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This page was generated on 2024-07-24 11:38 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4284
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 1432/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.13.1  (landing page)
Denes Turei
Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 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  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for OmnipathR on nebbiolo2

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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.13.1.tar.gz
StartedAt: 2024-07-24 02:07:03 -0400 (Wed, 24 Jul 2024)
EndedAt: 2024-07-24 02:35:23 -0400 (Wed, 24 Jul 2024)
EllapsedTime: 1699.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘3.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:07:23] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:07:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-24 02:07:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:07:23] [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
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:07:32] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:07:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-24 02:07:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:07:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-24 02:07:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:07:33] [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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-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
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:36:37] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] Contains 6 files.
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:36:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:36:37] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:36:39] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:36:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-23 15:36:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:36:39] [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 4.4.1 (2024-06-14) -- "Race for Your Life"
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)
[2024-07-24 02:24:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-24 02:24:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:24:11] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:24:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-24 02:24:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:24:11] [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 
 25.515   1.397  83.079

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0200.0000.021
all_uniprots0.0100.0000.011
ancestors0.010.000.01
annotated_network1.9430.2367.157
annotation_categories93.650 0.13595.471
biomart_query1.1590.0457.015
bioplex10.0270.0000.027
bioplex20.0270.0000.027
bioplex30.0280.0000.028
bioplex_all0.0270.0000.028
bioplex_hct116_10.0220.0040.026
bma_motif_es0.8460.0681.963
bma_motif_vs0.4380.0121.128
collectri151.239 4.537162.286
common_name0.0570.0000.057
consensuspathdb_download000
consensuspathdb_raw_table0.0250.0040.029
curated_ligand_receptor_interactions 5.660 0.93216.917
curated_ligrec_stats 49.791 3.389136.889
database_summary1.3130.0203.757
descendants0.0100.0040.014
dorothea84.789 0.90895.068
ensembl_dataset0.0170.0000.016
ensembl_id_mapping_table 1.306 0.15332.463
ensembl_id_type0.0040.0000.004
ensembl_name0.0850.0040.089
ensembl_organisms0.2290.0200.249
ensembl_organisms_raw0.2260.0120.240
ensembl_orthology000
enzsub_graph3.7070.2396.977
evex_download0.0230.0040.027
evidences000
extra_attr_values13.372 0.34316.444
extra_attrs4.8560.0364.892
extra_attrs_to_cols 9.905 0.11510.021
filter_by_resource 9.572 0.60613.000
filter_extra_attrs36.319 0.73056.777
filter_intercell10.154 1.39319.938
filter_intercell_network0.0470.0000.085
find_all_paths 9.104 0.15618.409
from_evidences000
get_annotation_resources0.2160.0041.363
get_complex_genes2.2820.0236.857
get_complex_resources0.2200.0081.209
get_db0.0010.0000.000
get_enzsub_resources0.2400.0081.334
get_interaction_resources0.3760.0041.338
get_intercell_categories0.7500.0161.689
get_intercell_generic_categories0.2420.0040.467
get_intercell_resources0.2180.0041.258
get_ontology_db0.0370.0000.077
get_resources0.2500.0321.366
get_signed_ptms7.4870.0838.724
giant_component20.395 1.64843.019
go_annot_download12.541 2.16116.717
