Multiple platform build/check report for BioC 3.20 - CHECK results for OmnipathR on palomino8

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4688
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4284
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4455
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4404
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*

CHECK results for OmnipathR on palomino8

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: 3.13.1

Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings OmnipathR_3.13.1.tar.gz

StartedAt: 2024-07-24 02:31:40 -0400 (Wed, 24 Jul 2024)

EndedAt: 2024-07-24 02:45:04 -0400 (Wed, 24 Jul 2024)

EllapsedTime: 803.3 seconds

RetCode: 1

Status: ERROR

CheckDir: OmnipathR.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings OmnipathR_3.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OmnipathR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OmnipathR' version '3.13.1'
* 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 whether package 'OmnipathR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:32:08] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:32:08] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-24 02:32:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:32:08] [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
[2024-07-24 02:32:23] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-24 02:32:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:32:23] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-24 02:32:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-24 02:32:23] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-24 02:32:24] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-24 02:32:24] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-24 02:32:24] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-24 02:32:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:32:24] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-24 02:32:24] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-24 02:32:24] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-24 02:32:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:32:24] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-24 02:32:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:32:24] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-24 02:32:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:32:24] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-24 02:32:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:32:24] [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 ... ERROR
Running examples in 'OmnipathR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: organism_for
> ### Title: Make sure the resource supports the organism and it has the ID
> ### Aliases: organism_for
> 
> ### ** Examples
> 
> organism_for(10116, 'chalmers-gem')
[1] "Rat"
> # [1] "Rat"
> organism_for(6239, 'chalmers-gem')
Error in organism_for(6239, "chalmers-gem") : 
  Organism `6239` (common_name: `Caenorhabditis elegans (Nematode, N2)`; common_name: `Caenorhabditis elegans (Nematode, N2)`) is not supported by resource `chalmers-gem`. Supported organisms: Human, Mouse, Rat, Zebrafish, Drosophila melanogaster (Fruit fly), Caenorhabditis elegans (PRJNA13758).
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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
[2024-07-23 15:46:35] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 15:46:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:46:35] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-23 15:46:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-23 15:46:35] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-23 15:46:35] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-23 15:46:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-23 15:46:35] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 15:46:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:46:35] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-23 15:46:35] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-23 15:46:35] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-23 15:46:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:46:35] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-23 15:46:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:46:36] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-23 15:46:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:46:36] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-23 15:46:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:46:36] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:46:38] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:46:38] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-23 15:46:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 15:46:38] [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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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)
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:44:09] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:44:09] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-24 02:44:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-24 02:44:09] [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 
  11.20    1.43   30.95

