Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2024-07-23 11:38 -0400 (Tue, 23 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4280
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1432/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.13.1  (landing page)
Denes Turei
Snapshot Date: 2024-07-22 14:00 -0400 (Mon, 22 Jul 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 1cdbb59
git_last_commit_date: 2024-05-29 08:38:09 -0400 (Wed, 29 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for OmnipathR on nebbiolo2

To the developers/maintainers of the OmnipathR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: OmnipathR
Version: 3.13.1
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.13.1.tar.gz
StartedAt: 2024-07-23 02:26:48 -0400 (Tue, 23 Jul 2024)
EndedAt: 2024-07-23 02:55:14 -0400 (Tue, 23 Jul 2024)
EllapsedTime: 1706.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

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


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.13.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:27:07] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:27:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:27:07] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:27:17] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:27:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:27:17] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: organism_for
> ### Title: Make sure the resource supports the organism and it has the ID
> ### Aliases: organism_for
> 
> ### ** Examples
> 
> organism_for(10116, 'chalmers-gem')
[1] "Rat"
> # [1] "Rat"
> organism_for(6239, 'chalmers-gem')
Error in organism_for(6239, "chalmers-gem") : 
  Organism `6239` (common_name: `Caenorhabditis elegans (Nematode, N2)`; common_name: `Caenorhabditis elegans (Nematode, N2)`) is not supported by resource `chalmers-gem`. Supported organisms: Human, Mouse, Rat, Zebrafish, Drosophila melanogaster (Fruit fly), Caenorhabditis elegans (PRJNA13758).
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

Installation output

OmnipathR.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 15:33:00] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] Contains 8 files.
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 15:33:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 15:33:00] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 15:33:02] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 15:33:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 15:33:02] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

Tests output

OmnipathR.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2024
> #  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> #  File author(s): Alberto Valdeolivas
> #                  Dénes Türei (turei.denes@gmail.com)
> #                  Attila Gábor
> #
> #  Distributed under the MIT (Expat) License.
> #  See accompanying file `LICENSE` or find a copy at
> #      https://directory.fsf.org/wiki/License:Expat
> #
> #  Website: https://r.omnipathdb.org/
> #  Git repo: https://github.com/saezlab/OmnipathR
> #
> 
> 
> library(testthat)
> library(OmnipathR)
[2024-07-23 02:44:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 02:44:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:44:14] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 02:44:14] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-23 02:44:14] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 02:44:14] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-23 02:44:14] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-23 02:44:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 02:44:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:44:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-23 02:44:14] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-23 02:44:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-23 02:44:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:44:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-23 02:44:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:44:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-23 02:44:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:44:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-23 02:44:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 02:44:15] [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 
 21.140   1.982  61.648