go_annot_slim0.0010.0000.000
go_ontology_download0.0100.0040.014
guide2pharma_download0.0120.0000.012
harmonizome_download0.0120.0000.011
has_extra_attrs8.2890.2478.672
homologene_download0.0240.0090.050
homologene_raw0.0430.0000.075
homologene_uniprot_orthology0.0220.0000.039
hpo_download3.5700.4595.177
htridb_download0.0260.0000.026
import_all_interactions4.1780.3918.182
import_intercell_network0.0220.0080.030
import_kinaseextra_interactions2.3890.2146.706
import_ligrecextra_interactions1.4900.1203.922
import_lncrna_mrna_interactions1.1050.0862.856
import_mirnatarget_interactions1.9310.1454.658
import_omnipath_annotations1.1310.0972.540
import_omnipath_complexes1.2250.1254.164
import_omnipath_enzsub2.0100.1333.124
import_omnipath_interactions0.4770.0321.384
import_omnipath_intercell0.7900.0981.780
import_pathwayextra_interactions1.4750.2013.680
import_post_translational_interactions1.3040.2623.340
import_small_molecule_protein_interactions0.4740.0520.750
import_tf_mirna_interactions0.9080.1672.315
import_tf_target_interactions1.4110.5933.761
import_transcriptional_interactions3.9950.3226.077
inbiomap_download000
inbiomap_raw000
interaction_datasets0.0570.0120.069
interaction_graph0.6890.0561.943
interaction_types0.0850.0120.097
intercell_categories0.1210.0080.129
intercell_consensus_filter2.4690.2476.124
is_ontology_id0.0010.0000.004
is_swissprot0.0740.0080.155
is_trembl0.0690.0120.162
is_uniprot0.0330.0090.073
kegg_info0.0180.0080.026
kegg_open0.0250.0000.025
kegg_pathway_annotations000
kegg_pathway_download0.0280.0000.028
kegg_pathway_list0.2850.0360.444
kegg_pathways_download0.0000.0000.001
kegg_picture0.2830.0444.932
kegg_process0.0580.0040.122
latin_name0.1060.0000.105
load_db0.1800.0160.322
ncbi_taxid0.1140.0000.315
nichenet_build_model000
nichenet_expression_data0.0250.0040.061
nichenet_gr_network0.0790.0080.223
nichenet_gr_network_evex0.0260.0040.082
nichenet_gr_network_harmonizome0.0270.0120.083
nichenet_gr_network_htridb0.0280.0000.064
nichenet_gr_network_omnipath25.209 0.57230.910
nichenet_gr_network_pathwaycommons0.0240.0000.024
nichenet_gr_network_regnetwork0.0190.0000.019
nichenet_gr_network_remap0.0140.0030.017
nichenet_gr_network_trrust0.0110.0040.016
nichenet_ligand_activities000
nichenet_ligand_target_links000
nichenet_ligand_target_matrix0.0000.0000.001
nichenet_lr_network0.0600.0040.077
nichenet_lr_network_guide2pharma0.020.000.02
nichenet_lr_network_omnipath0.0490.0040.053
nichenet_lr_network_ramilowski0.0150.0000.014
nichenet_main000
nichenet_networks0.0510.0040.102
nichenet_optimization000
nichenet_remove_orphan_ligands0.0250.0040.028
nichenet_results_dir000
nichenet_signaling_network0.0290.0000.028
nichenet_signaling_network_cpdb0.0100.0000.009
nichenet_signaling_network_evex0.0100.0000.009
nichenet_signaling_network_harmonizome0.0100.0000.009
nichenet_signaling_network_inbiomap0.0000.0000.001
nichenet_signaling_network_omnipath17.060 0.71536.551
nichenet_signaling_network_pathwaycommons0.0330.0000.081
nichenet_signaling_network_vinayagam0.0280.0040.064
nichenet_test0.0010.0000.000
nichenet_workarounds0.0010.0000.000
obo_parser0.2530.0610.813
oma_code0.0530.0040.057
oma_organisms0.2690.0480.443
oma_pairwise0.0360.0000.044
oma_pairwise_genesymbols0.0330.0000.033
oma_pairwise_translated0.0320.0000.032
omnipath6.5400.3168.266
omnipath_cache_autoclean000
omnipath_cache_clean0.0110.0040.016
omnipath_cache_clean_db0.1800.0080.188
omnipath_cache_download_ready0.9530.0651.117
omnipath_cache_filter_versions0.2370.0240.305
omnipath_cache_get0.2050.0320.238
omnipath_cache_key0.0000.0020.002
omnipath_cache_latest_or_new0.1560.0050.161
omnipath_cache_load1.2550.1133.851
omnipath_cache_move_in0.3060.0440.362
omnipath_cache_remove0.1830.0400.238
omnipath_cache_save0.3620.0400.515
omnipath_cache_search0.0010.0000.001
omnipath_cache_set_ext0.2080.0480.269
omnipath_cache_update_status0.1040.0190.124
omnipath_cache_wipe0.0000.0000.001
omnipath_get_config_path0.0010.0000.001
omnipath_load_config000
omnipath_log000
omnipath_logfile0.0020.0000.002
omnipath_msg0.0070.0000.007
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0290.0040.033
omnipath_set_console_loglevel0.0040.0000.004
omnipath_set_logfile_loglevel0.0000.0040.003
omnipath_set_loglevel0.0000.0020.002
omnipath_show_db0.0630.0010.065
omnipath_unlock_cache_db0.0000.0010.000
only_from0.0000.0010.000
ontology_ensure_id0.0000.0010.001
ontology_ensure_name0.0000.0010.001
ontology_name_id0.0000.0000.001