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This page was generated on 2024-05-13 11:32:09 -0400 (Mon, 13 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4378
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Package 1422/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.13.0  (landing page)
Denes Turei
Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 May 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 8bb9bf7
git_last_commit_date: 2024-04-30 11:18:21 -0400 (Tue, 30 Apr 2024)
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  

CHECK results for OmnipathR on kjohnson1


To the developers/maintainers of the OmnipathR package:
- 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: 3.13.0
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_3.13.0.tar.gz
StartedAt: 2024-05-12 21:47:55 -0400 (Sun, 12 May 2024)
EndedAt: 2024-05-12 21:57:26 -0400 (Sun, 12 May 2024)
EllapsedTime: 571.2 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_3.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/OmnipathR.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.13.0’
* 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 whether startup messages can be suppressed ... NOTE
[2024-05-12 21:48:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-12 21:48:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:48:15] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-12 21:48:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-12 21:48:15] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-12 21:48:15] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-12 21:48:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-12 21:48:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-12 21:48:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:48:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-12 21:48:15] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-05-12 21:48:15] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-12 21:48:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:48:15] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-12 21:48:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:48:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-12 21:48:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:48:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-12 21:48:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:48:16] [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
[2024-05-12 21:48:27] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-12 21:48:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:48:27] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-12 21:48:27] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-12 21:48:27] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-12 21:48:27] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-12 21:48:27] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-12 21:48:27] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-12 21:48:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:48:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-12 21:48:28] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-05-12 21:48:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-12 21:48:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:48:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-12 21:48:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:48:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-12 21:48:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:48:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-12 21:48:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:48:28] [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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/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-arm64/Resources/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
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:32] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:32] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:34] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-11 11:39:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:34] [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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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
> #  2018-2024
> #  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)
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:56:55] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:56:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-12 21:56:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-12 21:56:55] [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 
  9.933   0.888  14.601

