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

This page was generated on 2024-05-04 11:36:55 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 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    OK    ERROR    OK  
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 nebbiolo1


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

raw results


Summary

Package: OmnipathR
Version: 3.12.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OmnipathR_3.12.0.tar.gz
StartedAt: 2024-05-04 01:47:28 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 02:21:34 -0400 (Sat, 04 May 2024)
EllapsedTime: 2046.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OmnipathR_3.12.0.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: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.12.0’
* 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
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 01:47:48] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 01:47:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-04 01:47:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 01:47:48] [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
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 01:47:58] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 01:47:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-04 01:47:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 01:47:58] [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: omnipath_cache_load
> ### Title: Loads an R object from the cache
> ### Aliases: omnipath_cache_load
> 
> ### ** Examples
> 
> url <- paste0(
+     'https://omnipathdb.org/intercell?resources=Adhesome,Almen2009,',
+     'Baccin2019,CSPA,CellChatDB&license=academic'
+ )
> result <- read.delim(url, sep = '\t')
> omnipath_cache_save(result, url = url)
[2024-05-04 02:08:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 02:08:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:08:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 02:08:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:08:07] [INFO]    [OmnipathR] Cache item `31d0d863d41fbc3d10dd489849f900bd2ee741c9` version 1: status changed from `unknown` to `started`.
[2024-05-04 02:08:07] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/31d0d863d41fbc3d10dd489849f900bd2ee741c9-1.rds`.
[2024-05-04 02:08:07] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/31d0d863d41fbc3d10dd489849f900bd2ee741c9-1.rds`.
[2024-05-04 02:08:07] [INFO]    [OmnipathR] Download ready [key=31d0d863d41fbc3d10dd489849f900bd2ee741c9, version=1]
[2024-05-04 02:08:07] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 02:08:07] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:08:07] [INFO]    [OmnipathR] Cache item `31d0d863d41fbc3d10dd489849f900bd2ee741c9` version 1: status changed from `started` to `ready`.
> # works only if you have already this item in the cache
> intercell_data <- omnipath_cache_load(url = url)
[2024-05-04 02:08:07] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/31d0d863d41fbc3d10dd489849f900bd2ee741c9-1.rds`.
> class(intercell_data)
[1] "data.frame"
> # [1] "data.frame"
> nrow(intercell_data)
[1] 17377
> # [1] 16622
> attr(intercell_data, 'origin')
[1] "cache"
> # [1] "cache"
> 
> # basic example of saving and loading to and from the cache:
> bioc_url <- 'https://bioconductor.org/'
> bioc_html <- readChar(url(bioc_url), nchars = 99999)
Warning in readChar(url(bioc_url), nchars = 99999) :
  URL 'https://bioconductor.org/': status was 'SSL connect error'
Error in readChar(url(bioc_url), nchars = 99999) : 
  cannot open the connection to 'https://bioconductor.org/'
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.


Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:27:32] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] Contains 8 files.
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:27:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:27:32] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:27:34] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:27:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-03 15:27:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:27:34] [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: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2024
> #  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> #  File author(s): Alberto Valdeolivas
> #                  Dénes Türei (turei.denes@gmail.com)
> #                  Attila Gábor
> #
> #  Distributed under the MIT (Expat) License.
> #  See accompanying file `LICENSE` or find a copy at
> #      https://directory.fsf.org/wiki/License:Expat
> #
> #  Website: https://r.omnipathdb.org/
> #  Git repo: https://github.com/saezlab/OmnipathR
> #
> 
> 
> library(testthat)
> library(OmnipathR)
[2024-05-04 02:08:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 02:08:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:08:31] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 02:08:31] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-04 02:08:31] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 02:08:31] [TRACE]   [OmnipathR] Contains 2 files.
[2024-05-04 02:08:31] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-04 02:08:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 02:08:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:08:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-04 02:08:31] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-04 02:08:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-04 02:08:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:08:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-04 02:08:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:08:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-04 02:08:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:08:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-04 02:08:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 02:08:32] [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 
 22.842   1.836  78.644 

