Denes Turei
| Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_18 |
| git_last_commit: b1b2bab |
| git_last_commit_date: 2023-10-25 11:47:10 -0500 (Wed, 25 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:38 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| 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 1452/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.10.1 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 3.10.1 |
| 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_3.10.1.tar.gz |
| StartedAt: 2024-03-03 22:18:00 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 22:32:42 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 882.2 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_3.10.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/OmnipathR.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.10.1’
* 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 startup messages can be suppressed ... NOTE
[2024-03-03 22:18:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 22:18:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:24] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:18:24] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-03-03 22:18:24] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:18:24] [TRACE] [OmnipathR] Contains 1 files.
[2024-03-03 22:18:24] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-03-03 22:18:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 22:18:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:18:24] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-03 22:18:24] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-03 22:18:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:24] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-03 22:18:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:24] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-03 22:18:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:24] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-03 22:18:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:24] [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
[2024-03-03 22:18:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 22:18:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:39] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:18:39] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-03-03 22:18:39] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:18:39] [TRACE] [OmnipathR] Contains 1 files.
[2024-03-03 22:18:39] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-03-03 22:18:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 22:18:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:18:39] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-03 22:18:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-03 22:18:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-03 22:18:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-03 22:18:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-03 22:18:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:39] [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
collectri 94.563 1.413 99.506
annotation_categories 63.386 0.644 66.063
dorothea 49.632 1.105 64.423
curated_ligrec_stats 28.746 8.388 122.133
filter_extra_attrs 25.033 0.904 38.342
nichenet_gr_network_omnipath 12.740 0.643 15.735
pivot_annotations 10.896 1.129 20.382
extra_attrs_to_cols 11.273 0.131 24.581
nichenet_signaling_network_omnipath 10.257 0.678 13.690
giant_component 10.243 0.390 13.423
go_annot_download 8.823 1.037 9.338
extra_attr_values 8.587 0.397 17.672
with_extra_attrs 8.500 0.261 11.139
filter_intercell 6.019 0.594 14.431
has_extra_attrs 6.345 0.159 6.562
extra_attrs 6.229 0.175 7.288
filter_by_resource 5.849 0.430 15.277
find_all_paths 5.975 0.182 8.584
print_interactions 5.834 0.279 10.317
static_table 5.665 0.433 11.889
get_signed_ptms 5.151 0.082 5.836
curated_ligand_receptor_interactions 4.384 0.356 14.292
pubmed_open 4.535 0.197 6.983
enzsub_graph 2.491 0.131 6.279
annotated_network 1.657 0.199 10.939
ensembl_id_mapping_table 1.140 0.126 17.216
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
‘/Users/biocbuild/bbs-3.18-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/4.3-x86_64/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 [2024-03-03 15:27:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-03 15:27:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:35] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-03 15:27:35] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:35] [TRACE] [OmnipathR] Contains 1 files. [2024-03-03 15:27:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-03 15:27:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-03 15:27:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:35] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-03-03 15:27:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-03 15:27:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-03 15:27:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-03 15:27:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-03 15:27:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:35] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-03-03 15:27:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-03 15:27:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:38] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:38] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-03 15:27:38] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:38] [TRACE] [OmnipathR] Contains 1 files. [2024-03-03 15:27:38] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-03 15:27:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-03 15:27:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2024-03-03 15:27:38] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-03-03 15:27:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-03 15:27:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-03 15:27:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-03 15:27:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-03 15:27:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-03 15:27:38] [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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
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
> # 2018-2023
> # 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)
[2024-03-03 22:31:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 22:31:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:31:48] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:31:48] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-03-03 22:31:48] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:31:48] [TRACE] [OmnipathR] Contains 17 files.
