Denes Turei
| Snapshot Date: 2024-10-13 14:00 -0400 (Sun, 13 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_19 |
| git_last_commit: edb3c69 |
| git_last_commit_date: 2024-10-02 06:46:04 -0400 (Wed, 02 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-15 21:55 -0400 (Tue, 15 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4529 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4479 |
| 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 1467/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.12.4 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 3.12.4 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.12.4.tar.gz |
| StartedAt: 2024-10-15 06:04:30 -0400 (Tue, 15 Oct 2024) |
| EndedAt: 2024-10-15 06:16:17 -0400 (Tue, 15 Oct 2024) |
| EllapsedTime: 706.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.12.4.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.12.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for 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 ... NOTE
License stub is invalid DCF.
* 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
[2024-10-15 06:04:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-15 06:04:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:04:54] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:04:54] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-15 06:04:54] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:04:54] [TRACE] [OmnipathR] Contains 1 files.
[2024-10-15 06:04:54] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-15 06:04:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-15 06:04:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:04:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:04:54] [TRACE] [OmnipathR] Pandoc version: `3.1.2`.
[2024-10-15 06:04:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-15 06:04:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:04:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-15 06:04:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:04:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-15 06:04:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:04:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-15 06:04:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:04:54] [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
[2024-10-15 06:05:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-15 06:05:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:05:08] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:05:08] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-15 06:05:08] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:05:08] [TRACE] [OmnipathR] Contains 1 files.
[2024-10-15 06:05:08] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-15 06:05:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-15 06:05:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:05:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:05:08] [TRACE] [OmnipathR] Pandoc version: `3.1.2`.
[2024-10-15 06:05:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-15 06:05:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:05:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-15 06:05:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:05:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-15 06:05:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:05:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-15 06:05:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:05:09] [TRACE] [OmnipathR] Cache locked: FALSE
oma_organisms: no visible binding for global variable ‘ncbi_tax_id’
Undefined global functions or variables:
ncbi_tax_id
* 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
collectri 106.923 0.938 110.918
annotation_categories 96.350 0.362 98.282
dorothea 58.511 0.376 62.195
curated_ligrec_stats 25.698 1.454 32.654
filter_extra_attrs 18.056 0.100 18.470
go_annot_download 12.192 0.635 12.822
nichenet_gr_network_omnipath 11.293 0.944 12.432
extra_attr_values 11.448 0.155 11.800
pivot_annotations 10.088 0.757 10.973
giant_component 9.962 0.414 10.747
extra_attrs_to_cols 9.461 0.078 9.849
nichenet_signaling_network_omnipath 9.058 0.324 9.628
with_extra_attrs 7.652 0.135 8.060
filter_intercell 6.982 0.352 7.746
static_table 6.939 0.298 7.215
extra_attrs 6.464 0.044 6.650
has_extra_attrs 6.039 0.076 6.160
find_all_paths 5.637 0.146 5.871
curated_ligand_receptor_interactions 5.062 0.272 6.410
filter_by_resource 5.209 0.096 5.495
get_signed_ptms 5.226 0.063 5.398
print_interactions 4.784 0.317 5.451
ensembl_id_mapping_table 1.176 0.076 71.327
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 [2024-10-13 17:01:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-13 17:01:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-13 17:01:47] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-13 17:01:47] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-13 17:01:47] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-13 17:01:47] [TRACE] [OmnipathR] Contains 1 files. [2024-10-13 17:01:47] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-13 17:01:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-13 17:01:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-13 17:01:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-13 17:01:48] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2024-10-13 17:01:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-13 17:01:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-13 17:01:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-13 17:01:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-13 17:01:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-13 17:01:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-13 17:01:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-13 17:01:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-13 17:01:48] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-10-13 17:01:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-13 17:01:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-13 17:01:50] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-13 17:01:50] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-13 17:01:50] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-13 17:01:50] [TRACE] [OmnipathR] Contains 1 files. [2024-10-13 17:01:50] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-13 17:01:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-13 17:01:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-13 17:01:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-10-13 17:01:50] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2024-10-13 17:01:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-13 17:01:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-13 17:01:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-13 17:01:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-13 17:01:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-13 17:01:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-13 17:01:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-13 17:01:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-13 17:01:50] [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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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)
[2024-10-15 06:15:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-15 06:15:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:15:40] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:15:40] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-10-15 06:15:40] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:15:40] [TRACE] [OmnipathR] Contains 17 files.
