* using log directory 'd:/Rcompile/CRANpkg/local/4.5/MixviR.Rcheck'
* using R version 4.5.2 (2025-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.3.0
    GNU Fortran (GCC) 14.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'MixviR/DESCRIPTION' ... OK
* this is package 'MixviR' version '3.5.0'
* 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 whether package 'MixviR' can be installed ... OK
* 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 ... [0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s] OK
* checking whether the package can be unloaded cleanly ... [0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s] OK
* checking loading without being on the library search path ... [0s] 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 ... [6s] OK
* checking Rd files ... [1s] 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] ERROR
Running examples in 'MixviR-Ex.R' failed
The error most likely occurred in:

> ### Name: create_ref
> ### Title: Create MixVir-formatted reference genome object
> ### Aliases: create_ref
> ### Keywords: reference
> 
> ### ** Examples
> 
> site1 <- "https://raw.githubusercontent.com/mikesovic/MixviR/main/raw_files/GCF_ASM985889v3.fa"
> site2 <- "https://raw.githubusercontent.com/mikesovic/MixviR/main/raw_files/sars_cov2_genes.bed"
> 
> if (httr::http_error(site1) | httr::http_error(site2)) {
+      message("No internet connection or data source broken.") 
+      return(NULL)
+ } else { 
+ create_ref(
+  genome = site1,
+  feature.bed = site2,
+  code.num = "1")
+ }
Rows: 12 Columns: 6
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (4): X1, X4, X5, X6
dbl (2): X2, X3

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
trying URL 'https://raw.githubusercontent.com/mikesovic/MixviR/main/raw_files/GCF_ASM985889v3.fa'
Content type 'text/plain; charset=utf-8' length 30290 bytes (29 KB)
==================================================
downloaded 29 KB

Error in `dplyr::summarise()`:
ℹ In argument: `translation = translate_fwd(REF_BASE, code = code.num)`.
ℹ In group 1: `GENE = "E"`.
Caused by error:
! `translation` must be size 1, not 228.
ℹ To return more or less than 1 row per group, use `reframe()`.
Backtrace:
     ▆
  1. ├─MixviR::create_ref(genome = site1, feature.bed = site2, code.num = "1")
  2. │ └─... %>% dplyr::pull(translation)
  3. ├─dplyr::pull(., translation)
  4. ├─dplyr::arrange(., GENE, POS)
  5. ├─dplyr::summarise(...)
  6. ├─dplyr:::summarise.grouped_df(...)
  7. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
  8. │   └─base::withCallingHandlers(...)
  9. ├─dplyr:::dplyr_internal_error(...)
 10. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
 11. │   └─rlang:::signal_abort(cnd, .file)
 12. │     └─base::signalCondition(cnd)
 13. └─dplyr (local) `<fn>`(`<dpl:::__>`)
 14.   └─dplyr (local) handler(cnd)
 15.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [9s] OK
* checking PDF version of manual ... [19s] OK
* checking HTML version of manual ... [2s] OK
* DONE
Status: 1 ERROR