[2024-03-03 22:31:48] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-03-03 22:31:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 22:31:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:31:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:31:48] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-03 22:31:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-03 22:31:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:31:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-03 22:31:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:31:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-03 22:31:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:31:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-03 22:31:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:31:48] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
11.474 1.287 39.518
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.000 | 0.001 | |
| all_uniprot_acs | 0.027 | 0.003 | 0.032 | |
| all_uniprots | 0.014 | 0.002 | 0.016 | |
| ancestors | 0.020 | 0.002 | 0.022 | |
| annotated_network | 1.657 | 0.199 | 10.939 | |
| annotation_categories | 63.386 | 0.644 | 66.063 | |
| biomart_query | 0.817 | 0.092 | 3.973 | |
| bioplex1 | 0.013 | 0.002 | 0.015 | |
| bioplex2 | 0.011 | 0.002 | 0.013 | |
| bioplex3 | 0.010 | 0.002 | 0.012 | |
| bioplex_all | 0.009 | 0.001 | 0.010 | |
| bioplex_hct116_1 | 0.011 | 0.002 | 0.013 | |
| bma_motif_es | 0.397 | 0.058 | 1.208 | |
| bma_motif_vs | 0.149 | 0.009 | 0.769 | |
| collectri | 94.563 | 1.413 | 99.506 | |
| common_name | 0.022 | 0.001 | 0.023 | |
| consensuspathdb_download | 0.000 | 0.001 | 0.000 | |
| consensuspathdb_raw_table | 0.015 | 0.002 | 0.018 | |
| curated_ligand_receptor_interactions | 4.384 | 0.356 | 14.292 | |
| curated_ligrec_stats | 28.746 | 8.388 | 122.133 | |
| database_summary | 1.335 | 0.061 | 4.043 | |
| descendants | 0.015 | 0.002 | 0.017 | |
| dorothea | 49.632 | 1.105 | 64.423 | |
| ensembl_dataset | 0.010 | 0.001 | 0.011 | |
| ensembl_id_mapping_table | 1.140 | 0.126 | 17.216 | |
| ensembl_id_type | 0.002 | 0.001 | 0.003 | |
| ensembl_name | 0.059 | 0.001 | 0.102 | |
| ensembl_organisms | 0.150 | 0.006 | 0.272 | |
| ensembl_organisms_raw | 0.155 | 0.006 | 0.292 | |
| ensembl_orthology | 0.001 | 0.001 | 0.001 | |
| enzsub_graph | 2.491 | 0.131 | 6.279 | |
| evex_download | 0.026 | 0.004 | 0.047 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 8.587 | 0.397 | 17.672 | |
| extra_attrs | 6.229 | 0.175 | 7.288 | |
| extra_attrs_to_cols | 11.273 | 0.131 | 24.581 | |
| filter_by_resource | 5.849 | 0.430 | 15.277 | |
| filter_extra_attrs | 25.033 | 0.904 | 38.342 | |
| filter_intercell | 6.019 | 0.594 | 14.431 | |
| filter_intercell_network | 0.030 | 0.004 | 0.035 | |
| find_all_paths | 5.975 | 0.182 | 8.584 | |
| from_evidences | 0.000 | 0.001 | 0.001 | |
| get_annotation_resources | 0.070 | 0.006 | 0.836 | |
| get_complex_genes | 1.570 | 0.087 | 4.436 | |
