- using R Under development (unstable) (2026-02-10 r89394)
- 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: 2026-03-13 14:48:49 UTC
- 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 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 ‘MixviR’ can be installed ... [4s/5s] 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 ... [0s/0s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/0s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
- checking loading without being on the library search path ... [0s/0s] 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 ... [4s/9s] OK
- checking Rd files ... [0s/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 ... [4s/11s] 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 ... [14s/35s] OK
- checking PDF version of manual ... [7s/8s] OK
- DONE
Status: 1 ERROR
- using check arguments '--no-clean-on-error '