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This page was generated on 2024-05-30 12:37:10 -0400 (Thu, 30 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4669
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4404
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4431
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4384
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 1422/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.13.1  (landing page)
Denes Turei
Snapshot Date: 2024-05-29 11:04:14 -0400 (Wed, 29 May 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  
palomino4Windows 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: 3.13.1
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: 2024-05-30 04:58:47 -0400 (Thu, 30 May 2024)
EndedAt: 2024-05-30 05:27:01 -0400 (Thu, 30 May 2024)
EllapsedTime: 1694.4 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 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* 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
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 04:59:29] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 04:59:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 04:59:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 04:59:29] [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
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 04:59:56] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 04:59:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 04:59:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 04:59:56] [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
[2024-05-29 12:48:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 12:48:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 12:48:34] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 12:48:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 12:48:34] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 12:48:34] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 12:48:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 12:48:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 12:48:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 12:48:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 12:48:37] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 12:48:37] [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).
[2024-05-29 12:48:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 12:48:38] [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).
[2024-05-29 12:48:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 12:48:38] [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).
[2024-05-29 12:48:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 12:48:38] [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).
[2024-05-29 12:48:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 12:48:38] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 12:48:42] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 12:48:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-29 12:48:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 12:48:42] [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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
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)
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 05:24:49] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 05:24:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 05:24:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 05:24:49] [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 
 21.694   1.646  97.351

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0020.002
all_uniprot_acs0.0480.0040.059
all_uniprots0.0240.0020.026
ancestors0.0240.0020.027
annotated_network 3.053 0.25513.475
annotation_categories101.757 0.660115.750
biomart_query 1.340 0.12922.930
bioplex10.0250.0020.058
bioplex20.0250.0020.031
bioplex30.0240.0020.027
bioplex_all0.0250.0020.028
bioplex_hct116_10.0240.0020.027
bma_motif_es0.6380.0531.592
bma_motif_vs0.3450.0100.791
collectri306.707 2.975356.154
common_name0.0460.0020.051
consensuspathdb_download0.0010.0010.002
consensuspathdb_raw_table0.0700.0030.081
curated_ligand_receptor_interactions 8.999 0.40819.566
curated_ligrec_stats 57.385 1.926114.010
database_summary2.7400.0674.005
descendants0.0240.0030.028
dorothea160.778 1.500247.355
ensembl_dataset0.0150.0010.028
ensembl_id_mapping_table 1.405 0.09467.537
ensembl_id_type0.0040.0000.008
ensembl_name0.0920.0020.102
ensembl_organisms0.2660.0060.304
ensembl_organisms_raw0.2690.0070.304
ensembl_orthology0.0010.0010.002
enzsub_graph 4.077 0.14511.641
evex_download0.0250.0030.029
evidences0.0010.0000.001
extra_attr_values28.681 0.47034.227
extra_attrs15.837 0.10417.432
extra_attrs_to_cols26.113 0.21341.593
filter_by_resource14.119 0.30222.215
filter_extra_attrs53.799 0.41391.410
filter_intercell 8.931 0.75711.129
filter_intercell_network0.0500.0050.061
find_all_paths11.903 0.13713.740
from_evidences0.0000.0010.001
get_annotation_resources0.1280.0080.577