| get_complex_resources | 0.072 | 0.007 | 0.702 | |
| get_db | 0.000 | 0.001 | 0.000 | |
| get_enzsub_resources | 0.063 | 0.006 | 0.604 | |
| get_interaction_resources | 0.068 | 0.008 | 0.605 | |
| get_intercell_categories | 0.362 | 0.049 | 0.646 | |
| get_intercell_generic_categories | 0.041 | 0.005 | 0.046 | |
| get_intercell_resources | 0.062 | 0.006 | 0.600 | |
| get_ontology_db | 0.014 | 0.001 | 0.016 | |
| get_resources | 0.064 | 0.005 | 0.601 | |
| get_signed_ptms | 5.151 | 0.082 | 5.836 | |
| giant_component | 10.243 | 0.390 | 13.423 | |
| go_annot_download | 8.823 | 1.037 | 9.338 | |
| go_annot_slim | 0.000 | 0.001 | 0.000 | |
| go_ontology_download | 0.013 | 0.002 | 0.015 | |
| guide2pharma_download | 0.013 | 0.002 | 0.015 | |
| harmonizome_download | 0.010 | 0.001 | 0.012 | |
| has_extra_attrs | 6.345 | 0.159 | 6.562 | |
| homologene_download | 0.012 | 0.003 | 0.014 | |
| homologene_raw | 0.022 | 0.003 | 0.026 | |
| homologene_uniprot_orthology | 0.012 | 0.002 | 0.014 | |
| hpo_download | 2.174 | 0.284 | 3.653 | |
| htridb_download | 0.014 | 0.002 | 0.015 | |
| import_all_interactions | 1.710 | 0.114 | 4.601 | |
| import_intercell_network | 0.012 | 0.001 | 0.014 | |
| import_kinaseextra_interactions | 1.346 | 0.091 | 3.599 | |
| import_ligrecextra_interactions | 0.588 | 0.058 | 2.155 | |
| import_lncrna_mrna_interactions | 0.479 | 0.055 | 1.291 | |
| import_mirnatarget_interactions | 0.838 | 0.064 | 2.473 | |
| import_omnipath_annotations | 0.420 | 0.035 | 1.287 | |
| import_omnipath_complexes | 0.510 | 0.044 | 2.387 | |
| import_omnipath_enzsub | 1.056 | 0.036 | 1.649 | |
| import_omnipath_interactions | 0.283 | 0.010 | 0.828 | |
| import_omnipath_intercell | 0.383 | 0.048 | 0.951 | |
| import_pathwayextra_interactions | 0.720 | 0.067 | 2.592 | |
| import_post_translational_interactions | 0.760 | 0.076 | 2.505 | |
| import_small_molecule_protein_interactions | 0.374 | 0.033 | 0.639 | |
| import_tf_mirna_interactions | 0.631 | 0.056 | 1.753 | |
| import_tf_target_interactions | 1.240 | 0.080 | 2.962 | |
| import_transcriptional_interactions | 2.324 | 0.115 | 4.759 | |
| inbiomap_download | 0.000 | 0.000 | 0.001 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.495 | 0.039 | 1.006 | |
| interaction_graph | 0.416 | 0.012 | 0.961 | |
| interaction_types | 0.046 | 0.004 | 0.060 | |
| intercell_categories | 0.067 | 0.005 | 0.076 | |
| intercell_consensus_filter | 1.403 | 0.136 | 2.995 | |
| is_ontology_id | 0.000 | 0.000 | 0.001 | |
| is_swissprot | 0.040 | 0.005 | 0.052 | |
| is_trembl | 0.040 | 0.005 | 0.049 | |
| is_uniprot | 0.017 | 0.002 | 0.021 | |
| kegg_info | 0.015 | 0.002 | 0.017 | |
| kegg_open | 0.015 | 0.002 | 0.017 | |
| kegg_pathway_annotations | 0.001 | 0.001 | 0.001 | |
| kegg_pathway_download | 0.016 | 0.002 | 0.018 | |
| kegg_pathway_list | 0.015 | 0.002 | 0.017 | |
| kegg_pathways_download | 0.000 | 0.001 | 0.001 | |
| kegg_picture | 0.086 | 0.016 | 4.021 | |