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

name	user	system	elapsed
OmnipathR	0	0	0
all_uniprot_acs	0.02	0.00	0.01
all_uniprots	0.02	0.00	0.01
ancestors	0.01	0.00	0.02
annotated_network	1.83	0.22	5.72
annotation_categories	77.27	0.05	78.01
biomart_query	0.78	0.12	8.74
bioplex1	0.02	0.00	0.01
bioplex2	0.01	0.00	0.02
bioplex3	0.02	0.00	0.02
bioplex_all	0.03	0.00	0.03
bioplex_hct116_1	0.01	0.00	0.01
bma_motif_es	0.41	0.09	1.17
bma_motif_vs	0.12	0.02	0.57
collectri	140.15	1.98	142.22
common_name	0.03	0.00	0.03
consensuspathdb_download	0	0	0
consensuspathdb_raw_table	0.03	0.00	0.03
curated_ligand_receptor_interactions	4.39	0.32	10.65
curated_ligrec_stats	31.03	1.95	76.47
database_summary	1.59	0.08	2.44
descendants	0.02	0.00	0.03
dorothea	86.53	1.25	91.06
ensembl_dataset	0	0	0
ensembl_id_mapping_table	1.14	0.04	27.50
ensembl_id_type	0	0	0
ensembl_name	0.06	0.00	0.06
ensembl_organisms	0.26	0.00	0.49
ensembl_organisms_raw	0.19	0.00	0.20
ensembl_orthology	0	0	0
enzsub_graph	2.52	0.10	7.67
evex_download	0.03	0.00	0.03
evidences	0	0	0
extra_attr_values	12.86	0.26	15.71
extra_attrs	8.20	0.05	8.50
extra_attrs_to_cols	13.16	0.09	14.53
filter_by_resource	8.12	0.38	16.26
filter_extra_attrs	24.07	0.25	26.02
filter_intercell	6.59	0.42	7.03
filter_intercell_network	0.03	0.00	0.03
find_all_paths	5.41	0.11	5.53
from_evidences	0	0	0
get_annotation_resources	0.04	0.01	0.45
get_complex_genes	1.39	0.11	2.19
get_complex_resources	0.07	0.00	0.47
get_db	0	0	0
get_enzsub_resources	0.07	0.00	0.48
get_interaction_resources	0.07	0.02	0.49
get_intercell_categories	0.59	0.01	0.89
get_intercell_generic_categories	0.05	0.00	0.04
get_intercell_resources	0.08	0.00	0.49
get_ontology_db	0.01	0.00	0.01
get_resources	0.06	0.02	0.49
get_signed_ptms	5.47	0.08	5.95
giant_component	11.07	0.24	11.68
go_annot_download	10.57	1.00	10.66
go_annot_slim	0	0	0
go_ontology_download	0.02	0.00	0.02
guide2pharma_download	0.01	0.00	0.01
harmonizome_download	0.02	0.00	0.02
has_extra_attrs	6.56	0.04	6.61
homologene_download	0.03	0.00	0.03
homologene_raw	0.04	0.00	0.03
homologene_uniprot_orthology	0.03	0.00	0.03
hpo_download	2.45	0.08	2.92
htridb_download	0.02	0.00	0.02
import_all_interactions	2.54	0.27	4.36
import_intercell_network	0.02	0.00	0.01
import_kinaseextra_interactions	1.19	0.12	2.32
import_ligrecextra_interactions	0.65	0.14	1.62
import_lncrna_mrna_interactions	0.58	0.03	1.30
import_mirnatarget_interactions	1.11	0.10	2.03
import_omnipath_annotations	0.48	0.03	1.40
import_omnipath_complexes	0.68	0.01	1.65
import_omnipath_enzsub	1.21	0.00	1.62
import_omnipath_interactions	0.32	0.00	0.72
import_omnipath_intercell	0.62	0.05	1.11
import_pathwayextra_interactions	0.80	0.08	1.81
import_post_translational_interactions	0.94	0.06	1.99
import_small_molecule_protein_interactions	0.51	0.02	0.82
import_tf_mirna_interactions	0.67	0.04	1.61
import_tf_target_interactions	1.07	0.05	2.16
import_transcriptional_interactions	2.29	0.10	3.33
inbiomap_download	0	0	0
inbiomap_raw	0	0	0
interaction_datasets	0.02	0.01	0.04
interaction_graph	0.45	0.03	0.88
interaction_types	0.06	0.00	0.06
