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This page was generated on 2024-05-30 12:36:03 -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 palomino4


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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings OmnipathR_3.13.1.tar.gz
StartedAt: 2024-05-30 00:30:25 -0400 (Thu, 30 May 2024)
EndedAt: 2024-05-30 00:43:14 -0400 (Thu, 30 May 2024)
EllapsedTime: 769.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings OmnipathR_3.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 00:30:50] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:30:50] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:30:50] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 00:30:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:30:50] [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 00:31:04] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 00:31:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:31:04] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 00:31:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 00:31:04] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 00:31:04] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 00:31:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 00:31:04] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 00:31:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:31:04] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 00:31:05] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 00:31:05] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 00:31:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:31:05] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 00:31:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:31:05] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 00:31:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:31:05] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 00:31:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:31:05] [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
  'F:/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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 13:17:45] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:17:45] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:17:45] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:17:45] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-29 13:17:47] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 13:17:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:17:47] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:17:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 13:17:47] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:17:47] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 13:17:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 13:17:47] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 13:17:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:17:47] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-29 13:17:48] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 13:17:48] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-29 13:17:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:17:48] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-29 13:17:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:17:48] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-29 13:17:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:17:48] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-29 13:17:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 13:17:48] [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 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 00:42:22] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 00:42:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:42:22] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 00:42:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 00:42:22] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 00:42:22] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 00:42:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 00:42:22] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 00:42:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:42:22] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-30 00:42:23] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 00:42:23] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 00:42:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:42:23] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 00:42:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:42:23] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 00:42:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:42:23] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 00:42:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:42:23] [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 
  10.73    1.45   30.07

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.030.000.03
all_uniprots0.020.000.01
ancestors0.010.000.02
annotated_network1.990.295.87
annotation_categories74.68 0.0775.34
biomart_query0.760.035.16
bioplex10.020.000.02
bioplex20.010.000.01
bioplex30.020.000.02
bioplex_all0.010.000.01
