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This page was generated on 2024-07-12 17:41 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
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 1467/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.12.1  (landing page)
Denes Turei
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_19
git_last_commit: a310819
git_last_commit_date: 2024-05-29 08:39:10 -0400 (Wed, 29 May 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for OmnipathR on merida1

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: 3.12.1
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_3.12.1.tar.gz
StartedAt: 2024-07-11 08:49:32 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 09:17:06 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 1654.2 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_3.12.1.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: 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 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.12.1’
* 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
[2024-07-11 08:50:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-11 08:50:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 08:50:16] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 08:50:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-11 08:50:16] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 08:50:16] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-11 08:50:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-11 08:50:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-11 08:50:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 08:50:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 08:50:16] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-11 08:50:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-11 08:50:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 08:50:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-11 08:50:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 08:50:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-11 08:50:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 08:50:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-11 08:50:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 08:50:17] [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
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 08:50:46] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 08:50:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 08:50:46] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘oma_pairwise_translated’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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, 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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
[2024-07-10 16:07:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-10 16:07:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-10 16:07:14] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-10 16:07:14] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-10 16:07:14] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-10 16:07:14] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-10 16:07:14] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-10 16:07:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-10 16:07:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-10 16:07:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-10 16:07:16] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-10 16:07:16] [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).
[2024-07-10 16:07:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-10 16:07:16] [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).
[2024-07-10 16:07:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-10 16:07:16] [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).
[2024-07-10 16:07:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-10 16:07:16] [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).
[2024-07-10 16:07:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-10 16:07:16] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-10 16:07:20] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-10 16:07:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-10 16:07:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-10 16:07:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-10 16:07:21] [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)
[2024-07-11 09:15:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-11 09:15:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 09:15:46] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 09:15:46] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-11 09:15:46] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 09:15:46] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-11 09:15:46] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-11 09:15:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-11 09:15:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 09:15:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-11 09:15:47] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-11 09:15:47] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-11 09:15:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 09:15:47] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-11 09:15:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 09:15:47] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-11 09:15:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 09:15:47] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-11 09:15:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-11 09:15:47] [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 
 21.767   1.591  50.094

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0010.0010.002
all_uniprot_acs0.0500.0040.062
all_uniprots0.0250.0020.029
ancestors0.0250.0020.030
annotated_network 3.101 0.26813.397
annotation_categories101.418 0.666121.839
biomart_query1.3380.1293.532
bioplex10.0260.0020.030
bioplex20.0250.0020.031
bioplex30.0240.0020.037
bioplex_all0.0250.0020.031
