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This page was generated on 2024-06-17 12:23 -0400 (Mon, 17 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4685
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4400
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 1428/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.13.1  (landing page)
Denes Turei
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 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  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped

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: 2024-06-17 01:42:04 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 02:12:02 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 1798.8 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 4.4.0 RC (2024-04-16 r86468)
* 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
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:42:23] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:42:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-17 01:42:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:42:23] [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
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:42:33] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:42:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-17 01:42:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:42:33] [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
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-16 15:32:37] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] Contains 8 files.
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-16 15:32:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-16 15:32:37] [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).
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-16 15:32:37] [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).
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-16 15:32:37] [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).
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-16 15:32:37] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-06-16 15:32:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-16 15:32:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-16 15:32:38] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-06-16 15:32:38] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-16 15:32:38] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-06-16 15:32:38] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-16 15:32:38] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-16 15:32:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-16 15:32:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-16 15:32:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-06-16 15:32:38] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-16 15:32:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-16 15:32:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-16 15:32:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-16 15:32:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-16 15:32:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-16 15:32:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-16 15:32:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-16 15:32:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-16 15:32:39] [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 4.4.0 RC (2024-04-16 r86468) -- "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)
[2024-06-17 01:58:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-17 01:58:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:58:37] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-06-17 01:58:37] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-17 01:58:37] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-06-17 01:58:37] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-17 01:58:37] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-17 01:58:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-17 01:58:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:58:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-06-17 01:58:37] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-17 01:58:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-17 01:58:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:58:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-17 01:58:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:58:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-17 01:58:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:58:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-17 01:58:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-17 01:58:38] [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 
 23.427   1.999  88.033

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0210.0000.022
all_uniprots0.0110.0000.011
ancestors0.0110.0000.010
annotated_network1.9110.1947.754
annotation_categories 96.488 0.074100.652
biomart_query1.1030.0325.796
bioplex10.0290.0000.029
bioplex20.0230.0000.023
bioplex30.0220.0000.022
bioplex_all0.0180.0040.022
bioplex_hct116_10.0210.0000.021
bma_motif_es0.8420.0452.216
bma_motif_vs0.3800.0081.228
collectri148.972 1.697161.929
common_name0.0420.0000.043
consensuspathdb_download0.0010.0000.000
consensuspathdb_raw_table0.0240.0000.024
curated_ligand_receptor_interactions 5.761 0.67921.220
curated_ligrec_stats 48.131 3.741145.738
database_summary2.6180.1376.697
descendants0.0250.0000.058
