[ Started: 2023-12-03 13:51:37 CET ]
[ OmnipathR v3.8.2 for BioC-3.17 from https://github.com/saezlab/OmnipathR@RELEASE_3_17 ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-12-03_1345/OmnipathR/OmnipathR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.8.2’
* 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  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
* 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
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-03 13:51:54] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] Contains 1 files.
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-03 13:51:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-12-03_1345/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-12-03_1345/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-12-03_1345/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-12-03_1345/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-12-03 13:51:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-03 13:51:54] [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
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-03 13:52:00] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] Contains 1 files.
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-03 13:52:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-12-03_1345/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-12-03_1345/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-12-03_1345/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-12-03_1345/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-12-03 13:52:00] [TRACE]   [OmnipathR] Cache locked: FALSE
uniprot_idmapping_id_types: no visible binding for global variable
  ‘groups’
uniprot_idmapping_id_types: no visible binding for global variable
  ‘items’
Undefined global functions or variables:
  groups items
* 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: collectri
> ### Title: TF-target interactions from CollecTRI
> ### Aliases: collectri
> 
> ### ** Examples
> 
> collectri_grn <- collectri()
[2023-12-03 13:53:14] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-12-03 13:53:14] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-12-03 13:53:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-12-03 13:53:17] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 1/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
[2023-12-03 13:53:22] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-12-03 13:53:25] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 2/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
[2023-12-03 13:53:30] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic`
[2023-12-03 13:53:33] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&dorothea_levels=A,B&fields=evidences,sources,references,curation_effort&license=academic` (attempt 3/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
Error in (function (con, what, n = 1L, size = NA_integer_, signed = TRUE,  : 
  OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
Calls: collectri ... <Anonymous> -> do.call -> <Anonymous> -> download_base
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-3.17/2023-12-03_1345/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2023-12-03 13:59:22 CET ]