Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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: 2024-06-12 14:00 -0400 (Wed, 12 Jun 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  
palomino3Windows Server 2022 Datacenter / x64  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: 2024-06-13 01:44:08 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 02:12:41 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 1713.5 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 4.4.0 (2024-04-24)
* 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
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:44:29] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:44:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-13 01:44:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:44:29] [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
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:44:39] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:44:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-13 01:44:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:44:39] [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
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-12 15:33:08] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] Contains 4 files.
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-12 15:33:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-12 15:33:08] [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).
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-12 15:33:08] [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).
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-12 15:33:08] [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).
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-12 15:33:08] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-12 15:33:10] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-12 15:33:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-12 15:33:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-12 15:33:10] [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 (2024-04-24) -- "Puppy Cup"
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)
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:59:48] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:59:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-13 01:59:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-13 01:59:48] [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 
 21.970   1.612  69.655

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0010.0010.001
all_uniprot_acs0.0210.0000.021
all_uniprots0.0110.0000.010
ancestors0.010.000.01
annotated_network1.9770.1637.862
annotation_categories 99.986 0.116102.680
biomart_query1.4940.1405.574
bioplex10.0260.0040.062
bioplex20.0220.0040.059
bioplex30.0300.0000.061
bioplex_all0.0310.0000.047
bioplex_hct116_10.0290.0000.029
bma_motif_es0.9990.0572.741
bma_motif_vs0.5140.0681.595
collectri148.575 2.773154.862
common_name0.0320.0000.031
consensuspathdb_download0.0000.0000.001
consensuspathdb_raw_table0.0130.0030.016
curated_ligand_receptor_interactions 6.423 0.27419.017
curated_ligrec_stats 46.980 3.766135.580
database_summary2.2830.2205.930
descendants0.0200.0120.032
dorothea83.683 1.23194.726
ensembl_dataset0.0140.0000.014
ensembl_id_mapping_table1.7440.0776.819
ensembl_id_type0.0020.0020.004
ensembl_name0.1210.0040.125
ensembl_organisms0.2920.0000.292
ensembl_organisms_raw0.2580.0000.258
ensembl_orthology0.0000.0010.001
enzsub_graph3.0190.3205.999
evex_download0.0230.0000.075
evidences000
extra_attr_values18.645 0.64521.782
extra_attrs5.4140.0085.422
extra_attrs_to_cols11.399 0.18311.586
filter_by_resource10.903 0.12414.282
filter_extra_attrs17.325 0.09918.183
filter_intercell10.152 0.92914.655
filter_intercell_network0.0500.0040.054
find_all_paths7.9330.1848.117
from_evidences000
get_annotation_resources0.1500.0041.117
get_complex_genes1.0570.0523.292
get_complex_resources0.1490.0000.821
get_db000
get_enzsub_resources0.1830.0000.884
get_interaction_resources0.2200.0000.995
get_intercell_categories0.3170.0190.586
get_intercell_generic_categories0.0740.0000.074
get_intercell_resources0.1190.0000.834
get_ontology_db0.0080.0040.012
get_resources0.1360.0080.837
get_signed_ptms8.8610.0809.691
giant_component18.045 0.69228.891
go_annot_download11.304 1.22015.936
go_annot_slim0.0010.0000.001
