[ Started: 2023-05-30 01:59:26 CEST ] [ OmnipathR v3.9.3 for BioC-3.17 from https://github.com/saezlab/OmnipathR@master ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-05-30_0153/OmnipathR/OmnipathR.Rcheck’ * using R version 4.3.0 (2023-04-21) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.9.3’ * 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 executable files ... 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 ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: doc 5.4Mb * 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 R 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 startup messages can be suppressed ... NOTE [2023-05-30 01:59:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-05-30 01:59:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-30 01:59:45] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-05-30 01:59:45] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-05-30 01:59:45] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-05-30 01:59:45] [TRACE] [OmnipathR] Contains 1 files. [2023-05-30 01:59:45] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-05-30 01:59:45] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-05-30 01:59:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-30 01:59:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-05-30 01:59:45] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-05-30 01:59:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-05-30_0153/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-05-30 01:59:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-30 01:59:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-05-30_0153/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-05-30 01:59:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-30 01:59:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-05-30_0153/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-05-30 01:59:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-30 01:59:45] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-05-30_0153/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-05-30 01:59:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-30 01:59:45] [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 [2023-05-30 01:59:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-05-30 01:59:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-30 01:59:51] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-05-30 01:59:51] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-05-30 01:59:51] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-05-30 01:59:51] [TRACE] [OmnipathR] Contains 1 files. [2023-05-30 01:59:51] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-05-30 01:59:51] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-05-30 01:59:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-30 01:59:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-05-30 01:59:51] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-05-30 01:59:51] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-05-30_0153/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-05-30 01:59:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-30 01:59:51] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-05-30_0153/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-05-30 01:59:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-30 01:59:51] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-05-30_0153/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-05-30 01:59:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-30 01:59:51] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-05-30_0153/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-05-30 01:59:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-05-30 01:59:51] [TRACE] [OmnipathR] Cache locked: FALSE complex_orthology : comp_prod: no visible binding for global variable ‘complexes’ complex_orthology: no visible global function definition for ‘vars’ oma_pairwise: no visible binding for global variable ‘id_organism_a’ oma_pairwise: no visible binding for global variable ‘id_organism_b’ oma_pairwise: no visible binding for global variable ‘mapping’ orthology_translate: no visible binding for global variable ‘d’ orthology_translate_column: no visible global function definition for ‘join_by’ subnetwork: no visible global function definition for ‘igraph_vs’ Undefined global functions or variables: complexes d id_organism_a id_organism_b igraph_vs join_by mapping vars * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > ### Name: from_evidences > ### Title: Recreate interaction records from evidences columns > ### Aliases: from_evidences > > ### ** Examples > > ci <- collectri(evidences = TRUE) [2023-05-30 02:05:12] [TRACE] [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/099e7af92f71a88d7560d65cea14c1970f66c0b6-1.rds`. [2023-05-30 02:05:12] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` [2023-05-30 02:05:12] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2023-05-30 02:05:15] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any [2023-05-30 02:05:19] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: collectri; and resources: any [2023-05-30 02:06:33] [SUCCESS] [OmnipathR] Downloaded 64495 interactions. > ci <- filter_evidences(datasets = 'collectri') Error: argument "data" is missing, with no default 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK ‘db_manager.Rmd’ using ‘UTF-8’... OK ‘drug_targets.Rmd’ using ‘UTF-8’... OK ‘extra_attrs.Rmd’ using ‘UTF-8’... OK ‘nichenet.Rmd’ using ‘UTF-8’... OK ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK ‘paths.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-05-30_0153/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2023-05-30 02:12:20 CEST ]