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This page was generated on 2024-03-04 11:39:37 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 1437/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.11.3  (landing page)
Denes Turei
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 4183d8d
git_last_commit_date: 2024-02-16 10:54:02 -0500 (Fri, 16 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for OmnipathR on merida1


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: 3.11.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.11.3.tar.gz
StartedAt: 2024-03-02 07:55:42 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 08:19:59 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 1457.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.11.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.11.3’
* 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 ... WARNING
Found the following significant warnings:
  Warning: OmnipathR.Rd:3: docType ‘_PACKAGE’ is unrecognized
See ‘/Users/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00install.out’ for details.
* 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 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 whether startup messages can be suppressed ... NOTE
[2024-03-02 07:56:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 07:56:25] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 07:56:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-02 07:56:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 07:56:25] [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
[2024-03-02 07:56:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-02 07:56:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 07:56:51] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 07:56:51] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-02 07:56:51] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 07:56:51] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-02 07:56:51] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-02 07:56:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-02 07:56:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 07:56:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 07:56:52] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-02 07:56:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-02 07:56:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 07:56:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-02 07:56:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 07:56:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-02 07:56:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 07:56:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-02 07:56:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 07:56:52] [TRACE]   [OmnipathR] Cache locked: FALSE
oma_pairwise_genesymbols: no visible binding for global variable
  ‘id_organism_a’
oma_pairwise_genesymbols: no visible binding for global variable
  ‘id_organism_b’
Undefined global functions or variables:
  id_organism_a id_organism_b
* checking Rd files ... WARNING
prepare_Rd: OmnipathR.Rd:3: docType ‘_PACKAGE’ is unrecognized
* 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: oma_pairwise_genesymbols
> ### Title: Orthologous pairs of gene symbols between two organisms
> ### Aliases: oma_pairwise_genesymbols
> 
> ### ** Examples
> 
> oma_pairwise_genesmybols("human", "mouse")
Error in oma_pairwise_genesmybols("human", "mouse") : 
  could not find function "oma_pairwise_genesmybols"
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: OmnipathR.Rd:3: docType ‘_PACKAGE’ is unrecognized
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2024-03-01 16:04:03] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-01 16:04:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:03] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:03] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-01 16:04:03] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:04] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:08] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-01 16:04:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:08] [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) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2023
> #  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)
[2024-03-02 08:18:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-02 08:18:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 08:18:36] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 08:18:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-02 08:18:37] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 08:18:37] [TRACE]   [OmnipathR] Contains 64 files.
[2024-03-02 08:18:37] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-02 08:18:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-02 08:18:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 08:18:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 08:18:37] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-02 08:18:37] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-02 08:18:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 08:18:37] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-02 08:18:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 08:18:37] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-02 08:18:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 08:18:37] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-02 08:18:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 08:18:37] [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 
