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+ message("Perl version is outdated.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)...

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s6.sam -i s6 -g gr  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s6_1.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s11.sam -i s11 -g cu  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s11_2.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s13.sam -i s13 -g p  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s13_3.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s14.sam -i s14 -g p  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s14_4.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s18.sam -i s18 -g gr  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s18_5.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s22.sam -i s22 -g cu  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s22_6.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s24.sam -i s24 -g cu  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s24_7.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s25.sam -i s25 -g p  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s25_8.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s32.sam -i s32 -g w  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s32_9.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s34.sam -i s34 -g cu  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s34_10.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s39.sam -i s39 -g p  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s39_11.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s43.sam -i s43 -g w  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s43_12.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s44.sam -i s44 -g w  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s44_13.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s49.sam -i s49 -g p  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s49_14.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s54.sam -i s54 -g gr  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s54_15.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s56.sam -i s56 -g w  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s56_16.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s58.sam -i s58 -g cu  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s58_17.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s77.sam -i s77 -g gr  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s77_18.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s78.sam -i s78 -g gr  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s78_19.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/sebastes.vcf  -s D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\s81.sam -i s81 -g w  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s81_20.summary 

d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>type D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_*.summary  1>D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj/intermed/all.summary 

D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s11_2.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s13_3.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s14_4.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s18_5.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s22_6.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s24_7.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s25_8.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s32_9.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s34_10.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s39_11.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s43_12.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s44_13.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s49_14.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s54_15.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s56_16.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s58_17.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s6_1.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s77_18.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s78_19.summary



D:\temp\2026_02_28_01_50_00_3652\Rtmpctlilj\intermed\sebastes_s81_20.summary


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