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This page was generated on 2024-07-24 09:03 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4747
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4489
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4518
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4467
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 1467/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.12.1  (landing page)
Denes Turei
Snapshot Date: 2024-07-21 14:00 -0400 (Sun, 21 Jul 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_19
git_last_commit: a310819
git_last_commit_date: 2024-05-29 08:39:10 -0400 (Wed, 29 May 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for OmnipathR on nebbiolo1

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: 3.12.1
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OmnipathR_3.12.1.tar.gz
StartedAt: 2024-07-22 03:05:10 -0400 (Mon, 22 Jul 2024)
EndedAt: 2024-07-22 03:35:26 -0400 (Mon, 22 Jul 2024)
EllapsedTime: 1815.4 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OmnipathR_3.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-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 ‘3.12.1’
* 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
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:05:31] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:05:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-22 03:05:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:05:31] [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
[2024-07-22 03:05:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 03:05:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:05:41] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 03:05:41] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-22 03:05:41] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 03:05:41] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-22 03:05:41] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-22 03:05:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 03:05:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:05:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 03:05:41] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-22 03:05:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-22 03:05:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:05:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-22 03:05:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:05:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-22 03:05:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:05:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-22 03:05:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:05:42] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘oma_pairwise_translated’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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
[2024-07-21 16:08:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-21 16:08:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:08:17] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-21 16:08:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-21 16:08:17] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-21 16:08:17] [TRACE]   [OmnipathR] Contains 6 files.
[2024-07-21 16:08:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-21 16:08:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-21 16:08:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:08:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-21 16:08:17] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-21 16:08:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-21 16:08:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:08:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-21 16:08:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:08:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-21 16:08:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:08:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-21 16:08:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:08:18] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:08:19] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:08:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-21 16:08:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:08:19] [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)
[2024-07-22 03:21:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 03:21:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:21:58] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 03:21:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-22 03:21:58] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 03:21:59] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-22 03:21:59] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-22 03:21:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-22 03:21:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:21:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-07-22 03:21:59] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-22 03:21:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-22 03:21:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:21:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-22 03:21:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:21:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-22 03:21:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:21:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-22 03:21:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-22 03:21:59] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 23.960   1.929  70.727

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0010.0000.000
all_uniprot_acs0.0220.0000.022
all_uniprots0.0120.0000.013
ancestors0.0070.0040.011
annotated_network1.8680.2567.039
annotation_categories81.751 0.07383.629
biomart_query 1.160 0.06913.868
bioplex10.0280.0000.060
bioplex20.0250.0000.057
bioplex30.0220.0040.042
