From cae66c82523dbed6445b3aed537467d7ed0d3412 Mon Sep 17 00:00:00 2001 From: Thierry Gosselin Date: Wed, 24 Apr 2024 10:11:56 -0400 Subject: [PATCH] * works with latest R 4.3.3 * remove rland dependecies with integers --- DESCRIPTION | 7 +++--- NEWS.md | 3 ++- R/filter_individuals.R | 8 ------- R/filter_rad.R | 22 ------------------- R/genlight.R | 3 ++- README.Rmd | 1 - README.md | 4 +--- docs/articles/get_started.html | 2 +- docs/articles/life_cycle.html | 2 +- .../articles/rad_genomics_computer_setup.html | 2 +- docs/index.html | 3 +-- docs/news/index.html | 5 +++-- docs/pkgdown.yml | 2 +- 13 files changed, 17 insertions(+), 47 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9cb0a2fa..d6e01df3 100644 --- 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 = "thierrygosselin@icloud.com", role = c("aut", "cre")), @@ -12,7 +12,7 @@ Authors@R: c( Maintainer: Thierry Gosselin 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 index 83d60712..e2f0cc96 100644 --- 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 index e87b337a..32d426fd 100644 --- 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 index 123802f5..6d4aa910 100644 --- 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 index a7973589..172d553c 100644 --- 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 index 56ad947a..f2469312 100644 --- a/README.Rmd +++ b/README.Rmd @@ -12,7 +12,6 @@ version <- gsub(" ", "", gsub("Version:", "", grep("Version:", description, valu [![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 index a33f2e95..8ab55992 100644 --- 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) diff --git a/docs/articles/get_started.html b/docs/articles/get_started.html index d3e9ebdc..dfebac0e 100644 --- a/docs/articles/get_started.html +++ b/docs/articles/get_started.html @@ -91,7 +91,7 @@

Get Started

Thierry Gosselin

-

2024-04-23

+

2024-04-24

Source: vignettes/get_started.Rmd diff --git a/docs/articles/life_cycle.html b/docs/articles/life_cycle.html index 3f500905..78af7636 100644 --- a/docs/articles/life_cycle.html +++ b/docs/articles/life_cycle.html @@ -91,7 +91,7 @@

Life Cycle

Thierry Gosselin

-

2024-04-23

+

2024-04-24

Source: vignettes/life_cycle.Rmd diff --git a/docs/articles/rad_genomics_computer_setup.html b/docs/articles/rad_genomics_computer_setup.html index d991720e..834f4399 100644 --- a/docs/articles/rad_genomics_computer_setup.html +++ b/docs/articles/rad_genomics_computer_setup.html @@ -90,7 +90,7 @@

RADseq Genomics in R

computer setup

-

2024-04-23

+

2024-04-24

Source: vignettes/rad_genomics_computer_setup.Rmd diff --git a/docs/index.html b/docs/index.html index 8071d1a2..0b4f0649 100644 --- a/docs/index.html +++ b/docs/index.html @@ -176,9 +176,8 @@

Dev status

diff --git a/docs/news/index.html b/docs/news/index.html index 332602d9..db134455 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -67,8 +67,9 @@

Changelog

-

radiator 1.3.1 2024-04-23

-
  • Updated DArT code that use COUNT files to check more for problematic markers usually stemming from merged project
    • +

    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

radiator 1.3.0 2024-02-22

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index b1ccb46f..20f8fba7 100644 --- 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