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+ message("Perl version is outdated.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
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
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
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
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
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
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
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
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory