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This page was generated on 2024-05-18 11:36:14 -0400 (Sat, 18 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 3.12.0  (landing page)
Denes Turei
Snapshot Date: 2024-05-17 14:00:11 -0400 (Fri, 17 May 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_19
git_last_commit: 330f65c
git_last_commit_date: 2024-04-30 11:18:21 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for OmnipathR on nebbiolo1


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: 3.12.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OmnipathR_3.12.0.tar.gz
StartedAt: 2024-05-18 01:08:47 -0400 (Sat, 18 May 2024)
EndedAt: 2024-05-18 01:44:59 -0400 (Sat, 18 May 2024)
EllapsedTime: 2172.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OmnipathR_3.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.12.0’
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-05-18 01:09:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 01:09:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:09:29] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-18 01:09:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-18 01:09:29] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-18 01:09:29] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-18 01:09:29] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-18 01:09:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 01:09:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:09:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-18 01:09:29] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-18 01:09:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-18 01:09:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:09:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-18 01:09:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:09:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-18 01:09:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:09:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-18 01:09:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:09:30] [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
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:09:40] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:09:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-18 01:09:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:09:40] [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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 15:27:34] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] Contains 8 files.
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 15:27:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 15:27:34] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 15:27:36] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 15:27:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-17 15:27:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-17 15:27:36] [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 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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)
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:33:55] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:33:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-18 01:33:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-18 01:33:55] [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 
 14.853   1.539  62.243

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0000.001
all_uniprot_acs0.020.000.02
all_uniprots0.010.000.01
ancestors0.0100.0000.009
annotated_network 1.879 0.17117.389
annotation_categories 96.491 0.132107.212
biomart_query 0.873 0.06455.905
bioplex10.0100.0000.011
bioplex20.0020.0080.009
bioplex30.010.000.01
bioplex_all0.010.000.01
bioplex_hct116_10.0090.0000.010
bma_motif_es0.7470.0532.575
bma_motif_vs0.4040.0041.617
collectri163.722 4.311239.720
common_name0.0370.0000.037
consensuspathdb_download0.0010.0000.001
consensuspathdb_raw_table0.0310.0000.031
curated_ligand_receptor_interactions 7.625 0.95432.198
curated_ligrec_stats 49.361 3.303179.524
database_summary 1.331 0.14012.989
descendants0.0120.0000.012
dorothea119.961 1.875210.529
ensembl_dataset0.010.000.01
ensembl_id_mapping_table 1.347 0.08541.057
ensembl_id_type0.0040.0000.020
ensembl_name0.0820.0040.165
ensembl_organisms0.2330.0200.372
ensembl_organisms_raw0.2260.0120.283
ensembl_orthology000
enzsub_graph 3.862 0.30010.026
evex_download0.0300.0040.066
evidences000
extra_attr_values21.710 0.63527.614
extra_attrs9.3570.1369.495
extra_attrs_to_cols17.646 0.20320.950
filter_by_resource 9.292 0.22915.376
filter_extra_attrs37.446 0.10357.718
filter_intercell 8.298 0.77817.992
filter_intercell_network0.0400.0110.163
find_all_paths 5.072 0.70851.305
from_evidences0.0000.0000.001
get_annotation_resources0.1090.0001.110
get_complex_genes1.3890.1313.916