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.0160.0040.020
all_uniprots0.0070.0040.011
ancestors0.0060.0030.010
annotated_network 1.845 0.15354.161
annotation_categories 98.567 0.091100.364
biomart_query1.1000.0485.054
bioplex10.0210.0000.021
bioplex20.0230.0000.023
bioplex30.0220.0000.022
bioplex_all0.0230.0000.023
bioplex_hct116_10.0240.0000.023
bma_motif_es0.7720.0282.101
bma_motif_vs0.3510.0121.180
collectri149.237 3.405169.359
common_name0.0290.0000.029
consensuspathdb_download0.0010.0000.001
consensuspathdb_raw_table0.0130.0040.016
curated_ligand_receptor_interactions 5.376 0.67917.879
curated_ligrec_stats 46.590 4.127136.529
database_summary1.3470.0843.915
descendants0.0130.0000.013
dorothea78.606 0.94987.519
ensembl_dataset0.0170.0000.017
ensembl_id_mapping_table 1.446 0.04912.715
ensembl_id_type0.0040.0000.004
ensembl_name0.0800.0040.084
ensembl_organisms0.2060.0000.206
ensembl_organisms_raw0.2040.0000.204
ensembl_orthology0.0000.0000.001
enzsub_graph2.7510.0726.878
evex_download0.0170.0040.022
evidences000
extra_attr_values23.276 0.37339.570
extra_attrs4.4800.0034.505
extra_attrs_to_cols 9.053 0.06810.426
filter_by_resource 5.550 7.41226.381
filter_extra_attrs34.590 2.77655.009
filter_intercell 8.912 7.07136.795
filter_intercell_network0.0480.0040.097
find_all_paths 9.775 0.26925.267
from_evidences0.0010.0000.001
get_annotation_resources0.2290.0001.157
get_complex_genes2.2410.2596.226
get_complex_resources0.2500.0281.120
get_db0.0000.0000.001
get_enzsub_resources0.2410.0321.055
get_interaction_resources0.4490.0601.237
get_intercell_categories0.6730.0521.203
get_intercell_generic_categories0.1980.0110.209
get_intercell_resources0.2240.0120.933
get_ontology_db0.0450.0000.045
get_resources0.2400.0280.948
get_signed_ptms6.8670.2609.815
giant_component 9.691 0.56813.152
go_annot_download16.043 1.07727.092
go_annot_slim0.0000.0000.001
go_ontology_download0.0230.0010.035
guide2pharma_download0.0210.0000.020
harmonizome_download0.0230.0000.038
has_extra_attrs10.323 0.08210.932
homologene_download0.0220.0000.023
homologene_raw0.1360.0000.136
homologene_uniprot_orthology0.0260.0160.041
hpo_download3.3410.4534.674
htridb_download0.0290.0000.029
import_all_interactions3.8860.2747.864
import_intercell_network0.0220.0000.022
import_kinaseextra_interactions2.4550.1935.003
import_ligrecextra_interactions1.2720.0473.322
import_lncrna_mrna_interactions0.9040.0362.157
import_mirnatarget_interactions1.7210.0904.149
import_omnipath_annotations1.0420.0152.521
import_omnipath_complexes1.1580.0643.469
import_omnipath_enzsub2.0870.0684.160
import_omnipath_interactions0.5270.0151.481
import_omnipath_intercell1.1120.0622.729
import_pathwayextra_interactions1.5510.1346.564
import_post_translational_interactions1.7560.1575.074
import_small_molecule_protein_interactions1.0430.0402.267
import_tf_mirna_interactions1.4210.1983.800
import_tf_target_interactions2.7130.2476.060
import_transcriptional_interactions4.2970.2998.112
inbiomap_download000
inbiomap_raw000
interaction_datasets0.0470.0000.055
interaction_graph0.4720.0321.268
interaction_types0.0310.0040.036
intercell_categories0.0460.0120.058
intercell_consensus_filter1.2551.2379.501
is_ontology_id0.0000.0000.001
is_swissprot0.0460.0160.081
is_trembl0.0300.0080.037
is_uniprot0.0100.0030.013
kegg_info0.0140.0040.018
kegg_open0.0140.0040.019
kegg_pathway_annotations000
kegg_pathway_download0.0150.0040.019
kegg_pathway_list0.0130.0040.018
kegg_pathways_download0.0000.0010.001
kegg_picture0.2240.0394.955
kegg_process0.0450.0080.078
latin_name0.0720.0150.164
load_db0.2680.0410.835
ncbi_taxid0.0920.0000.117
nichenet_build_model0.0010.0000.000
nichenet_expression_data0.0250.0010.071
nichenet_gr_network0.0630.0060.129
nichenet_gr_network_evex0.0200.0040.056
nichenet_gr_network_harmonizome0.0250.0000.053
nichenet_gr_network_htridb0.0260.0000.042
nichenet_gr_network_omnipath 20.720 13.329129.006
nichenet_gr_network_pathwaycommons0.0290.0970.196
nichenet_gr_network_regnetwork0.0070.0080.016
nichenet_gr_network_remap0.0120.0040.016
nichenet_gr_network_trrust0.0170.0080.028
nichenet_ligand_activities0.0010.0000.000
nichenet_ligand_target_links0.0000.0000.001
nichenet_ligand_target_matrix0.0000.0000.001
nichenet_lr_network0.0350.0090.050
nichenet_lr_network_guide2pharma0.0150.0000.015
nichenet_lr_network_omnipath0.0290.0120.042
nichenet_lr_network_ramilowski0.0110.0040.025
nichenet_main000
nichenet_networks0.0630.1790.496
nichenet_optimization000
nichenet_remove_orphan_ligands0.0370.1030.279
nichenet_results_dir000
nichenet_signaling_network0.0310.0120.044
nichenet_signaling_network_cpdb0.0070.0040.011
nichenet_signaling_network_evex0.0550.0290.084
nichenet_signaling_network_harmonizome0.0160.0040.020
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath 8.22949.88673.193
nichenet_signaling_network_pathwaycommons0.0080.0070.018
nichenet_signaling_network_vinayagam0.0110.0040.015
nichenet_test000
nichenet_workarounds0.0010.0000.000
obo_parser0.0911.5403.753
oma_code0.0220.0040.031
oma_organisms0.0620.0000.088
oma_pairwise0.0140.0000.014
oma_pairwise_genesymbols0.0090.0040.017
omnipath 4.360 3.93610.466
omnipath_cache_autoclean0.0000.0000.001
omnipath_cache_clean0.0080.0020.012
omnipath_cache_clean_db0.0820.0280.113
omnipath_cache_download_ready0.5030.0891.245
omnipath_cache_filter_versions0.0910.0050.102
omnipath_cache_get0.1230.0040.129
omnipath_cache_key0.0010.0000.001
omnipath_cache_latest_or_new0.0590.0000.059