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This page was generated on 2023-04-12 10:55:39 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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

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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1413/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.7.15  (landing page)
Denes Turei
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 394681b
git_last_commit_date: 2023-04-10 12:20:04 -0400 (Mon, 10 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: OmnipathR
Version: 3.7.15
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OmnipathR_3.7.15.tar.gz
StartedAt: 2023-04-12 08:00:25 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 08:28:50 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 1705.1 seconds
RetCode: 0
Status:   OK  
CheckDir: OmnipathR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OmnipathR_3.7.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.7.15’
* 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 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
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:00:55] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:00:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:00:55] [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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
annotation_categories                77.983  0.039  79.521
curated_ligrec_stats                 39.454  1.201 112.729
filter_extra_attrs                   38.637  0.195  40.034
has_extra_attrs                      10.294 25.066 183.932
with_extra_attrs                     21.843  0.157  33.965
giant_component                      20.007  0.176  45.807
go_annot_download                    16.019  4.042  71.163
extra_attr_values                    17.487  0.420  20.293
nichenet_gr_network_omnipath         16.685  0.196  21.095
pivot_annotations                    15.883  0.414  31.758
extra_attrs_to_cols                  15.193  0.172  15.366
find_all_paths                       12.865  0.111  27.223
extra_attrs                          10.858  0.160  11.039
get_signed_ptms                      10.581  0.012  19.871
nichenet_signaling_network_omnipath  10.443  0.137  13.060
filter_intercell                      9.601  0.328  23.244
pubmed_open                           9.221  0.172  12.087
filter_by_resource                    8.301  0.142  10.706
print_interactions                    7.187  0.179  11.201
curated_ligand_receptor_interactions  6.476  0.229  16.600
collectri                             4.607  0.120   6.447
print_path_vs                         3.442  0.134   7.048
import_transcriptional_interactions   2.824  0.061   7.126
enzsub_graph                          2.558  0.108   5.104
intercell_consensus_filter            2.380  0.088   7.081
dorothea                              2.202  0.104   5.001
biomart_query                         1.742  0.056   9.511
ensembl_id_mapping_table              1.248  0.040  21.631
kegg_picture                          0.135  0.023   5.593
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK
  ‘db_manager.Rmd’ using ‘UTF-8’... OK
  ‘drug_targets.Rmd’ using ‘UTF-8’... OK
  ‘extra_attrs.Rmd’ using ‘UTF-8’... OK
  ‘nichenet.Rmd’ using ‘UTF-8’... OK
  ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK
  ‘paths.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 01:51:20] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] Contains 6 files.
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 01:51:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 01:51:20] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 01:51:21] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 01:51:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-12 01:51:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 01:51:21] [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 Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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
> #  2018-2023
> #  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)
[2023-04-12 08:17:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 08:17:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:17:48] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 08:17:48] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-12 08:17:48] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 08:17:48] [TRACE]   [OmnipathR] Contains 15 files.
