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This page was generated on 2025-03-17 12:12 -0400 (Mon, 17 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" 4399
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: 2025-03-13 13:00 -0400 (Thu, 13 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    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for OmnipathR on taishan

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: 3.14.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.14.0.tar.gz
StartedAt: 2025-03-14 08:43:47 -0000 (Fri, 14 Mar 2025)
EndedAt: 2025-03-14 09:01:46 -0000 (Fri, 14 Mar 2025)
EllapsedTime: 1078.2 seconds
RetCode: 0
Status:   OK  
CheckDir: OmnipathR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --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: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.14.0’
* 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
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:44:19] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:44:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-14 08:44:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:44:19] [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
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:44:36] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:44:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-14 08:44:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:44:36] [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                100.853  0.041 107.745
curated_ligrec_stats                  33.228  2.263 146.371
omnipath-interactions                 27.817  0.552  60.250
filter_extra_attrs                    24.786  0.095  28.469
nichenet_gr_network_omnipath          14.736  0.151  31.648
extra_attr_values                     13.285  0.323  16.196
extra_attrs_to_cols                   12.096  0.023  12.471
go_annot_download                     11.564  0.242  31.456
giant_component                       10.281  0.250  13.198
with_extra_attrs                       9.982  0.122  11.662
nichenet_signaling_network_omnipath    9.917  0.079  15.094
pivot_annotations                      9.673  0.254  21.544
omnipath_for_cosmos                    9.312  0.064  33.495
has_extra_attrs                        7.461  0.035  10.429
extra_attrs                            7.315  0.063   7.629
translate_ids_multi                    7.023  0.043  26.308
filter_by_resource                     6.473  0.084   8.901
static_table                           6.034  0.165  12.660
print_interactions                     6.132  0.039   9.932
find_all_paths                         6.066  0.018   6.737
curated_ligand_receptor_interactions   5.572  0.305  20.542
signed_ptms                            5.317  0.088   6.323
filter_intercell                       5.343  0.060  10.008
hpo_download                           2.351  0.175  22.954
enzsub_graph                           2.296  0.047  10.735
print_path_vs                          2.094  0.043   5.234
ensembl_id_mapping_table               1.423  0.056  25.344
translate_ids                          1.213  0.024  20.981
all_uniprots                           0.921  0.065  27.564
annotated_network                      0.868  0.084   5.061
uniprot_full_id_mapping_table          0.915  0.004  22.579
* 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: 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/R/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.3/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
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 20:56:01] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] Contains 2 files.
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 20:56:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 20:56:01] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 20:56:04] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 20:56:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-13 20:56:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 20:56:04] [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: 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)
