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

This page was generated on 2025-03-20 12:05 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4756
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4487
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4441
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4406
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 1456/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.14.0  (landing page)
Denes Turei
Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_20
git_last_commit: 3c7d7f1
git_last_commit_date: 2024-10-29 10:41:00 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for OmnipathR on nebbiolo2

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

raw results


Summary

Package: OmnipathR
Version: 3.14.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.14.0.tar.gz
StartedAt: 2025-03-18 01:25:40 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 01:52:09 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 1589.3 seconds
RetCode: 0
Status:   OK  
CheckDir: OmnipathR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.14.0’
* 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 ... OK
* 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
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:26:04] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:26:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 01:26:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:26:04] [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
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:26:16] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:26:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:26:16] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
annotation_categories                95.864  0.068  97.441
omnipath-interactions                42.926  2.016  92.080
filter_extra_attrs                   35.346  0.419  55.077
curated_ligrec_stats                 29.773  1.423 103.542
nichenet_signaling_network_omnipath  19.130  0.617  32.232
giant_component                      17.206  1.411  24.926
nichenet_gr_network_omnipath         17.820  0.768  24.790
pivot_annotations                    15.245  1.016  37.938
go_annot_download                    13.049  1.625  17.257
omnipath_for_cosmos                  12.577  0.561  27.377
has_extra_attrs                      10.483  0.579  21.506
find_all_paths                       10.436  0.595  18.388
filter_by_resource                    9.726  0.246  15.860
extra_attr_values                     9.530  0.232  12.293
filter_intercell                      7.997  1.089  12.333
extra_attrs_to_cols                   8.190  0.048   8.238
with_extra_attrs                      7.196  0.249   9.859
print_interactions                    7.140  0.299  15.688
translate_ids_multi                   6.011  0.177  15.454
omnipath_query                        6.000  0.030   6.035
static_table                          5.613  0.302   6.636
extra_attrs                           5.192  0.091   5.283
curated_ligand_receptor_interactions  4.426  0.419  15.137
hpo_download                          3.314  0.224   5.980
intercell_consensus_filter            2.327  0.136   5.351
ensembl_id_mapping_table              1.180  0.065  10.320
all_uniprots                          0.948  0.130  87.653
translate_ids                         0.815  0.016  18.367
uniprot_full_id_mapping_table         0.678  0.053  21.588
kegg_picture                          0.206  0.006   5.298
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.


Installation output

OmnipathR.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-03-17 16:30:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 16:30:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:30:26] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-17 16:30:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-17 16:30:26] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-17 16:30:26] [TRACE]   [OmnipathR] Contains 8 files.
[2025-03-17 16:30:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-17 16:30:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 16:30:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:30:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-17 16:30:27] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-17 16:30:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-17 16:30:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:30:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-17 16:30:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:30:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-17 16:30:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:30:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-17 16:30:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:30:27] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-03-17 16:30:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 16:30:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:30:28] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-17 16:30:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-17 16:30:28] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-17 16:30:28] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-17 16:30:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-17 16:30:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 16:30:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:30:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-17 16:30:29] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-17 16:30:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-17 16:30:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:30:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-17 16:30:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:30:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-17 16:30:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:30:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-17 16:30:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:30:29] [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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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)
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:41:54] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] Contains 21 files.
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:41:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 01:41:54] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 11.526   1.124  41.629 

