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This page was generated on 2024-07-18 11:41 -0400 (Thu, 18 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4683
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4379
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4450
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4399
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 1432/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.13.1  (landing page)
Denes Turei
Snapshot Date: 2024-07-17 14:00 -0400 (Wed, 17 Jul 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 1cdbb59
git_last_commit_date: 2024-05-29 08:38:09 -0400 (Wed, 29 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for OmnipathR on lconway

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.

raw results


Summary

Package: OmnipathR
Version: 3.13.1
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_3.13.1.tar.gz
StartedAt: 2024-07-17 23:03:34 -0400 (Wed, 17 Jul 2024)
EndedAt: 2024-07-17 23:18:51 -0400 (Wed, 17 Jul 2024)
EllapsedTime: 917.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### 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_3.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 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 ‘3.13.1’
* 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 ... 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
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:04:00] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:04:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-17 23:04:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:04:00] [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
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:04:16] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:04:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-17 23:04:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:04:16] [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 ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: organism_for
> ### Title: Make sure the resource supports the organism and it has the ID
> ### Aliases: organism_for
> 
> ### ** Examples
> 
> organism_for(10116, 'chalmers-gem')
[1] "Rat"
> # [1] "Rat"
> organism_for(6239, 'chalmers-gem')
Error in organism_for(6239, "chalmers-gem") : 
  Organism `6239` (common_name: `Caenorhabditis elegans (Nematode, N2)`; common_name: `Caenorhabditis elegans (Nematode, N2)`) is not supported by resource `chalmers-gem`. Supported organisms: Human, Mouse, Rat, Zebrafish, Drosophila melanogaster (Fruit fly), Caenorhabditis elegans (PRJNA13758).
Execution halted
* 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: 1 ERROR, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

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-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
[2024-07-17 15:26:19] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-17 15:26:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 15:26:19] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 15:26:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-17 15:26:19] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 15:26:19] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-17 15:26:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-17 15:26:19] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-17 15:26:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 15:26:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 15:26:20] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-17 15:26:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-17 15:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 15:26:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-17 15:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 15:26:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-17 15:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 15:26:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-17 15:26:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 15:26:20] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 15:26:22] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 15:26:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 15:26:22] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-17 15:26:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 15:26:23] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

Tests output

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: x86_64-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)
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:17:47] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:17:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-17 23:17:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-17 23:17:47] [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 
 12.400   1.306  43.262

