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This page was generated on 2024-05-30 11:35:11 -0400 (Thu, 30 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4753
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4518
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: 2024-05-29 14:00:10 -0400 (Wed, 29 May 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  
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: 3.12.1
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_3.12.1.tar.gz
StartedAt: 2024-05-30 00:56:42 -0400 (Thu, 30 May 2024)
EndedAt: 2024-05-30 01:26:24 -0400 (Thu, 30 May 2024)
EllapsedTime: 1782.1 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_3.12.1.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 ‘3.12.1’
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-05-30 00:57:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 00:57:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:57:03] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 00:57:03] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 00:57:03] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 00:57:03] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 00:57:03] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 00:57:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 00:57:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:57:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 00:57:03] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 00:57:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 00:57:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:57:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 00:57:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:57:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 00:57:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:57:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 00:57:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:57:04] [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 00:57:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:57:14] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:57:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 00:57:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 00:57:14] [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
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:36] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] Contains 8 files.
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 15:27:36] [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).
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:36] [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).
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:36] [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).
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:36] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:38] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-29 15:27:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:38] [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)
[2024-05-30 01:12:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 01:12:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 01:12:58] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 01:12:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 01:12:58] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 01:12:58] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 01:12:58] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 01:12:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 01:12:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 01:12:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 01:12:58] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 01:12:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 01:12:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 01:12:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 01:12:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 01:12:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 01:12:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 01:12:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 01:12:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 01:12:59] [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 
 18.969   1.550  95.644

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0010.0000.001
all_uniprot_acs0.0220.0000.022
all_uniprots0.0120.0000.012
ancestors0.0070.0040.010
annotated_network1.9590.1807.740
annotation_categories85.892 0.07787.541
biomart_query0.6260.0483.132
bioplex10.0110.0000.011
bioplex20.010.000.01
bioplex30.0100.0000.011
bioplex_all0.0100.0000.011
bioplex_hct116_10.010.000.01
bma_motif_es0.4560.0481.434
bma_motif_vs0.2430.0001.016
collectri142.801 2.646152.353
common_name0.0210.0000.021
consensuspathdb_download000
consensuspathdb_raw_table0.0130.0040.017
curated_ligand_receptor_interactions 8.455 0.99623.712
curated_ligrec_stats 47.231 4.129136.113
database_summary1.4860.1464.561
descendants0.0140.0000.015
dorothea87.398 0.74593.615
ensembl_dataset0.0080.0000.008
ensembl_id_mapping_table 1.391 0.06411.663
ensembl_id_type0.0050.0000.005
ensembl_name0.0890.0040.092
ensembl_organisms0.2560.0080.266
ensembl_organisms_raw0.2170.0080.305
ensembl_orthology0.0010.0000.001
