Last updated on 2026-02-04 04:50:53 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| microhaplot | 3 | 3 | 7 |
Current CRAN status: ERROR: 3, NOTE: 3, OK: 7
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+ message("Perl version is outdated.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
Flavor: r-devel-linux-x86_64-debian-gcc
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