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alex-sandercockalex-sandercock
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Merge pull request #21 from alex-sandercock/development
Added Tests and Cleaned Documentation
2 parents 26392d0 + 2482015 commit ded03aa

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‎.Rbuildignore‎

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^.*\.Rproj$
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^\.Rproj\.user$
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^dev$
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^doc$
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^LICENSE\.md$
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^revdep$
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^cran-comments\.md$

‎.github/workflows/R-CMD-check.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, development]
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pull_request:
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branches: [main, development]
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name: R-CMD-check
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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with:
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upload-snapshots: true

‎.github/workflows/rhub.yaml‎

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# R-hub's generic GitHub Actions workflow file. It's canonical location is at
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# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
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# You can update this file to a newer version using the rhub2 package:
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#
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# rhub::rhub_setup()
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#
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# It is unlikely that you need to modify this file manually.
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name: R-hub
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run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
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on:
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workflow_dispatch:
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inputs:
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config:
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description: 'A comma separated list of R-hub platforms to use.'
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type: string
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default: 'linux,windows,macos'
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name:
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description: 'Run name. You can leave this empty now.'
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type: string
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id:
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description: 'Unique ID. You can leave this empty now.'
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type: string
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jobs:
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setup:
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runs-on: ubuntu-latest
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outputs:
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containers: ${{ steps.rhub-setup.outputs.containers }}
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platforms: ${{ steps.rhub-setup.outputs.platforms }}
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steps:
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# NO NEED TO CHECKOUT HERE
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- uses: r-hub/actions/setup@v1
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with:
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config: ${{ github.event.inputs.config }}
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id: rhub-setup
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linux-containers:
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needs: setup
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if: ${{ needs.setup.outputs.containers != '[]' }}
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runs-on: ubuntu-latest
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name: ${{ matrix.config.label }}
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strategy:
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fail-fast: false
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matrix:
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config: ${{ fromJson(needs.setup.outputs.containers) }}
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container:
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image: ${{ matrix.config.container }}
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steps:
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- uses: r-hub/actions/checkout@v1
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- uses: r-hub/actions/platform-info@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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- uses: r-hub/actions/setup-deps@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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- uses: r-hub/actions/run-check@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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other-platforms:
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needs: setup
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if: ${{ needs.setup.outputs.platforms != '[]' }}
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.label }}
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strategy:
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fail-fast: false
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matrix:
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config: ${{ fromJson(needs.setup.outputs.platforms) }}
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steps:
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- uses: r-hub/actions/checkout@v1
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- uses: r-hub/actions/setup-r@v1
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with:
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job-config: ${{ matrix.config.job-config }}
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token: ${{ secrets.RHUB_TOKEN }}
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- uses: r-hub/actions/platform-info@v1
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with:
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token: ${{ secrets.RHUB_TOKEN }}
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job-config: ${{ matrix.config.job-config }}
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- uses: r-hub/actions/setup-deps@v1
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with:
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job-config: ${{ matrix.config.job-config }}
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token: ${{ secrets.RHUB_TOKEN }}
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- uses: r-hub/actions/run-check@v1
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with:
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job-config: ${{ matrix.config.job-config }}
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token: ${{ secrets.RHUB_TOKEN }}

‎.gitignore‎

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.Rhistory
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.RData
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.Ruserdata
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revdep/

‎DESCRIPTION‎

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Package: BIGr
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Title: (B)reeding (I)nsight (G)enomics Functions for Polypoid and Diploid Species
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Version: 0.4.3
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Author: Alexander M. Sandercock, Cristiane Taniguti, Josue Chinchilla-Vargas, Shufen Chen, Manoj Sapkota, Meng Lin, Dongyan Zhao, and Breeding Insight Team
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Title: Breeding Insight Genomics Functions for Polypoid and Diploid Species
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Version: 0.5.0
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Author: Alexander M. Sandercock, Cristiane H. Taniguti, Josue
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Chinchilla-Vargas, Shufen Chen, Manoj Sapkota, Meng Lin, Dongyan Zhao,
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and Breeding Insight Team
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Maintainer: Alexander M. Sandercock <[email protected]>
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Description: This package contains the functions developed within Breeding Insight to analyze diploid and polyploid breeding and genetic data.
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License: Apache License 2.0
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Encoding: UTF-8
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.2
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Depends: R (>= 4.4.0)
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Description: Functions developed within Breeding Insight to analyze diploid and polyploid
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breeding and genetic data. 'BIGr' provides the ability to filter VCF files, extract SNPs from the DArT MADC file,
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and manipulate genotype data for both diploid and polyploid species. It also serves
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as the core dependency for the 'BIGapp' Shiny app, which provides a user-friendly interface for performing routine genotype analysis tasks
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such as dosage calling, filtering, PCA, GWAS, and Genomic Prediction.
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URL: https://github.com/Breeding-Insight/BIGr
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BugReports: https://github.com/Breeding-Insight/BIGr/issues
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License: Apache License (>= 2)
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Depends:
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R (>= 4.4.0)
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Imports:
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Biostrings,
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doParallel,
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dplyr,
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foreach,
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janitor,
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methods,
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parallel,
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pwalign,
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Rdpack (>= 0.7),
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readr (>= 2.1.5),
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reshape2 (>= 1.4.4),
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stats,
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tibble,
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tidyr (>= 1.3.1),
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vcfR (>= 1.15.0),
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Biostrings,
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pwalign
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Remotes:
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RdMacros: Rdpack
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utils,
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vcfR (>= 1.15.0)
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Suggests:
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testthat (>= 3.0.0)
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RdMacros:
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Rdpack
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Encoding: UTF-8
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.2

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