Denes Turei
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_17 |
| git_last_commit: b12b9bf |
| git_last_commit_date: 2023-09-15 08:58:47 -0400 (Fri, 15 Sep 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:08 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1425/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.8.2 (landing page) Denes Turei
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the OmnipathR package: - 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: 3.8.2 |
| 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_3.8.2.tar.gz |
| StartedAt: 2023-10-18 12:26:49 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 12:44:38 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 1069.7 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_3.8.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/OmnipathR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.8.2’
* 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
[2023-10-18 12:27:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-18 12:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:27:20] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-18 12:27:20] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-10-18 12:27:20] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-18 12:27:20] [TRACE] [OmnipathR] Contains 1 files.
[2023-10-18 12:27:20] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-10-18 12:27:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-18 12:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:27:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-18 12:27:20] [TRACE] [OmnipathR] Pandoc version: `3.1.2`.
[2023-10-18 12:27:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-18 12:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:27:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-18 12:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:27:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-18 12:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:27:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-18 12:27:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:27:20] [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
[2023-10-18 12:27:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-18 12:27:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:27:38] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-18 12:27:38] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-10-18 12:27:38] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-18 12:27:38] [TRACE] [OmnipathR] Contains 1 files.
[2023-10-18 12:27:38] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-10-18 12:27:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-18 12:27:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:27:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-18 12:27:38] [TRACE] [OmnipathR] Pandoc version: `3.1.2`.
[2023-10-18 12:27:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-18 12:27:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:27:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-18 12:27:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:27:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-18 12:27:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:27:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-18 12:27:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:27:39] [TRACE] [OmnipathR] Cache locked: FALSE
uniprot_idmapping_id_types: no visible binding for global variable
‘groups’
uniprot_idmapping_id_types: no visible binding for global variable
‘items’
Undefined global functions or variables:
groups items
* 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 126.996 1.633 191.990
dorothea 65.328 0.829 99.681
annotation_categories 55.907 0.429 83.119
curated_ligrec_stats 25.131 2.155 106.646
filter_extra_attrs 18.667 0.173 29.602
nichenet_gr_network_omnipath 13.936 0.354 22.202
giant_component 11.579 0.300 19.537
extra_attr_values 11.073 0.256 18.451
pivot_annotations 10.242 0.782 20.367
extra_attrs_to_cols 10.024 0.084 15.435
go_annot_download 9.031 0.658 23.270
nichenet_signaling_network_omnipath 9.360 0.307 15.626
with_extra_attrs 8.840 0.196 14.814
has_extra_attrs 6.447 0.088 9.458
filter_by_resource 6.026 0.210 10.810
filter_intercell 5.773 0.418 13.784
extra_attrs 5.821 0.055 8.986
print_interactions 5.453 0.272 10.752
find_all_paths 5.489 0.111 8.575
get_signed_ptms 5.044 0.062 8.507
pubmed_open 4.653 0.195 8.365
curated_ligand_receptor_interactions 4.129 0.494 14.280
omnipath 3.838 0.032 5.846
database_summary 1.870 1.087 5.969
import_transcriptional_interactions 2.349 0.125 5.172
print_path_vs 2.086 0.108 5.449
biomart_query 1.391 0.158 6.208
ensembl_id_mapping_table 0.877 0.069 24.333
kegg_picture 0.185 0.089 8.123
* 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-3.17-bioc-mac-arm64/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-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 [2023-10-15 17:52:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 17:52:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 17:52:26] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 17:52:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-10-15 17:52:26] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 17:52:26] [TRACE] [OmnipathR] Contains 1 files. [2023-10-15 17:52:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-10-15 17:52:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 17:52:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 17:52:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 17:52:27] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2023-10-15 17:52:27] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-10-15 17:52:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 17:52:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-10-15 17:52:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 17:52:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-10-15 17:52:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 17:52:28] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-10-15 17:52:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 17:52:28] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2023-10-15 17:52:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 17:52:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 17:52:31] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 17:52:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-10-15 17:52:31] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 17:52:31] [TRACE] [OmnipathR] Contains 1 files. [2023-10-15 17:52:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-10-15 17:52:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2023-10-15 17:52:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 17:52:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2023-10-15 17:52:31] [TRACE] [OmnipathR] Pandoc version: `3.1.2`. [2023-10-15 17:52:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-10-15 17:52:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 17:52:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-10-15 17:52:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 17:52:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-10-15 17:52:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 17:52:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-10-15 17:52:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-10-15 17:52:31] [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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-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)
[2023-10-18 12:43:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-18 12:43:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:43:25] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-18 12:43:25] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-10-18 12:43:25] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-18 12:43:25] [TRACE] [OmnipathR] Contains 16 files.
[2023-10-18 12:43:25] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-10-18 12:43:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2023-10-18 12:43:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:43:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2023-10-18 12:43:25] [TRACE] [OmnipathR] Pandoc version: `3.1.2`.
[2023-10-18 12:43:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-10-18 12:43:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:43:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-10-18 12:43:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:43:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-10-18 12:43:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:43:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-10-18 12:43:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-10-18 12:43:25] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
10.354 1.232 39.826
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.025 | 0.003 | 0.041 | |
| all_uniprots | 0.012 | 0.001 | 0.022 | |
| ancestors | 0.020 | 0.002 | 0.033 | |
| annotated_network | 0.969 | 0.174 | 4.166 | |
| annotation_categories | 55.907 | 0.429 | 83.119 | |
| biomart_query | 1.391 | 0.158 | 6.208 | |
| bioplex1 | 0.013 | 0.002 | 0.019 | |
| bioplex2 | 0.014 | 0.002 | 0.018 | |
| bioplex3 | 0.014 | 0.002 | 0.020 | |
| bioplex_all | 0.015 | 0.002 | 0.020 | |
| bioplex_hct116_1 | 0.014 | 0.002 | 0.020 | |
| bma_motif_es | 0.344 | 0.068 | 1.520 | |
| bma_motif_vs | 0.143 | 0.010 | 0.719 | |
| collectri | 126.996 | 1.633 | 191.990 | |
| common_name | 0.033 | 0.001 | 0.042 | |
| consensuspathdb_download | 0.000 | 0.000 | 0.001 | |
| consensuspathdb_raw_table | 0.012 | 0.002 | 0.020 | |
| curated_ligand_receptor_interactions | 4.129 | 0.494 | 14.280 | |
| curated_ligrec_stats | 25.131 | 2.155 | 106.646 | |
| database_summary | 1.870 | 1.087 | 5.969 | |
| descendants | 0.013 | 0.002 | 0.018 | |
| dorothea | 65.328 | 0.829 | 99.681 | |
| ensembl_dataset | 0.013 | 0.001 | 0.021 | |
| ensembl_id_mapping_table | 0.877 | 0.069 | 24.333 | |
| ensembl_id_type | 0.006 | 0.000 | 0.009 | |
| ensembl_name | 0.119 | 0.004 | 0.186 | |
| ensembl_organisms | 0.200 | 0.005 | 0.319 | |
| ensembl_organisms_raw | 0.171 | 0.005 | 0.267 | |
| ensembl_orthology | 0.000 | 0.001 | 0.001 | |
| enzsub_graph | 1.849 | 0.114 | 4.135 | |
| evex_download | 0.014 | 0.002 | 0.026 | |
| evidences | 0.000 | 0.000 | 0.001 | |
| extra_attr_values | 11.073 | 0.256 | 18.451 | |
| extra_attrs | 5.821 | 0.055 | 8.986 | |
| extra_attrs_to_cols | 10.024 | 0.084 | 15.435 | |
| filter_by_resource | 6.026 | 0.210 | 10.810 | |
| filter_extra_attrs | 18.667 | 0.173 | 29.602 | |
| filter_intercell | 5.773 | 0.418 | 13.784 | |
| filter_intercell_network | 0.028 | 0.004 | 0.050 | |
| find_all_paths | 5.489 | 0.111 | 8.575 | |