bioplex_hct116_10.020.000.02
bma_motif_es0.340.061.04
bma_motif_vs0.170.020.58
collectri118.02 1.75120.11
common_name0.030.000.03
consensuspathdb_download000
consensuspathdb_raw_table0.030.000.03
curated_ligand_receptor_interactions 4.78 0.3710.63
curated_ligrec_stats30.16 2.0574.14
database_summary1.420.032.18
descendants0.010.000.01
dorothea60.44 0.8662.04
ensembl_dataset0.020.000.01
ensembl_id_mapping_table 1.04 0.0858.89
ensembl_id_type0.020.000.02
ensembl_name0.060.000.08
ensembl_organisms0.280.000.28
ensembl_organisms_raw0.210.000.20
ensembl_orthology000
enzsub_graph2.510.093.83
evex_download0.010.000.02
evidences000
extra_attr_values13.94 0.3017.53
extra_attrs8.140.099.59
extra_attrs_to_cols13.64 0.1114.79
filter_by_resource 7.77 0.3418.65
filter_extra_attrs27.61 0.2529.22
filter_intercell 7.28 0.4710.66
filter_intercell_network0.040.000.04
find_all_paths6.630.107.13
from_evidences000
get_annotation_resources0.050.000.44
get_complex_genes1.450.092.17
get_complex_resources0.060.020.45
get_db000
get_enzsub_resources0.080.000.47
get_interaction_resources0.060.000.45
get_intercell_categories0.300.060.64
get_intercell_generic_categories0.050.000.05
get_intercell_resources0.060.000.45
get_ontology_db0.030.000.04
get_resources0.110.000.50
get_signed_ptms4.450.065.04
giant_component 9.55 0.2510.39
go_annot_download9.500.538.96
go_annot_slim000
go_ontology_download0.020.000.01
guide2pharma_download0.020.000.01
harmonizome_download0.010.000.02
has_extra_attrs6.140.036.17
homologene_download0.020.000.02
homologene_raw0.030.000.03
homologene_uniprot_orthology0.020.020.03
hpo_download2.260.202.72
htridb_download0.030.000.03
import_all_interactions2.550.163.95
import_intercell_network0.010.000.02
import_kinaseextra_interactions1.160.042.22
import_ligrecextra_interactions0.770.101.67
import_lncrna_mrna_interactions0.390.051.09
import_mirnatarget_interactions0.870.091.89
import_omnipath_annotations0.460.041.12
import_omnipath_complexes0.510.031.50
import_omnipath_enzsub0.990.061.42
import_omnipath_interactions0.290.020.69
import_omnipath_intercell0.420.100.92
import_pathwayextra_interactions0.910.111.88
import_post_translational_interactions0.800.111.81
import_small_molecule_protein_interactions0.390.070.74
import_tf_mirna_interactions0.810.061.62
import_tf_target_interactions1.250.082.17
import_transcriptional_interactions2.230.093.33
inbiomap_download000
inbiomap_raw000
interaction_datasets0.030.020.04
interaction_graph0.390.000.77
interaction_types0.030.010.05
intercell_categories0.100.000.11
intercell_consensus_filter1.400.142.03
is_ontology_id000
is_swissprot0.070.000.06
is_trembl0.040.000.05
is_uniprot0.020.020.03
kegg_info0.010.000.01
kegg_open000
kegg_pathway_annotations000
kegg_pathway_download0.020.000.01
kegg_pathway_list0.030.000.04
kegg_pathways_download000
kegg_picture0.160.002.12
kegg_process0.030.020.05
latin_name0.060.000.06
load_db0.050.030.08
ncbi_taxid0.030.020.04
nichenet_build_model000
nichenet_expression_data0.030.000.04
nichenet_gr_network0.060.000.06
nichenet_gr_network_evex0.020.000.01
nichenet_gr_network_harmonizome0.030.000.04
nichenet_gr_network_htridb0.020.000.01
nichenet_gr_network_omnipath12.34 0.5713.38
nichenet_gr_network_pathwaycommons0.010.000.01
nichenet_gr_network_regnetwork0.020.000.02
nichenet_gr_network_remap0.020.000.01
nichenet_gr_network_trrust0.030.000.03
nichenet_ligand_activities000
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.030.020.07
nichenet_lr_network_guide2pharma0.010.000.01
nichenet_lr_network_omnipath0.050.000.05
nichenet_lr_network_ramilowski0.020.000.01
nichenet_main000
nichenet_networks0.040.030.08
nichenet_optimization000
nichenet_remove_orphan_ligands0.070.000.07
nichenet_results_dir000
nichenet_signaling_network0.040.000.04
nichenet_signaling_network_cpdb0.020.000.02
nichenet_signaling_network_evex0.000.020.01
nichenet_signaling_network_harmonizome0.010.000.02
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath 9.80 0.3710.87
nichenet_signaling_network_pathwaycommons0.020.000.02
nichenet_signaling_network_vinayagam0.000.020.02
nichenet_test000
nichenet_workarounds000
obo_parser0.110.000.34
oma_code0.030.000.03
oma_organisms0.080.000.09
oma_pairwise0.030.000.04
oma_pairwise_genesymbols0.000.010.01
oma_pairwise_translated0.010.000.03
omnipath3.120.023.14
omnipath_cache_autoclean000
omnipath_cache_clean0.020.000.02
omnipath_cache_clean_db0.090.000.09
omnipath_cache_download_ready0.580.080.78
omnipath_cache_filter_versions0.140.030.24
omnipath_cache_get0.120.010.16
omnipath_cache_key000
omnipath_cache_latest_or_new0.110.020.14
omnipath_cache_load0.640.011.44
omnipath_cache_move_in0.240.050.34
omnipath_cache_remove0.230.020.30
omnipath_cache_save0.270.030.34
omnipath_cache_search000
omnipath_cache_set_ext0.140.030.22
omnipath_cache_update_status0.080.090.17
omnipath_cache_wipe000
omnipath_get_config_path000
omnipath_load_config000
omnipath_log000
omnipath_logfile000
omnipath_msg0.020.000.02
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.040.000.04
omnipath_set_console_loglevel000
omnipath_set_logfile_loglevel0.020.000.02
omnipath_set_loglevel000
omnipath_show_db0.170.000.17
omnipath_unlock_cache_db000
only_from000
ontology_ensure_id000
ontology_ensure_name000
ontology_name_id000