[2024-10-15 06:15:40] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-10-15 06:15:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-15 06:15:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:15:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:15:41] [TRACE] [OmnipathR] Pandoc version: `3.1.2`.
[2024-10-15 06:15:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-15 06:15:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:15:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-15 06:15:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:15:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-15 06:15:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:15:41] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-15 06:15:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:15:41] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
9.895 1.092 13.960
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.001 | 0.001 | |
| all_uniprot_acs | 0.021 | 0.003 | 0.024 | |
| all_uniprots | 0.010 | 0.002 | 0.011 | |
| ancestors | 0.012 | 0.002 | 0.016 | |
| annotated_network | 1.611 | 0.169 | 3.399 | |
| annotation_categories | 96.350 | 0.362 | 98.282 | |
| biomart_query | 1.075 | 0.097 | 2.688 | |
| bioplex1 | 0.010 | 0.001 | 0.012 | |
| bioplex2 | 0.006 | 0.000 | 0.007 | |
| bioplex3 | 0.047 | 0.002 | 0.049 | |
| bioplex_all | 0.004 | 0.001 | 0.005 | |
| bioplex_hct116_1 | 0.010 | 0.001 | 0.011 | |
| bma_motif_es | 0.310 | 0.032 | 0.426 | |
| bma_motif_vs | 0.168 | 0.008 | 0.227 | |
| collectri | 106.923 | 0.938 | 110.918 | |
| common_name | 0.031 | 0.001 | 0.032 | |
| consensuspathdb_download | 0.001 | 0.001 | 0.000 | |
| consensuspathdb_raw_table | 0.013 | 0.002 | 0.015 | |
| curated_ligand_receptor_interactions | 5.062 | 0.272 | 6.410 | |
| curated_ligrec_stats | 25.698 | 1.454 | 32.654 | |
| database_summary | 0.885 | 0.040 | 1.007 | |
| descendants | 0.008 | 0.001 | 0.009 | |
| dorothea | 58.511 | 0.376 | 62.195 | |
| ensembl_dataset | 0.011 | 0.000 | 0.012 | |
| ensembl_id_mapping_table | 1.176 | 0.076 | 71.327 | |
| ensembl_id_type | 0.002 | 0.000 | 0.003 | |
| ensembl_name | 0.063 | 0.000 | 0.064 | |
| ensembl_organisms | 0.103 | 0.004 | 0.114 | |
| ensembl_organisms_raw | 0.098 | 0.003 | 0.102 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 1.567 | 0.058 | 1.732 | |
| evex_download | 0.053 | 0.006 | 0.059 | |
| evidences | 0.000 | 0.001 | 0.000 | |
| extra_attr_values | 11.448 | 0.155 | 11.800 | |
| extra_attrs | 6.464 | 0.044 | 6.650 | |
| extra_attrs_to_cols | 9.461 | 0.078 | 9.849 | |
| filter_by_resource | 5.209 | 0.096 | 5.495 | |
| filter_extra_attrs | 18.056 | 0.100 | 18.470 | |
| filter_intercell | 6.982 | 0.352 | 7.746 | |
| filter_intercell_network | 0.023 | 0.003 | 0.026 | |
| find_all_paths | 5.637 | 0.146 | 5.871 | |
| from_evidences | 0.000 | 0.000 | 0.001 | |
| get_annotation_resources | 0.064 | 0.006 | 0.117 | |
| get_complex_genes | 1.027 | 0.051 | 1.166 | |