get_complex_resources0.1830.0000.868
get_db0.0010.0000.001
get_enzsub_resources0.1820.0040.878
get_interaction_resources0.2830.0040.973
get_intercell_categories0.6280.0520.992
get_intercell_generic_categories0.1880.0340.304
get_intercell_resources0.2080.0041.029
get_ontology_db0.0320.0000.031
get_resources0.2210.0161.139
get_signed_ptms 9.082 0.24315.052
giant_component19.082 4.15289.551
go_annot_download15.445 1.31346.383
go_annot_slim0.0000.0000.001
go_ontology_download0.0090.0030.012
guide2pharma_download0.0120.0000.014
harmonizome_download0.0080.0040.012
has_extra_attrs5.7340.1036.406
homologene_download0.0130.0000.015
homologene_raw0.0630.0000.063
homologene_uniprot_orthology0.0140.0000.015
hpo_download1.8860.2496.562
htridb_download0.0130.0000.013
import_all_interactions1.9540.1018.900
import_intercell_network0.0100.0000.011
import_kinaseextra_interactions1.3840.0765.895
import_ligrecextra_interactions0.7050.0813.543
import_lncrna_mrna_interactions0.5520.0654.635
import_mirnatarget_interactions1.0230.1769.407
import_omnipath_annotations0.5280.0571.715
import_omnipath_complexes0.5990.0763.030
import_omnipath_enzsub0.9360.0281.655
import_omnipath_interactions0.2960.0162.177
import_omnipath_intercell0.4380.0521.111
import_pathwayextra_interactions0.7580.0776.452
import_post_translational_interactions0.7300.0526.186
import_small_molecule_protein_interactions0.4310.0240.735
import_tf_mirna_interactions0.7010.0401.913
import_tf_target_interactions1.1840.0937.088
import_transcriptional_interactions 2.236 0.16810.943
inbiomap_download0.0000.0000.001
inbiomap_raw0.0000.0000.001
interaction_datasets0.0360.0040.040
interaction_graph0.5180.0081.296
interaction_types0.0390.0000.039
intercell_categories0.0580.0040.062
intercell_consensus_filter1.2500.1453.964
is_ontology_id0.0010.0000.001
is_swissprot0.0290.0040.033
is_trembl0.0270.0040.031
is_uniprot0.0130.0000.014
kegg_info0.0100.0030.015
kegg_open0.0130.0000.014
kegg_pathway_annotations000
kegg_pathway_download0.0120.0000.012
kegg_pathway_list0.0130.0000.012
kegg_pathways_download0.0010.0000.000
kegg_picture0.1690.0484.826
kegg_process0.0320.0040.037
latin_name0.0480.0040.052
load_db0.1090.0320.141
ncbi_taxid0.0310.0080.039
nichenet_build_model0.0000.0000.001
nichenet_expression_data0.0120.0000.013
nichenet_gr_network0.0300.0030.033
nichenet_gr_network_evex0.0110.0000.011
nichenet_gr_network_harmonizome0.0120.0000.012
nichenet_gr_network_htridb0.0060.0070.014
nichenet_gr_network_omnipath11.020 0.33613.846
nichenet_gr_network_pathwaycommons0.0110.0000.011
nichenet_gr_network_regnetwork0.0090.0000.010
nichenet_gr_network_remap0.010.000.01
nichenet_gr_network_trrust0.0100.0000.009
nichenet_ligand_activities0.0000.0000.001
nichenet_ligand_target_links0.0000.0000.001
nichenet_ligand_target_matrix000
nichenet_lr_network0.0260.0040.029
nichenet_lr_network_guide2pharma0.010.000.01
nichenet_lr_network_omnipath0.0240.0040.029
nichenet_lr_network_ramilowski0.010.000.01
nichenet_main0.0010.0000.000
nichenet_networks0.0460.0000.046
nichenet_optimization000
nichenet_remove_orphan_ligands0.0260.0030.028
nichenet_results_dir000
nichenet_signaling_network0.030.000.03
nichenet_signaling_network_cpdb0.0100.0000.011
nichenet_signaling_network_evex0.0440.0000.044
nichenet_signaling_network_harmonizome0.0110.0000.011
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath 7.811 0.29020.773
nichenet_signaling_network_pathwaycommons0.0130.0000.013
nichenet_signaling_network_vinayagam0.0110.0000.012
nichenet_test0.0000.0000.001
nichenet_workarounds000
obo_parser0.1090.0040.163
oma_code0.0290.0000.029
oma_organisms0.0740.0000.076
oma_pairwise0.0200.0000.019
oma_pairwise_genesymbols0.0150.0000.015
omnipath3.4790.1533.659
omnipath_cache_autoclean0.0000.0010.000
omnipath_cache_clean0.0030.0030.005
omnipath_cache_clean_db0.0730.0040.076
omnipath_cache_download_ready0.7620.0924.978
omnipath_cache_filter_versions0.2120.0120.239
omnipath_cache_get0.2670.0240.291
omnipath_cache_key0.0020.0000.002
omnipath_cache_latest_or_new0.1250.0000.125
omnipath_cache_load1.2200.0524.652
omnipath_cache_move_in0.5710.0640.936
omnipath_cache_remove0.2250.0360.554
omnipath_cache_save0.5070.0761.430
omnipath_cache_search0.0000.0010.001
omnipath_cache_set_ext0.2020.0100.383
omnipath_cache_update_status0.2140.0200.279
omnipath_cache_wipe0.0010.0000.001
omnipath_get_config_path0.0010.0000.003
omnipath_load_config000
omnipath_log0.0010.0000.001
omnipath_logfile0.0000.0020.004
omnipath_msg0.0130.0010.014
omnipath_reset_config0.0000.0000.001
omnipath_save_config0.0010.0000.000
omnipath_set_cachedir0.3260.0200.372
omnipath_set_console_loglevel0.0030.0000.003
omnipath_set_logfile_loglevel0.0000.0030.003
omnipath_set_loglevel0.0020.0000.001
omnipath_show_db0.1220.0040.127
omnipath_unlock_cache_db0.0000.0010.001
only_from0.0000.0010.000
ontology_ensure_id0.0010.0000.002
ontology_ensure_name0.0010.0000.001
ontology_name_id0.0000.0020.002