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:59:44] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] Contains 21 files.
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:59:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-14 08:59:44] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 12.405   1.211 113.280

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0210.0040.025
all_uniprots 0.921 0.06527.564
ancestors0.0120.0000.024
annotated_network0.8680.0845.061
annotation_categories100.853 0.041107.745
annotation_resources0.0980.0031.061
annotations0.3350.0161.968
biomart_query0.9280.0213.160
bioplex10.0110.0000.010
bioplex20.0110.0000.011
bioplex30.0110.0000.011
bioplex_all0.0110.0000.011
bioplex_hct116_10.0110.0000.011
bma_motif_es0.4520.0122.164
bma_motif_vs0.2350.0041.352
chalmers_gem0.0130.0000.024
chalmers_gem_id_mapping_table0.0120.0000.020
chalmers_gem_id_type0.0020.0000.003
chalmers_gem_metabolites0.0110.0000.016
chalmers_gem_network0.0110.0000.011
chalmers_gem_raw0.010.000.01
chalmers_gem_reactions0.0110.0000.011
common_name0.0360.0000.037
complex_genes0.5070.0232.772
complex_resources0.0870.0001.052
complexes0.2040.0041.189
consensuspathdb_download0.0010.0000.000
consensuspathdb_raw_table0.0110.0000.011
cosmos_pkn000
curated_ligand_receptor_interactions 5.572 0.30520.542
curated_ligrec_stats 33.228 2.263146.371
database_summary1.5930.1003.997
descendants0.0120.0000.012
ensembl_dataset0.0130.0000.013
ensembl_id_mapping_table 1.423 0.05625.344
ensembl_id_type0.0020.0000.003
ensembl_name0.0690.0000.069
ensembl_organisms0.1480.0160.164
ensembl_organisms_raw0.1780.0040.183
ensembl_orthology000
enzsub_graph 2.296 0.04710.735
enzsub_resources0.0900.0041.014
enzyme_substrate1.3690.0303.730
evex_download0.010.000.01
evidences000
extra_attr_values13.285 0.32316.196
extra_attrs7.3150.0637.629
extra_attrs_to_cols12.096 0.02312.471
filter_by_resource6.4730.0848.901
filter_extra_attrs24.786 0.09528.469
filter_intercell 5.343 0.06010.008
filter_intercell_network0.0230.0000.022
find_all_paths6.0660.0186.737
from_evidences000
get_db000
get_ontology_db0.0110.0000.010
giant_component10.281 0.25013.198
go_annot_download11.564 0.24231.456
go_annot_slim000
go_ontology_download0.0120.0000.021
guide2pharma_download0.0080.0040.023
harmonizome_download0.0110.0000.023
has_extra_attrs 7.461 0.03510.429
hmdb_id_mapping_table0.0120.0000.013
hmdb_id_type0.0030.0000.004
hmdb_metabolite_fields0.0010.0000.000
hmdb_protein_fields0.0010.0000.000
hmdb_table0.0120.0000.013
homologene_download0.0080.0040.013
homologene_raw0.0240.0000.025
homologene_uniprot_orthology0.0120.0000.025
hpo_download 2.351 0.17522.954
htridb_download0.0120.0000.013
id_translation_resources0.0010.0000.001
id_types0.0540.0000.062
inbiomap_download000
inbiomap_raw000
interaction_datasets0.3730.0871.255
interaction_graph0.3780.0401.725
interaction_resources0.1320.0081.150
interaction_types0.0510.0040.111
intercell0.4780.0161.455
intercell_categories0.3850.0471.025
intercell_consensus_filter1.1990.0443.311
intercell_generic_categories0.0640.0000.064
intercell_network0.0130.0000.014
intercell_resources0.0940.0041.065
intercell_summary0.0550.0040.063
is_ontology_id000
is_swissprot0.0340.0000.034
is_trembl0.0370.0000.037
is_uniprot0.0120.0000.012
kegg_info0.0110.0000.011
kegg_open0.0110.0000.020
kegg_pathway_annotations0.0000.0000.001
kegg_pathway_download0.0120.0000.025
kegg_pathway_list0.0120.0000.025
kegg_pathways_download000
kegg_picture0.1040.0241.320
kegg_process0.0240.0000.049
latin_name0.0700.0040.160
load_db0.0980.0000.199
ncbi_taxid0.0740.0000.146
nichenet_build_model000
nichenet_expression_data0.0130.0000.020
nichenet_gr_network0.0330.0040.073
nichenet_gr_network_evex0.0090.0040.025
nichenet_gr_network_harmonizome0.0130.0000.025
nichenet_gr_network_htridb0.0120.0000.024
nichenet_gr_network_omnipath14.736 0.15131.648
nichenet_gr_network_pathwaycommons0.0110.0000.011
nichenet_gr_network_regnetwork0.0120.0000.012
nichenet_gr_network_remap0.0100.0000.011
nichenet_gr_network_trrust0.0100.0000.011