| get_complex_resources | 0.112 | 0.005 | 0.366 | |
| get_db | 0.000 | 0.000 | 0.001 | |
| get_enzsub_resources | 0.062 | 0.006 | 0.118 | |
| get_interaction_resources | 0.069 | 0.006 | 0.119 | |
| get_intercell_categories | 0.302 | 0.042 | 0.374 | |
| get_intercell_generic_categories | 0.038 | 0.003 | 0.042 | |
| get_intercell_resources | 0.116 | 0.005 | 0.204 | |
| get_ontology_db | 0.016 | 0.002 | 0.021 | |
| get_resources | 0.068 | 0.005 | 0.145 | |
| get_signed_ptms | 5.226 | 0.063 | 5.398 | |
| giant_component | 9.962 | 0.414 | 10.747 | |
| go_annot_download | 12.192 | 0.635 | 12.822 | |
| go_annot_slim | 0.000 | 0.000 | 0.001 | |
| go_ontology_download | 0.013 | 0.002 | 0.015 | |
| guide2pharma_download | 0.013 | 0.002 | 0.015 | |
| harmonizome_download | 0.013 | 0.002 | 0.015 | |
| has_extra_attrs | 6.039 | 0.076 | 6.160 | |
| homologene_download | 0.060 | 0.002 | 0.061 | |
| homologene_raw | 0.024 | 0.002 | 0.025 | |
| homologene_uniprot_orthology | 0.012 | 0.002 | 0.014 | |
| hpo_download | 1.816 | 0.118 | 3.206 | |
| htridb_download | 0.012 | 0.001 | 0.016 | |
| import_all_interactions | 1.851 | 0.109 | 2.107 | |
| import_intercell_network | 0.012 | 0.001 | 0.012 | |
| import_kinaseextra_interactions | 1.314 | 0.056 | 1.470 | |
| import_ligrecextra_interactions | 0.640 | 0.050 | 0.791 | |
| import_lncrna_mrna_interactions | 0.436 | 0.035 | 0.546 | |
| import_mirnatarget_interactions | 0.876 | 0.048 | 1.038 | |
| import_omnipath_annotations | 0.442 | 0.034 | 0.561 | |
| import_omnipath_complexes | 0.565 | 0.036 | 0.706 | |
| import_omnipath_enzsub | 1.020 | 0.012 | 1.079 | |
| import_omnipath_interactions | 0.238 | 0.007 | 0.291 | |
| import_omnipath_intercell | 0.456 | 0.036 | 0.533 | |
| import_pathwayextra_interactions | 0.732 | 0.046 | 0.895 | |
| import_post_translational_interactions | 0.819 | 0.048 | 0.982 | |
| import_small_molecule_protein_interactions | 0.413 | 0.033 | 0.486 | |
| import_tf_mirna_interactions | 0.644 | 0.041 | 0.810 | |
| import_tf_target_interactions | 1.226 | 0.051 | 1.364 | |
| import_transcriptional_interactions | 2.030 | 0.114 | 2.266 | |
| inbiomap_download | 0.000 | 0.001 | 0.000 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.041 | 0.004 | 0.048 | |
| interaction_graph | 0.363 | 0.012 | 0.439 | |
| interaction_types | 0.037 | 0.004 | 0.041 | |
| intercell_categories | 0.059 | 0.004 | 0.065 | |
| intercell_consensus_filter | 0.862 | 0.088 | 1.021 | |
| is_ontology_id | 0.000 | 0.001 | 0.000 | |
| is_swissprot | 0.027 | 0.002 | 0.029 | |
| is_trembl | 0.025 | 0.002 | 0.027 | |
| is_uniprot | 0.005 | 0.001 | 0.005 | |
| kegg_info | 0.003 | 0.000 | 0.004 | |
| kegg_open | 0.003 | 0.001 | 0.004 | |
| kegg_pathway_annotations | 0.000 | 0.000 | 0.001 | |
| kegg_pathway_download | 0.004 | 0.001 | 0.004 | |
| kegg_pathway_list | 0.009 | 0.001 | 0.011 | |
| kegg_pathways_download | 0.000 | 0.000 | 0.001 | |
| kegg_picture | 0.075 | 0.011 | 3.048 | |