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0130.0020.016
all_uniprots 0.948 0.13087.653
ancestors0.0090.0020.011
annotated_network0.7130.1483.946
annotation_categories95.864 0.06897.441
annotation_resources0.1220.0100.912
annotations0.3410.0191.382
biomart_query0.7720.0532.430
bioplex10.0070.0010.009
bioplex20.0070.0010.008
bioplex30.0070.0000.008
bioplex_all0.0060.0010.008
bioplex_hct116_10.0400.0090.050
bma_motif_es0.3600.0611.302
bma_motif_vs0.2430.0030.950
chalmers_gem0.0080.0010.008
chalmers_gem_id_mapping_table0.0080.0000.007
chalmers_gem_id_type0.0020.0000.002
chalmers_gem_metabolites0.0070.0000.007
chalmers_gem_network0.0080.0000.007
chalmers_gem_raw0.0070.0000.006
chalmers_gem_reactions0.0070.0000.007
common_name0.0280.0000.028
complex_genes0.4970.0142.351
complex_resources0.1400.0000.941
complexes0.2340.0490.916
consensuspathdb_download000
consensuspathdb_raw_table0.0080.0000.007
cosmos_pkn000
curated_ligand_receptor_interactions 4.426 0.41915.137
curated_ligrec_stats 29.773 1.423103.542
database_summary1.3860.0193.962
descendants0.0080.0000.008
ensembl_dataset0.0110.0000.011
ensembl_id_mapping_table 1.180 0.06510.320
ensembl_id_type0.0010.0000.002
ensembl_name0.060.000.06
ensembl_organisms0.1100.0250.134
ensembl_organisms_raw0.1240.0110.135
ensembl_orthology000
enzsub_graph1.9130.0464.174
enzsub_resources0.0990.0020.780
enzyme_substrate1.1860.0101.882
evex_download0.0070.0000.007
evidences000
extra_attr_values 9.530 0.23212.293
extra_attrs5.1920.0915.283
extra_attrs_to_cols8.1900.0488.238
filter_by_resource 9.726 0.24615.860
filter_extra_attrs35.346 0.41955.077
filter_intercell 7.997 1.08912.333
filter_intercell_network0.0150.0010.016
find_all_paths10.436 0.59518.388
from_evidences0.0010.0000.000
get_db0.0010.0000.000
get_ontology_db0.0190.0000.019
giant_component17.206 1.41124.926
go_annot_download13.049 1.62517.257
go_annot_slim000
go_ontology_download0.0090.0000.010
guide2pharma_download0.0080.0000.009
harmonizome_download0.0060.0010.008
has_extra_attrs10.483 0.57921.506
hmdb_id_mapping_table0.0200.0010.046
hmdb_id_type0.0050.0000.009
hmdb_metabolite_fields0.0000.0000.001
hmdb_protein_fields000
hmdb_table0.0190.0000.038
homologene_download0.0210.0000.038
homologene_raw0.0440.0010.091
homologene_uniprot_orthology0.0190.0020.044
hpo_download3.3140.2245.980
htridb_download0.0260.0000.037
id_translation_resources000
id_types0.1370.0020.207
inbiomap_download000
inbiomap_raw000
interaction_datasets0.9230.0282.129
interaction_graph0.7580.0471.726
interaction_resources0.3200.0171.421
interaction_types0.0950.0050.236
intercell0.9990.0512.118
intercell_categories0.8520.0211.724
intercell_consensus_filter2.3270.1365.351
intercell_generic_categories0.1170.0000.117
intercell_network0.0220.0020.024
intercell_resources0.2110.0110.926
intercell_summary0.1250.0030.257
is_ontology_id0.0000.0000.001
is_swissprot0.0830.0020.170
is_trembl0.0790.0020.159
is_uniprot0.0330.0000.065
kegg_info0.0250.0000.052
kegg_open0.0230.0000.050
kegg_pathway_annotations000
kegg_pathway_download0.0250.0000.051
kegg_pathway_list0.0250.0000.049
kegg_pathways_download000
kegg_picture0.2060.0065.298
kegg_process0.0800.0000.103
latin_name0.1050.0000.106
load_db0.1340.0010.258
ncbi_taxid0.1100.0000.175
nichenet_build_model000
nichenet_expression_data0.0160.0000.016
nichenet_gr_network0.0400.0010.041
nichenet_gr_network_evex0.0130.0020.014
nichenet_gr_network_harmonizome0.0130.0010.015
nichenet_gr_network_htridb0.0140.0000.014
nichenet_gr_network_omnipath17.820 0.76824.790
nichenet_gr_network_pathwaycommons0.0170.0000.017
nichenet_gr_network_regnetwork0.0150.0000.015
nichenet_gr_network_remap0.0130.0010.014
nichenet_gr_network_trrust0.0130.0010.014
nichenet_ligand_activities0.0000.0000.001
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0380.0000.039
nichenet_lr_network_guide2pharma0.0130.0000.012
nichenet_lr_network_omnipath0.0410.0010.042
