnipathR] Contains 21 files.
[2025-03-18 04:25:07] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-18 04:25:07] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 04:25:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:25:07] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-18 04:25:07] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 04:25:07] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 04:25:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:25:07] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 04:25:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:25:08] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 04:25:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:25:08] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 04:25:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 04:25:08] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
12.21 1.31 31.73
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.01 | 0.01 | 0.03 | |
| all_uniprots | 0.77 | 0.19 | 157.50 | |
| ancestors | 0.01 | 0.00 | 0.01 | |
| annotated_network | 0.91 | 0.09 | 2.94 | |
| annotation_categories | 58.17 | 0.06 | 58.97 | |
| annotation_resources | 0.06 | 0.00 | 0.48 | |
| annotations | 0.25 | 0.02 | 1.00 | |
| biomart_query | 1.11 | 0.07 | 2.77 | |
| bioplex1 | 0.02 | 0.00 | 0.01 | |
| bioplex2 | 0.01 | 0.00 | 0.02 | |
| bioplex3 | 0.02 | 0.00 | 0.01 | |
| bioplex_all | 0.01 | 0.00 | 0.02 | |
| bioplex_hct116_1 | 0.07 | 0.00 | 0.06 | |
| bma_motif_es | 0.40 | 0.07 | 1.17 | |
| bma_motif_vs | 0.21 | 0.00 | 0.63 | |
| chalmers_gem | 0.01 | 0.00 | 0.01 | |
| chalmers_gem_id_mapping_table | 0.02 | 0.00 | 0.02 | |
| chalmers_gem_id_type | 0 | 0 | 0 | |
| chalmers_gem_metabolites | 0 | 0 | 0 | |
| chalmers_gem_network | 0.02 | 0.00 | 0.02 | |
| chalmers_gem_raw | 0.01 | 0.00 | 0.02 | |
| chalmers_gem_reactions | 0.02 | 0.00 | 0.01 | |
| common_name | 0.03 | 0.00 | 0.03 | |
| complex_genes | 0.47 | 0.03 | 1.55 | |
| complex_resources | 0.08 | 0.00 | 0.48 | |
| complexes | 0.20 | 0.00 | 0.63 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.02 | 0.00 | 0.01 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 5.22 | 0.38 | 12.30 | |
| curated_ligrec_stats | 31.21 | 1.47 | 78.13 | |
| database_summary | 1.47 | 0.01 | 2.26 | |
| descendants | 0.02 | 0.00 | 0.02 | |
| ensembl_dataset | 0.01 | 0.00 | 0.01 | |
| ensembl_id_mapping_table | 1.82 | 0.07 | 29.11 | |
| ensembl_id_type | 0 | 0 | 0 | |
| ensembl_name | 0.11 | 0.00 | 0.11 | |
| ensembl_organisms | 0.15 | 0.01 | 0.17 | |
| ensembl_organisms_raw | 0.30 | 0.02 | 0.32 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 2.91 | 0.04 | 12.47 | |
| enzsub_resources | 0.07 | 0.00 | 0.68 | |
| enzyme_substrate | 1.35 | 0.04 | 1.80 | |
| evex_download | 0.03 | 0.00 | 0.03 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 14.20 | 0.14 | 16.69 | |
| extra_attrs | 8.19 | 0.07 | 8.47 | |
| extra_attrs_to_cols | 13.01 | 0.08 | 13.41 | |
| filter_by_resource | 7.41 | 0.14 | 10.98 | |
| filter_extra_attrs | 24.81 | 0.19 | 26.03 | |
| filter_intercell | 7.66 | 0.59 | 16.08 | |
| filter_intercell_network | 0.03 | 0.00 | 0.03 | |
| find_all_paths | 7.48 | 0.19 | 7.83 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0 | 0 | 0 | |
| giant_component | 11.79 | 0.31 | 13.89 | |
| go_annot_download | 14.91 | 1.13 | 18.66 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.02 | 0.00 | 0.01 | |
| guide2pharma_download | 0.01 | 0.00 | 0.08 | |
| harmonizome_download | 0.02 | 0.00 | 0.02 | |