| kegg_process | 0.027 | 0.005 | 0.039 | |
| latin_name | 0.045 | 0.001 | 0.058 | |
| load_db | 0.078 | 0.005 | 0.084 | |
| ncbi_taxid | 0.043 | 0.002 | 0.047 | |
| nichenet_build_model | 0.000 | 0.001 | 0.001 | |
| nichenet_expression_data | 0.014 | 0.003 | 0.017 | |
| nichenet_gr_network | 0.041 | 0.007 | 0.050 | |
| nichenet_gr_network_evex | 0.015 | 0.002 | 0.018 | |
| nichenet_gr_network_harmonizome | 0.015 | 0.003 | 0.018 | |
| nichenet_gr_network_htridb | 0.015 | 0.002 | 0.019 | |
| nichenet_gr_network_omnipath | 12.740 | 0.643 | 15.735 | |
| nichenet_gr_network_pathwaycommons | 0.014 | 0.002 | 0.016 | |
| nichenet_gr_network_regnetwork | 0.016 | 0.003 | 0.022 | |
| nichenet_gr_network_remap | 0.013 | 0.002 | 0.018 | |
| nichenet_gr_network_trrust | 0.014 | 0.002 | 0.016 | |
| nichenet_ligand_activities | 0.000 | 0.001 | 0.002 | |
| nichenet_ligand_target_links | 0.000 | 0.002 | 0.002 | |
| nichenet_ligand_target_matrix | 0.000 | 0.001 | 0.001 | |
| nichenet_lr_network | 0.042 | 0.006 | 0.049 | |
| nichenet_lr_network_guide2pharma | 0.015 | 0.002 | 0.019 | |
| nichenet_lr_network_omnipath | 0.032 | 0.005 | 0.038 | |
| nichenet_lr_network_ramilowski | 0.015 | 0.002 | 0.021 | |
| nichenet_main | 0.000 | 0.001 | 0.001 | |
| nichenet_networks | 0.067 | 0.011 | 0.083 | |
| nichenet_optimization | 0.000 | 0.001 | 0.001 | |
| nichenet_remove_orphan_ligands | 0.038 | 0.005 | 0.047 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.042 | 0.006 | 0.052 | |
| nichenet_signaling_network_cpdb | 0.013 | 0.002 | 0.015 | |
| nichenet_signaling_network_evex | 0.013 | 0.001 | 0.015 | |
| nichenet_signaling_network_harmonizome | 0.013 | 0.002 | 0.017 | |
| nichenet_signaling_network_inbiomap | 0.001 | 0.000 | 0.001 | |
| nichenet_signaling_network_omnipath | 10.257 | 0.678 | 13.690 | |
| nichenet_signaling_network_pathwaycommons | 0.013 | 0.002 | 0.015 | |
| nichenet_signaling_network_vinayagam | 0.014 | 0.003 | 0.016 | |
| nichenet_test | 0.000 | 0.001 | 0.000 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.106 | 0.010 | 2.825 | |
| oma_code | 0.025 | 0.001 | 0.025 | |
| oma_organisms | 0.058 | 0.003 | 0.062 | |
| oma_pairwise | 0.055 | 0.006 | 0.061 | |
| omnipath | 3.761 | 0.036 | 3.830 | |
| omnipath_cache_autoclean | 0.000 | 0.001 | 0.001 | |
| omnipath_cache_clean | 0.004 | 0.001 | 0.005 | |
| omnipath_cache_clean_db | 0.099 | 0.010 | 0.113 | |
| omnipath_cache_download_ready | 0.529 | 0.064 | 0.683 | |
| omnipath_cache_filter_versions | 0.190 | 0.030 | 0.248 | |
| omnipath_cache_get | 0.121 | 0.024 | 0.153 | |
| omnipath_cache_key | 0.001 | 0.001 | 0.002 | |
| omnipath_cache_latest_or_new | 0.091 | 0.019 | 0.121 | |
| omnipath_cache_load | 0.667 | 0.058 | 3.514 | |
| omnipath_cache_move_in | 0.257 | 0.046 | 0.325 | |
| omnipath_cache_remove | 0.135 | 0.025 | 0.179 | |
| omnipath_cache_save | 0.190 | 0.034 | 0.276 | |
| omnipath_cache_search | 0.001 | 0.001 | 0.001 | |
| omnipath_cache_set_ext | 0.102 | 0.021 | 0.140 | |
