Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-08-08 11:46 -0400 (Thu, 08 Aug 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4703
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4402
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4471
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4420
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4413
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 1436/2254HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.13.1  (landing page)
Denes Turei
Snapshot Date: 2024-08-07 14:00 -0400 (Wed, 07 Aug 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  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for OmnipathR on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: OmnipathR
Version: 3.13.1
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.13.1.tar.gz
StartedAt: 2024-08-08 07:44:59 -0000 (Thu, 08 Aug 2024)
EndedAt: 2024-08-08 08:08:07 -0000 (Thu, 08 Aug 2024)
EllapsedTime: 1387.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --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: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.13.1’
* 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
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 07:45:23] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] Contains 1 files.
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 07:45:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-08-08 07:45:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 07:45:23] [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
[2024-08-08 07:45:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-08 07:45:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 07:45:36] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-08-08 07:45:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-08-08 07:45:36] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-08-08 07:45:36] [TRACE]   [OmnipathR] Contains 1 files.
[2024-08-08 07:45:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-08-08 07:45:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-08 07:45:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 07:45:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-08-08 07:45:36] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-08-08 07:45:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-08-08 07:45:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 07:45:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-08-08 07:45:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 07:45:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-08-08 07:45:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 07:45:37] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-08-08 07:45:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 07:45:37] [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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package textcomp Error: Symbol \textrightarrow not provided by
(textcomp)                font family ptm in TS1 encoding.
(textcomp)                Default family used instead.

See the textcomp package documentation for explanation.
* checking PDF version of manual without index ... ERROR
* DONE

Status: 2 ERRORs, 1 WARNING, 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/R/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/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
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-07 19:41:05] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] Contains 6 files.
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-07 19:41:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-07 19:41:05] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-07 19:41:07] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] Contains 1 files.
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-07 19:41:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-08-07 19:41:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-07 19:41:07] [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: aarch64-unknown-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)
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 08:06:42] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] Contains 1 files.
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 08:06:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-08-08 08:06:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-08-08 08:06:42] [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 
 12.288   1.027  69.229

