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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.14.0’
* 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 ... 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:16] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 00:41:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:16] [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
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:28] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 00:41:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:28] [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')
[2025-01-31 00:41:54] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-31 00:41:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 00:41:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:55] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-31 00:41:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 00:41:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:55] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-31 00:41:55] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-31 00:41:55] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-31 00:41:55] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-31 00:41:56] [TRACE]   [OmnipathR] HTTP 200
[2025-01-31 00:41:56] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-01-31 00:41:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 00:41:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:56] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-01-31 00:41:56] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-31 00:41:56] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-01-31 00:41:56] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-31 00:41:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 00:41:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 00:41:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:56] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-01-31 00:41:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-31 00:41:56] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-01-31 00:41:56] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-01-31 00:41:57] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-31 00:41:57] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-01-31 00:41:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 00:41:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:57] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-01-31 00:41:57] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-01-31 00:41:57] [TRACE]   [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id
[2025-01-31 00:41:57] [TRACE]   [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`.
[2025-01-31 00:41:57] [INFO]    [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-01-31 00:41:57] [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`.
[2025-01-31 00:41:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 00:41:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 00:41:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 00:41:57] [INFO]    [OmnipathR] Cache item `80e22dce504c916061293773267b3f34dea718f3` version 1: status changed from `unknown` to `started`.
[2025-01-31 00:41:57] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/80e22dce504c916061293773267b3f34dea718f3-1.rds`.
[2025-01-31 00:41:57] [INFO]    [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-01-31 00:41:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-01-31 00:42:59] [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)
[2025-01-31 00:43:04] [TRACE]   [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-01-31 00:44:06] [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)
[2025-01-31 00:44:12] [TRACE]   [OmnipathR] Attempt 3/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id&query=organism_id:9606%20AND%20reviewed:true`
[2025-01-31 00:45:13] [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’
 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.