go_ontology_download0.0070.0080.015
guide2pharma_download0.0130.0000.013
harmonizome_download0.0130.0000.013
has_extra_attrs8.5810.1238.704
homologene_download0.0270.0000.027
homologene_raw0.0350.0080.043
homologene_uniprot_orthology0.0250.0000.025
hpo_download3.6760.2035.752
htridb_download0.0290.0000.028
import_all_interactions3.0500.2459.448
import_intercell_network0.0570.0040.061
import_kinaseextra_interactions4.0030.2669.029
import_ligrecextra_interactions1.5310.1585.157
import_lncrna_mrna_interactions1.0530.0983.804
import_mirnatarget_interactions1.9870.1196.903
import_omnipath_annotations1.0990.0733.726
import_omnipath_complexes1.2470.0614.589
import_omnipath_enzsub1.8520.0483.996
import_omnipath_interactions0.5790.0081.746
import_omnipath_intercell0.9350.1233.204
import_pathwayextra_interactions1.6660.1635.734
import_post_translational_interactions1.3980.1533.426
import_small_molecule_protein_interactions0.6050.0280.925
import_tf_mirna_interactions0.8640.0872.194
import_tf_target_interactions1.7620.2805.650
import_transcriptional_interactions 4.437 0.22712.200
inbiomap_download0.0000.0010.001
inbiomap_raw000
interaction_datasets0.0920.0050.122
interaction_graph1.0780.0562.657
interaction_types0.1190.0080.127
intercell_categories0.1820.0240.207
intercell_consensus_filter2.9450.2605.728
is_ontology_id0.0000.0010.001
is_swissprot0.0670.0160.179
is_trembl0.0900.0080.184
is_uniprot0.0330.0040.084
kegg_info0.0240.0040.044
kegg_open0.0290.0000.053
kegg_pathway_annotations0.0010.0000.017
kegg_pathway_download0.0280.0000.044
kegg_pathway_list0.0230.0040.059
kegg_pathways_download0.0010.0000.000
kegg_picture0.2710.0084.571
kegg_process0.1450.0160.196
latin_name0.0890.0000.121
load_db0.1480.0080.156
ncbi_taxid0.1040.0000.104
nichenet_build_model0.0000.0000.001
nichenet_expression_data0.0230.0030.026
nichenet_gr_network0.0630.0120.075
nichenet_gr_network_evex0.0270.0000.028
nichenet_gr_network_harmonizome0.0270.0000.026
nichenet_gr_network_htridb0.0270.0000.027
nichenet_gr_network_omnipath19.482 0.55123.850
nichenet_gr_network_pathwaycommons0.0240.0070.031
nichenet_gr_network_regnetwork0.0190.0080.027
nichenet_gr_network_remap0.0240.0000.024
nichenet_gr_network_trrust0.0230.0000.023
nichenet_ligand_activities0.0010.0000.001
nichenet_ligand_target_links0.0010.0000.001
nichenet_ligand_target_matrix0.0010.0000.001
nichenet_lr_network0.0710.0000.071
nichenet_lr_network_guide2pharma0.0210.0000.021
nichenet_lr_network_omnipath0.070.000.07
nichenet_lr_network_ramilowski0.0230.0000.023
nichenet_main0.0000.0000.001
nichenet_networks0.0990.0040.102
nichenet_optimization0.0000.0000.001
nichenet_remove_orphan_ligands0.0610.0070.067
nichenet_results_dir0.0000.0000.001
nichenet_signaling_network0.0680.0000.068
nichenet_signaling_network_cpdb0.0210.0030.024
nichenet_signaling_network_evex0.0240.0080.032
nichenet_signaling_network_harmonizome0.0210.0040.025
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath16.596 0.17128.929
nichenet_signaling_network_pathwaycommons0.0270.0000.027
nichenet_signaling_network_vinayagam0.0280.0000.028
nichenet_test0.0000.0000.001
nichenet_workarounds000
obo_parser0.1740.0090.355
oma_code0.0330.0060.039
oma_organisms0.2240.0000.229
oma_pairwise0.0230.0040.027
oma_pairwise_genesymbols0.0230.0040.027
omnipath6.5950.0516.807
omnipath_cache_autoclean000
omnipath_cache_clean0.0070.0020.009
omnipath_cache_clean_db0.1220.0000.121
omnipath_cache_download_ready0.7800.0280.891
omnipath_cache_filter_versions0.2380.0000.275
omnipath_cache_get0.1130.0040.117
omnipath_cache_key0.0020.0000.002
omnipath_cache_latest_or_new0.0800.0120.091
omnipath_cache_load0.8350.0444.260
omnipath_cache_move_in0.1610.0160.182
omnipath_cache_remove0.1760.0200.200
omnipath_cache_save0.2000.0170.335
omnipath_cache_search0.0010.0000.001
omnipath_cache_set_ext0.1300.0200.154
omnipath_cache_update_status0.1150.0160.131
omnipath_cache_wipe0.0010.0000.000
omnipath_get_config_path0.0010.0000.000
omnipath_load_config000
omnipath_log0.0000.0000.001
omnipath_logfile0.0000.0010.001
omnipath_msg0.0050.0020.007
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0270.0000.027
omnipath_set_console_loglevel0.0020.0000.001
omnipath_set_logfile_loglevel0.0000.0010.001
omnipath_set_loglevel0.0000.0010.001
omnipath_show_db0.0570.0000.057
omnipath_unlock_cache_db0.0010.0000.000
only_from000
ontology_ensure_id0.0010.0000.001
ontology_ensure_name000
ontology_name_id0.0000.0010.001