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This page was generated on 2024-05-30 11:35:46 -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 lconway


To the developers/maintainers of the OmnipathR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: OmnipathR
Version: 3.12.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.12.1.tar.gz
StartedAt: 2024-05-29 22:34:45 -0400 (Wed, 29 May 2024)
EndedAt: 2024-05-29 22:50:27 -0400 (Wed, 29 May 2024)
EllapsedTime: 941.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.12.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-05-29 22:35:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 22:35:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:35:11] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 22:35:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 22:35:11] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 22:35:11] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 22:35:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 22:35:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 22:35:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:35:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 22:35:11] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 22:35:11] [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 22:35:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:35:11] [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 22:35:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:35:11] [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 22:35:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:35:11] [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 22:35:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:35:11] [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
[2024-05-29 22:35:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 22:35:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:35:26] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 22:35:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 22:35:26] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 22:35:26] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 22:35:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 22:35:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 22:35:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:35:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 22:35:27] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 22:35:27] [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 22:35:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:35:27] [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 22:35:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:35:27] [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 22:35:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:35:27] [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 22:35:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:35:27] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘oma_pairwise_translated’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: organism_for
> ### Title: Make sure the resource supports the organism and it has the ID
> ### Aliases: organism_for
> 
> ### ** Examples
> 
> organism_for(10116, 'chalmers-gem')
[1] "Rat"
> # [1] "Rat"
> organism_for(6239, 'chalmers-gem')
Error in organism_for(6239, "chalmers-gem") : 
  Organism `6239` (common_name: `Caenorhabditis elegans (Nematode, N2)`; common_name: `Caenorhabditis elegans (Nematode, N2)`) is not supported by resource `chalmers-gem`. Supported organisms: Human, Mouse, Rat, Zebrafish, Drosophila melanogaster (Fruit fly), Caenorhabditis elegans (PRJNA13758).
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2024-05-29 15:23:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 15:23:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:23:49] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 15:23:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 15:23:49] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 15:23:50] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 15:23:50] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 15:23:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 15:23:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:23:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 15:23:51] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 15:23:51] [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 15:23:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:23:51] [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 15:23:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:23:51] [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 15:23:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:23:51] [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 15:23:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:23:51] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-29 15:23:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 15:23:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:23:54] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 15:23:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 15:23:54] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 15:23:54] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 15:23:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 15:23:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 15:23:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:23:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 15:23:54] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 15:23:54] [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 15:23:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:23:54] [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 15:23:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:23:54] [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 15:23:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:23:54] [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 15:23:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:23:54] [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-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)
[2024-05-29 22:49:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 22:49:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:49:25] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 22:49:25] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 22:49:25] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 22:49:25] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 22:49:25] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 22:49:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 22:49:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:49:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-29 22:49:25] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 22:49:25] [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 22:49:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:49:25] [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 22:49:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:49:25] [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 22:49:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:49:25] [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 22:49:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 22:49:25] [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 
