[ Started: 2024-05-02 15:52:42 CEST ] [ OmnipathR v3.11.15 for BioC-3.19 from https://github.com/saezlab/OmnipathR@master (88f8b50 2024-04-30 14:35:31) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-02_1545/OmnipathR/OmnipathR.Rcheck’ * using R version 4.4.0 alpha (2024-04-04 r86334) * 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 ‘3.11.15’ * 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 6.0Mb sub-directories of 1Mb or more: doc 4.8Mb * 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 [2024-05-02 15:53:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-02 15:53:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-02 15:53:02] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-02 15:53:02] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-02 15:53:02] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-02 15:53:02] [TRACE] [OmnipathR] Contains 1 files. [2024-05-02 15:53:02] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-02 15:53:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-02 15:53:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-02 15:53:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-02 15:53:02] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-02 15:53:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-02_1545/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-02 15:53:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-02 15:53:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-02_1545/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-02 15:53:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-02 15:53:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-02_1545/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-02 15:53:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-02 15:53:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-02_1545/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-02 15:53:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-02 15:53:02] [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 [2024-05-02 15:53:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-02 15:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-02 15:53:08] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-02 15:53:08] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-02 15:53:08] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-02 15:53:08] [TRACE] [OmnipathR] Contains 1 files. [2024-05-02 15:53:08] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-02 15:53:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-02 15:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-02 15:53:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-02 15:53:08] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-02 15:53:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-02_1545/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-02 15:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-02 15:53:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-02_1545/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-02 15:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-02 15:53:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-02_1545/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-02 15:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-02 15:53:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-02_1545/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-02 15:53:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-02 15:53:09] [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 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: import_mirnatarget_interactions > ### Title: Imports interactions from the miRNA-target dataset of OmniPath > ### Aliases: import_mirnatarget_interactions > ### import_miRNAtarget_Interactions > > ### ** Examples > > interactions <- + import_mirnatarget_interactions( + resources = c('miRTarBase', 'miRecords') + ) Error in file(con, "r") : cannot open the connection to 'https://omnipathdb.org/resources' Calls: import_mirnatarget_interactions ... %>% -> omnipath_check_param -> get_resources -> safe_json 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, 4 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-02_1545/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2024-05-02 16:05:43 CEST ]