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This page was generated on 2024-05-09 11:41:12 -0400 (Thu, 09 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4748
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4484
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4514
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 3.12.0  (landing page)
Denes Turei
Snapshot Date: 2024-05-08 14:00:19 -0400 (Wed, 08 May 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_19
git_last_commit: 330f65c
git_last_commit_date: 2024-04-30 11:18:21 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for OmnipathR on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: OmnipathR
Version: 3.12.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings OmnipathR_3.12.0.tar.gz
StartedAt: 2024-05-09 10:12:54 -0000 (Thu, 09 May 2024)
EndedAt: 2024-05-09 10:30:44 -0000 (Thu, 09 May 2024)
EllapsedTime: 1070.2 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings OmnipathR_3.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.12.0’
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:13:21] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:13:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-09 10:13:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:13:21] [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
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:13:34] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:13:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-09 10:13:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:13:34] [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 ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package textcomp Error: Symbol \textrightarrow not provided by
(textcomp)                font family ptm in TS1 encoding.
(textcomp)                Default family used instead.

See the textcomp package documentation for explanation.
* checking PDF version of manual without index ... ERROR
* DONE

Status: 2 ERRORs, 2 WARNINGs, 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/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-08 20:39:33] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] Contains 6 files.
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-08 20:39:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-08 20:39:33] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-08 20:39:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-08 20:39:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-08 20:39:35] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-08 20:39:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-08 20:39:35] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-08 20:39:35] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-08 20:39:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-08 20:39:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-08 20:39:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-08 20:39:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-08 20:39:35] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-05-08 20:39:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-08 20:39:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-08 20:39:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-08 20:39:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-08 20:39:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-08 20:39:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-08 20:39:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-08 20:39:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-08 20:39:36] [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 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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)
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:29:32] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:29:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-09 10:29:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-09 10:29:32] [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 
 12.248   0.683  57.428

