[ Started: 2024-05-15 15:33:37 CEST ]
[ OmnipathR v3.11.16 for BioC-3.19 from https://github.com/saezlab/OmnipathR@master (e19dca9 2024-05-14 11:59:08) ]

* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-15_1525/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 ‘3.11.16’
* 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
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:33:58] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:33:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-15_1525/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-15_1525/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-15_1525/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-15_1525/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-15 15:33:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:33:58] [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
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:34:05] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:34:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-15_1525/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-15_1525/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-15_1525/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.19/2024-05-15_1525/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-15 15:34:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-15 15:34:05] [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: organism_for
> ### Title: Make sure the resource supports the organism and it has the ID
> ### Aliases: organism_for
> 
> ### ** Examples
> 
> organism_for(10116, 'chalmers-gem')
[1] "Rat"
> # [1] "Rat"
> organism_for(6239, 'chalmers-gem')
Error in organism_for(6239, "chalmers-gem") : 
  Organism `6239` (common_name: `Caenorhabditis elegans (Nematode, N2)`; common_name: `Caenorhabditis elegans (Nematode, N2)`) is not supported by resource `chalmers-gem`. Supported organisms: Human, Mouse, Rat, Zebrafish, Drosophila melanogaster (Fruit fly), Caenorhabditis elegans (PRJNA13758).
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-3.19/2024-05-15_1525/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.

[ Finished: 2024-05-15 15:46:17 CEST ]