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This page was generated on 2024-07-24 09:06 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4747
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4489
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4518
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4467
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: 2024-07-21 14:00 -0400 (Sun, 21 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 12.7.5 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: 2024-07-22 09:35:06 -0400 (Mon, 22 Jul 2024)
EndedAt: 2024-07-22 10:03:19 -0400 (Mon, 22 Jul 2024)
EllapsedTime: 1692.5 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
[2024-07-22 09:35:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 09:35:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 09:35:52] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 09:35:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-22 09:35:52] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 09:35:52] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-22 09:35:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-22 09:35:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 09:35:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 09:35:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 09:35:53] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-22 09:35:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-22 09:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 09:35:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-22 09:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 09:35:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-22 09:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 09:35:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-22 09:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 09:35:53] [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
[2024-07-22 09:36:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 09:36:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 09:36:23] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 09:36:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-22 09:36:23] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 09:36:23] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-22 09:36:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-22 09:36:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 09:36:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 09:36:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 09:36:23] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-22 09:36:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-22 09:36:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 09:36:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-22 09:36:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 09:36:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-22 09:36:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 09:36:24] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-22 09:36:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 09:36:24] [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
[2024-07-21 16:05:03] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-21 16:05:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:05:03] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-21 16:05:03] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-21 16:05:03] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-21 16:05:03] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-21 16:05:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-21 16:05:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-21 16:05:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:05:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-21 16:05:04] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-21 16:05:04] [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).
[2024-07-21 16:05:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:05:04] [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).
[2024-07-21 16:05:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:05:04] [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).
[2024-07-21 16:05:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:05:04] [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).
[2024-07-21 16:05:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:05:04] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:05:08] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:05:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-21 16:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:05:08] [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)
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 10:02:04] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 10:02:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-22 10:02:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 10:02:04] [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 
 21.680   1.632  45.412

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0010.002
all_uniprot_acs0.0500.0040.069
all_uniprots0.0260.0030.037
ancestors0.0250.0020.031
annotated_network3.0130.2569.886
annotation_categories 99.405 0.605124.943
biomart_query 1.335 0.13110.919
bioplex10.0260.0020.036
bioplex20.0250.0020.034
bioplex30.0250.0020.034
bioplex_all0.0270.0020.036
bioplex_hct116_10.0260.0020.035
bma_motif_es0.6240.0491.448
bma_motif_vs0.3280.0100.794
collectri308.141 2.941386.921
common_name0.0420.0010.049
consensuspathdb_download0.0010.0010.001
consensuspathdb_raw_table0.0240.0020.030
curated_ligand_receptor_interactions 9.691 0.47818.437
curated_ligrec_stats 56.203 2.287120.455
