- using R version 4.6.0 alpha (2026-03-30 r89743)
- 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 Ventura 13.3.1
- using session charset: UTF-8
* current time: 2026-04-07 16:37:21 UTC
- checking for file ‘annotaR/DESCRIPTION’ ... OK
- this is package ‘annotaR’ version ‘0.1.1’
- 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 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 ‘annotaR’ can be installed ... [15s/23s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking ‘build’ 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 ... [5s/7s] OK
- checking whether the package can be loaded with stated dependencies ... [5s/6s] OK
- checking whether the package can be unloaded cleanly ... [5s/7s] OK
- checking whether the namespace can be loaded with stated dependencies ... [5s/7s] OK
- checking whether the namespace can be unloaded cleanly ... [5s/7s] OK
- checking loading without being on the library search path ... [5s/7s] 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 ... [11s/15s] OK
- checking Rd files ... [0s/0s] 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 installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [6s/9s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [6s/8s] OK
Running ‘testthat.R’ [6s/8s]
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [16s/47s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘annotaR-workflow.Rmd’ using rmarkdown
Quitting from annotaR-workflow.Rmd:45-56 [annotation]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/httr2_failure>
Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.ensembl.org]:
Operation timed out after 10001 milliseconds with 0 bytes received
---
Backtrace:
▆
1. ├─... %>% add_drug_links()
2. ├─annotaR::add_drug_links(.)
3. │ └─"gene" %in% names(annotaR_object)
4. └─annotaR::add_disease_links(.)
5. ├─biomaRt::getBM(...)
6. │ └─biomaRt:::martCheck(mart)
7. └─biomaRt::useEnsembl("genes", "hsapiens_gene_ensembl")
8. └─biomaRt:::.listEnsembl(version = version, GRCh = GRCh, mirror = mirror)
9. └─biomaRt:::.currentEnsemblVersion()
10. └─biomaRt::listEnsemblArchives()
11. └─biomaRt:::.listEnsemblArchives(http_config = list())
12. └─biomaRt:::.checkArchiveList(http_config)
13. └─biomaRt:::.getArchiveList(http_config = http_config)
14. └─httr2::req_perform(html_request)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'annotaR-workflow.Rmd' failed with diagnostics:
Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.ensembl.org]:
Operation timed out after 10001 milliseconds with 0 bytes received
--- failed re-building ‘annotaR-workflow.Rmd’
SUMMARY: processing the following file failed:
‘annotaR-workflow.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [6s/8s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '