• using R Under development (unstable) (2026-01-26 r89334)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-12) 15.2.0     GNU Fortran (Debian 15.2.0-12) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘annotaR/DESCRIPTION’ ... OK
• this is package ‘annotaR’ version ‘0.1.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/1s] OK
• 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 serialization versions ... OK
• checking whether package ‘annotaR’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... 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/6s] OK
• checking whether the package can be loaded with stated dependencies ... [5s/6s] OK
• checking whether the package can be unloaded cleanly ... [5s/9s] OK
• checking whether the namespace can be loaded with stated dependencies ... [5s/6s] OK
• checking whether the namespace can be unloaded cleanly ... [6s/8s] OK
• checking loading without being on the library search path ... [7s/9s] OK
• checking use of S3 registration ... 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 ... [25s/32s] OK
• checking Rd files ... [0s/0s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... 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 ... [7s/26s] 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 ... [4s/6s] OK
• checking HTML version of manual ... [0s/0s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR