Last updated on 2026-02-06 07:51:52 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.1 | 2.07 | 36.01 | 38.08 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | ERROR | ||||
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 60.91 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 69.00 | ERROR | |||
| r-devel-windows-x86_64 | 1.0.1 | 6.00 | 65.00 | 71.00 | OK | |
| r-patched-linux-x86_64 | 1.0.1 | 1.94 | 30.59 | 32.53 | ERROR | |
| r-release-linux-x86_64 | 1.0.1 | 2.06 | 30.98 | 33.04 | OK | |
| r-release-macos-arm64 | 1.0.1 | OK | ||||
| r-release-macos-x86_64 | 1.0.1 | 2.00 | 46.00 | 48.00 | OK | |
| r-release-windows-x86_64 | 1.0.1 | 5.00 | 65.00 | 70.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.1 | NOTE | ||||
| r-oldrel-macos-x86_64 | 1.0.1 | 2.00 | 47.00 | 49.00 | NOTE | |
| r-oldrel-windows-x86_64 | 1.0.1 | 6.00 | 78.00 | 84.00 | ERROR |
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘microhaplot-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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+ message("Perl version is outdated.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
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64
Version: 1.0.1
Check: dependencies in R code
Result: NOTE
Namespaces in Imports field not imported from:
‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
‘shinyWidgets’ ‘tidyr’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.1
Check: examples
Result: 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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.1
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.0.1
Check: examples
Result: 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\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s6.sam -i s6 -g gr 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s6_1.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s11.sam -i s11 -g cu 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s11_2.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s13.sam -i s13 -g p 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s13_3.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s14.sam -i s14 -g p 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s14_4.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s18.sam -i s18 -g gr 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s18_5.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s22.sam -i s22 -g cu 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s22_6.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s24.sam -i s24 -g cu 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s24_7.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s25.sam -i s25 -g p 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s25_8.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s32.sam -i s32 -g w 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s32_9.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s34.sam -i s34 -g cu 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s34_10.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s39.sam -i s39 -g p 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s39_11.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s43.sam -i s43 -g w 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s43_12.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s44.sam -i s44 -g w 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s44_13.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s49.sam -i s49 -g p 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s49_14.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s54.sam -i s54 -g gr 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s54_15.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s56.sam -i s56 -g w 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s56_16.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s58.sam -i s58 -g cu 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s58_17.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s77.sam -i s77 -g gr 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s77_18.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s78.sam -i s78 -g gr 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s78_19.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>perl D:/RCompile/CRANpkg/lib/4.4/microhaplot/perl/hapture -v D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/sebastes.vcf -s D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\s81.sam -i s81 -g w 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s81_20.summary
d:\Rcompile\CRANpkg\local\4.4\microhaplot.Rcheck>type D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_*.summary 1>D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6/intermed/all.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s11_2.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s13_3.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s14_4.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s18_5.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s22_6.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s24_7.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s25_8.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s32_9.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s34_10.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s39_11.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s43_12.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s44_13.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s49_14.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s54_15.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s56_16.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s58_17.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s6_1.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s77_18.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\intermed\sebastes_s78_19.summary
D:\temp\2026_02_04_01_50_01_15123\RtmpeEDym6\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
Flavor: r-oldrel-windows-x86_64