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0010.0010.001
all_uniprot_acs0.0210.0020.023
all_uniprots0.0110.0010.012
ancestors0.0100.0020.011
annotated_network1.6560.1553.336
annotation_categories104.808 0.214105.336
biomart_query0.8630.0702.565
bioplex10.0120.0010.013
bioplex20.0090.0010.011
bioplex30.0100.0020.012
bioplex_all0.0100.0010.011
bioplex_hct116_10.0100.0010.011
bma_motif_es0.2890.0320.600
bma_motif_vs0.1520.0080.213
collectri98.030 0.59898.956
common_name0.0210.0000.021
consensuspathdb_download000
consensuspathdb_raw_table0.0500.0020.051
curated_ligand_receptor_interactions3.8900.2384.914
curated_ligrec_stats25.846 1.17635.532
database_summary1.1300.0361.248
descendants0.0120.0010.014
dorothea56.031 0.36156.581
ensembl_dataset0.0080.0010.008
ensembl_id_mapping_table 0.910 0.07413.131
ensembl_id_type0.0040.0010.004
ensembl_name0.0500.0010.050
ensembl_organisms0.1200.0040.125
ensembl_organisms_raw0.1060.0020.109
ensembl_orthology0.0000.0010.001
enzsub_graph1.0570.0571.246
evex_download0.0060.0010.007
evidences000
extra_attr_values 9.702 0.13510.055
extra_attrs5.5160.0285.556
extra_attrs_to_cols9.8710.0449.941
filter_by_resource5.1930.0895.376
filter_extra_attrs18.276 0.07218.427
filter_intercell6.6970.3797.449
filter_intercell_network0.0210.0030.024
find_all_paths4.3180.1404.472
from_evidences000
get_annotation_resources0.0350.0040.198
get_complex_genes1.2700.0471.471
get_complex_resources0.0590.0050.117
get_db0.0000.0000.001
get_enzsub_resources0.0580.0040.110
get_interaction_resources0.1000.0060.154
get_intercell_categories0.2740.0380.342
get_intercell_generic_categories0.0360.0040.040
get_intercell_resources0.0580.0040.214
get_ontology_db0.0110.0010.013
get_resources0.0620.0060.297
get_signed_ptms5.1940.1045.362
giant_component10.238 0.30310.730
go_annot_download 9.735 0.43110.436
go_annot_slim0.0000.0010.000
go_ontology_download0.0100.0010.012
guide2pharma_download0.0090.0010.011
harmonizome_download0.0090.0020.010
has_extra_attrs4.9850.0715.075
homologene_download0.0090.0020.011
homologene_raw0.0180.0020.019
homologene_uniprot_orthology0.0080.0010.009
hpo_download2.5750.1333.723
htridb_download0.0100.0010.012
import_all_interactions1.8480.0862.142
import_intercell_network0.0110.0010.013
import_kinaseextra_interactions0.7770.0520.971
import_ligrecextra_interactions0.3930.0310.647
import_lncrna_mrna_interactions0.4270.0330.542
import_mirnatarget_interactions0.8170.0510.963
import_omnipath_annotations0.5810.0440.874
import_omnipath_complexes0.5450.0380.695
import_omnipath_enzsub1.0130.0101.070
import_omnipath_interactions0.1850.0050.420
import_omnipath_intercell0.4350.0360.514
import_pathwayextra_interactions0.7460.0451.156
import_post_translational_interactions0.7480.0481.081
import_small_molecule_protein_interactions0.3680.0260.424
import_tf_mirna_interactions0.6230.0441.013
import_tf_target_interactions1.1660.0471.317
import_transcriptional_interactions1.6980.0621.856
inbiomap_download000
inbiomap_raw000
interaction_datasets0.0360.0030.039
interaction_graph0.3530.0060.408
interaction_types0.0800.0030.082
intercell_categories0.0490.0030.052
intercell_consensus_filter0.9450.0741.081
is_ontology_id0.0010.0000.001
is_swissprot0.0300.0020.033
is_trembl0.0190.0020.022
is_uniprot0.0060.0000.007
kegg_info0.0120.0020.013
kegg_open0.0100.0010.012
kegg_pathway_annotations0.0000.0000.001
kegg_pathway_download0.0100.0010.011
kegg_pathway_list0.0100.0010.011
kegg_pathways_download000
kegg_picture0.0790.0102.990
kegg_process0.0220.0020.024
latin_name0.0420.0000.042
load_db0.0710.0030.074
ncbi_taxid0.0370.0010.038
nichenet_build_model000
nichenet_expression_data0.0110.0010.012
nichenet_gr_network0.0280.0030.031
nichenet_gr_network_evex0.0100.0010.010
nichenet_gr_network_harmonizome0.0100.0010.011
nichenet_gr_network_htridb0.0550.0020.056
nichenet_gr_network_omnipath11.857 0.70312.703
nichenet_gr_network_pathwaycommons0.0140.0020.016
nichenet_gr_network_regnetwork0.0120.0010.012
nichenet_gr_network_remap0.0110.0010.012
nichenet_gr_network_trrust0.0120.0020.013
nichenet_ligand_activities0.0000.0000.001
nichenet_ligand_target_links0.0000.0010.001
nichenet_ligand_target_matrix0.0000.0000.001
nichenet_lr_network0.0330.0040.037
nichenet_lr_network_guide2pharma0.0110.0010.012
nichenet_lr_network_omnipath0.0280.0030.031
nichenet_lr_network_ramilowski0.0090.0010.010
nichenet_main0.0000.0000.001
nichenet_networks0.1010.0070.108
nichenet_optimization000
nichenet_remove_orphan_ligands0.0400.0040.043
nichenet_results_dir000
nichenet_signaling_network0.0420.0030.046
nichenet_signaling_network_cpdb0.0090.0010.011
nichenet_signaling_network_evex0.0110.0010.012
nichenet_signaling_network_harmonizome0.0130.0010.015
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath 9.783 0.52610.416
nichenet_signaling_network_pathwaycommons0.0110.0020.013
nichenet_signaling_network_vinayagam0.0100.0010.012
nichenet_test0.0000.0010.000
nichenet_workarounds000
obo_parser0.1500.0100.572
oma_code0.0250.0000.025
oma_organisms0.0630.0020.065
oma_pairwise0.0130.0020.015
oma_pairwise_genesymbols0.0120.0020.013
omnipath4.0740.0554.129
omnipath_cache_autoclean000
omnipath_cache_clean0.0060.0000.007
omnipath_cache_clean_db0.0800.0090.089
omnipath_cache_download_ready0.4200.0480.660
omnipath_cache_filter_versions0.1110.0220.150
omnipath_cache_get0.1140.0140.127
omnipath_cache_key0.0010.0010.002
omnipath_cache_latest_or_new0.0560.0090.066
omnipath_cache_load0.3670.0390.826
omnipath_cache_move_in0.1490.0260.187
omnipath_cache_remove0.0950.0150.122
omnipath_cache_save0.1850.0330.348
omnipath_cache_search0.0000.0000.001
omnipath_cache_set_ext0.0830.0140.109
omnipath_cache_update_status0.0990.0180.120
omnipath_cache_wipe000
omnipath_get_config_path0.0010.0000.001
omnipath_load_config0.0000.0000.001
omnipath_log0.0010.0000.000
omnipath_logfile0.0010.0010.001
omnipath_msg0.0060.0010.007
omnipath_reset_config000
omnipath_save_config0.0000.0010.001
omnipath_set_cachedir0.0250.0030.030
omnipath_set_console_loglevel0.0010.0000.001
omnipath_set_logfile_loglevel0.0010.0000.001
omnipath_set_loglevel0.0010.0000.000
omnipath_show_db0.0440.0010.044
omnipath_unlock_cache_db000
only_from0.0000.0010.000
ontology_ensure_id000
ontology_ensure_name000
ontology_name_id0.0000.0000.001