| from_evidences | 0 | 0 | 0 | |
| get_annotation_resources | 0.098 | 0.006 | 0.715 | |
| get_complex_genes | 1.197 | 0.109 | 2.973 | |
| get_complex_resources | 0.062 | 0.005 | 0.714 | |
| get_db | 0.000 | 0.000 | 0.001 | |
| get_enzsub_resources | 0.060 | 0.005 | 0.739 | |
| get_interaction_resources | 0.063 | 0.007 | 0.788 | |
| get_intercell_categories | 0.336 | 0.083 | 0.849 | |
| get_intercell_generic_categories | 0.027 | 0.004 | 0.044 | |
| get_intercell_resources | 0.063 | 0.005 | 0.854 | |
| get_ontology_db | 0.014 | 0.002 | 0.024 | |
| get_resources | 0.062 | 0.008 | 0.858 | |
| get_signed_ptms | 5.044 | 0.062 | 8.507 | |
| giant_component | 11.579 | 0.300 | 19.537 | |
| go_annot_download | 9.031 | 0.658 | 23.270 | |
| go_annot_slim | 0.000 | 0.000 | 0.001 | |
| go_ontology_download | 0.015 | 0.002 | 0.024 | |
| guide2pharma_download | 0.015 | 0.002 | 0.026 | |
| harmonizome_download | 0.013 | 0.002 | 0.022 | |
| has_extra_attrs | 6.447 | 0.088 | 9.458 | |
| homologene_download | 0.013 | 0.002 | 0.024 | |
| homologene_raw | 0.025 | 0.002 | 0.043 | |
| homologene_uniprot_orthology | 0.013 | 0.002 | 0.023 | |
| homology_translate | 0 | 0 | 0 | |
| hpo_download | 2.231 | 0.186 | 4.301 | |
| htridb_download | 0.013 | 0.002 | 0.024 | |
| import_all_interactions | 0.433 | 0.078 | 2.005 | |
| import_intercell_network | 0.015 | 0.003 | 0.023 | |
| import_kinaseextra_interactions | 1.296 | 0.104 | 3.402 | |
| import_ligrecextra_interactions | 0.600 | 0.088 | 1.949 | |
| import_lncrna_mrna_interactions | 0.420 | 0.074 | 1.510 | |
| import_mirnatarget_interactions | 0.889 | 0.091 | 2.439 | |
| import_omnipath_annotations | 0.424 | 0.071 | 1.605 | |
| import_omnipath_complexes | 0.523 | 0.081 | 2.136 | |
| import_omnipath_enzsub | 1.035 | 0.015 | 1.898 | |
| import_omnipath_interactions | 0.256 | 0.009 | 1.096 | |
| import_omnipath_intercell | 0.449 | 0.083 | 1.128 | |
| import_pathwayextra_interactions | 0.802 | 0.096 | 2.602 | |
| import_post_translational_interactions | 0.794 | 0.090 | 2.656 | |
| import_small_molecule_protein_interactions | 0.401 | 0.069 | 0.885 | |
| import_tf_mirna_interactions | 0.617 | 0.082 | 2.262 | |
| import_tf_target_interactions | 1.229 | 0.101 | 3.212 | |
| import_transcriptional_interactions | 2.349 | 0.125 | 5.172 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.396 | 0.030 | 0.979 | |
| interaction_graph | 0.403 | 0.012 | 1.353 | |
| interaction_types | 0.024 | 0.002 | 0.043 | |
| intercell_categories | 0.044 | 0.003 | 0.070 | |
| intercell_consensus_filter | 1.267 | 0.141 | 2.777 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.039 | 0.004 | 0.069 | |
| is_trembl | 0.040 | 0.004 | 0.071 | |
| is_uniprot | 0.015 | 0.002 | 0.026 | |
| kegg_info | 0.012 | 0.002 | 0.022 | |
| kegg_open | 0.013 | 0.002 | 0.024 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.015 | 0.002 | 0.029 | |