nichenet_lr_network_ramilowski0.0150.0000.015
nichenet_main000
nichenet_networks0.0740.0020.075
nichenet_optimization000
nichenet_remove_orphan_ligands0.0450.0010.045
nichenet_results_dir0.0000.0000.001
nichenet_signaling_network0.0440.0030.047
nichenet_signaling_network_cpdb0.0160.0000.016
nichenet_signaling_network_evex0.0160.0000.017
nichenet_signaling_network_harmonizome0.0170.0000.017
nichenet_signaling_network_inbiomap0.0010.0000.000
nichenet_signaling_network_omnipath19.130 0.61732.232
nichenet_signaling_network_pathwaycommons0.0190.0010.020
nichenet_signaling_network_vinayagam0.0110.0010.012
nichenet_test0.0000.0000.001
nichenet_workarounds000
obo_parser0.1220.0040.184
oma_code0.0440.0000.045
oma_organisms0.0600.0010.062
oma_pairwise0.0110.0000.011
oma_pairwise_genesymbols0.0090.0000.009
oma_pairwise_translated0.0090.0000.009
omnipath-interactions42.926 2.01692.080
omnipath_cache_autoclean000
omnipath_cache_clean0.0100.0010.011
omnipath_cache_clean_db0.1580.0100.168
omnipath_cache_download_ready0.9470.0431.085
omnipath_cache_filter_versions0.2000.0040.352
omnipath_cache_get0.1550.0050.192
omnipath_cache_key0.0020.0000.006
omnipath_cache_latest_or_new0.1150.0040.171
omnipath_cache_load1.0880.0164.180
omnipath_cache_move_in0.2860.0140.504
omnipath_cache_remove0.1870.0100.278
omnipath_cache_save0.3550.0410.679
omnipath_cache_search0.0010.0000.001
omnipath_cache_set_ext0.1500.0080.195
omnipath_cache_update_status0.2030.0340.236
omnipath_cache_wipe000
omnipath_config_path0.0020.0000.006
omnipath_for_cosmos12.577 0.56127.377
omnipath_load_config0.0010.0000.001
omnipath_log000
omnipath_logfile0.0020.0000.002
omnipath_msg0.0080.0010.009
omnipath_query6.0000.0306.035
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0520.0020.054
omnipath_set_console_loglevel0.0080.0000.008
omnipath_set_logfile_loglevel0.0060.0000.006
omnipath_set_loglevel0.0030.0000.003
omnipath_show_db0.1340.0000.134
omnipath_unlock_cache_db0.0010.0000.001
only_from000
ontology_ensure_id0.0010.0000.001
ontology_ensure_name0.0010.0000.001
ontology_name_id0.0020.0000.002
organism_for0.1440.0010.145
pathwaycommons_download0.0020.0000.002
pivot_annotations15.245 1.01637.938
preppi_download0.0000.0010.002
preppi_filter0.0010.0000.002
print_bma_motif_es0.4020.0581.408
print_bma_motif_vs0.2160.0031.001
print_interactions 7.140 0.29915.688
print_path_es0.4810.0322.202
print_path_vs1.9220.1564.823
pubmed_open3.1640.0903.254
query_info0.1190.0240.410
ramilowski_download0.0010.0000.001
ramp_id_mapping_table000
ramp_id_type0.0010.0020.003
ramp_sqlite0.0000.0010.000
ramp_table0.0010.0000.001
ramp_tables0.0010.0000.001
regnetwork_directions000
regnetwork_download000
relations_list_to_table0.0900.0130.138
relations_table_to_graph000
relations_table_to_list0.0650.0040.082
remap_dorothea_download000
remap_filtered0.0000.0000.001
remap_tf_target_download000
resource_info0.1950.0140.890
resources0.0800.0030.860
resources_colname0.5810.0582.868
resources_in2.7380.1122.850
show_network0.0000.0000.001
signed_ptms3.8950.0704.659
simplify_intercell_network0.0010.0000.001
static_table5.6130.3026.636
static_tables0.0470.0010.129
stitch_actions0.0010.0000.001
stitch_links0.0000.0010.000
stitch_network0.0000.0010.000
stitch_remove_prefixes0.0070.0000.006
swap_relations0.1110.0010.122
swissprots_only0.0320.0000.032
tfcensus_download0.1480.0080.297
translate_ids 0.815 0.01618.367
translate_ids_multi 6.011 0.17715.454
trembls_only0.030.000.03
trrust_download0.0000.0000.001
uniprot_full_id_mapping_table 0.678 0.05321.588
uniprot_genesymbol_cleanup000
uniprot_id_mapping_table0.0000.0010.000
uniprot_id_type0.0010.0010.002
uniprot_idmapping_id_types0.2060.0090.785
unique_intercell_network0.0010.0000.001
unnest_evidences000
uploadlists_id_type0.0030.0000.003
vinayagam_download0.0010.0000.001
walk_ontology_tree0.0010.0000.001
with_extra_attrs7.1960.2499.859
with_references0.3680.0531.681
zenodo_download0.0010.0000.001