| has_extra_attrs | 8.04 | 0.06 | 8.48 | |
| hmdb_id_mapping_table | 0 | 0 | 0 | |
| hmdb_id_type | 0 | 0 | 0 | |
| hmdb_metabolite_fields | 0 | 0 | 0 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.02 | 0.00 | 0.02 | |
| homologene_download | 0.01 | 0.00 | 0.01 | |
| homologene_raw | 0.08 | 0.00 | 0.08 | |
| homologene_uniprot_orthology | 0.03 | 0.00 | 0.03 | |
| hpo_download | 2.39 | 0.28 | 2.94 | |
| htridb_download | 0.02 | 0.00 | 0.01 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.09 | 0.02 | 0.11 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.40 | 0.01 | 1.36 | |
| interaction_graph | 0.49 | 0.02 | 0.92 | |
| interaction_resources | 0.06 | 0.00 | 0.49 | |
| interaction_types | 0.06 | 0.00 | 0.27 | |
| intercell | 0.56 | 0.03 | 6.18 | |
| intercell_categories | 0.52 | 0.04 | 0.89 | |
| intercell_consensus_filter | 1.48 | 0.04 | 2.10 | |
| intercell_generic_categories | 0.07 | 0.00 | 0.07 | |
| intercell_network | 0.01 | 0.00 | 0.01 | |
| intercell_resources | 0.03 | 0.01 | 0.47 | |
| intercell_summary | 0.05 | 0.03 | 0.08 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.05 | 0.00 | 0.05 | |
| is_trembl | 0.03 | 0.00 | 0.03 | |
| is_uniprot | 0 | 0 | 0 | |
| kegg_info | 0.00 | 0.02 | 0.02 | |
| kegg_open | 0 | 0 | 0 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.02 | 0.00 | 0.01 | |
| kegg_pathway_list | 0.03 | 0.00 | 0.03 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.12 | 0.00 | 22.05 | |
| kegg_process | 0.03 | 0.00 | 0.03 | |
| latin_name | 0.10 | 0.00 | 0.09 | |
| load_db | 0.09 | 0.00 | 0.10 | |
| ncbi_taxid | 0.08 | 0.00 | 0.08 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.00 | 0.01 | 0.02 | |
| nichenet_gr_network | 0.03 | 0.00 | 0.03 | |
| nichenet_gr_network_evex | 0.02 | 0.00 | 0.01 | |
| nichenet_gr_network_harmonizome | 0.01 | 0.00 | 0.02 | |
| nichenet_gr_network_htridb | 0.02 | 0.00 | 0.02 | |
| nichenet_gr_network_omnipath | 13.48 | 1.17 | 15.14 | |
| nichenet_gr_network_pathwaycommons | 0.02 | 0.00 | 0.01 | |
| nichenet_gr_network_regnetwork | 0.01 | 0.00 | 0.02 | |
| nichenet_gr_network_remap | 0.02 | 0.00 | 0.01 | |
| nichenet_gr_network_trrust | 0 | 0 | 0 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.02 | 0.02 | 0.03 | |
| nichenet_lr_network_guide2pharma | 0.02 | 0.00 | 0.02 | |
| nichenet_lr_network_omnipath | 0.03 | 0.00 | 0.03 | |
| nichenet_lr_network_ramilowski | 0 | 0 | 0 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.07 | 0.00 | 0.06 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.04 | 0.01 | 0.07 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.03 | 0.00 | 0.03 | |
| nichenet_signaling_network_cpdb | 0.01 | 0.00 | 0.02 | |
| nichenet_signaling_network_evex | 0.02 | 0.00 | 0.02 | |
| nichenet_signaling_network_harmonizome | 0.02 | 0.00 | 0.01 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 9.18 | 0.50 | 10.25 | |
| nichenet_signaling_network_pathwaycommons | 0 | 0 | 0 | |
| nichenet_signaling_network_vinayagam | 0.01 | 0.00 | 0.01 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.15 | 0.00 | 0.42 | |
| oma_code | 0.04 | 0.00 | 0.05 | |
| oma_organisms | 0.08 | 0.00 | 0.08 | |
| oma_pairwise | 0.02 | 0.00 | 0.01 | |
| oma_pairwise_genesymbols | 0.01 | 0.00 | 0.02 | |
| oma_pairwise_translated | 0.02 | 0.00 | 0.02 | |
| omnipath-interactions | 28.50 | 1.07 | 43.00 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.01 | 0.00 | 0.01 | |
| omnipath_cache_clean_db | 0.10 | 0.01 | 0.11 | |
