[ Started: 2023-05-23 02:40:04 CEST ]
[ OmnipathR v3.6.6 for BioC-3.16 from https://github.com/saezlab/OmnipathR@RELEASE_3_16 ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.16/2023-05-23_0227/OmnipathR/OmnipathR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.6.6’
* 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 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
[2023-05-23 02:40:27] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-05-23 02:40:27] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-23 02:40:27] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-05-23 02:40:27] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-23 02:40:27] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-23 02:40:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-05-23 02:40:27] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-23 02:40:27] [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: curated_ligrec_stats
> ### Title: Statistics about literature curated ligand-receptor interactions
> ### Aliases: curated_ligrec_stats
> 
> ### ** Examples
> 
> clr <- curated_ligrec_stats()
[2023-05-23 02:43:42] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/69503cb1a01671e7c77c0e80e6ca0ce4110a89fe-1.rds`.
[2023-05-23 02:43:42] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Guide2Pharma,HPMR,ICELLNET,Kirouac2010,CellTalkDB,connectomeDB2020&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-05-23 02:43:42] [SUCCESS] [OmnipathR] Loaded 4568 interactions from cache.
[2023-05-23 02:43:42] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/ec8c89037e2c920468342c7c2326c74a5474eedc-1.rds`.
[2023-05-23 02:43:42] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellPhoneDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-05-23 02:43:43] [SUCCESS] [OmnipathR] Loaded 2879 interactions from cache.
[2023-05-23 02:43:43] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/8173bc9dfc09711dc80f48d9c3c5bd57af3d8be5-1.rds`.
[2023-05-23 02:43:43] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=Cellinker&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-05-23 02:43:43] [SUCCESS] [OmnipathR] Loaded 3765 interactions from cache.
[2023-05-23 02:43:44] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/b2de51666493a9c70a7b375972a2557903c14763-1.rds`.
[2023-05-23 02:43:44] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=talklr&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-05-23 02:43:44] [SUCCESS] [OmnipathR] Loaded 2484 interactions from cache.
[2023-05-23 02:43:45] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/fedf7fd37a8e863f804aa073f2ae480ff78001e5-1.rds`.
[2023-05-23 02:43:45] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CellChatDB&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=extra_attrs,sources,references,curation_effort&license=academic`
[2023-05-23 02:43:45] [SUCCESS] [OmnipathR] Loaded 1894 interactions from cache.
[2023-05-23 02:43:45] [TRACE]   [OmnipathR] Loaded data from RDS `/home/omnipath/.cache/OmnipathR/95ee739b50bbfea2c48e5c86a64525084a1dab30-1.rds`.
[2023-05-23 02:43:45] [INFO]    [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=SignaLink3&datasets=omnipath&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2023-05-23 02:43:45] [SUCCESS] [OmnipathR] Loaded 1796 interactions from cache.
Error in file(con, "r") : 
  cannot open the connection to 'https://omnipathdb.org/resources'
Calls: curated_ligrec_stats ... import_omnipath -> omnipath_check_param -> get_resources -> safe_json
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [2023-05-23 02:44:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
  [2023-05-23 02:44:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
  [2023-05-23 02:44:47] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
  [2023-05-23 02:44:47] [TRACE]   [OmnipathR] Cache locked: FALSE
  > 
  > test_check('OmnipathR')
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 33 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (???): interactions (mirnatarget): numof rows ───────────────────────
  nrow(response) is not strictly more than 10. Difference: -10
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 33 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.16/2023-05-23_0227/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2023-05-23 02:56:36 CEST ]