* works with latest R 4.3.3

* remove rland dependecies with integers
thierrygosselin · Apr 24, 2024 · cae66c8 · cae66c8
1 parent 899436d
commit cae66c8
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Showing 13 changed files with 17 additions and 47 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: radiator
 Type: Package
 Title: RADseq Data Exploration, Manipulation and Visualization using R
 Version: 1.3.1
-Date: 2024-04-23
+Date: 2024-04-24
 Encoding: UTF-8
 Authors@R: c(
   person("Thierry", "Gosselin", email = "[email protected]", role = c("aut", "cre")),
@@ -12,7 +12,7 @@ Authors@R: c(
 Maintainer: Thierry Gosselin <[email protected]>
 Description: RADseq Data Exploration, Manipulation and Visualization using R.
 Depends:
-    R (>= 4.0)
+    R (>= 4.3)
 biocViews:
 Imports:
     carrier,
@@ -51,7 +51,8 @@ Suggests:
     tibble,
     tidyr (>= 1.1.0),
     tidyselect,
-    utils
+    utils,
+    vctrs
 License: GPL-3
 LazyLoad: yes
 VignetteBuilder:

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,6 @@
-# radiator 1.3.1 2024-04-23
+# radiator 1.3.1 2024-04-24
 
+* works with R 4.3.3
 * Updated DArT code that use COUNT files to check more for problematic markers usually stemming from merged projects
 
 

diff --git a/R/filter_individuals.R b/R/filter_individuals.R
@@ -222,14 +222,6 @@ filter_individuals <- function(
     variant.select <- subsample <- NULL
     subsample.markers.stats <- 1
 
-    # id.stats <- generate_id_stats(
-    #   gds = data,
-    #   subsample = variant.select,
-    #   path.folder = path.folder,
-    #   file.date = file.date,
-    #   parallel.core = parallel.core,
-    #   verbose = verbose)
-
     id.stats <- generate_stats(
       gds = data,
       individuals = TRUE,

diff --git a/R/filter_rad.R b/R/filter_rad.R
@@ -920,28 +920,6 @@ filter_rad <- function(
     verbose = verbose
   )
 
-  # id.stats <- generate_id_stats(
-  #   gds = gds,
-  #   # subsample = variant.select,
-  #   path.folder = path.folder,
-  #   file.date = file.date,
-  #   parallel.core = parallel.core,
-  #   verbose = verbose
-  # ) %$% info
-
-  # Markers stats
-  # markers.stats <- generate_stats(
-  #   gds = gds,
-  #   individuals = FALSE,
-  #   path.folder = path.folder,
-  #   filename = NULL,
-  #   file.date = file.date,
-  #   parallel.core = parallel.core,
-  #   verbose = verbose
-  #   # ,
-  #   # subsample = variant.select
-  # ) %$% info
-
   # genomic_converter-----------------------------------------------------------
   if (verbose) message("\nTransferring data to genomic converter...")
   res$output <- genomic_converter(

diff --git a/R/genlight.R b/R/genlight.R
@@ -114,7 +114,8 @@ tidy_genlight <- function(
   if (is.null(data@position)) {
     if (verbose) message("    POS: no")
     pos.info <- FALSE
-    data@position <- rlang::as_integer(seq(from = 1, to = n.markers, by = 1))
+    # data@position <- rlang::as_integer(seq(from = 1, to = n.markers, by = 1))
+    data@position <- vctrs::vec_cast(x = seq(from = 1, to = n.markers, by = 1), to = integer())
   } else {
     if (verbose) message("    POS: yes")
     pos.info <- TRUE

diff --git a/README.Rmd b/README.Rmd
@@ -12,7 +12,6 @@ version <- gsub(" ", "", gsub("Version:", "", grep("Version:", description, valu
 <!-- badges: start -->
 [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://tidyverse.org/lifecycle/#maturing)
 [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
-[![minimal R version](https://img.shields.io/badge/R%3E%3D-`r rvers`-6666ff.svg)](https://cran.r-project.org/)
 [![packageversion](https://img.shields.io/badge/Package%20version-`r version`-orange.svg)](commits/master)
 [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-brightgreen.svg)](/commits/master)
 [![R-CMD-check](https://github.com/thierrygosselin/radiator/workflows/R-CMD-check/badge.svg)](https://github.com/thierrygosselin/radiator/actions)

diff --git a/README.md b/README.md
@@ -5,10 +5,8 @@
 [![Project Status: Active – The project has reached a stable, usable
 state and is being actively
 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
-[![minimal R
-version](https://img.shields.io/badge/R%3E%3D-NA-6666ff.svg)](https://cran.r-project.org/)
 [![packageversion](https://img.shields.io/badge/Package%20version-1.3.1-orange.svg)](commits/master)
-[![Last-changedate](https://img.shields.io/badge/last%20change-2024--04--23-brightgreen.svg)](/commits/master)
+[![Last-changedate](https://img.shields.io/badge/last%20change-2024--04--24-brightgreen.svg)](/commits/master)
 [![R-CMD-check](https://github.com/thierrygosselin/radiator/workflows/R-CMD-check/badge.svg)](https://github.com/thierrygosselin/radiator/actions)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3687060.svg)](https://doi.org/10.5281/zenodo.3687060)
 <!-- badges: end -->

diff --git a/docs/articles/get_started.html b/docs/articles/get_started.html
diff --git a/docs/articles/life_cycle.html b/docs/articles/life_cycle.html
diff --git a/docs/articles/rad_genomics_computer_setup.html b/docs/articles/rad_genomics_computer_setup.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -5,5 +5,5 @@ articles:
   get_started: get_started.html
   life_cycle: life_cycle.html
   rad_genomics_computer_setup: rad_genomics_computer_setup.html
-last_built: 2024-04-23T22:04Z
+last_built: 2024-04-24T14:02Z