bioplex_all0.0280.0000.060
bioplex_hct116_10.0270.0000.059
bma_motif_es0.7590.0282.208
bma_motif_vs0.4670.0041.550
collectri161.062 4.000173.920
common_name0.0420.0000.041
consensuspathdb_download0.0000.0000.001
consensuspathdb_raw_table0.0200.0030.023
curated_ligand_receptor_interactions 8.266 0.48419.506
curated_ligrec_stats 49.151 5.656134.397
database_summary2.4460.1615.466
descendants0.0330.0000.033
dorothea83.585 1.46188.464
ensembl_dataset0.0090.0000.009
ensembl_id_mapping_table 1.521 0.02121.991
ensembl_id_type0.0060.0000.006
ensembl_name0.1450.0000.289
ensembl_organisms0.3380.0000.587
ensembl_organisms_raw0.2950.0120.592
ensembl_orthology000
enzsub_graph2.8530.1005.185
evex_download0.0140.0000.014
evidences000
extra_attr_values21.856 0.74826.402
extra_attrs8.9460.1639.145
extra_attrs_to_cols17.089 0.47919.139
filter_by_resource5.7640.1938.024
filter_extra_attrs31.032 0.23934.615
filter_intercell5.9630.3629.781
filter_intercell_network0.0200.0030.023
find_all_paths7.3680.0797.447
from_evidences000
get_annotation_resources0.1930.0040.977
get_complex_genes2.0230.1044.005
get_complex_resources0.2150.0121.248
get_db0.0000.0010.001
get_enzsub_resources0.2240.0001.040
get_interaction_resources0.3200.0081.049
get_intercell_categories0.7150.0361.449
get_intercell_generic_categories0.1690.0000.257
get_intercell_resources0.1950.0120.943
get_ontology_db0.0320.0000.032
get_resources0.1990.0110.868
get_signed_ptms6.9360.0037.664
giant_component13.557 0.17717.236
go_annot_download20.486 1.16545.436
go_annot_slim000
go_ontology_download0.0210.0040.041
guide2pharma_download0.0210.0040.057
harmonizome_download0.0310.0000.071
has_extra_attrs16.394 1.06223.753
homologene_download0.0200.0020.022
homologene_raw0.0380.0040.042
homologene_uniprot_orthology0.0320.0000.032
hpo_download3.7270.6787.981
htridb_download0.0140.0160.031
import_all_interactions 3.860 0.41810.405
import_intercell_network0.0250.0000.041
import_kinaseextra_interactions2.4570.1897.167
import_ligrecextra_interactions1.7870.2665.449
import_lncrna_mrna_interactions1.2220.2044.075
import_mirnatarget_interactions2.1810.1695.507
import_omnipath_annotations1.1230.1302.787
import_omnipath_complexes1.0180.1293.290
import_omnipath_enzsub1.8900.1652.727
import_omnipath_interactions0.5510.0321.316
import_omnipath_intercell0.7950.0891.374
import_pathwayextra_interactions1.4340.1703.661
import_post_translational_interactions1.4020.1543.341
import_small_molecule_protein_interactions0.8740.2372.072
import_tf_mirna_interactions1.4920.1604.283
import_tf_target_interactions2.5370.3756.399
import_transcriptional_interactions4.6000.3779.372
inbiomap_download000
inbiomap_raw0.0000.0000.001
interaction_datasets0.2380.0190.256
interaction_graph0.8030.0601.685
interaction_types0.0880.0060.095
intercell_categories0.1400.0040.144
intercell_consensus_filter2.6280.5107.000
is_ontology_id0.0000.0000.001
is_swissprot0.0760.0080.184
is_trembl0.0950.0080.218
is_uniprot0.0410.0000.072
kegg_info0.0330.0040.069
kegg_open0.0310.0000.062
kegg_pathway_annotations0.0000.0000.001
kegg_pathway_download0.0340.0000.067
kegg_pathway_list0.0340.0000.067
kegg_pathways_download0.0000.0000.017
kegg_picture0.5910.0725.277
kegg_process0.0560.0060.070
latin_name0.0970.0000.097
load_db0.1740.0120.186
ncbi_taxid0.0850.0100.095
nichenet_build_model0.0000.0000.001
nichenet_expression_data0.0270.0040.030
nichenet_gr_network0.0890.0120.101
nichenet_gr_network_evex0.0230.0070.030
nichenet_gr_network_harmonizome0.0310.0000.030
nichenet_gr_network_htridb0.0190.0080.027
nichenet_gr_network_omnipath18.513 0.79121.391
nichenet_gr_network_pathwaycommons0.0150.0000.015
nichenet_gr_network_regnetwork0.0130.0000.012
nichenet_gr_network_remap0.0120.0000.012
nichenet_gr_network_trrust0.0080.0040.012
nichenet_ligand_activities0.0010.0000.001
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0330.0050.038
nichenet_lr_network_guide2pharma0.0130.0000.014
nichenet_lr_network_omnipath0.1240.0000.124
nichenet_lr_network_ramilowski0.0240.0000.024
nichenet_main0.0000.0010.001
nichenet_networks0.0820.0070.089
nichenet_optimization0.0010.0000.000
nichenet_remove_orphan_ligands0.0350.0000.035
nichenet_results_dir0.0000.0000.001
nichenet_signaling_network0.0320.0040.037
nichenet_signaling_network_cpdb0.0120.0000.012
nichenet_signaling_network_evex0.0120.0000.012
nichenet_signaling_network_harmonizome0.0120.0000.012
nichenet_signaling_network_inbiomap0.0010.0000.000
nichenet_signaling_network_omnipath15.531 1.08127.980
nichenet_signaling_network_pathwaycommons0.0390.0000.102
nichenet_signaling_network_vinayagam0.0320.0040.066
nichenet_test0.0000.0000.001
nichenet_workarounds000
obo_parser0.2210.0200.407
oma_code0.0630.0000.128
oma_organisms0.3040.0200.628
oma_pairwise0.0310.0080.072
oma_pairwise_genesymbols0.0420.0000.074
omnipath7.4850.3338.761
omnipath_cache_autoclean000
omnipath_cache_clean0.0170.0000.017
omnipath_cache_clean_db0.2290.0030.233
omnipath_cache_download_ready1.1500.1261.897
omnipath_cache_filter_versions0.3220.0480.394
omnipath_cache_get0.2350.0240.259
omnipath_cache_key0.0030.0000.003
omnipath_cache_latest_or_new0.1840.0080.194
omnipath_cache_load1.1550.1294.170
omnipath_cache_move_in0.2390.0290.272
omnipath_cache_remove0.1220.0230.152
omnipath_cache_save0.3260.0410.506
omnipath_cache_search0.0020.0000.001
omnipath_cache_set_ext0.2250.0720.302
omnipath_cache_update_status0.2060.0120.218
omnipath_cache_wipe0.0010.0000.001
omnipath_get_config_path0.0010.0000.001
omnipath_load_config000
omnipath_log0.0000.0010.001
omnipath_logfile0.0000.0020.002
omnipath_msg0.0140.0000.014
omnipath_reset_config000
omnipath_save_config0.0000.0010.000
omnipath_set_cachedir0.0600.0160.078
omnipath_set_console_loglevel0.0030.0000.003
omnipath_set_logfile_loglevel0.0020.0000.002
omnipath_set_loglevel0.0020.0000.001
omnipath_show_db0.1040.0120.117
omnipath_unlock_cache_db0.0000.0000.001
only_from0.0010.0000.000
ontology_ensure_id0.0010.0000.001
ontology_ensure_name0.0010.0000.001
ontology_name_id0.0020.0000.002