diff --git a/BIGf90_0.3.2_manual.pdf b/BIGf90_0.3.2_manual.pdf deleted file mode 100644 index e79e18a..0000000 Binary files a/BIGf90_0.3.2_manual.pdf and /dev/null differ diff --git a/R/zzz.R b/R/zzz.R index 3ef5431..cb6e2d8 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -1,15 +1,19 @@ -.onLoad <- function(libname, pkgname){ +# Register the dplyr NSE column names used across the package so R CMD check +# does not flag them as undefined global variables. +utils::globalVariables(c("V1", "V2", "V3", "trait.effect")) + +.onAttach <- function(libname, pkgname){ msg <- paste0("\nBIGf90 is a wrapper package for BLUPf90 family of programs, please use the following citations:\n\n", "BIGf90 Reference: \n", "Chinchilla-Vargas J, Taniguti C, Sandercock A, Breeding Insight Team (2024). BIGf90: - Breeding Insight Genomics R front face to blupf90 modules. R package version 0.3.2, - https://github.com/josuechinchilla/BIGf90 \n\n", + Breeding Insight Genomics R front face to blupf90 modules. R package version 0.4.0, + https://github.com/Breeding-Insight/BIGf90 \n\n", "BLUPF90 Reference: \n", "Misztal, I., S. Tsuruta, D.A.L. Lourenco, I. Aguilar, A. Legarra, and Z. Vitezica. 2014.\n", "Manual for BLUPF90 family of programs: http://nce.ads.uga.edu/wiki/lib/exe/fetch.php?media=blupf90_all2.pdf \n\n", "The BLUPF90 programs are free for research, but their use should be acknowledged in publications. For commercial use, -please contact Ignacy Misztal (ignacy@uga.edu) or Daniela Lourenco (danilino@uga.edu). Provide your name, company, and purpose of use in the email." +please contact Ignacy Misztal (ignacy@uga.edu) or Daniela Lourenco (danilino@uga.edu). Provide your name, company, and purpose of use in the email." ) - + packageStartupMessage(msg) } diff --git a/README.md b/README.md index 0bf748f..150e333 100644 --- a/README.md +++ b/README.md @@ -2,19 +2,19 @@ ## (B)reeding (I)nsight (G)enomics f90 -[![Development Status](https://img.shields.io/badge/status-active%20development-yellow)](https://github.com/josuechinchilla/BIGf90) -[![R-CMD-check](https://github.com/josuechinchilla/BIGf90/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/josuechinchilla/BIGf90/actions/workflows/R-CMD-check.yaml) +[![Development Status](https://img.shields.io/badge/status-active%20development-yellow)](https://github.com/Breeding-Insight/BIGf90) +[![R-CMD-check](https://github.com/Breeding-Insight/BIGf90/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Breeding-Insight/BIGf90/actions/workflows/R-CMD-check.yaml) [![R](https://img.shields.io/badge/R-%3E%3D%204.3-blue)](https://www.r-project.org/) [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://www.apache.org/licenses/LICENSE-2.0) -[![GitHub issues](https://img.shields.io/github/issues/josuechinchilla/BIGf90)](https://github.com/josuechinchilla/BIGf90/issues) -[![GitHub pull requests](https://img.shields.io/github/issues-pr/josuechinchilla/BIGf90)](https://github.com/josuechinchilla/BIGf90/pulls) -[![GitHub Release](https://img.shields.io/github/v/release/josuechinchilla/BIGf90?include_prereleases)](https://github.com/josuechinchilla/BIGf90/releases/latest) +[![GitHub issues](https://img.shields.io/github/issues/Breeding-Insight/BIGf90)](https://github.com/Breeding-Insight/BIGf90/issues) +[![GitHub pull requests](https://img.shields.io/github/issues-pr/Breeding-Insight/BIGf90)](https://github.com/Breeding-Insight/BIGf90/pulls) +[![GitHub Release](https://img.shields.io/github/v/release/Breeding-Insight/BIGf90?include_prereleases)](https://github.com/Breeding-Insight/BIGf90/releases/latest) BIGf90 is a wrapper package for BLUPf90 family of programs, please use the following citations: #### BIGf90 Reference: - Chinchilla-Vargas J, Taniguti C, Sandercock A, Breeding Insight Team (2024). BIGf90: Breeding Insight Genomics R front face to blupf90 modules. R package version 0.4.0, https://github.com/josuechinchilla/BIGf90 + Chinchilla-Vargas J, Taniguti C, Sandercock A, Breeding Insight Team (2024). BIGf90: Breeding Insight Genomics R front face to blupf90 modules. R package version 0.4.0, https://github.com/Breeding-Insight/BIGf90 #### BLUPF90 Reference: Misztal, I., S. Tsuruta, D.A.L. Lourenco, I. Aguilar, A. Legarra, and Z. Vitezica. 2014. Manual for BLUPF90 family of programs: http://nce.ads.uga.edu/wiki/lib/exe/fetch.php?media=blupf90_all2.pdf") @@ -37,5 +37,5 @@ When running on windows always run RStudio as administrator to avoid issues with ### To install package: install.packages("devtools") #If not already installed library(devtools) -devtools::install_github("josuechinchilla/BIGf90") +devtools::install_github("Breeding-Insight/BIGf90") library("BIGf90") diff --git a/inst/CITATION b/inst/CITATION index 7cd7881..0f0cda0 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -8,6 +8,6 @@ bibentry( person(given = "Breeding Insight Team", role = "aut") ), year = "2024", - note = "R package version 0.3.2", - url = "https://github.com/Breeding-Insight/BIGr" + note = "R package version 0.4.0", + url = "https://github.com/Breeding-Insight/BIGf90" )