enzsub_graph3.8660.4037.666
evex_download0.0390.0000.039
evidences0.0000.0000.001
extra_attr_values11.374 0.50114.286
extra_attrs 8.335 0.08812.468
extra_attrs_to_cols16.281 0.18816.544
filter_by_resource5.4690.3388.265
filter_extra_attrs27.338 0.49131.298
filter_intercell 7.417 0.51514.421
filter_intercell_network0.0510.0040.112
find_all_paths 8.268 0.05622.228
from_evidences0.0010.0000.000
get_annotation_resources0.2080.0161.223
get_complex_genes3.1850.1267.851
get_complex_resources0.2020.0091.434
get_db0.0000.0000.001
get_enzsub_resources0.2010.0111.258
get_interaction_resources0.2150.0071.242
get_intercell_categories0.7140.0411.865
get_intercell_generic_categories0.0750.0000.155
get_intercell_resources0.1880.0041.175
get_ontology_db0.0270.0040.103
get_resources0.2280.0321.118
get_signed_ptms7.4460.3599.197
giant_component20.607 0.61226.474
go_annot_download17.340 0.97425.248
go_annot_slim000
go_ontology_download0.0400.0090.158
guide2pharma_download0.0360.0000.132
harmonizome_download0.0310.0010.063
has_extra_attrs11.355 0.06916.919
homologene_download0.0210.0000.021
homologene_raw0.0350.0000.035
homologene_uniprot_orthology0.0210.0000.020
hpo_download3.7760.2716.025
htridb_download0.0310.0000.030
import_all_interactions3.9930.2007.575
import_intercell_network0.0260.0040.031
import_kinaseextra_interactions2.7150.1245.586
import_ligrecextra_interactions1.4420.0933.454
import_lncrna_mrna_interactions1.1750.0862.516
import_mirnatarget_interactions2.1150.0944.361
import_omnipath_annotations1.0560.0402.397
import_omnipath_complexes0.9120.0523.036
import_omnipath_enzsub1.7560.0242.573
import_omnipath_interactions0.3820.0081.062
import_omnipath_intercell0.7550.0732.137
import_pathwayextra_interactions1.4290.0754.325
import_post_translational_interactions1.5670.1374.459
import_small_molecule_protein_interactions0.9590.0521.723
import_tf_mirna_interactions1.3080.1314.480
import_tf_target_interactions2.6600.2326.304
import_transcriptional_interactions4.2710.4827.000
inbiomap_download000
inbiomap_raw000
interaction_datasets0.0470.0030.050
interaction_graph0.4380.0041.191
interaction_types0.0340.0000.034
intercell_categories0.0420.0080.051
intercell_consensus_filter1.3150.2193.035
is_ontology_id0.0000.0010.000
is_swissprot0.0290.0030.032
is_trembl0.0310.0000.030
is_uniprot0.0130.0000.012
kegg_info0.0070.0040.011
kegg_open0.0100.0000.011
kegg_pathway_annotations000
kegg_pathway_download0.0110.0000.012
kegg_pathway_list0.0110.0040.014
kegg_pathways_download000
kegg_picture0.1970.0125.027
kegg_process0.1430.0240.358
latin_name0.0990.0040.220
load_db0.1850.0200.460
ncbi_taxid0.1040.0080.232
nichenet_build_model0.0000.0000.001
nichenet_expression_data0.0370.0040.089
nichenet_gr_network0.0950.0040.196
nichenet_gr_network_evex0.0280.0040.064
nichenet_gr_network_harmonizome0.0290.0000.061
nichenet_gr_network_htridb0.0280.0000.060
nichenet_gr_network_omnipath21.759 0.46444.355
nichenet_gr_network_pathwaycommons0.0130.0000.013
nichenet_gr_network_regnetwork0.0110.0000.011
nichenet_gr_network_remap0.0060.0040.010
nichenet_gr_network_trrust0.0090.0000.009
nichenet_ligand_activities0.0000.0000.001
nichenet_ligand_target_links0.0000.0000.001
nichenet_ligand_target_matrix0.0000.0000.001
nichenet_lr_network0.0220.0050.028
nichenet_lr_network_guide2pharma0.0100.0000.018
nichenet_lr_network_omnipath0.0280.0000.028
nichenet_lr_network_ramilowski0.010.000.01
nichenet_main0.0010.0000.001
nichenet_networks0.0390.0080.064
nichenet_optimization000
nichenet_remove_orphan_ligands0.0270.0000.028
nichenet_results_dir0.0000.0000.001
nichenet_signaling_network0.0290.0000.030
nichenet_signaling_network_cpdb0.0100.0000.009
nichenet_signaling_network_evex0.0060.0040.010
nichenet_signaling_network_harmonizome0.0090.0000.010
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath12.893 1.15821.286
nichenet_signaling_network_pathwaycommons0.0100.0040.014
nichenet_signaling_network_vinayagam0.0120.0000.013
nichenet_test0.0000.0000.001
nichenet_workarounds0.0000.0000.001
obo_parser0.1650.0080.511
oma_code0.0410.0000.042
oma_organisms0.1710.0040.196
oma_pairwise0.0230.0000.023
oma_pairwise_genesymbols0.0210.0000.037
omnipath7.2810.1207.559
omnipath_cache_autoclean0.0010.0000.001
omnipath_cache_clean0.0040.0080.012
omnipath_cache_clean_db0.1620.0160.179
omnipath_cache_download_ready1.0780.0441.352
omnipath_cache_filter_versions0.2290.0040.259
omnipath_cache_get0.1740.0200.267
omnipath_cache_key0.0020.0000.002
omnipath_cache_latest_or_new0.1610.0210.398
omnipath_cache_load1.1710.1034.331
omnipath_cache_move_in0.3910.0550.664
omnipath_cache_remove0.2350.0240.449
omnipath_cache_save0.4820.0480.995
omnipath_cache_search0.0010.0000.001
omnipath_cache_set_ext0.2110.0080.432
omnipath_cache_update_status0.2470.0120.271
omnipath_cache_wipe0.0010.0000.001
omnipath_get_config_path0.0010.0000.001
omnipath_load_config0.0010.0000.001
omnipath_log000
omnipath_logfile0.0020.0000.002
omnipath_msg0.0160.0000.041
omnipath_reset_config0.0010.0000.000
omnipath_save_config000
omnipath_set_cachedir0.0600.0120.136
omnipath_set_console_loglevel0.0010.0020.003
omnipath_set_logfile_loglevel0.0030.0000.003
omnipath_set_loglevel0.0010.0000.001
omnipath_show_db0.2130.0120.477
omnipath_unlock_cache_db0.0010.0000.025
only_from000
ontology_ensure_id0.0010.0000.001
ontology_ensure_name0.0010.0000.001
ontology_name_id0.0020.0000.002