| omnipath_cache_update_status | 0.283 | 0.027 | 0.323 | |
| omnipath_cache_wipe | 0.000 | 0.001 | 0.000 | |
| omnipath_get_config_path | 0.001 | 0.000 | 0.001 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0.000 | 0.000 | 0.001 | |
| omnipath_logfile | 0.001 | 0.000 | 0.001 | |
| omnipath_msg | 0.006 | 0.001 | 0.008 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.036 | 0.006 | 0.046 | |
| omnipath_set_console_loglevel | 0.001 | 0.000 | 0.002 | |
| omnipath_set_logfile_loglevel | 0.001 | 0.000 | 0.001 | |
| omnipath_set_loglevel | 0.001 | 0.000 | 0.001 | |
| omnipath_show_db | 0.062 | 0.001 | 0.064 | |
| omnipath_unlock_cache_db | 0.000 | 0.000 | 0.001 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.001 | |
| ontology_name_id | 0.001 | 0.000 | 0.001 | |
| pathwaycommons_download | 0.000 | 0.000 | 0.001 | |
| pivot_annotations | 10.896 | 1.129 | 20.382 | |
| preppi_download | 0.001 | 0.002 | 0.002 | |
| preppi_filter | 0.001 | 0.001 | 0.002 | |
| print_bma_motif_es | 0.165 | 0.035 | 0.960 | |
| print_bma_motif_vs | 0.143 | 0.011 | 0.688 | |
| print_interactions | 5.834 | 0.279 | 10.317 | |
| print_path_es | 0.415 | 0.042 | 2.321 | |
| print_path_vs | 1.954 | 0.069 | 4.601 | |
| pubmed_open | 4.535 | 0.197 | 6.983 | |
| query_info | 0.084 | 0.011 | 0.480 | |
| ramilowski_download | 0.001 | 0.000 | 0.001 | |
| regnetwork_directions | 0.001 | 0.000 | 0.001 | |
| regnetwork_download | 0.000 | 0.001 | 0.000 | |
| relations_list_to_table | 0.091 | 0.007 | 0.102 | |
| relations_table_to_graph | 0.000 | 0.000 | 0.001 | |
| relations_table_to_list | 0.073 | 0.003 | 0.081 | |
| remap_dorothea_download | 0 | 0 | 0 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0.000 | 0.001 | 0.001 | |
| resource_info | 0.143 | 0.054 | 0.731 | |
| resources_colname | 0.556 | 0.049 | 2.543 | |
| show_network | 0 | 0 | 0 | |
| simplify_intercell_network | 0.000 | 0.000 | 0.001 | |
| static_table | 5.665 | 0.433 | 11.889 | |
| static_tables | 0.052 | 0.002 | 0.061 | |
| swap_relations | 0.080 | 0.004 | 0.089 | |
| swissprots_only | 0.028 | 0.000 | 0.029 | |
| tfcensus_download | 0.202 | 0.023 | 0.406 | |
| translate_ids | 0.001 | 0.000 | 0.001 | |
| trembls_only | 0.023 | 0.000 | 0.024 | |
| trrust_download | 0.000 | 0.001 | 0.001 | |
| uniprot_full_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| uniprot_genesymbol_cleanup | 0.000 | 0.001 | 0.000 | |
| uniprot_id_mapping_table | 0.000 | 0.000 | 0.001 | |
| uniprot_id_type | 0.002 | 0.000 | 0.002 | |
| uniprot_idmapping_id_types | 0.145 | 0.014 | 1.125 | |
| unique_intercell_network | 0.001 | 0.000 | 0.000 | |
| unnest_evidences | 0.000 | 0.000 | 0.001 | |
| uploadlists_id_type | 0.003 | 0.000 | 0.003 | |
| vinayagam_download | 0 | 0 | 0 | |
| walk_ontology_tree | 0.001 | 0.000 | 0.001 | |
| with_extra_attrs | 8.500 | 0.261 | 11.139 | |
| with_references | 0.400 | 0.042 | 1.739 | |
| zenodo_download | 0.001 | 0.001 | 0.002 | |