- using R Under development (unstable) (2026-02-07 r89380)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
* current time: 2026-02-09 11:14:30 UTC
- using option ‘--no-stop-on-test-error’
- checking for file ‘microhaplot/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘microhaplot’ version ‘1.0.1’
- 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 ‘microhaplot’ can be installed ... OK
See the install log for details.
- 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 ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... OK
- checking use of S3 registration ... OK
- checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
‘shinyWidgets’ ‘tidyr’
All declared Imports should be used.
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... OK
- checking Rd files ... 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 LazyData ... INFO
'LazyData' is specified without a 'data' directory
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [10s/12s] ERROR
Running examples in ‘microhaplot-Ex.R’ failed
The error most likely occurred in:
> ### Name: prepHaplotFiles
> ### Title: Extracts haplotype from alignment reads.
> ### Aliases: prepHaplotFiles
>
> ### ** Examples
>
>
> run.label <- "sebastes"
>
> sam.path <- tempdir()
> untar(system.file("extdata",
+ "sebastes_sam.tar.gz",
+ package="microhaplot"),
+ exdir = sam.path)
>
>
> label.path <- file.path(sam.path, "label.txt")
> vcf.path <- file.path(sam.path, "sebastes.vcf")
>
> mvShinyHaplot(tempdir())
[1] TRUE
> app.path <- file.path(tempdir(), "microhaplot")
>
> # retrieve system Perl version number
> perl.version <- as.numeric(system('perl -e "print $];"', intern=TRUE))
>
> if (perl.version >= 5.014) {
+ haplo.read.tbl <- prepHaplotFiles(run.label = run.label,
+ sam.path = sam.path,
+ out.path = tempdir(),
+ label.path = label.path,
+ vcf.path = vcf.path,
+ app.path = app.path)
+ }else {
+ message("Perl version is outdated. Must >= 5.014.")}
Perl is found in system
...running Hapture.pl to extract haplotype information (takes a while)...
Error:
! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct.
ℹ Please use `tibble::as_tibble()` instead.
Backtrace:
▆
1. ├─microhaplot::prepHaplotFiles(...)
2. │ └─... %>% dplyr::tbl_df()
3. └─dplyr::tbl_df(.)
4. └─lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()")
5. └─lifecycle:::deprecate_stop0(msg)
6. └─rlang::cnd_signal(...)
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [20s/26s] OK
- checking PDF version of manual ... OK
- checking HTML version of manual ... OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR, 1 NOTE