[ Started: 2024-03-18 13:14:24 CET ]
[ OmnipathR v3.11.4 for BioC-3.18 from https://github.com/saezlab/OmnipathR@master ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-18_1307/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 ‘3.11.4’
* 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 ... WARNING
Found the following significant warnings:
  Warning: OmnipathR.Rd: docType ‘_PACKAGE’ is unrecognized
See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-18_1307/OmnipathR/OmnipathR.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
* 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
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:14:43] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:14:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-18_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-18_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-18_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-18_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-18 13:14:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:14:43] [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
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:14:50] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:14:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-18_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-18_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-18_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-18_1307/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:14:50] [TRACE]   [OmnipathR] Cache locked: FALSE
oma_pairwise_genesymbols: no visible binding for global variable
  ‘id_organism_a’
oma_pairwise_genesymbols: no visible binding for global variable
  ‘id_organism_b’
Undefined global functions or variables:
  id_organism_a id_organism_b
* checking Rd files ... WARNING
prepare_Rd: OmnipathR.Rd: docType ‘_PACKAGE’ is unrecognized
* 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: dorothea
> ### Title: TF-target interactions from DoRothEA
> ### Aliases: dorothea import_tfregulons_interactions
> ###   import_dorothea_interactions
> 
> ### ** Examples
> 
> dorothea_grn <- dorothea(
+     resources = c('DoRothEA', 'ARACNe-GTEx_DoRothEA'),
+     organism = 9606,
+     dorothea_levels = c('A', 'B', 'C')
+ )
[2024-03-18 13:18:03] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-03-18 13:18:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:18:03] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-18 13:18:03] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-18 13:18:03] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-18 13:18:03] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-18 13:18:03] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-18 13:18:03] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-18 13:18:03] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-18 13:18:06] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` (attempt 1/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
[2024-03-18 13:18:11] [TRACE]   [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-18 13:18:14] [WARN]    [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` (attempt 2/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
[2024-03-18 13:18:19] [TRACE]   [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-18 13:18:23] [ERROR]   [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic` (attempt 3/3); error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
[2024-03-18 13:18:23] [WARN]    [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`; error: OpenSSL SSL_read: error:0A000126:SSL routines::unexpected eof while reading, errno 0
[2024-03-18 13:18:23] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=DoRothEA,ARACNe-GTEx_DoRothEA&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C&fields=evidences,sources,references,curation_effort,dorothea_level&license=academic`
[2024-03-18 13:18:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-18 13:18:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:18:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-18 13:18:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:18:23] [INFO]    [OmnipathR] Cache item `bbd46c752473f3189c754e4248ac33e41bda2b16` version 1: status changed from `unknown` to `started`.
[2024-03-18 13:18:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/bbd46c752473f3189c754e4248ac33e41bda2b16-1.rds`.
[2024-03-18 13:18:23] [TRACE]   [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/bbd46c752473f3189c754e4248ac33e41bda2b16-1.rds`.
[2024-03-18 13:18:23] [INFO]    [OmnipathR] Download ready [key=bbd46c752473f3189c754e4248ac33e41bda2b16, version=1]
[2024-03-18 13:18:23] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-18 13:18:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-18 13:18:23] [INFO]    [OmnipathR] Cache item `bbd46c752473f3189c754e4248ac33e41bda2b16` version 1: status changed from `started` to `ready`.
[2024-03-18 13:18:23] [ERROR]   [OmnipathR] `only_from` can be called only on data frames with `evidences` column.
Error in do.call(stop, list(m), envir = env) : 
  `only_from` can be called only on data frames with `evidences` column.
Calls: dorothea ... only_from -> must_have_evidences -> do.call -> <Anonymous>
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, 2 WARNINGs, 3 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-03-18_1307/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2024-03-18 13:24:22 CET ]