bioplex_hct116_10.0250.0020.030
bma_motif_es0.6310.0501.712
bma_motif_vs0.3280.0100.782
collectri302.671 3.051354.939
common_name0.0430.0010.049
consensuspathdb_download0.0000.0010.001
consensuspathdb_raw_table0.0230.0020.027
curated_ligand_receptor_interactions 9.674 0.47120.312
curated_ligrec_stats 56.350 2.267130.282
database_summary2.6990.0734.165
descendants0.0270.0020.034
dorothea164.548 1.392214.403
ensembl_dataset0.0180.0010.057
ensembl_id_mapping_table 1.433 0.10624.197
ensembl_id_type0.0040.0010.018
ensembl_name0.0920.0010.216
ensembl_organisms0.2810.0050.688
ensembl_organisms_raw0.2700.0070.689
ensembl_orthology0.0010.0020.003
enzsub_graph 4.178 0.11011.227
evex_download0.0260.0020.074
evidences0.0000.0010.001
extra_attr_values30.222 0.46266.465
extra_attrs16.860 0.17935.464
extra_attrs_to_cols25.462 0.18929.393
filter_by_resource13.784 0.29416.030
filter_extra_attrs53.329 0.37268.584
filter_intercell 9.022 0.85314.123
filter_intercell_network0.0510.0050.121
find_all_paths12.387 0.18224.199
from_evidences0.0000.0010.002
get_annotation_resources0.1360.0080.585
get_complex_genes2.2490.1255.116
get_complex_resources0.2060.0060.799
get_db0.0000.0010.013
get_enzsub_resources0.1310.0060.630
get_interaction_resources0.1380.0110.627
get_intercell_categories0.6580.0781.862
get_intercell_generic_categories0.2970.0110.712
get_intercell_resources0.1330.0060.632
get_ontology_db0.0250.0020.062
get_resources0.1370.0090.758
get_signed_ptms12.119 0.12226.057
giant_component22.125 0.45233.834
go_annot_download15.607 1.55618.277
go_annot_slim0.0010.0010.001
go_ontology_download0.0250.0020.032
guide2pharma_download0.0250.0030.034
harmonizome_download0.0260.0030.031
has_extra_attrs16.171 0.13420.416
homologene_download0.0260.0030.038
homologene_raw0.0430.0030.062
homologene_uniprot_orthology0.0270.0030.037
hpo_download3.6550.3885.032
htridb_download0.0260.0030.033
import_all_interactions4.2300.1738.998
import_intercell_network0.0280.0030.037
import_kinaseextra_interactions2.9050.1165.111
import_ligrecextra_interactions1.2630.0772.843
import_lncrna_mrna_interactions0.9060.0601.757
import_mirnatarget_interactions1.8590.0803.384
import_omnipath_annotations0.9050.0501.874
import_omnipath_complexes1.0490.0612.230
import_omnipath_enzsub2.5190.0263.404
import_omnipath_interactions0.5580.0101.053
import_omnipath_intercell0.8850.0621.482
import_pathwayextra_interactions1.5220.0883.191
import_post_translational_interactions1.4950.0873.091
import_small_molecule_protein_interactions0.8390.0471.252
import_tf_mirna_interactions1.4250.0722.474
import_tf_target_interactions2.7200.0944.862
import_transcriptional_interactions5.5180.1389.376
inbiomap_download0.0000.0010.001
inbiomap_raw0.0000.0000.001
interaction_datasets0.0740.0040.092
interaction_graph0.7240.0111.234
interaction_types0.0740.0040.090
intercell_categories0.1140.0050.156
intercell_consensus_filter2.1720.1343.785
is_ontology_id0.0000.0010.001
is_swissprot0.0630.0050.078
is_trembl0.0640.0050.075
is_uniprot0.0270.0020.036
kegg_info0.0250.0030.031
kegg_open0.0250.0020.031
kegg_pathway_annotations0.0000.0010.001
kegg_pathway_download0.0250.0030.031
kegg_pathway_list0.0250.0020.032
kegg_pathways_download0.0010.0010.005
kegg_picture0.1470.0151.547
kegg_process0.0490.0040.053
latin_name0.0810.0010.083
load_db0.2170.0110.251
ncbi_taxid0.0850.0010.098
nichenet_build_model0.0010.0010.001
nichenet_expression_data0.0250.0030.035
nichenet_gr_network0.0750.0060.095
nichenet_gr_network_evex0.0250.0020.030
nichenet_gr_network_harmonizome0.0260.0030.033
nichenet_gr_network_htridb0.0240.0030.029
nichenet_gr_network_omnipath26.270 0.68030.878
nichenet_gr_network_pathwaycommons0.0270.0030.034
nichenet_gr_network_regnetwork0.0250.0020.030
nichenet_gr_network_remap0.0240.0020.028
nichenet_gr_network_trrust0.0260.0020.033
nichenet_ligand_activities0.0010.0010.001
nichenet_ligand_target_links0.0000.0020.002
nichenet_ligand_target_matrix0.0010.0010.001
nichenet_lr_network0.0750.0050.090
nichenet_lr_network_guide2pharma0.0260.0020.030
nichenet_lr_network_omnipath0.0770.0070.097
nichenet_lr_network_ramilowski0.0240.0020.031
nichenet_main0.0000.0010.001
nichenet_networks0.1870.0120.216
nichenet_optimization0.0000.0010.001
nichenet_remove_orphan_ligands0.0780.0060.093
nichenet_results_dir0.0000.0010.000
nichenet_signaling_network0.0810.0060.096
nichenet_signaling_network_cpdb0.0250.0030.033
nichenet_signaling_network_evex0.0240.0020.027
nichenet_signaling_network_harmonizome0.0270.0020.030
nichenet_signaling_network_inbiomap0.0000.0000.001
nichenet_signaling_network_omnipath20.784 0.56627.220
nichenet_signaling_network_pathwaycommons0.0240.0020.033
nichenet_signaling_network_vinayagam0.0240.0020.031
nichenet_test0.0010.0010.001
nichenet_workarounds0.0000.0010.001
obo_parser0.2260.0136.391
oma_code0.0440.0010.045
oma_organisms0.1190.0040.138
oma_pairwise0.0250.0020.029
oma_pairwise_genesymbols0.0230.0020.030
omnipath 9.203 0.07710.839
omnipath_cache_autoclean0.0000.0010.003
omnipath_cache_clean0.0160.0020.023
omnipath_cache_clean_db0.2090.0160.280
omnipath_cache_download_ready1.0880.1041.457
omnipath_cache_filter_versions0.2440.0250.363
omnipath_cache_get0.2180.0240.290
omnipath_cache_key0.0020.0010.004
omnipath_cache_latest_or_new0.1530.0160.194
omnipath_cache_load1.0470.0512.297
omnipath_cache_move_in0.3730.0420.529
omnipath_cache_remove0.2430.0270.334
omnipath_cache_save0.4000.0370.617
omnipath_cache_search0.0010.0010.001
omnipath_cache_set_ext0.1890.0210.246
omnipath_cache_update_status0.2290.0250.311
omnipath_cache_wipe0.0000.0010.001
omnipath_get_config_path0.0010.0010.004
omnipath_load_config0.0000.0010.000
omnipath_log0.0010.0000.001
omnipath_logfile0.0010.0010.002
omnipath_msg0.0140.0020.018
omnipath_reset_config0.0000.0000.001
omnipath_save_config0.0000.0010.001
omnipath_set_cachedir0.0630.0070.157
omnipath_set_console_loglevel0.0030.0010.003
omnipath_set_logfile_loglevel0.0020.0010.004
omnipath_set_loglevel0.0020.0010.002
omnipath_show_db0.1160.0030.137
omnipath_unlock_cache_db0.0000.0010.001
only_from0.0000.0000.001
ontology_ensure_id0.0010.0010.002
ontology_ensure_name0.0000.0010.003
ontology_name_id0.0020.0010.004