| kegg_pathway_list | 0.015 | 0.002 | 0.026 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.185 | 0.089 | 8.123 | |
| kegg_process | 0.027 | 0.004 | 0.047 | |
| latin_name | 0.070 | 0.002 | 0.111 | |
| load_db | 0.100 | 0.005 | 0.159 | |
| ncbi_taxid | 0.073 | 0.002 | 0.115 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.014 | 0.002 | 0.025 | |
| nichenet_gr_network | 0.040 | 0.006 | 0.072 | |
| nichenet_gr_network_evex | 0.015 | 0.003 | 0.025 | |
| nichenet_gr_network_harmonizome | 0.067 | 0.003 | 0.109 | |
| nichenet_gr_network_htridb | 0.014 | 0.002 | 0.025 | |
| nichenet_gr_network_omnipath | 13.936 | 0.354 | 22.202 | |
| nichenet_gr_network_pathwaycommons | 0.013 | 0.002 | 0.025 | |
| nichenet_gr_network_regnetwork | 0.012 | 0.002 | 0.023 | |
| nichenet_gr_network_remap | 0.013 | 0.002 | 0.023 | |
| nichenet_gr_network_trrust | 0.013 | 0.002 | 0.023 | |
| nichenet_ligand_activities | 0.000 | 0.001 | 0.001 | |
| nichenet_ligand_target_links | 0.001 | 0.001 | 0.000 | |
| nichenet_ligand_target_matrix | 0.000 | 0.001 | 0.000 | |
| nichenet_lr_network | 0.073 | 0.006 | 0.121 | |
| nichenet_lr_network_guide2pharma | 0.013 | 0.002 | 0.026 | |
| nichenet_lr_network_omnipath | 0.039 | 0.005 | 0.070 | |
| nichenet_lr_network_ramilowski | 0.013 | 0.002 | 0.023 | |
| nichenet_main | 0.001 | 0.000 | 0.001 | |
| nichenet_networks | 0.059 | 0.009 | 0.104 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.037 | 0.005 | 0.063 | |
| nichenet_results_dir | 0.000 | 0.000 | 0.001 | |
| nichenet_signaling_network | 0.043 | 0.006 | 0.079 | |
| nichenet_signaling_network_cpdb | 0.014 | 0.002 | 0.023 | |
| nichenet_signaling_network_evex | 0.014 | 0.002 | 0.025 | |
| nichenet_signaling_network_harmonizome | 0.013 | 0.002 | 0.021 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 9.360 | 0.307 | 15.626 | |
| nichenet_signaling_network_pathwaycommons | 0.016 | 0.002 | 0.026 | |
| nichenet_signaling_network_vinayagam | 0.018 | 0.002 | 0.027 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.114 | 0.008 | 0.289 | |
| omnipath | 3.838 | 0.032 | 5.846 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.013 | 0.001 | 0.020 | |
| omnipath_cache_clean_db | 0.085 | 0.007 | 0.151 | |
| omnipath_cache_download_ready | 0.574 | 0.051 | 0.932 | |
| omnipath_cache_filter_versions | 0.121 | 0.020 | 0.207 | |
| omnipath_cache_get | 0.178 | 0.021 | 0.311 | |
| omnipath_cache_key | 0.001 | 0.000 | 0.002 | |
| omnipath_cache_latest_or_new | 0.086 | 0.014 | 0.151 | |
| omnipath_cache_load | 0.595 | 0.040 | 2.886 | |
| omnipath_cache_move_in | 0.272 | 0.036 | 0.446 | |
| omnipath_cache_remove | 0.128 | 0.023 | 0.226 | |
| omnipath_cache_save | 0.251 | 0.030 | 0.555 | |
| omnipath_cache_search | 0.001 | 0.001 | 0.003 | |
| omnipath_cache_set_ext | 0.104 | 0.015 | 0.185 | |
| omnipath_cache_update_status | 0.121 | 0.018 | 0.215 | |