 20.919   1.572  46.696

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0010.002
all_uniprot_acs0.0490.0040.057
all_uniprots0.0230.0030.027
ancestors0.0240.0020.028
annotated_network 2.872 0.24613.124
annotation_categories101.621 0.746119.891
biomart_query1.2850.1293.405
bioplex10.0230.0030.030
bioplex20.0240.0030.028
bioplex30.0230.0020.028
bioplex_all0.0250.0020.032
bioplex_hct116_10.0260.0030.036
bma_motif_es0.6300.0501.465
bma_motif_vs0.3140.0111.026
collectri227.216 2.967269.654
common_name0.0410.0020.049
consensuspathdb_download0.0000.0010.001
consensuspathdb_raw_table0.0230.0020.028
curated_ligand_receptor_interactions 8.588 0.40518.683
curated_ligrec_stats 54.805 2.069120.269
database_summary2.4750.0723.927
descendants0.0230.0030.035
dorothea120.457 1.233163.618
ensembl_dataset0.0140.0000.018
ensembl_id_mapping_table 1.359 0.10121.776
ensembl_id_type0.0040.0010.005
ensembl_name0.0800.0020.184
ensembl_organisms0.3330.0080.740
ensembl_organisms_raw0.2520.0070.552
ensembl_orthology0.0010.0010.012
enzsub_graph 3.975 0.12610.154
evex_download0.0300.0030.080
evidences0.0000.0000.001
extra_attr_values27.817 0.62154.498
extra_attrs15.969 0.24732.572
extra_attrs_to_cols23.516 0.23727.601
filter_by_resource13.010 0.32015.845
filter_extra_attrs49.485 0.45468.579
filter_intercell 8.918 1.00830.816
filter_intercell_network0.0470.0070.550
find_all_paths12.120 0.36125.042
from_evidences0.0000.0000.001
get_annotation_resources0.1340.0150.903
get_complex_genes2.0290.1365.624
get_complex_resources0.1250.0060.656
get_db0.0010.0010.002
get_enzsub_resources0.1820.0090.782
get_interaction_resources0.1340.0110.815
get_intercell_categories0.6190.0781.845
get_intercell_generic_categories0.0700.0050.180
get_intercell_resources0.1260.0060.675
get_ontology_db0.0230.0020.091
get_resources0.1650.0090.746
get_signed_ptms11.282 0.11118.380
giant_component20.787 0.71929.711
go_annot_download13.947 1.43624.687
go_annot_slim0.0000.0010.002
go_ontology_download0.0230.0030.032
guide2pharma_download0.0240.0030.032
harmonizome_download0.0230.0030.030
has_extra_attrs15.198 0.18318.931
homologene_download0.0230.0030.039
homologene_raw0.0370.0030.050
homologene_uniprot_orthology0.0240.0030.040
hpo_download3.4650.5546.866
htridb_download0.0240.0020.034
import_all_interactions4.0850.2068.616
import_intercell_network0.0240.0020.030
import_kinaseextra_interactions2.5960.1284.230
import_ligrecextra_interactions1.3570.0912.640
import_lncrna_mrna_interactions0.7990.0621.880
import_mirnatarget_interactions1.8100.0903.442
import_omnipath_annotations0.8310.0501.838
import_omnipath_complexes0.9780.0652.482
import_omnipath_enzsub2.3560.0343.271
import_omnipath_interactions0.4730.0111.040
import_omnipath_intercell0.8300.0691.472
import_pathwayextra_interactions1.3970.0922.838
import_post_translational_interactions1.4620.0892.928
import_small_molecule_protein_interactions0.7870.0481.331
import_tf_mirna_interactions1.2750.0772.500
import_tf_target_interactions2.5310.1114.351
import_transcriptional_interactions4.8830.1647.309
inbiomap_download0.0000.0010.001
inbiomap_raw000
interaction_datasets0.0670.0040.084
interaction_graph0.7610.0141.393
interaction_types0.0720.0040.094
intercell_categories0.1020.0050.131
intercell_consensus_filter2.4400.2093.832
is_ontology_id0.0010.0010.001
is_swissprot0.0580.0040.077
is_trembl0.0580.0050.079
is_uniprot0.0240.0030.033
kegg_info0.0230.0020.029
kegg_open0.0230.0020.030
kegg_pathway_annotations0.0010.0010.001
kegg_pathway_download0.0240.0030.033
kegg_pathway_list0.0230.0030.034
kegg_pathways_download0.0000.0000.001
kegg_picture0.1330.0141.572
kegg_process0.0430.0040.047
latin_name0.0820.0010.100
load_db0.1560.0060.197
ncbi_taxid0.0830.0010.104
nichenet_build_model0.0000.0000.001
nichenet_expression_data0.0230.0020.034
nichenet_gr_network0.0720.0060.095
nichenet_gr_network_evex0.0240.0020.033
nichenet_gr_network_harmonizome0.0250.0020.034
nichenet_gr_network_htridb0.0240.0020.036
nichenet_gr_network_omnipath23.310 0.76431.420
nichenet_gr_network_pathwaycommons0.0230.0020.029
nichenet_gr_network_regnetwork0.0230.0020.031
nichenet_gr_network_remap0.0240.0030.032
nichenet_gr_network_trrust0.0230.0020.030
nichenet_ligand_activities0.0010.0020.002
nichenet_ligand_target_links0.0000.0010.002
nichenet_ligand_target_matrix0.0000.0000.001
nichenet_lr_network0.0710.0060.092
nichenet_lr_network_guide2pharma0.0240.0030.032
nichenet_lr_network_omnipath0.0690.0060.094
nichenet_lr_network_ramilowski0.0230.0020.027
nichenet_main0.0010.0000.001
nichenet_networks0.1570.0120.198
nichenet_optimization0.0000.0000.001
nichenet_remove_orphan_ligands0.0700.0050.095
nichenet_results_dir000
nichenet_signaling_network0.0750.0070.127
nichenet_signaling_network_cpdb0.0250.0030.029
nichenet_signaling_network_evex0.0250.0020.031
nichenet_signaling_network_harmonizome0.0240.0020.033
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath18.213 0.51323.161
nichenet_signaling_network_pathwaycommons0.0830.0050.102
nichenet_signaling_network_vinayagam0.0250.0020.034
nichenet_test0.0000.0010.001
nichenet_workarounds0.0000.0000.001
obo_parser0.1710.0090.264
oma_code0.0410.0010.048
oma_organisms0.1070.0040.131
oma_pairwise0.0230.0020.030