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0290.0000.028
all_uniprots0.0150.0000.015
ancestors0.0140.0000.014
annotated_network 1.983 0.245378.031
annotation_categories105.137 0.089122.469
biomart_query0.8260.0526.473
bioplex10.0160.0000.017
bioplex20.0150.0000.016
bioplex30.0160.0000.016
bioplex_all0.0160.0000.016
bioplex_hct116_10.0150.0000.016
bma_motif_es0.3960.0121.866
bma_motif_vs0.2260.0001.224
collectri164.471 1.253194.059
common_name0.030.000.03
consensuspathdb_download000
consensuspathdb_raw_table0.0150.0000.016
curated_ligand_receptor_interactions 5.227 0.81418.676
curated_ligrec_stats 31.430 2.641132.643
database_summary1.4830.0203.251
descendants0.0490.0000.049
dorothea86.466 0.63489.543
ensembl_dataset0.0110.0000.010
ensembl_id_mapping_table 0.930 0.02411.187
ensembl_id_type0.0020.0000.003
ensembl_name0.0570.0000.057
ensembl_organisms0.1470.0000.147
ensembl_organisms_raw0.1400.0000.141
ensembl_orthology000
enzsub_graph2.1520.1394.539
evex_download0.0170.0000.017
evidences0.0010.0000.000
extra_attr_values14.781 0.46316.602
extra_attrs7.0710.0877.173
extra_attrs_to_cols12.699 0.11512.843
filter_by_resource7.2170.2898.903
filter_extra_attrs25.776 0.26027.002
filter_intercell 6.946 0.20711.477
filter_intercell_network0.0280.0040.032
find_all_paths6.2480.0486.307
from_evidences000
get_annotation_resources0.0780.0031.043
get_complex_genes1.2240.0442.863
get_complex_resources0.0790.0001.043
get_db000
get_enzsub_resources0.1410.0001.057
get_interaction_resources0.0790.0041.015
get_intercell_categories0.3420.0201.019
get_intercell_generic_categories0.0470.0000.047
get_intercell_resources0.0810.0001.045
get_ontology_db0.0150.0000.015
get_resources0.1510.0001.084
get_signed_ptms5.8180.0326.825
giant_component11.371 0.10412.616
go_annot_download11.198 0.37818.189
go_annot_slim000
go_ontology_download0.0100.0040.015
guide2pharma_download0.0100.0040.014
harmonizome_download0.0130.0000.013
has_extra_attrs7.3410.0087.362
homologene_download0.0160.0000.015
homologene_raw0.0240.0000.023
homologene_uniprot_orthology0.0140.0000.014
hpo_download 2.468 0.15729.951
htridb_download0.0120.0040.015
import_all_interactions2.2380.0655.273
import_intercell_network0.0140.0000.014
import_kinaseextra_interactions1.3540.0523.753
import_ligrecextra_interactions0.6700.0392.652
import_lncrna_mrna_interactions0.6020.0402.256
import_mirnatarget_interactions0.9700.0603.117
import_omnipath_annotations0.5010.0041.965
import_omnipath_complexes0.5860.0122.683
import_omnipath_enzsub1.1910.0082.127
import_omnipath_interactions0.2500.0041.218
import_omnipath_intercell0.5080.0191.339
import_pathwayextra_interactions0.8070.0252.923
import_post_translational_interactions0.7840.0402.897
import_small_molecule_protein_interactions0.4480.0360.981
import_tf_mirna_interactions0.7190.0242.524
import_tf_target_interactions1.3450.0673.489
import_transcriptional_interactions2.6150.0484.978
inbiomap_download0.0010.0000.000
inbiomap_raw000
interaction_datasets0.0450.0000.046
interaction_graph0.3510.0241.340
interaction_types0.0410.0040.045
intercell_categories0.0620.0040.066
intercell_consensus_filter1.4370.0602.770
is_ontology_id0.0010.0000.000
is_swissprot0.0960.0000.096
is_trembl0.0370.0000.037
is_uniprot0.0120.0040.016
kegg_info0.0150.0000.014
kegg_open0.0150.0000.014
kegg_pathway_annotations000
kegg_pathway_download0.0140.0000.015
kegg_pathway_list0.0150.0000.015
kegg_pathways_download0.0000.0000.001
kegg_picture0.0860.0121.485
kegg_process0.0280.0000.028
latin_name0.0520.0000.051
load_db0.0900.0040.094
ncbi_taxid0.0510.0000.051
nichenet_build_model000
nichenet_expression_data0.0150.0000.015
nichenet_gr_network0.0420.0000.042
nichenet_gr_network_evex0.0100.0040.014
nichenet_gr_network_harmonizome0.0150.0000.015
nichenet_gr_network_htridb0.0150.0000.014
nichenet_gr_network_omnipath14.993 0.23116.558
nichenet_gr_network_pathwaycommons0.0140.0000.014
nichenet_gr_network_regnetwork0.0130.0000.014
nichenet_gr_network_remap0.0140.0000.014
nichenet_gr_network_trrust0.0100.0040.014
nichenet_ligand_activities000
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0370.0040.041
nichenet_lr_network_guide2pharma0.0140.0000.014
nichenet_lr_network_omnipath0.0420.0000.042
nichenet_lr_network_ramilowski0.0140.0000.014
nichenet_main0.0000.0000.001
nichenet_networks0.0630.0040.067
nichenet_optimization000
nichenet_remove_orphan_ligands0.0410.0000.040
nichenet_results_dir000
nichenet_signaling_network0.0430.0000.043
nichenet_signaling_network_cpdb0.0150.0000.015
nichenet_signaling_network_evex0.0140.0000.015
nichenet_signaling_network_harmonizome0.0140.0000.014
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath 9.795 0.24011.489
nichenet_signaling_network_pathwaycommons0.0140.0000.014
nichenet_signaling_network_vinayagam0.0140.0000.014
nichenet_test000
nichenet_workarounds0.0010.0000.000
obo_parser0.0970.0081.099
oma_code0.0260.0000.026
oma_organisms0.1080.0000.108
oma_pairwise0.0150.0000.014
oma_pairwise_genesymbols0.0140.0000.014
oma_pairwise_translated0.0130.0000.014
omnipath4.4670.0234.509
omnipath_cache_autoclean000
omnipath_cache_clean0.0090.0000.009
omnipath_cache_clean_db0.1080.0080.116
omnipath_cache_download_ready0.5610.0350.616
omnipath_cache_filter_versions0.1280.0130.148
omnipath_cache_get0.1230.0000.124
omnipath_cache_key0.0020.0000.001
omnipath_cache_latest_or_new0.1310.0040.136
omnipath_cache_load0.5420.0112.948
omnipath_cache_move_in0.2090.0160.231
omnipath_cache_remove0.1730.0080.186
omnipath_cache_save0.2090.0120.402
omnipath_cache_search000
omnipath_cache_set_ext0.1090.0040.142
omnipath_cache_update_status0.1320.0040.137
omnipath_cache_wipe000
omnipath_get_config_path0.0010.0000.001
omnipath_load_config000
omnipath_log000
omnipath_logfile0.0020.0000.002
omnipath_msg0.0080.0000.008
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0400.0000.041
omnipath_set_console_loglevel0.0050.0000.005
omnipath_set_logfile_loglevel0.0050.0000.005
omnipath_set_loglevel0.0020.0000.002
omnipath_show_db0.0650.0000.066
omnipath_unlock_cache_db0.0000.0000.001
only_from000
ontology_ensure_id0.0010.0000.000
ontology_ensure_name0.0010.0000.000
ontology_name_id0.0010.0000.001