[2023-04-12 08:17:48] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-12 08:17:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 08:17:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:17:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 08:17:48] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-12 08:17:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-12 08:17:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:17:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-12 08:17:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:17:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-12 08:17:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:17:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-12 08:17:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:17:49] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 16.879   1.365  60.058

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0360.0000.035
all_uniprots0.0140.0000.014
ancestors0.0120.0000.012
annotated_network1.3470.0654.523
annotation_categories77.983 0.03979.521
biomart_query1.7420.0569.511
bioplex10.0130.0000.013
bioplex20.0120.0000.013
bioplex30.0120.0000.012
bioplex_all0.0120.0000.012
bioplex_hct116_10.0080.0040.013
bma_motif_es0.4590.0201.357
bma_motif_vs0.1530.0000.946
collectri4.6070.1206.447
common_name0.0560.0000.057
consensuspathdb_download0.0000.0000.001
consensuspathdb_raw_table0.0110.0000.011
curated_ligand_receptor_interactions 6.476 0.22916.600
curated_ligrec_stats 39.454 1.201112.729
database_summary1.8530.3264.785
descendants0.0130.0000.014
dorothea2.2020.1045.001
ensembl_dataset0.0140.0000.014
ensembl_id_mapping_table 1.248 0.04021.631
ensembl_id_type0.0090.0000.009
ensembl_name0.1010.0040.104
ensembl_organisms0.4140.0040.420
ensembl_organisms_raw0.3260.0000.328
ensembl_orthology0.0000.0000.001
enzsub_graph2.5580.1085.104
evex_download0.0120.0000.013
extra_attr_values17.487 0.42020.293
extra_attrs10.858 0.16011.039
extra_attrs_to_cols15.193 0.17215.366
filter_by_resource 8.301 0.14210.706
filter_extra_attrs38.637 0.19540.034
filter_intercell 9.601 0.32823.244
filter_intercell_network0.0520.0000.140
find_all_paths12.865 0.11127.223
get_annotation_resources0.1140.0121.073
get_complex_genes1.4970.0604.166
get_complex_resources0.1010.0001.000
get_db0.0000.0000.001
get_enzsub_resources0.1320.0000.842
get_interaction_resources0.1700.0041.041
get_intercell_categories0.4210.0081.002
get_intercell_generic_categories0.0410.0000.041
get_intercell_resources0.1700.0001.014
get_ontology_db0.0200.0040.068
get_resources0.0990.0160.833
get_signed_ptms10.581 0.01219.871
giant_component20.007 0.17645.807
go_annot_download16.019 4.04271.163
go_annot_slim0.0050.0041.128
go_ontology_download0.0180.0000.027
guide2pharma_download0.0140.0000.035
harmonizome_download0.0080.0000.008
has_extra_attrs 10.294 25.066183.932
homologene_download0.0130.0000.018
homologene_raw0.0160.0120.079
homologene_uniprot_orthology0.0070.0040.010
homology_translate0.0010.0000.000
hpo_download1.2440.1112.403
htridb_download0.0130.0000.012
import_all_interactions1.4270.1364.470
import_intercell_network0.0060.0040.010
import_kinaseextra_interactions1.0480.0713.391
import_ligrecextra_interactions0.5870.0752.282
import_lncrna_mrna_interactions0.4750.0211.517
import_mirnatarget_interactions0.8050.0622.643
import_omnipath_annotations0.3500.0331.422
import_omnipath_complexes0.4440.0152.227
import_omnipath_enzsub0.9820.0071.625
import_omnipath_interactions0.2650.0041.271
import_omnipath_intercell0.3620.0400.956
import_pathwayextra_interactions1.0890.1184.142
import_post_translational_interactions1.2290.0353.857
import_small_molecule_protein_interactions0.5480.0111.147
import_tf_mirna_interactions0.9840.0462.901
import_tf_target_interactions1.0590.0362.906
import_transcriptional_interactions2.8240.0617.126
inbiomap_download000
inbiomap_raw000
interaction_datasets0.6060.0201.845
interaction_graph0.5210.0091.985
interaction_types0.0330.0040.069
intercell_categories0.1420.0000.284
intercell_consensus_filter2.3800.0887.081
is_ontology_id0.0010.0000.000
is_swissprot0.0600.0000.119
