• using R Under development (unstable) (2026-02-13 r89414 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 * current time: 2026-02-14 15:13:24 UTC
• 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 hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'microhaplot' can be installed ... 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] 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 ... [2s] OK
• checking Rd files ... [0s] 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 LazyData ... INFO   'LazyData' is specified without a 'data' directory
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ... [18s] 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)... d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.6/microhaplot/perl/hapture -v D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s6.sam -i s6 -g gr 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s11.sam -i s11 -g cu 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s13.sam -i s13 -g p 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s14.sam -i s14 -g p 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s18.sam -i s18 -g gr 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s22.sam -i s22 -g cu 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s24.sam -i s24 -g cu 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s25.sam -i s25 -g p 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s32.sam -i s32 -g w 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s34.sam -i s34 -g cu 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s39.sam -i s39 -g p 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s43.sam -i s43 -g w 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s44.sam -i s44 -g w 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s49.sam -i s49 -g p 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s54.sam -i s54 -g gr 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s56.sam -i s56 -g w 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s58.sam -i s58 -g cu 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s77.sam -i s77 -g gr 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s78.sam -i s78 -g gr 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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_14_01_50_00_18536\RtmpUXpr1N/sebastes.vcf -s D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\s81.sam -i s81 -g w 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s81_20.summary d:\Rcompile\CRANpkg\local\4.6\microhaplot.Rcheck>type D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_*.summary 1>D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N/intermed/all.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s11_2.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s13_3.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s14_4.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s18_5.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s22_6.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s24_7.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s25_8.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s32_9.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s34_10.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s39_11.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s43_12.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s44_13.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s49_14.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s54_15.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s56_16.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s58_17.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s6_1.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s77_18.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\intermed\sebastes_s78_19.summary D:\temp\2026_02_14_01_50_00_18536\RtmpUXpr1N\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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [7s] OK
• checking PDF version of manual ... [19s] OK
• checking HTML version of manual ... [1s] OK
• DONE

Status: 1 ERROR