nichenet_ligand_activities0.0000.0000.001
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.0290.0000.031
nichenet_lr_network_guide2pharma0.0110.0000.011
nichenet_lr_network_omnipath0.0320.0000.033
nichenet_lr_network_ramilowski0.0060.0040.011
nichenet_main0.0000.0000.001
nichenet_networks0.0530.0000.055
nichenet_optimization000
nichenet_remove_orphan_ligands0.0330.0000.033
nichenet_results_dir0.0000.0000.001
nichenet_signaling_network0.0350.0000.036
nichenet_signaling_network_cpdb0.0110.0000.011
nichenet_signaling_network_evex0.0110.0000.011
nichenet_signaling_network_harmonizome0.0120.0000.012
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath 9.917 0.07915.094
nichenet_signaling_network_pathwaycommons0.0090.0040.014
nichenet_signaling_network_vinayagam0.0120.0000.012
nichenet_test0.0000.0000.001
nichenet_workarounds000
obo_parser0.1040.0071.045
oma_code0.0380.0000.040
oma_organisms0.0590.0040.113
oma_pairwise0.0130.0000.013
oma_pairwise_genesymbols0.0090.0040.013
oma_pairwise_translated0.0120.0000.013
omnipath-interactions27.817 0.55260.250
omnipath_cache_autoclean000
omnipath_cache_clean0.0090.0000.009
omnipath_cache_clean_db0.1080.0040.112
omnipath_cache_download_ready0.5520.0200.590
omnipath_cache_filter_versions0.1170.0120.134
omnipath_cache_get0.1030.0000.104
omnipath_cache_key0.0010.0000.002
omnipath_cache_latest_or_new0.0650.0080.073
omnipath_cache_load0.5910.0083.031
omnipath_cache_move_in0.1790.0000.184
omnipath_cache_remove0.1070.0080.120
omnipath_cache_save0.1840.0040.297
omnipath_cache_search000
omnipath_cache_set_ext0.0890.0040.098
omnipath_cache_update_status0.1010.0040.106
omnipath_cache_wipe000
omnipath_config_path0.0000.0010.003
omnipath_for_cosmos 9.312 0.06433.495
omnipath_load_config000
omnipath_log000
omnipath_logfile0.0020.0000.002
omnipath_msg0.0060.0000.007
omnipath_query4.4080.0004.419
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.0260.0040.030
omnipath_set_console_loglevel0.0040.0000.005
omnipath_set_logfile_loglevel0.0040.0000.004
omnipath_set_loglevel0.0020.0000.003
omnipath_show_db0.0620.0000.063
omnipath_unlock_cache_db0.0000.0000.001
only_from000
ontology_ensure_id0.0010.0000.000
ontology_ensure_name000
ontology_name_id0.0010.0000.001
organism_for0.0490.0000.049
pathwaycommons_download0.0010.0000.000
pivot_annotations 9.673 0.25421.544
preppi_download0.0010.0000.001
preppi_filter0.0010.0000.001
print_bma_motif_es0.2090.0201.609
print_bma_motif_vs0.1450.0041.051
print_interactions6.1320.0399.932
print_path_es0.4880.0202.386
print_path_vs2.0940.0435.234
pubmed_open4.4210.1314.565
query_info0.1100.0040.690
ramilowski_download0.0010.0010.001
ramp_id_mapping_table0.0000.0010.001
ramp_id_type0.0000.0020.002
ramp_sqlite0.0000.0000.001
ramp_table0.0000.0000.001
ramp_tables0.0000.0000.001
regnetwork_directions0.0000.0000.001
regnetwork_download0.0010.0000.001
relations_list_to_table0.1000.0010.861
relations_table_to_graph000
relations_table_to_list0.0860.0000.362
remap_dorothea_download0.0010.0000.000
remap_filtered000
remap_tf_target_download000
resource_info0.1540.0151.081
resources0.0740.0000.973
resources_colname0.5980.0322.080
resources_in4.0810.0924.183
show_network000
signed_ptms5.3170.0886.323
simplify_intercell_network0.0010.0000.001
static_table 6.034 0.16512.660
static_tables0.0610.0000.227
stitch_actions0.0000.0010.001
stitch_links0.0000.0000.001
stitch_network0.0000.0010.001
stitch_remove_prefixes0.0090.0000.008
swap_relations0.0920.0040.362
swissprots_only0.0410.0000.041
tfcensus_download0.1990.0000.221
translate_ids 1.213 0.02420.981
translate_ids_multi 7.023 0.04326.308
trembls_only0.0380.0000.037
trrust_download0.0010.0000.001
uniprot_full_id_mapping_table 0.915 0.00422.579
uniprot_genesymbol_cleanup000
uniprot_id_mapping_table0.0010.0000.001
uniprot_id_type0.0020.0000.002
uniprot_idmapping_id_types0.1880.0041.053
unique_intercell_network0.0010.0000.001
unnest_evidences000
uploadlists_id_type0.0020.0000.002
vinayagam_download0.0000.0000.001
walk_ontology_tree0.0010.0000.001
with_extra_attrs 9.982 0.12211.662
with_references0.4460.0392.192
zenodo_download0.0010.0010.001