database_summary2.7030.0744.543
descendants0.0270.0020.038
dorothea164.590 1.631230.863
ensembl_dataset0.0150.0000.030
ensembl_id_mapping_table 1.440 0.11528.043
ensembl_id_type0.0040.0000.016
ensembl_name0.0910.0020.212
ensembl_organisms0.2820.0060.683
ensembl_organisms_raw0.3550.0120.905
ensembl_orthology0.0000.0010.002
enzsub_graph 4.077 0.12910.619
evex_download0.0260.0030.068
evidences000
extra_attr_values29.658 0.61362.574
extra_attrs16.629 0.35432.012
extra_attrs_to_cols24.907 0.22531.063
filter_by_resource13.571 0.30717.251
filter_extra_attrs52.425 0.31071.159
filter_intercell 9.005 0.93114.709
filter_intercell_network0.0530.0050.071
find_all_paths12.317 0.21323.611
from_evidences0.0000.0010.002
get_annotation_resources0.1350.0100.656
get_complex_genes2.2020.1314.874
get_complex_resources0.2260.0090.831
get_db0.0010.0010.001
get_enzsub_resources0.1400.0080.660
get_interaction_resources0.1310.0110.620
get_intercell_categories0.6980.0841.868
get_intercell_generic_categories0.2810.0130.632
get_intercell_resources0.1310.0060.617
get_ontology_db0.0250.0030.060
get_resources0.1380.0110.808
get_signed_ptms12.063 0.15924.327
giant_component21.603 0.53238.044
go_annot_download15.362 1.54919.159
go_annot_slim0.0010.0020.001
go_ontology_download0.0260.0030.046
guide2pharma_download0.0260.0030.058
harmonizome_download0.0270.0020.060
has_extra_attrs15.849 0.13919.246
homologene_download0.0250.0020.035
homologene_raw0.0390.0040.051
homologene_uniprot_orthology0.0240.0020.031
hpo_download3.5710.3794.806
htridb_download0.0250.0030.033
import_all_interactions4.1950.1996.961
import_intercell_network0.0260.0030.034
import_kinaseextra_interactions2.8600.1394.870
import_ligrecextra_interactions1.2540.0872.705
import_lncrna_mrna_interactions0.9010.0601.952
import_mirnatarget_interactions1.8460.0793.298
import_omnipath_annotations0.8700.0461.685
import_omnipath_complexes1.0290.0642.363
import_omnipath_enzsub2.4730.0233.412
import_omnipath_interactions0.5440.0121.094
import_omnipath_intercell0.8910.0681.532
import_pathwayextra_interactions1.4610.0942.831
import_post_translational_interactions1.4980.1003.178
import_small_molecule_protein_interactions0.8460.0491.421
import_tf_mirna_interactions1.4070.0772.820
import_tf_target_interactions2.6690.1024.385
import_transcriptional_interactions5.4930.1897.800
inbiomap_download0.0010.0010.001
inbiomap_raw0.0000.0010.004
interaction_datasets0.0730.0040.093
interaction_graph0.7180.0141.490
interaction_types0.0720.0040.090
intercell_categories0.1070.0050.135
intercell_consensus_filter2.1500.1903.284
is_ontology_id0.0000.0010.000
is_swissprot0.0620.0040.077
is_trembl0.0620.0040.073
is_uniprot0.0260.0030.033
kegg_info0.0250.0020.031
kegg_open0.0260.0030.034
kegg_pathway_annotations0.0010.0010.000
kegg_pathway_download0.0240.0030.031
kegg_pathway_list0.0240.0020.034
kegg_pathways_download0.0000.0010.001
kegg_picture0.1460.0161.452
kegg_process0.0480.0030.051
latin_name0.0790.0010.080
load_db0.2110.0120.243
ncbi_taxid0.0860.0010.096
nichenet_build_model0.0000.0010.001
nichenet_expression_data0.0240.0020.032
nichenet_gr_network0.0740.0060.095
nichenet_gr_network_evex0.0240.0020.030
nichenet_gr_network_harmonizome0.0250.0030.029
nichenet_gr_network_htridb0.0240.0020.033
nichenet_gr_network_omnipath26.040 0.84033.353
nichenet_gr_network_pathwaycommons0.0250.0020.073
nichenet_gr_network_regnetwork0.0260.0020.034
nichenet_gr_network_remap0.0240.0030.031
nichenet_gr_network_trrust0.0220.0020.024
nichenet_ligand_activities0.0000.0010.002
nichenet_ligand_target_links0.0010.0010.002
nichenet_ligand_target_matrix0.0000.0000.001
nichenet_lr_network0.0740.0060.095
nichenet_lr_network_guide2pharma0.0250.0020.033
nichenet_lr_network_omnipath0.0710.0050.088
nichenet_lr_network_ramilowski0.0250.0020.032
nichenet_main0.0010.0010.001
nichenet_networks0.1830.0120.275
nichenet_optimization0.0010.0010.001
nichenet_remove_orphan_ligands0.0770.0060.101
nichenet_results_dir0.0000.0000.002
nichenet_signaling_network0.0820.0060.112
nichenet_signaling_network_cpdb0.0230.0020.029
nichenet_signaling_network_evex0.0260.0020.032
nichenet_signaling_network_harmonizome0.0260.0020.031
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath20.271 0.63024.781
nichenet_signaling_network_pathwaycommons0.0260.0020.064
nichenet_signaling_network_vinayagam0.0240.0020.033
nichenet_test0.0000.0010.001
nichenet_workarounds0.0000.0010.001
obo_parser0.2110.0140.322
oma_code0.0420.0020.059
oma_organisms0.1130.0030.140
oma_pairwise0.0240.0030.030
oma_pairwise_genesymbols0.0240.0020.029
omnipath 9.084 0.07210.952
omnipath_cache_autoclean0.0000.0000.001
omnipath_cache_clean0.0150.0010.021
omnipath_cache_clean_db0.2060.0140.273
omnipath_cache_download_ready1.0990.0911.467
omnipath_cache_filter_versions0.2540.0290.341
omnipath_cache_get0.2080.0220.270
omnipath_cache_key0.0020.0010.003
omnipath_cache_latest_or_new0.1520.0160.208
omnipath_cache_load1.0590.0532.166
omnipath_cache_move_in0.3640.0400.527
omnipath_cache_remove0.2430.0250.347
omnipath_cache_save0.4010.0340.609
omnipath_cache_search0.0000.0010.002
omnipath_cache_set_ext0.1880.0190.244
omnipath_cache_update_status0.2200.0230.287
omnipath_cache_wipe0.0000.0000.001
omnipath_get_config_path0.0010.0020.007
omnipath_load_config000
omnipath_log000
omnipath_logfile0.0010.0000.002
omnipath_msg0.0140.0020.018
omnipath_reset_config0.0000.0010.001
omnipath_save_config0.0000.0000.001
omnipath_set_cachedir0.0640.0060.089
omnipath_set_console_loglevel0.0020.0000.003
omnipath_set_logfile_loglevel0.0030.0000.004
omnipath_set_loglevel0.0010.0000.002
omnipath_show_db0.1170.0010.144
omnipath_unlock_cache_db0.0010.0010.001
only_from0.0000.0010.001
ontology_ensure_id0.0010.0010.001
ontology_ensure_name0.0010.0000.003
ontology_name_id0.0010.0000.002