is_trembl0.0560.0000.104
is_uniprot0.0200.0000.035
kegg_info0.0200.0120.064
kegg_open0.0190.0030.038
kegg_pathway_annotations000
kegg_pathway_download0.0150.0070.038
kegg_pathway_list0.0160.0080.056
kegg_pathways_download000
kegg_picture0.1350.0235.593
kegg_process0.0480.0000.120
latin_name0.1360.0030.348
load_db0.1730.0050.365
ncbi_taxid0.1250.0000.236
nichenet_build_model000
nichenet_expression_data0.0260.0010.059
nichenet_gr_network0.0770.0160.189
nichenet_gr_network_evex0.0160.0030.035
nichenet_gr_network_harmonizome0.0120.0080.035
nichenet_gr_network_htridb0.0190.0000.035
nichenet_gr_network_omnipath16.685 0.19621.095
nichenet_gr_network_pathwaycommons0.0210.0000.020
nichenet_gr_network_regnetwork0.0200.0000.019
nichenet_gr_network_remap0.020.000.02
nichenet_gr_network_trrust0.0190.0000.019
nichenet_ligand_activities000
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0680.0000.068
nichenet_lr_network_guide2pharma0.0200.0040.024
nichenet_lr_network_omnipath0.0610.0030.065
nichenet_lr_network_ramilowski0.0230.0000.022
nichenet_main0.0000.0000.001
nichenet_networks0.0830.0240.107
nichenet_optimization000
nichenet_remove_orphan_ligands0.0540.0040.059
nichenet_results_dir000
nichenet_signaling_network0.060.000.06
nichenet_signaling_network_cpdb0.020.000.02
nichenet_signaling_network_evex0.0820.0040.085
nichenet_signaling_network_harmonizome0.0220.0000.022
nichenet_signaling_network_inbiomap0.0000.0000.001
nichenet_signaling_network_omnipath10.443 0.13713.060
nichenet_signaling_network_pathwaycommons0.010.000.01
nichenet_signaling_network_vinayagam0.0090.0000.009
nichenet_test000
nichenet_workarounds000
obo_parser0.0940.0000.131
omnipath3.2580.0013.259
omnipath_cache_autoclean000
omnipath_cache_clean0.0130.0000.013
omnipath_cache_clean_db0.1000.0080.108
omnipath_cache_download_ready0.3990.0200.439
omnipath_cache_filter_versions0.2290.0040.257
omnipath_cache_get0.1310.0080.139
omnipath_cache_key0.0020.0000.001
omnipath_cache_latest_or_new0.0950.0080.102
omnipath_cache_load0.8470.0233.786
omnipath_cache_move_in0.4010.0250.705
omnipath_cache_remove0.2910.0030.332
omnipath_cache_save0.3340.0090.502
omnipath_cache_search0.0000.0010.005
omnipath_cache_set_ext0.1450.0040.228
omnipath_cache_update_status0.1690.0000.272
omnipath_cache_wipe000
omnipath_get_config_path0.0010.0000.001
omnipath_load_config0.0000.0000.001
omnipath_log000
omnipath_logfile0.0010.0000.001
omnipath_msg0.0100.0000.024
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0460.0030.085
omnipath_set_console_loglevel0.0020.0000.002
omnipath_set_logfile_loglevel0.0010.0000.001
omnipath_set_loglevel0.0000.0020.013
omnipath_show_db0.1510.0010.288
omnipath_unlock_cache_db000
ontology_ensure_id0.0010.0000.001
ontology_ensure_name0.0010.0000.001
ontology_name_id0.0000.0000.001
pathwaycommons_download000
pivot_annotations15.883 0.41431.758
preppi_download0.0000.0000.001
preppi_filter0.0010.0000.001
print_bma_motif_es0.2380.0171.293
print_bma_motif_vs0.1550.0000.950
print_interactions 7.187 0.17911.201
print_path_es0.7320.0173.249
print_path_vs3.4420.1347.048
pubmed_open 9.221 0.17212.087
query_info0.0990.0040.468
ramilowski_download0.0000.0000.001
regnetwork_directions0.0010.0000.001
regnetwork_download0.0010.0000.000
relations_list_to_table0.1720.0010.206
relations_table_to_graph000
relations_table_to_list0.150.000.20
remap_dorothea_download0.0000.0000.001
remap_filtered0.0010.0000.000
remap_tf_target_download0.0010.0000.000
resource_info0.1920.0120.899
resources_colname0.7640.0342.826
simplify_intercell_network0.0010.0000.001
swap_relations0.2080.0080.284
swissprots_only0.0550.0000.055
tfcensus_download0.2240.0040.557
translate_ids0.0010.0000.001
trembls_only0.060.000.10
trrust_download0.0000.0010.001
uniprot_full_id_mapping_table0.0000.0010.001
uniprot_genesymbol_cleanup000
uniprot_id_mapping_table0.0010.0000.017
uniprot_id_type0.0080.0000.009
unique_intercell_network0.0010.0000.001
uploadlists_id_type0.0080.0000.008
vinayagam_download0.0010.0000.001
walk_ontology_tree0.0010.0000.006
with_extra_attrs21.843 0.15733.965
with_references0.7080.0133.225
zenodo_download0.0010.0000.001