 11.403   1.267  45.264

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0010.0000.001
all_uniprot_acs0.0260.0040.029
all_uniprots0.0150.0020.016
ancestors0.0120.0010.013
annotated_network1.7180.1947.955
annotation_categories64.203 0.64667.453
biomart_query0.8550.0986.702
bioplex10.0140.0020.016
bioplex20.0130.0020.015
bioplex30.0140.0020.016
bioplex_all0.0130.0010.014
bioplex_hct116_10.0150.0020.017
bma_motif_es0.3510.0441.469
bma_motif_vs0.1880.0100.742
collectri132.967 1.754139.845
common_name0.0230.0010.026
consensuspathdb_download000
consensuspathdb_raw_table0.0530.0010.055
curated_ligand_receptor_interactions 4.230 0.37015.645
curated_ligrec_stats 30.103 9.032137.865
database_summary1.5970.0627.321
descendants0.0180.0020.051
dorothea 66.901 2.046116.741
ensembl_dataset0.0090.0040.074
ensembl_id_mapping_table 0.883 0.30941.454
ensembl_id_type0.0030.0020.004
ensembl_name0.0600.0070.073
ensembl_organisms0.1630.0380.220
ensembl_organisms_raw0.1610.0210.207
ensembl_orthology000
enzsub_graph2.4260.2426.749
evex_download0.0190.0030.035
evidences0.0000.0010.001
extra_attr_values13.896 0.58327.160
extra_attrs6.6100.1276.878
extra_attrs_to_cols10.766 0.25711.233
filter_by_resource6.4820.2129.541
filter_extra_attrs21.891 0.24922.943
filter_intercell 6.239 0.79111.499
filter_intercell_network0.0270.0030.030
find_all_paths5.7360.2846.256
from_evidences0.0000.0000.001
get_annotation_resources0.0670.0070.672
get_complex_genes1.2430.0943.629
get_complex_resources0.0650.0060.686
get_db0.0010.0000.001
get_enzsub_resources0.0620.0050.634
get_interaction_resources0.1030.0080.788
get_intercell_categories0.3070.0440.634
get_intercell_generic_categories0.0430.0040.047
get_intercell_resources0.0720.0060.734
get_ontology_db0.0130.0020.014
get_resources0.0630.0060.743
get_signed_ptms5.4410.1216.339
giant_component10.276 0.41917.195
go_annot_download9.0561.0979.730
go_annot_slim0.0000.0000.001
go_ontology_download0.0120.0010.014
guide2pharma_download0.0110.0010.013
harmonizome_download0.0090.0010.011
has_extra_attrs6.5400.1086.693
homologene_download0.0150.0020.017
homologene_raw0.0250.0020.027
homologene_uniprot_orthology0.0160.0020.017
hpo_download2.2260.3203.603
htridb_download0.0150.0020.017
import_all_interactions2.2640.1465.577
import_intercell_network0.0140.0020.016
import_kinaseextra_interactions1.3910.0854.421
import_ligrecextra_interactions0.6500.0632.484
import_lncrna_mrna_interactions0.5470.0571.526
import_mirnatarget_interactions0.9760.0712.742
import_omnipath_annotations0.5470.0551.443
import_omnipath_complexes0.5680.0462.540
import_omnipath_enzsub1.0780.0171.678
import_omnipath_interactions0.2540.0090.961
import_omnipath_intercell0.5050.0491.111
import_pathwayextra_interactions0.7340.0642.998
import_post_translational_interactions0.7630.0683.067
import_small_molecule_protein_interactions0.4470.0330.722
import_tf_mirna_interactions0.6850.0622.005
import_tf_target_interactions1.3310.0774.021
import_transcriptional_interactions2.4630.1065.102
inbiomap_download0.0000.0000.001
inbiomap_raw000
interaction_datasets0.0420.0030.046
interaction_graph0.3680.0110.995
interaction_types0.0990.0040.106
intercell_categories0.0580.0030.063
intercell_consensus_filter1.3790.1244.529
is_ontology_id0.0010.0000.001
is_swissprot0.0420.0040.047
is_trembl0.0340.0040.038
is_uniprot0.0140.0010.016
kegg_info0.0160.0010.018
kegg_open0.0130.0020.016
kegg_pathway_annotations000
kegg_pathway_download0.0120.0020.015
kegg_pathway_list0.0110.0020.012
kegg_pathways_download000
kegg_picture0.0870.0163.798
kegg_process0.0290.0030.033
latin_name0.0530.0000.054
load_db0.0940.0040.100
ncbi_taxid0.0540.0020.055
nichenet_build_model000
nichenet_expression_data0.0150.0020.017
nichenet_gr_network0.0450.0050.050
nichenet_gr_network_evex0.0110.0020.013
nichenet_gr_network_harmonizome0.0130.0020.015
nichenet_gr_network_htridb0.0660.0020.068
nichenet_gr_network_omnipath12.947 0.59916.008
nichenet_gr_network_pathwaycommons0.0150.0010.018
nichenet_gr_network_regnetwork0.0110.0010.013
nichenet_gr_network_remap0.0150.0020.016
nichenet_gr_network_trrust0.0150.0020.016
nichenet_ligand_activities0.0000.0010.000
nichenet_ligand_target_links0.0000.0010.000
nichenet_ligand_target_matrix0.0000.0010.000
nichenet_lr_network0.0430.0060.049
nichenet_lr_network_guide2pharma0.0160.0020.018
nichenet_lr_network_omnipath0.0430.0050.049
nichenet_lr_network_ramilowski0.0110.0020.012
nichenet_main0.0010.0000.000
nichenet_networks0.1170.0130.132
nichenet_optimization000
nichenet_remove_orphan_ligands0.0440.0050.050
nichenet_results_dir0.0000.0000.001
nichenet_signaling_network0.0510.0050.057
nichenet_signaling_network_cpdb0.0150.0020.017
nichenet_signaling_network_evex0.0130.0020.015
nichenet_signaling_network_harmonizome0.0140.0010.016
nichenet_signaling_network_inbiomap0.0000.0000.001
nichenet_signaling_network_omnipath10.641 0.45114.091
nichenet_signaling_network_pathwaycommons0.0140.0010.016
nichenet_signaling_network_vinayagam0.0150.0020.017
nichenet_test000
nichenet_workarounds0.0000.0000.001
obo_parser0.1720.1046.702
oma_code0.0310.0200.117
oma_organisms0.0720.0030.081
oma_pairwise0.0170.0060.032
oma_pairwise_genesymbols0.0160.0030.020
omnipath4.2950.0834.425
omnipath_cache_autoclean000
omnipath_cache_clean0.0070.0000.008
omnipath_cache_clean_db0.0930.0060.101
omnipath_cache_download_ready0.5100.0560.645
omnipath_cache_filter_versions0.1390.0220.175
omnipath_cache_get0.1590.0200.183
omnipath_cache_key0.0020.0010.002
omnipath_cache_latest_or_new0.0890.0140.104
omnipath_cache_load0.6020.0453.406
omnipath_cache_move_in0.2010.0320.249
omnipath_cache_remove0.1280.0200.161
omnipath_cache_save0.2300.0360.322
omnipath_cache_search0.0000.0000.001
omnipath_cache_set_ext0.1080.0180.144
omnipath_cache_update_status0.1220.0190.144
omnipath_cache_wipe0.0000.0010.000
omnipath_get_config_path000
omnipath_load_config000
omnipath_log0.0010.0000.000
omnipath_logfile0.0010.0000.001
omnipath_msg0.0060.0010.007
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0300.0040.035
omnipath_set_console_loglevel0.0010.0000.002
omnipath_set_logfile_loglevel0.0010.0000.001
omnipath_set_loglevel0.0010.0000.001
omnipath_show_db0.0610.0010.063
omnipath_unlock_cache_db0.0000.0000.001
only_from0.0000.0000.001
ontology_ensure_id0.0000.0000.001
ontology_ensure_name000
ontology_name_id0.0010.0000.001