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0010.000
all_uniprot_acs0.0260.0030.029
all_uniprots0.0140.0010.016
ancestors0.0120.0020.013
annotated_network1.7770.1847.741
annotation_categories65.277 0.32267.706
biomart_query 0.900 0.09113.583
bioplex10.0160.0010.018
bioplex20.0160.0020.018
bioplex30.0150.0020.017
bioplex_all0.0150.0020.017
bioplex_hct116_10.0160.0020.018
bma_motif_es0.3650.0431.228
bma_motif_vs0.2100.0090.751
collectri139.726 2.095152.670
common_name0.0470.0010.049
consensuspathdb_download0.0000.0010.028
consensuspathdb_raw_table0.0130.0060.059
curated_ligand_receptor_interactions 4.665 1.64522.114
curated_ligrec_stats 30.371 4.772120.399
database_summary1.3870.1025.267
descendants0.0140.0020.019
dorothea57.736 0.92486.642
ensembl_dataset0.0150.0020.019
ensembl_id_mapping_table 1.113 0.13714.078
ensembl_id_type0.0030.0000.003
ensembl_name0.0620.0010.193
ensembl_organisms0.1590.0070.472
ensembl_organisms_raw0.1500.0060.476
ensembl_orthology000
enzsub_graph2.4520.1169.665
evex_download0.0190.0030.041
evidences0.0010.0010.000
extra_attr_values10.284 0.76133.068
extra_attrs 5.594 0.43712.381
extra_attrs_to_cols 9.465 0.46012.157
filter_by_resource6.6440.2528.937
filter_extra_attrs22.485 0.36923.582
filter_intercell5.1620.4749.286
filter_intercell_network0.0250.0030.028
find_all_paths5.8730.1506.066
from_evidences000
get_annotation_resources0.0690.0080.753
get_complex_genes1.2630.0783.155
get_complex_resources0.0670.0050.576
get_db0.0000.0010.000
get_enzsub_resources0.0690.0050.576
get_interaction_resources0.0680.0070.587
get_intercell_categories0.3950.0450.809
get_intercell_generic_categories0.0440.0030.048
get_intercell_resources0.0670.0050.568
get_ontology_db0.0160.0020.018
get_resources0.0650.0070.695
get_signed_ptms5.6530.1886.381
giant_component10.969 0.42616.810
go_annot_download10.184 0.70416.557
go_annot_slim000
go_ontology_download0.0160.0020.017
guide2pharma_download0.0150.0020.017
harmonizome_download0.0150.0020.017
has_extra_attrs6.8450.0806.958
homologene_download0.0130.0020.015
homologene_raw0.0210.0020.024
homologene_uniprot_orthology0.0110.0020.012
hpo_download2.2070.2583.701
htridb_download0.0120.0020.013
import_all_interactions2.1340.1187.402
import_intercell_network0.0120.0020.014
import_kinaseextra_interactions1.5330.1534.429
import_ligrecextra_interactions0.6470.0582.259
import_lncrna_mrna_interactions0.4880.0651.305
import_mirnatarget_interactions0.9220.0562.736
import_omnipath_annotations0.4800.0361.439
import_omnipath_complexes0.6080.0432.239
import_omnipath_enzsub1.1280.0151.652
import_omnipath_interactions0.2600.0090.766
import_omnipath_intercell0.5060.0461.089
import_pathwayextra_interactions0.7780.0612.828
import_post_translational_interactions0.8660.0653.037
import_small_molecule_protein_interactions0.4740.0320.741
import_tf_mirna_interactions0.6950.0541.743
import_tf_target_interactions1.4080.0663.831
import_transcriptional_interactions2.5710.0897.224
inbiomap_download0.0000.0000.001
inbiomap_raw000
interaction_datasets0.0460.0040.049
interaction_graph0.4490.0090.937
interaction_types0.0420.0040.046
intercell_categories0.0620.0040.066
intercell_consensus_filter1.3400.0973.983
is_ontology_id000
is_swissprot0.0400.0030.044
is_trembl0.0370.0030.040
is_uniprot0.0170.0020.020
kegg_info0.0160.0010.017
kegg_open0.0150.0010.017
kegg_pathway_annotations000
kegg_pathway_download0.0170.0020.020
kegg_pathway_list0.0150.0020.016
kegg_pathways_download000
kegg_picture0.0910.0159.992
kegg_process0.0260.0030.029
latin_name0.0510.0010.052
load_db0.1530.0090.163
ncbi_taxid0.0540.0000.054
nichenet_build_model0.0010.0000.000
nichenet_expression_data0.0140.0020.015
nichenet_gr_network0.0460.0050.050
nichenet_gr_network_evex0.0130.0010.014
nichenet_gr_network_harmonizome0.0140.0020.015
nichenet_gr_network_htridb0.0130.0020.015
nichenet_gr_network_omnipath12.633 0.56815.194
nichenet_gr_network_pathwaycommons0.0140.0020.015
nichenet_gr_network_regnetwork0.0120.0020.014
nichenet_gr_network_remap0.0130.0020.014
nichenet_gr_network_trrust0.0130.0020.015
nichenet_ligand_activities0.0000.0000.001
nichenet_ligand_target_links0.0000.0000.001
nichenet_ligand_target_matrix000
nichenet_lr_network0.0420.0050.046
nichenet_lr_network_guide2pharma0.0120.0010.013
nichenet_lr_network_omnipath0.0390.0050.044
nichenet_lr_network_ramilowski0.0160.0020.019
nichenet_main0.0000.0000.001
nichenet_networks0.1190.0090.129
nichenet_optimization000
nichenet_remove_orphan_ligands0.0380.0040.042
nichenet_results_dir000
nichenet_signaling_network0.0440.0050.049
nichenet_signaling_network_cpdb0.0160.0020.018
nichenet_signaling_network_evex0.0160.0010.018
nichenet_signaling_network_harmonizome0.0180.0020.021
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath10.166 0.40215.356
nichenet_signaling_network_pathwaycommons0.0140.0020.016
nichenet_signaling_network_vinayagam0.0150.0020.016
nichenet_test0.0000.0010.001
nichenet_workarounds000
obo_parser0.1700.0080.419
oma_code0.0260.0000.027
oma_organisms0.0780.0020.082
oma_pairwise0.0150.0020.017
oma_pairwise_genesymbols0.0140.0010.016
oma_pairwise_translated0.0130.0010.014
omnipath5.0110.0285.058
omnipath_cache_autoclean000
omnipath_cache_clean0.0120.0010.012
omnipath_cache_clean_db0.1020.0070.110
omnipath_cache_download_ready0.6710.0500.805
omnipath_cache_filter_versions0.1970.0210.274
omnipath_cache_get0.1370.0190.158
omnipath_cache_key0.0020.0000.002
omnipath_cache_latest_or_new0.0910.0130.105
omnipath_cache_load0.7060.0423.135
omnipath_cache_move_in0.2450.0320.288
omnipath_cache_remove0.1370.0190.162
omnipath_cache_save0.2620.0280.347
omnipath_cache_search0.0010.0010.001
omnipath_cache_set_ext0.1240.0160.146
omnipath_cache_update_status0.1290.0180.149
omnipath_cache_wipe000
omnipath_get_config_path0.0000.0010.000
omnipath_load_config0.0000.0000.001
omnipath_log000
omnipath_logfile0.0010.0000.001
omnipath_msg0.0090.0010.010
omnipath_reset_config000
omnipath_save_config0.0000.0000.001
omnipath_set_cachedir0.0780.0040.083
omnipath_set_console_loglevel0.0040.0000.005
omnipath_set_logfile_loglevel0.0040.0000.004
omnipath_set_loglevel0.0030.0010.003
omnipath_show_db0.0780.0010.078
omnipath_unlock_cache_db000
only_from000
ontology_ensure_id0.0010.0010.001
ontology_ensure_name0.0000.0000.001
ontology_name_id0.0010.0000.002