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0000.0010.001
all_uniprot_acs0.0330.0000.032
all_uniprots0.0160.0000.015
ancestors0.0160.0000.015
annotated_network 1.928 0.18610.216
annotation_categories108.419 0.060110.315
biomart_query0.8050.0366.919
bioplex10.0160.0000.016
bioplex20.0160.0000.016
bioplex30.0160.0000.016
bioplex_all0.0160.0000.016
bioplex_hct116_10.0170.0000.016
bma_motif_es0.3950.0282.408
bma_motif_vs0.2090.0001.367
collectri164.587 2.149168.843
common_name0.0310.0000.031
consensuspathdb_download0.0010.0000.000
consensuspathdb_raw_table0.0170.0000.017
curated_ligand_receptor_interactions 5.318 0.89023.049
curated_ligrec_stats 32.071 3.510170.515
database_summary1.7420.0684.933
descendants0.0190.0000.020
dorothea 89.149 0.909130.989
ensembl_dataset0.0100.0000.009
ensembl_id_mapping_table 0.975 0.02412.774
ensembl_id_type0.0020.0000.002
ensembl_name0.0570.0000.057
ensembl_organisms0.1510.0040.158
ensembl_organisms_raw0.1470.0000.147
ensembl_orthology000
enzsub_graph2.1940.0404.998
evex_download0.0170.0000.016
evidences000
extra_attr_values15.102 0.51017.387
extra_attrs7.2440.0367.295
extra_attrs_to_cols12.779 0.13112.936
filter_by_resource7.0930.0799.009
filter_extra_attrs26.629 0.11527.986
filter_intercell 6.760 0.18711.575
filter_intercell_network0.0330.0000.033
find_all_paths6.4850.0406.540
from_evidences000
get_annotation_resources0.0830.0001.264
get_complex_genes1.1770.0322.994
get_complex_resources0.0790.0041.334
get_db000
get_enzsub_resources0.0760.0081.367
get_interaction_resources0.1340.0001.302
get_intercell_categories0.3600.0201.009
get_intercell_generic_categories0.1000.0040.104
get_intercell_resources0.0850.0001.219
get_ontology_db0.0170.0000.017
get_resources0.0830.0001.227
get_signed_ptms6.0900.0447.280
giant_component12.890 0.24215.276
go_annot_download10.238 0.37716.762
go_annot_slim000
go_ontology_download0.0170.0000.016
guide2pharma_download0.0170.0000.017
harmonizome_download0.0170.0000.017
has_extra_attrs7.7210.0607.797
homologene_download0.0120.0040.016
homologene_raw0.0200.0040.024
homologene_uniprot_orthology0.0150.0000.016
hpo_download 2.331 0.13621.812
htridb_download0.0150.0000.015
import_all_interactions2.2380.1115.994
import_intercell_network0.0160.0000.016
import_kinaseextra_interactions1.5730.0954.433
import_ligrecextra_interactions0.7190.0563.089
import_lncrna_mrna_interactions0.5440.0562.330
import_mirnatarget_interactions1.0900.1043.622
import_omnipath_annotations0.4960.0322.278
import_omnipath_complexes0.6290.0363.310
import_omnipath_enzsub1.2120.0512.450
import_omnipath_interactions0.3050.0041.418
import_omnipath_intercell0.4800.0521.564
import_pathwayextra_interactions0.8840.0563.564
import_post_translational_interactions0.8170.0563.543
import_small_molecule_protein_interactions0.4970.0321.140
import_tf_mirna_interactions0.7690.0162.993
import_tf_target_interactions1.4190.0404.063
import_transcriptional_interactions2.9790.0645.728
inbiomap_download000
inbiomap_raw000
interaction_datasets0.050.000.05
interaction_graph0.3840.0161.570
interaction_types0.0400.0120.053
intercell_categories0.0670.0080.076
intercell_consensus_filter1.5540.1193.388
is_ontology_id0.0010.0000.000
is_swissprot0.0430.0000.043
is_trembl0.0420.0000.041
is_uniprot0.0160.0000.017
kegg_info0.0120.0040.016
kegg_open0.0770.0080.085
kegg_pathway_annotations0.0010.0000.000
kegg_pathway_download0.0160.0000.016
kegg_pathway_list0.0150.0000.016
kegg_pathways_download000
kegg_picture0.1040.0001.347
kegg_process0.0290.0040.033
latin_name0.0580.0000.058
load_db0.1080.0000.109
ncbi_taxid0.0560.0000.057
nichenet_build_model000
nichenet_expression_data0.0180.0000.018
nichenet_gr_network0.0490.0000.050
nichenet_gr_network_evex0.0180.0000.018
nichenet_gr_network_harmonizome0.0130.0040.017
nichenet_gr_network_htridb0.0160.0000.015
nichenet_gr_network_omnipath15.784 0.27817.906
nichenet_gr_network_pathwaycommons0.0160.0000.016
nichenet_gr_network_regnetwork0.0160.0000.016
nichenet_gr_network_remap0.0140.0000.015
nichenet_gr_network_trrust0.0150.0000.015
nichenet_ligand_activities0.0010.0000.001
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0420.0040.046
nichenet_lr_network_guide2pharma0.0160.0000.016
nichenet_lr_network_omnipath0.0440.0040.047
nichenet_lr_network_ramilowski0.0160.0000.016
nichenet_main000
nichenet_networks0.0700.0040.074
nichenet_optimization000
nichenet_remove_orphan_ligands0.0430.0040.046
nichenet_results_dir000
nichenet_signaling_network0.0430.0040.048
nichenet_signaling_network_cpdb0.0150.0000.016
nichenet_signaling_network_evex0.0160.0000.015
nichenet_signaling_network_harmonizome0.0170.0000.016
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath10.561 0.12312.651
nichenet_signaling_network_pathwaycommons0.0150.0000.016
nichenet_signaling_network_vinayagam0.0160.0000.016
nichenet_test0.0010.0000.000
nichenet_workarounds000
obo_parser0.1130.0000.923
oma_code0.0270.0000.028
oma_organisms0.1260.0000.127
oma_pairwise0.0180.0000.017
oma_pairwise_genesymbols0.0170.0000.016
omnipath4.6710.0444.724
omnipath_cache_autoclean000
omnipath_cache_clean0.010.000.01
omnipath_cache_clean_db0.1170.0080.126
omnipath_cache_download_ready0.6630.0240.704
omnipath_cache_filter_versions0.1490.0040.157
omnipath_cache_get0.1310.0000.132
omnipath_cache_key0.0010.0000.001
omnipath_cache_latest_or_new0.1410.0040.146
omnipath_cache_load0.5470.0232.701
omnipath_cache_move_in0.2740.0000.279
omnipath_cache_remove0.1550.0040.164
omnipath_cache_save0.2030.0160.239
omnipath_cache_search0.0010.0000.000
omnipath_cache_set_ext0.1660.0000.170
omnipath_cache_update_status0.1450.0000.145
omnipath_cache_wipe000
omnipath_get_config_path0.0010.0000.003
omnipath_load_config000
omnipath_log0.0010.0000.000
omnipath_logfile0.0010.0000.001
omnipath_msg0.0080.0000.008
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0380.0000.038
omnipath_set_console_loglevel0.0000.0020.001
omnipath_set_logfile_loglevel0.0000.0020.002
omnipath_set_loglevel0.0010.0000.001
omnipath_show_db0.0690.0000.068
omnipath_unlock_cache_db0.0010.0000.000
only_from000
ontology_ensure_id0.0000.0000.001
ontology_ensure_name0.0000.0000.001
ontology_name_id0.0010.0000.001