| omnipath_cache_wipe | 0.000 | 0.000 | 0.001 | |
| omnipath_get_config_path | 0.001 | 0.001 | 0.000 | |
| omnipath_load_config | 0.000 | 0.000 | 0.001 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.000 | 0.001 | 0.001 | |
| omnipath_msg | 0.008 | 0.001 | 0.010 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0.000 | 0.001 | 0.000 | |
| omnipath_set_cachedir | 0.032 | 0.005 | 0.050 | |
| omnipath_set_console_loglevel | 0.001 | 0.001 | 0.002 | |
| omnipath_set_logfile_loglevel | 0.001 | 0.000 | 0.003 | |
| omnipath_set_loglevel | 0.000 | 0.000 | 0.001 | |
| omnipath_show_db | 0.123 | 0.002 | 0.191 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0.001 | 0.001 | 0.000 | |
| ontology_ensure_id | 0.000 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.000 | 0.001 | 0.000 | |
| ontology_name_id | 0.000 | 0.001 | 0.001 | |
| pathwaycommons_download | 0.000 | 0.000 | 0.001 | |
| pivot_annotations | 10.242 | 0.782 | 20.367 | |
| preppi_download | 0 | 0 | 0 | |
| preppi_filter | 0.000 | 0.000 | 0.001 | |
| print_bma_motif_es | 0.190 | 0.069 | 1.235 | |
| print_bma_motif_vs | 0.159 | 0.013 | 0.820 | |
| print_interactions | 5.453 | 0.272 | 10.752 | |
| print_path_es | 0.446 | 0.070 | 2.014 | |
| print_path_vs | 2.086 | 0.108 | 5.449 | |
| pubmed_open | 4.653 | 0.195 | 8.365 | |
| query_info | 0.066 | 0.011 | 0.588 | |
| ramilowski_download | 0.001 | 0.001 | 0.001 | |
| regnetwork_directions | 0.001 | 0.001 | 0.004 | |
| regnetwork_download | 0.001 | 0.001 | 0.001 | |
| relations_list_to_table | 0.105 | 0.005 | 0.205 | |
| relations_table_to_graph | 0.000 | 0.000 | 0.001 | |
| relations_table_to_list | 0.083 | 0.005 | 0.171 | |
| remap_dorothea_download | 0.000 | 0.001 | 0.001 | |
| remap_filtered | 0.000 | 0.001 | 0.000 | |
| remap_tf_target_download | 0.001 | 0.001 | 0.001 | |
| resource_info | 0.126 | 0.074 | 1.058 | |
| resources_colname | 0.646 | 0.090 | 2.011 | |
| simplify_intercell_network | 0.000 | 0.000 | 0.001 | |
| swap_relations | 0.093 | 0.005 | 0.164 | |
| swissprots_only | 0.037 | 0.002 | 0.056 | |
| tfcensus_download | 0.213 | 0.018 | 0.888 | |
| translate_ids | 0.001 | 0.000 | 0.001 | |
| trembls_only | 0.037 | 0.001 | 0.055 | |
| trrust_download | 0.001 | 0.000 | 0.002 | |
| uniprot_full_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0.001 | 0.001 | 0.001 | |
| uniprot_id_type | 0.006 | 0.001 | 0.008 | |
| uniprot_idmapping_id_types | 0.158 | 0.013 | 0.794 | |
| unique_intercell_network | 0.000 | 0.001 | 0.001 | |
| unnest_evidences | 0.000 | 0.001 | 0.000 | |
| uploadlists_id_type | 0.006 | 0.000 | 0.010 | |
| vinayagam_download | 0.001 | 0.000 | 0.001 | |
| walk_ontology_tree | 0.001 | 0.000 | 0.001 | |
| with_extra_attrs | 8.840 | 0.196 | 14.814 | |
| with_references | 0.403 | 0.064 | 1.906 | |
| zenodo_download | 0.001 | 0.001 | 0.001 | |