| kegg_process | 0.021 | 0.003 | 0.024 | |
| latin_name | 0.090 | 0.004 | 0.094 | |
| load_db | 0.066 | 0.003 | 0.069 | |
| ncbi_taxid | 0.049 | 0.001 | 0.050 | |
| nichenet_build_model | 0.000 | 0.001 | 0.001 | |
| nichenet_expression_data | 0.010 | 0.001 | 0.013 | |
| nichenet_gr_network | 0.029 | 0.003 | 0.032 | |
| nichenet_gr_network_evex | 0.010 | 0.001 | 0.011 | |
| nichenet_gr_network_harmonizome | 0.010 | 0.001 | 0.012 | |
| nichenet_gr_network_htridb | 0.011 | 0.002 | 0.012 | |
| nichenet_gr_network_omnipath | 11.293 | 0.944 | 12.432 | |
| nichenet_gr_network_pathwaycommons | 0.074 | 0.003 | 0.080 | |
| nichenet_gr_network_regnetwork | 0.016 | 0.002 | 0.018 | |
| nichenet_gr_network_remap | 0.014 | 0.001 | 0.015 | |
| nichenet_gr_network_trrust | 0.016 | 0.001 | 0.020 | |
| nichenet_ligand_activities | 0.000 | 0.000 | 0.001 | |
| nichenet_ligand_target_links | 0.001 | 0.001 | 0.001 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.046 | 0.004 | 0.053 | |
| nichenet_lr_network_guide2pharma | 0.015 | 0.001 | 0.018 | |
| nichenet_lr_network_omnipath | 0.037 | 0.005 | 0.046 | |
| nichenet_lr_network_ramilowski | 0.011 | 0.002 | 0.012 | |
| nichenet_main | 0.000 | 0.000 | 0.001 | |
| nichenet_networks | 0.054 | 0.008 | 0.064 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.036 | 0.004 | 0.043 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.039 | 0.005 | 0.045 | |
| nichenet_signaling_network_cpdb | 0.011 | 0.002 | 0.013 | |
| nichenet_signaling_network_evex | 0.012 | 0.001 | 0.013 | |
| nichenet_signaling_network_harmonizome | 0.013 | 0.001 | 0.015 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 9.058 | 0.324 | 9.628 | |
| nichenet_signaling_network_pathwaycommons | 0.014 | 0.001 | 0.016 | |
| nichenet_signaling_network_vinayagam | 0.011 | 0.001 | 0.013 | |
| nichenet_test | 0.001 | 0.000 | 0.001 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.095 | 0.008 | 0.615 | |
| oma_code | 0.031 | 0.000 | 0.032 | |
| oma_organisms | 0.060 | 0.002 | 0.061 | |
| oma_pairwise | 0.012 | 0.001 | 0.014 | |
| oma_pairwise_genesymbols | 0.012 | 0.001 | 0.013 | |
| oma_pairwise_translated | 0.012 | 0.002 | 0.013 | |
| omnipath | 4.847 | 0.072 | 4.936 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.005 | 0.001 | 0.006 | |
| omnipath_cache_clean_db | 0.078 | 0.007 | 0.085 | |
| omnipath_cache_download_ready | 0.437 | 0.051 | 0.688 | |
| omnipath_cache_filter_versions | 0.111 | 0.019 | 0.138 | |
| omnipath_cache_get | 0.101 | 0.017 | 0.124 | |
| omnipath_cache_key | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.069 | 0.012 | 0.084 | |
| omnipath_cache_load | 0.434 | 0.034 | 0.772 | |
| omnipath_cache_move_in | 0.122 | 0.017 | 0.145 | |
| omnipath_cache_remove | 0.075 | 0.012 | 0.092 | |
| omnipath_cache_save | 0.113 | 0.017 | 0.189 | |
| omnipath_cache_search | 0 | 0 | 0 | |
| omnipath_cache_set_ext | 0.061 | 0.010 | 0.077 | |