intercell_categories	0.08	0.00	0.08
intercell_consensus_filter	1.71	0.14	2.36
is_ontology_id	0	0	0
is_swissprot	0.05	0.00	0.05
is_trembl	0.06	0.00	0.06
is_uniprot	0.02	0.00	0.02
kegg_info	0.01	0.02	0.03
kegg_open	0	0	0
kegg_pathway_annotations	0	0	0
kegg_pathway_download	0.02	0.01	0.03
kegg_pathway_list	0.01	0.00	0.02
kegg_pathways_download	0	0	0
kegg_picture	0.11	0.04	1.81
kegg_process	0.05	0.00	0.05
latin_name	0.05	0.00	0.04
load_db	0.12	0.00	0.13
ncbi_taxid	0.05	0.00	0.05
nichenet_build_model	0	0	0
nichenet_expression_data	0.01	0.00	0.01
nichenet_gr_network	0.05	0.00	0.05
nichenet_gr_network_evex	0.02	0.00	0.01
nichenet_gr_network_harmonizome	0.01	0.00	0.02
nichenet_gr_network_htridb	0.00	0.01	0.02
nichenet_gr_network_omnipath	13.27	0.61	14.35
nichenet_gr_network_pathwaycommons	0.00	0.00	0.02
nichenet_gr_network_regnetwork	0.00	0.02	0.02
nichenet_gr_network_remap	0.00	0.01	0.01
nichenet_gr_network_trrust	0.01	0.02	0.03
nichenet_ligand_activities	0	0	0
nichenet_ligand_target_links	0	0	0
nichenet_ligand_target_matrix	0	0	0
nichenet_lr_network	0.05	0.00	0.05
nichenet_lr_network_guide2pharma	0.02	0.00	0.02
nichenet_lr_network_omnipath	0.04	0.00	0.04
nichenet_lr_network_ramilowski	0.02	0.00	0.02
nichenet_main	0	0	0
nichenet_networks	0.08	0.00	0.08
nichenet_optimization	0	0	0
nichenet_remove_orphan_ligands	0.04	0.01	0.06
nichenet_results_dir	0	0	0
nichenet_signaling_network	0.03	0.02	0.05
nichenet_signaling_network_cpdb	0.00	0.01	0.01
nichenet_signaling_network_evex	0.00	0.02	0.01
nichenet_signaling_network_harmonizome	0.03	0.00	0.03
nichenet_signaling_network_inbiomap	0	0	0
nichenet_signaling_network_omnipath	7.99	0.64	9.11
nichenet_signaling_network_pathwaycommons	0.01	0.00	0.02
nichenet_signaling_network_vinayagam	0.03	0.00	0.03
nichenet_test	0	0	0
nichenet_workarounds	0	0	0
obo_parser	0.11	0.00	0.27
oma_code	0.02	0.00	0.01
oma_organisms	0.03	0.00	0.06
oma_pairwise	0.01	0.00	0.02
oma_pairwise_genesymbols	0.02	0.00	0.02
oma_pairwise_translated	0.00	0.01	0.02
omnipath	3.48	0.03	3.52
omnipath_cache_autoclean	0	0	0
omnipath_cache_clean	0	0	0
omnipath_cache_clean_db	0.08	0.02	0.11
omnipath_cache_download_ready	0.61	0.03	0.75
omnipath_cache_filter_versions	0.14	0.05	0.28
omnipath_cache_get	0.17	0.03	0.22
omnipath_cache_key	0	0	0
omnipath_cache_latest_or_new	0.08	0.04	0.12
omnipath_cache_load	0.48	0.04	1.30
omnipath_cache_move_in	0.27	0.07	0.40
omnipath_cache_remove	0.23	0.02	0.33
omnipath_cache_save	0.27	0.02	0.38
omnipath_cache_search	0	0	0
omnipath_cache_set_ext	0.15	0.01	0.22
omnipath_cache_update_status	0.11	0.08	0.18
omnipath_cache_wipe	0	0	0
omnipath_get_config_path	0	0	0
omnipath_load_config	0	0	0
omnipath_log	0	0	0
omnipath_logfile	0.02	0.00	0.02
omnipath_msg	0	0	0
omnipath_reset_config	0	0	0
omnipath_save_config	0	0	0
omnipath_set_cachedir	0.05	0.00	0.05
omnipath_set_console_loglevel	0.01	0.00	0.01
omnipath_set_logfile_loglevel	0	0	0
omnipath_set_loglevel	0	0	0
omnipath_show_db	0.05	0.00	0.05
omnipath_unlock_cache_db	0.01	0.00	0.01
only_from	0	0	0
ontology_ensure_id	0	0	0
ontology_ensure_name	0	0	0
ontology_name_id	0	0	0