dorothea79.237 1.12389.146
ensembl_dataset0.0220.0000.022
ensembl_id_mapping_table 1.644 0.10017.274
ensembl_id_type0.0040.0000.004
ensembl_name0.1000.0000.116
ensembl_organisms0.2270.0000.227
ensembl_organisms_raw0.2050.0040.209
ensembl_orthology0.0000.0000.001
enzsub_graph3.5620.0686.940
evex_download0.0250.0000.025
evidences000
extra_attr_values13.117 0.26718.326
extra_attrs 9.846 0.00410.473
extra_attrs_to_cols11.102 0.09911.785
filter_by_resource5.1380.1687.625
filter_extra_attrs26.373 0.01427.131
filter_intercell 5.545 0.43510.005
filter_intercell_network0.0220.0000.022
find_all_paths7.2140.0248.625
from_evidences0.0000.0000.001
get_annotation_resources0.2060.0081.178
get_complex_genes2.0810.0134.354
get_complex_resources0.1990.0000.959
get_db0.0010.0000.001
get_enzsub_resources0.1840.0001.021
get_interaction_resources0.3650.0081.205
get_intercell_categories0.7820.0251.349
get_intercell_generic_categories0.2490.0000.342
get_intercell_resources0.2270.0001.010
get_ontology_db0.0340.0000.034
get_resources0.2440.0041.068
get_signed_ptms7.1880.0278.875
giant_component22.138 0.19033.279
go_annot_download16.890 1.29427.059
go_annot_slim000
go_ontology_download0.0180.0040.022
guide2pharma_download0.0190.0040.023
harmonizome_download0.0220.0000.021
has_extra_attrs11.319 0.13119.531
homologene_download0.0290.0000.029
homologene_raw0.0550.0000.116
homologene_uniprot_orthology0.0270.0000.059
hpo_download3.7540.1427.638
htridb_download0.0270.0030.047
import_all_interactions 5.146 0.36812.860
import_intercell_network0.0500.0080.058
import_kinaseextra_interactions3.0810.1377.195
import_ligrecextra_interactions1.2560.1183.772
import_lncrna_mrna_interactions0.9300.0492.363
import_mirnatarget_interactions1.7430.0434.387
import_omnipath_annotations0.9020.0772.344
import_omnipath_complexes1.0730.0484.249
import_omnipath_enzsub1.8080.0345.306
import_omnipath_interactions0.7270.0042.081
import_omnipath_intercell0.9420.0582.241
import_pathwayextra_interactions1.5360.0584.688
import_post_translational_interactions1.7160.0625.107
import_small_molecule_protein_interactions0.9320.0161.784
import_tf_mirna_interactions1.7320.0914.441
import_tf_target_interactions3.1950.3076.478
import_transcriptional_interactions2.6750.1816.711
inbiomap_download000
inbiomap_raw000
interaction_datasets0.0700.0040.074
interaction_graph0.5410.0041.686
interaction_types0.0630.0000.062
intercell_categories0.0760.0000.075
intercell_consensus_filter2.4060.2184.734
is_ontology_id0.0010.0000.001
is_swissprot0.0740.0000.074
is_trembl0.0680.0000.068
is_uniprot0.0310.0000.032
kegg_info0.0260.0000.027
kegg_open0.0270.0000.027
kegg_pathway_annotations000
kegg_pathway_download0.0290.0000.029
kegg_pathway_list0.0260.0000.026
kegg_pathways_download0.0010.0000.000
kegg_picture0.3770.0085.143
kegg_process0.0540.0040.117
latin_name0.1050.0040.154
load_db0.1850.0040.331
ncbi_taxid0.10.00.1
nichenet_build_model0.0010.0000.000
nichenet_expression_data0.0260.0000.025
nichenet_gr_network0.0870.0000.168
nichenet_gr_network_evex0.0320.0000.064
nichenet_gr_network_harmonizome0.0200.0120.049
nichenet_gr_network_htridb0.0310.0000.031
nichenet_gr_network_omnipath19.929 0.58426.699
nichenet_gr_network_pathwaycommons0.0330.0000.065
nichenet_gr_network_regnetwork0.0300.0000.074
nichenet_gr_network_remap0.0250.0040.061
nichenet_gr_network_trrust0.0250.0050.046
nichenet_ligand_activities000
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0950.0000.188
nichenet_lr_network_guide2pharma0.0300.0000.062
nichenet_lr_network_omnipath0.0740.0040.126
nichenet_lr_network_ramilowski0.0270.0000.043
nichenet_main000
nichenet_networks0.1320.0030.224
nichenet_optimization0.0010.0000.000
nichenet_remove_orphan_ligands0.0880.0000.171
nichenet_results_dir0.0010.0000.000
nichenet_signaling_network0.0730.0080.129
nichenet_signaling_network_cpdb0.0220.0000.022
nichenet_signaling_network_evex0.0240.0000.029
nichenet_signaling_network_harmonizome0.0250.0000.058
nichenet_signaling_network_inbiomap0.0010.0000.000
nichenet_signaling_network_omnipath15.062 0.30425.614
nichenet_signaling_network_pathwaycommons0.0210.0040.025
nichenet_signaling_network_vinayagam0.0210.0000.021
nichenet_test000
nichenet_workarounds000
obo_parser0.2100.0080.413
oma_code0.0560.0000.056
oma_organisms0.2260.0030.233
oma_pairwise0.0250.0000.026
oma_pairwise_genesymbols0.0220.0000.022
oma_pairwise_translated0.0210.0000.021
omnipath6.8160.0437.792
omnipath_cache_autoclean000
omnipath_cache_clean0.010.000.01
omnipath_cache_clean_db0.1340.0110.145
omnipath_cache_download_ready1.0410.0401.134
omnipath_cache_filter_versions0.1930.0120.241
omnipath_cache_get0.1340.0040.137
omnipath_cache_key0.0010.0000.001
omnipath_cache_latest_or_new0.0730.0040.076
omnipath_cache_load0.8250.0203.932
omnipath_cache_move_in0.2180.0080.411
omnipath_cache_remove0.2000.0000.246
omnipath_cache_save0.4430.0240.617
omnipath_cache_search0.0010.0000.000
omnipath_cache_set_ext0.1550.0040.162
omnipath_cache_update_status0.1050.0120.116
omnipath_cache_wipe000
omnipath_get_config_path0.0010.0000.001
omnipath_load_config000
omnipath_log0.0010.0000.000
omnipath_logfile0.0020.0000.002
omnipath_msg0.0080.0000.008
omnipath_reset_config0.0010.0000.000
omnipath_save_config000
omnipath_set_cachedir0.0630.0000.063
omnipath_set_console_loglevel0.0070.0030.009
omnipath_set_logfile_loglevel0.0080.0000.008
omnipath_set_loglevel0.0040.0000.004
omnipath_show_db0.2290.0000.228
omnipath_unlock_cache_db0.0000.0000.001
only_from000
ontology_ensure_id0.0010.0000.014
ontology_ensure_name0.0010.0000.001
ontology_name_id0.0020.0000.001