* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/refseqR.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘refseqR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘refseqR’ version ‘1.1.5’
* 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 serialization versions ... OK
* checking whether package ‘refseqR’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/refseqR-00install.html' 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 ... [4s/5s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/5s] OK
* checking whether the package can be unloaded cleanly ... [4s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/6s] OK
* checking loading without being on the library search path ... [4s/6s] 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 ... [19s/29s] OK
* checking Rd files ... [0s/1s] 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 ... [5s/56s] ERROR
Running examples in ‘refseqR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: refseq_AAmol_wt
> ### Title: Extract the molecular weight from a protein accession
> ### Aliases: refseq_AAmol_wt
> 
> ### ** Examples
> 
>  # Get the molecular weight from a single protein accession
>  protein <- "XP_020244413"
>  refseq_AAmol_wt(protein)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [eutils.ncbi.nlm.nih.gov]: Resolving timed out after 10000 milliseconds
Calls: refseq_AAmol_wt ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [5s/92s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘refseqR.Rmd’ using rmarkdown

Quitting from lines 103-107 [unnamed-chunk-9] (refseqR.Rmd)
Error: processing vignette 'refseqR.Rmd' failed with diagnostics:
Timeout was reached [eutils.ncbi.nlm.nih.gov]: Resolving timed out after 10000 milliseconds
--- failed re-building ‘refseqR.Rmd’

SUMMARY: processing the following file failed:
  ‘refseqR.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [4s/6s] OK
* checking HTML version of manual ... [0s/1s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 2 ERRORs