Multiple platform build/check report for BioC 3.21 - CHECK results for OmnipathR on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4609
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4393
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	3839
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	3835
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4408
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for OmnipathR on lconway

To the developers/maintainers of the OmnipathR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: OmnipathR

Version: 3.15.0

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_3.15.0.tar.gz

StartedAt: 2025-01-23 19:42:55 -0500 (Thu, 23 Jan 2025)

EndedAt: 2025-01-23 19:51:09 -0500 (Thu, 23 Jan 2025)

EllapsedTime: 493.4 seconds

RetCode: 1

Status: ERROR

CheckDir: OmnipathR.Rcheck

Warnings: NA

Command output

##############################################################################
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###
### 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_3.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... OK
* 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
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:43:26] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:43:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-23 19:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:43:26] [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
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:43:45] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:43:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-23 19:43:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:43:45] [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 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: all_uniprots
> ### Title: A table with all UniProt records
> ### Aliases: all_uniprots
> 
> ### ** Examples
> 
> human_swissprot_entries <- all_uniprots(fields = 'id')
[2025-01-23 19:44:28] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-23 19:44:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 19:44:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:44:28] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-23 19:44:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 19:44:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:44:28] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-23 19:44:28] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-23 19:44:28] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-23 19:44:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-23 19:44:40] [TRACE]   [OmnipathR] HTTP 200
[2025-01-23 19:44:40] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-01-23 19:44:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 19:44:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:44:40] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-01-23 19:44:40] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-23 19:44:40] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-01-23 19:44:40] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-23 19:44:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 19:44:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:44:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 19:44:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:44:41] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-01-23 19:44:41] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-23 19:44:41] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-01-23 19:44:41] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-01-23 19:44:42] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-23 19:44:42] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-01-23 19:44:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 19:44:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:44:42] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-01-23 19:44:42] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-01-23 19:44:42] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id
[2025-01-23 19:44:42] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`.
[2025-01-23 19:44:42] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-01-23 19:44:42] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`.
[2025-01-23 19:44:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 19:44:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:44:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 19:44:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:44:42] [INFO]    [OmnipathR] Cache item `80e22dce504c916061293773267b3f34dea718f3` version 1: status changed from `unknown` to `started`.
[2025-01-23 19:44:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/80e22dce504c916061293773267b3f34dea718f3-1.rds`.
[2025-01-23 19:44:42] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-01-23 19:44:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-01-23 19:46:28] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` (attempt 1/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2025-01-23 19:46:33] [TRACE]   [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-01-23 19:47:35] [WARN]    [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` (attempt 2/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2025-01-23 19:47:40] [TRACE]   [OmnipathR] Attempt 3/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-01-23 19:49:31] [ERROR]   [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true` (attempt 3/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
Error in (function (con, what, n = 1L, size = NA_integer_, signed = TRUE,  : 
  Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
Calls: all_uniprots ... omnipath_cache_save -> saveRDS -> exec -> <Anonymous>
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:
  ── Error ('test_import.R:49:5'): (code run outside of `test_that()`) ───────────
  Error in `open.connection(con, "rb")`: cannot open the connection to 'https://omnipathdb.org/resources'
  Backtrace:
      ▆
   1. └─OmnipathR (local) get_resources_test(...) at test_import.R:162:9
   2.   └─jsonlite::fromJSON(txt = resources_url) at test_import.R:49:5
   3.     └─jsonlite:::parse_and_simplify(...)
   4.       └─jsonlite:::parseJSON(txt, bigint_as_char)
   5.         └─jsonlite:::parse_con(txt, bigint_as_char)
   6.           ├─base::open(con, "rb")
   7.           └─base::open.connection(con, "rb")
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
* 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: 2 ERRORs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘OmnipathR’ ...
** this is package ‘OmnipathR’ version ‘3.15.0’
** 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
[2025-01-23 15:28:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 15:28:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 15:28:02] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 15:28:02] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-23 15:28:02] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 15:28:02] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-23 15:28:02] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-23 15:28:02] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 15:28:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 15:28:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 15:28:03] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-23 15:28:03] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-23 15:28:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 15:28:03] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-23 15:28:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 15:28:03] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-23 15:28:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 15:28:03] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-23 15:28:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 15:28:03] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 15:28:06] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 15:28:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 15:28:06] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

Tests output

OmnipathR.Rcheck/tests/testthat.Rout.fail


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> #!/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)
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:49:34] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] Contains 3 files.
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:49:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-23 19:49:34] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 1 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_import.R:49:5'): (code run outside of `test_that()`) ───────────
Error in `open.connection(con, "rb")`: cannot open the connection to 'https://omnipathdb.org/resources'
Backtrace:
    ▆
 1. └─OmnipathR (local) get_resources_test(...) at test_import.R:162:9
 2.   └─jsonlite::fromJSON(txt = resources_url) at test_import.R:49:5
 3.     └─jsonlite:::parse_and_simplify(...)
 4.       └─jsonlite:::parseJSON(txt, bigint_as_char)
 5.         └─jsonlite:::parse_con(txt, bigint_as_char)
 6.           ├─base::open(con, "rb")
 7.           └─base::open.connection(con, "rb")

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 1 ]
Error: Test failures
Execution halted

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

name	user	system	elapsed
OmnipathR	0.000	0.001	0.001
all_uniprot_acs	0.017	0.002	0.020