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0010.0000.000
all_uniprot_acs0.0230.0000.023
all_uniprots0.010.000.01
ancestors0.0090.0000.010
annotated_network1.8250.0968.057
annotation_categories92.822 0.06797.932
biomart_query 1.379 0.04821.734
bioplex10.0270.0000.028
bioplex20.0240.0000.023
bioplex30.0240.0000.024
bioplex_all0.0250.0000.026
bioplex_hct116_10.0250.0000.042
bma_motif_es0.8150.1532.486
bma_motif_vs0.4380.0201.236
collectri149.788 4.326167.096
common_name0.0650.0030.068
consensuspathdb_download000
consensuspathdb_raw_table0.0340.0000.034
curated_ligand_receptor_interactions 6.018 0.90516.647
curated_ligrec_stats 50.414 8.380138.772
database_summary1.4470.4044.222
descendants0.0230.0000.023
dorothea86.020 1.60293.086
ensembl_dataset0.0090.0000.008
ensembl_id_mapping_table 1.392 0.27314.068
ensembl_id_type0.0050.0000.004
ensembl_name0.1060.0080.114
ensembl_organisms0.2370.0190.257
ensembl_organisms_raw0.2250.0040.263
ensembl_orthology0.0000.0000.001
enzsub_graph2.8010.3375.618
evex_download0.0190.0000.019
evidences000
extra_attr_values11.815 0.58914.487
extra_attrs 9.578 0.12014.244
extra_attrs_to_cols16.935 0.23026.193
filter_by_resource10.251 0.65113.405
filter_extra_attrs33.910 0.34939.898
filter_intercell 9.871 1.12920.900
filter_intercell_network0.0410.0040.046
find_all_paths 8.889 0.32215.523
from_evidences0.0010.0000.001
get_annotation_resources0.2290.0241.342
get_complex_genes2.7020.2037.069
get_complex_resources0.2300.0251.067
get_db000
get_enzsub_resources1.3150.1392.286
get_interaction_resources0.1930.0211.066
get_intercell_categories0.8290.1353.305
get_intercell_generic_categories0.1160.0070.157
get_intercell_resources0.1830.0360.988
get_ontology_db0.0400.0040.053
get_resources0.2040.1081.239
get_signed_ptms 7.646 0.59913.760
giant_component12.991 0.73219.092
go_annot_download18.526 1.17038.548
go_annot_slim0.0000.0000.001
go_ontology_download0.0250.0000.025
guide2pharma_download0.0210.0040.026
harmonizome_download0.0240.0030.026
has_extra_attrs11.162 0.16811.525
homologene_download0.0210.0000.022
homologene_raw0.0290.0040.034
homologene_uniprot_orthology0.020.000.02
hpo_download3.6860.2576.958
htridb_download0.0310.0000.030
import_all_interactions4.1220.4797.574
import_intercell_network0.0240.0000.024
import_kinaseextra_interactions1.7350.2554.002
import_ligrecextra_interactions1.0850.1712.858
import_lncrna_mrna_interactions1.1660.1312.946
import_mirnatarget_interactions2.3580.3956.157
import_omnipath_annotations1.0180.0732.350
import_omnipath_complexes1.1820.1413.720
import_omnipath_enzsub2.0290.1283.603
import_omnipath_interactions0.5040.0161.694
import_omnipath_intercell0.9210.1051.768
import_pathwayextra_interactions1.5560.1214.297
import_post_translational_interactions1.5650.1844.925
import_small_molecule_protein_interactions0.7860.0571.618
import_tf_mirna_interactions1.4970.1614.585
import_tf_target_interactions2.8860.5655.557
import_transcriptional_interactions4.3930.4229.762
inbiomap_download000
inbiomap_raw000
interaction_datasets0.0860.0200.218
interaction_graph0.8670.0972.516
interaction_types0.1090.0080.229
intercell_categories0.1450.0000.306
intercell_consensus_filter2.4680.1915.863
is_ontology_id0.0010.0000.001
is_swissprot0.0730.0040.120
is_trembl0.0800.0000.129
is_uniprot0.0280.0160.096
kegg_info0.0220.0030.041
kegg_open0.0230.0040.055
kegg_pathway_annotations0.0000.0000.001
kegg_pathway_download0.0280.0000.060
kegg_pathway_list0.0280.0000.060
kegg_pathways_download0.0010.0000.000
kegg_picture0.2680.0205.150
kegg_process0.0620.0000.118
latin_name0.2730.0250.606
load_db0.2140.0120.467
ncbi_taxid0.1450.0000.333
nichenet_build_model0.0010.0000.000
nichenet_expression_data0.0340.0000.066
nichenet_gr_network0.1080.0030.222
nichenet_gr_network_evex0.0350.0000.070
nichenet_gr_network_harmonizome0.0330.0040.068
nichenet_gr_network_htridb0.0290.0040.064
nichenet_gr_network_omnipath23.568 0.52433.534
nichenet_gr_network_pathwaycommons0.0260.0000.026
nichenet_gr_network_regnetwork0.0170.0090.026
nichenet_gr_network_remap0.0200.0030.024
nichenet_gr_network_trrust0.0250.0000.024
nichenet_ligand_activities000
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0780.0000.094
nichenet_lr_network_guide2pharma0.0290.0000.045
nichenet_lr_network_omnipath0.0830.0080.185
nichenet_lr_network_ramilowski0.1730.0020.359
nichenet_main0.0000.0000.001
nichenet_networks0.1560.0280.408
nichenet_optimization000
nichenet_remove_orphan_ligands0.0900.0090.195
nichenet_results_dir0.0000.0000.001
nichenet_signaling_network0.0860.0000.230
nichenet_signaling_network_cpdb0.0310.0000.064
nichenet_signaling_network_evex0.0320.0000.081
nichenet_signaling_network_harmonizome0.0260.0000.043
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath17.688 0.69132.332
nichenet_signaling_network_pathwaycommons0.0350.0000.067
nichenet_signaling_network_vinayagam0.0350.0000.064
nichenet_test000
nichenet_workarounds0.0000.0000.001
obo_parser0.2570.0220.656
oma_code0.0640.0000.126
oma_organisms0.1570.0080.342
oma_pairwise0.0250.0040.029
oma_pairwise_genesymbols0.0260.0000.026
oma_pairwise_translated0.0240.0000.024
omnipath5.4970.0976.668
omnipath_cache_autoclean000
omnipath_cache_clean0.0060.0000.006
omnipath_cache_clean_db0.1320.0080.140
omnipath_cache_download_ready0.6190.0610.714
omnipath_cache_filter_versions0.1980.0240.245
omnipath_cache_get0.1890.0040.193
omnipath_cache_key0.0020.0000.002
omnipath_cache_latest_or_new0.1190.0040.124
omnipath_cache_load0.6280.0673.193
omnipath_cache_move_in0.2320.0520.289
omnipath_cache_remove0.1060.0090.117
omnipath_cache_save0.2220.0400.377
omnipath_cache_search0.0000.0010.001
omnipath_cache_set_ext0.0960.0150.114
omnipath_cache_update_status0.1760.0770.253
omnipath_cache_wipe000
omnipath_get_config_path0.0000.0000.001
omnipath_load_config000
omnipath_log000
omnipath_logfile0.0020.0000.002
omnipath_msg0.0000.0080.008
omnipath_reset_config000
omnipath_save_config0.0010.0000.000
omnipath_set_cachedir0.0360.0000.036
omnipath_set_console_loglevel0.0040.0000.003
omnipath_set_logfile_loglevel0.0040.0000.003
omnipath_set_loglevel0.0020.0000.002
omnipath_show_db0.0680.0040.072
omnipath_unlock_cache_db0.0000.0000.001
only_from000
ontology_ensure_id0.0010.0000.001
ontology_ensure_name0.0000.0000.001
ontology_name_id0.0000.0010.001