get_complex_genes2.1970.1253.261
get_complex_resources0.1240.0060.566
get_db0.0000.0000.001
get_enzsub_resources0.1290.0050.565
get_interaction_resources0.1320.0120.754
get_intercell_categories0.6200.0730.981
get_intercell_generic_categories0.1450.0050.175
get_intercell_resources0.1280.0050.579
get_ontology_db0.0240.0020.025
get_resources0.1340.0080.748
get_signed_ptms11.936 0.26614.323
giant_component21.312 0.58724.521
go_annot_download13.516 1.45214.591
go_annot_slim0.0000.0010.001
go_ontology_download0.0250.0020.027
guide2pharma_download0.0240.0020.027
harmonizome_download0.0230.0020.025
has_extra_attrs15.881 0.13717.803
homologene_download0.0270.0020.035
homologene_raw0.0380.0030.044
homologene_uniprot_orthology0.0250.0030.031
hpo_download3.5360.3454.139
htridb_download0.0860.0230.117
import_all_interactions4.1470.1876.184
import_intercell_network0.0260.0020.033
import_kinaseextra_interactions2.6670.1204.217
import_ligrecextra_interactions1.2710.0782.382
import_lncrna_mrna_interactions0.8850.0581.657
import_mirnatarget_interactions1.8720.0833.202
import_omnipath_annotations0.9010.0471.665
import_omnipath_complexes0.9830.0882.166
import_omnipath_enzsub2.6620.0263.619
import_omnipath_interactions0.5010.0671.400
import_omnipath_intercell0.8910.0661.421
import_pathwayextra_interactions1.4280.0852.749
import_post_translational_interactions1.5020.0842.690
import_small_molecule_protein_interactions0.8300.0451.167
import_tf_mirna_interactions1.3640.0682.327
import_tf_target_interactions2.6730.1074.057
import_transcriptional_interactions5.1160.1516.725
inbiomap_download0.0000.0010.001
inbiomap_raw0.0000.0010.001
interaction_datasets0.0730.0040.086
interaction_graph0.7230.0111.361
interaction_types0.0790.0040.089
intercell_categories0.1870.0060.208
intercell_consensus_filter2.1170.1702.966
is_ontology_id0.0000.0010.002
is_swissprot0.0670.0050.073
is_trembl0.0620.0050.067
is_uniprot0.0260.0020.029
kegg_info0.0220.0020.024
kegg_open0.0180.0020.020
kegg_pathway_annotations0.0000.0010.002
kegg_pathway_download0.0250.0030.029
kegg_pathway_list0.0240.0030.027
kegg_pathways_download0.0000.0010.001
kegg_picture0.1510.0153.423
kegg_process0.0500.0040.055
latin_name0.1580.0130.171
load_db0.1720.0060.178
ncbi_taxid0.0890.0010.096
nichenet_build_model0.0000.0010.000
nichenet_expression_data0.0270.0030.032
nichenet_gr_network0.0770.0060.088
nichenet_gr_network_evex0.0250.0020.031
nichenet_gr_network_harmonizome0.0260.0020.030
nichenet_gr_network_htridb0.0250.0020.031
nichenet_gr_network_omnipath26.917 0.75931.840
nichenet_gr_network_pathwaycommons0.0250.0030.033
nichenet_gr_network_regnetwork0.0240.0020.026
nichenet_gr_network_remap0.0250.0030.028
nichenet_gr_network_trrust0.0250.0030.029
nichenet_ligand_activities0.0000.0010.002
nichenet_ligand_target_links0.0000.0010.002
nichenet_ligand_target_matrix0.0000.0010.001
nichenet_lr_network0.0700.0060.080
nichenet_lr_network_guide2pharma0.0240.0020.029
nichenet_lr_network_omnipath0.0740.0060.089
nichenet_lr_network_ramilowski0.0250.0020.027
nichenet_main0.0000.0010.001
nichenet_networks0.1180.0100.137
nichenet_optimization000
nichenet_remove_orphan_ligands0.0740.0050.084
nichenet_results_dir0.0000.0000.001
nichenet_signaling_network0.0730.0050.079
nichenet_signaling_network_cpdb0.0260.0020.028
nichenet_signaling_network_evex0.0240.0020.027
nichenet_signaling_network_harmonizome0.0260.0020.028
nichenet_signaling_network_inbiomap0.0010.0000.000
nichenet_signaling_network_omnipath18.675 0.57522.474
nichenet_signaling_network_pathwaycommons0.0250.0020.029
nichenet_signaling_network_vinayagam0.0250.0020.027
nichenet_test0.0000.0010.001
nichenet_workarounds0.0000.0010.001
obo_parser0.1800.0090.237
oma_code0.0440.0000.045
oma_organisms0.1190.0040.129
oma_pairwise0.0260.0030.030
oma_pairwise_genesymbols0.0250.0020.028
oma_pairwise_translated0.0240.0030.029
omnipath 9.506 0.05910.749
omnipath_cache_autoclean0.0000.0010.001
omnipath_cache_clean0.0160.0010.019
omnipath_cache_clean_db0.2670.0120.302
omnipath_cache_download_ready1.2120.1071.419
omnipath_cache_filter_versions0.2420.0260.297
omnipath_cache_get0.2190.0240.248
omnipath_cache_key0.0020.0000.003
omnipath_cache_latest_or_new0.1510.0160.168
omnipath_cache_load1.0650.0502.168
omnipath_cache_move_in0.3750.0410.463
omnipath_cache_remove0.2410.0260.304
omnipath_cache_save0.4060.0350.554
omnipath_cache_search0.0010.0000.001
omnipath_cache_set_ext0.1830.0200.205
omnipath_cache_update_status0.2140.0230.239
omnipath_cache_wipe0.0010.0010.001
omnipath_get_config_path0.0000.0000.001
omnipath_load_config0.0000.0010.001
omnipath_log0.0000.0000.001
omnipath_logfile0.0030.0010.003
omnipath_msg0.0130.0010.014
omnipath_reset_config0.0000.0010.001
omnipath_save_config0.0000.0000.001
omnipath_set_cachedir0.0610.0070.070
omnipath_set_console_loglevel0.0080.0000.008
omnipath_set_logfile_loglevel0.0070.0010.008
omnipath_set_loglevel0.0040.0000.004
omnipath_show_db0.1630.0030.169
omnipath_unlock_cache_db0.0000.0010.001
only_from000
ontology_ensure_id0.0010.0010.002
ontology_ensure_name0.0010.0010.002
ontology_name_id0.0020.0000.002