| omnipath_cache_update_status | 0.100 | 0.016 | 0.122 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_get_config_path | 0.000 | 0.001 | 0.000 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.001 | 0.000 | 0.001 | |
| omnipath_msg | 0.008 | 0.001 | 0.010 | |
| omnipath_reset_config | 0.000 | 0.000 | 0.001 | |
| omnipath_save_config | 0.000 | 0.000 | 0.001 | |
| omnipath_set_cachedir | 0.026 | 0.004 | 0.031 | |
| omnipath_set_console_loglevel | 0.001 | 0.000 | 0.001 | |
| omnipath_set_logfile_loglevel | 0.001 | 0.000 | 0.002 | |
| omnipath_set_loglevel | 0.001 | 0.000 | 0.001 | |
| omnipath_show_db | 0.051 | 0.001 | 0.051 | |
| omnipath_unlock_cache_db | 0.000 | 0.001 | 0.001 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.001 | 0.001 | 0.001 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.000 | |
| ontology_name_id | 0.001 | 0.001 | 0.001 | |
| organism_for | 0.072 | 0.001 | 0.072 | |
| pathwaycommons_download | 0.001 | 0.000 | 0.001 | |
| pivot_annotations | 10.088 | 0.757 | 10.973 | |
| preppi_download | 0.001 | 0.000 | 0.001 | |
| preppi_filter | 0.001 | 0.000 | 0.001 | |
| print_bma_motif_es | 0.161 | 0.035 | 0.313 | |
| print_bma_motif_vs | 0.139 | 0.008 | 0.206 | |
| print_interactions | 4.784 | 0.317 | 5.451 | |
| print_path_es | 0.429 | 0.031 | 0.564 | |
| print_path_vs | 1.679 | 0.065 | 1.904 | |
| pubmed_open | 4.547 | 0.156 | 4.722 | |
| query_info | 0.089 | 0.015 | 0.142 | |
| ramilowski_download | 0.001 | 0.000 | 0.000 | |
| regnetwork_directions | 0.001 | 0.001 | 0.001 | |
| regnetwork_download | 0.001 | 0.000 | 0.001 | |
| relations_list_to_table | 0.086 | 0.005 | 0.121 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.086 | 0.008 | 0.220 | |
| remap_dorothea_download | 0.000 | 0.001 | 0.001 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 0.142 | 0.054 | 0.365 | |
| resources_colname | 0.526 | 0.036 | 0.644 | |
| resources_in | 3.145 | 0.035 | 3.210 | |
| show_network | 0 | 0 | 0 | |
| simplify_intercell_network | 0.001 | 0.000 | 0.001 | |
| static_table | 6.939 | 0.298 | 7.215 | |
| static_tables | 0.048 | 0.001 | 0.060 | |
| swap_relations | 0.080 | 0.005 | 0.103 | |
| swissprots_only | 0.084 | 0.005 | 0.090 | |
| tfcensus_download | 0.155 | 0.016 | 0.277 | |
| translate_ids | 0.002 | 0.001 | 0.002 | |
| trembls_only | 0.026 | 0.000 | 0.028 | |
| trrust_download | 0 | 0 | 0 | |
| uniprot_full_id_mapping_table | 0.001 | 0.001 | 0.001 | |
| uniprot_genesymbol_cleanup | 0.000 | 0.001 | 0.001 | |
| uniprot_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| uniprot_id_type | 0.002 | 0.000 | 0.003 | |
| uniprot_idmapping_id_types | 0.130 | 0.010 | 0.336 | |
| unique_intercell_network | 0.001 | 0.000 | 0.001 | |
| unnest_evidences | 0.000 | 0.001 | 0.000 | |
| uploadlists_id_type | 0.003 | 0.000 | 0.003 | |
| vinayagam_download | 0.000 | 0.000 | 0.001 | |
| walk_ontology_tree | 0.001 | 0.001 | 0.001 | |
| with_extra_attrs | 7.652 | 0.135 | 8.060 | |
| with_references | 0.392 | 0.033 | 0.527 | |
| zenodo_download | 0.001 | 0.001 | 0.002 | |