##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.12.1’
* 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 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 ... OK
* 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 whether startup messages can be suppressed ... NOTE
[2024-07-23 05:21:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 05:21:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:21:15] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 05:21:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-23 05:21:15] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 05:21:15] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-23 05:21:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-23 05:21:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 05:21:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:21:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 05:21:15] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-07-23 05:21:15] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-23 05:21:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:21:15] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-23 05:21:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:21:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-23 05:21:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:21:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-23 05:21:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:21:16] [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
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:21:29] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:21:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:21:29] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘oma_pairwise_translated’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:58:38] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:58:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:58:38] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:58:40] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:58:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-21 16:58:40] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2024
> #  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> #  File author(s): Alberto Valdeolivas
> #                  Dénes Türei (turei.denes@gmail.com)
> #                  Attila Gábor
> #
> #  Distributed under the MIT (Expat) License.
> #  See accompanying file `LICENSE` or find a copy at
> #      https://directory.fsf.org/wiki/License:Expat
> #
> #  Website: https://r.omnipathdb.org/
> #  Git repo: https://github.com/saezlab/OmnipathR
> #
> 
> 
> library(testthat)
> library(OmnipathR)
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:30:26] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] Contains 1 files.
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:30:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-07-23 05:30:26] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
  9.624   0.866  14.016