| omnipath_cache_download_ready | 0.59 | 0.08 | 0.78 | |
| omnipath_cache_filter_versions | 0.13 | 0.00 | 0.22 | |
| omnipath_cache_get | 0.07 | 0.02 | 0.09 | |
| omnipath_cache_key | 0 | 0 | 0 | |
| omnipath_cache_latest_or_new | 0.08 | 0.00 | 0.08 | |
| omnipath_cache_load | 0.50 | 0.00 | 1.27 | |
| omnipath_cache_move_in | 0.24 | 0.04 | 0.36 | |
| omnipath_cache_remove | 0.14 | 0.03 | 0.29 | |
| omnipath_cache_save | 0.14 | 0.04 | 0.25 | |
| omnipath_cache_search | 0 | 0 | 0 | |
| omnipath_cache_set_ext | 0.06 | 0.04 | 0.18 | |
| omnipath_cache_update_status | 0.11 | 0.03 | 0.15 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0 | 0 | 0 | |
| omnipath_for_cosmos | 9.33 | 0.24 | 31.60 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0 | 0 | 0 | |
| omnipath_msg | 0 | 0 | 0 | |
| omnipath_query | 3.56 | 0.05 | 3.61 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.09 | 0.01 | 0.28 | |
| omnipath_set_console_loglevel | 0.02 | 0.00 | 0.01 | |
| omnipath_set_logfile_loglevel | 0 | 0 | 0 | |
| omnipath_set_loglevel | 0 | 0 | 0 | |
| omnipath_show_db | 0.03 | 0.02 | 0.05 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0 | 0 | 0 | |
| ontology_ensure_name | 0 | 0 | 0 | |
| ontology_name_id | 0 | 0 | 0 | |
| organism_for | 0.03 | 0.00 | 0.03 | |
| pathwaycommons_download | 0 | 0 | 0 | |
| pivot_annotations | 8.95 | 0.57 | 11.00 | |
| preppi_download | 0 | 0 | 0 | |
| preppi_filter | 0 | 0 | 0 | |
| print_bma_motif_es | 0.20 | 0.13 | 1.03 | |
| print_bma_motif_vs | 0.14 | 0.00 | 0.54 | |
| print_interactions | 6.02 | 0.20 | 8.28 | |
| print_path_es | 0.56 | 0.02 | 1.55 | |
| print_path_vs | 2.19 | 0.06 | 3.73 | |
| pubmed_open | 4.31 | 0.02 | 4.38 | |
| query_info | 0.11 | 0.00 | 0.59 | |
| ramilowski_download | 0 | 0 | 0 | |
| ramp_id_mapping_table | 0 | 0 | 0 | |
| ramp_id_type | 0 | 0 | 0 | |
| ramp_sqlite | 0 | 0 | 0 | |
| ramp_table | 0 | 0 | 0 | |
| ramp_tables | 0 | 0 | 0 | |
| regnetwork_directions | 0 | 0 | 0 | |
| regnetwork_download | 0 | 0 | 0 | |
| relations_list_to_table | 0.13 | 0.00 | 0.15 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.08 | 0.00 | 0.11 | |
| remap_dorothea_download | 0 | 0 | 0 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 0.17 | 0.07 | 0.71 | |
| resources | 0.04 | 0.02 | 0.46 | |
| resources_colname | 0.66 | 0.05 | 1.43 | |
| resources_in | 4.14 | 0.00 | 4.14 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 5.95 | 0.01 | 6.39 | |
| simplify_intercell_network | 0 | 0 | 0 | |
| static_table | 6.85 | 0.46 | 7.47 | |
| static_tables | 0.05 | 0.00 | 0.14 | |
| stitch_actions | 0 | 0 | 0 | |
| stitch_links | 0 | 0 | 0 | |
| stitch_network | 0 | 0 | 0 | |
| stitch_remove_prefixes | 0.01 | 0.00 | 0.01 | |
| swap_relations | 0.17 | 0.01 | 0.24 | |
| swissprots_only | 0.05 | 0.00 | 0.04 | |
| tfcensus_download | 0.17 | 0.00 | 0.30 | |
| translate_ids | 1.19 | 0.24 | 260.31 | |
| translate_ids_multi | 8.17 | 0.29 | 72.08 | |
| trembls_only | 0.06 | 0.00 | 0.06 | |
| trrust_download | 0 | 0 | 0 | |
| uniprot_full_id_mapping_table | 1.16 | 0.22 | 192.16 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0 | 0 | 0 | |
| uniprot_id_type | 0 | 0 | 0 | |
| uniprot_idmapping_id_types | 0.20 | 0.00 | 0.55 | |
| unique_intercell_network | 0 | 0 | 0 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0 | 0 | 0 | |
| vinayagam_download | 0 | 0 | 0 | |
| walk_ontology_tree | 0 | 0 | 0 | |
| with_extra_attrs | 9.08 | 0.22 | 9.74 | |
| with_references | 0.43 | 0.08 | 1.36 | |
| zenodo_download | 0 | 0 | 0 | |