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zankrut20 committed Sep 19, 2023
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1 change: 1 addition & 0 deletions .Rbuildignore
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^Meta$
^CRAN-SUBMISSION$
^\.httr-oauth$
^codecov\.yml$
22 changes: 1 addition & 21 deletions .github/workflows/R-CMD-check.yaml
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Expand Up @@ -10,33 +10,15 @@ name: R-CMD-check

jobs:
R-CMD-check:
runs-on: ${{ matrix.config.os }}

name: ${{ matrix.config.os }} (${{ matrix.config.r }})

strategy:
fail-fast: false
matrix:
config:
- {os: macos-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
- {os: ubuntu-latest, r: 'release'}
- {os: ubuntu-latest, r: 'oldrel-1'}

runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes

steps:
- uses: actions/checkout@v3

- uses: r-lib/actions/setup-pandoc@v2

- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true

- uses: r-lib/actions/setup-r-dependencies@v2
Expand All @@ -45,5 +27,3 @@ jobs:
needs: check

- uses: r-lib/actions/check-r-package@v2
with:
upload-snapshots: true
79 changes: 79 additions & 0 deletions .github/workflows/pr-commands.yaml
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
issue_comment:
types: [created]

name: Commands

jobs:
document:
if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
name: document
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v3

- uses: r-lib/actions/pr-fetch@v2
with:
repo-token: ${{ secrets.GITHUB_TOKEN }}

- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::roxygen2
needs: pr-document

- name: Document
run: roxygen2::roxygenise()
shell: Rscript {0}

- name: commit
run: |
git config --local user.name "$GITHUB_ACTOR"
git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
git add man/\* NAMESPACE
git commit -m 'Document'
- uses: r-lib/actions/pr-push@v2
with:
repo-token: ${{ secrets.GITHUB_TOKEN }}

style:
if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
name: style
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v3

- uses: r-lib/actions/pr-fetch@v2
with:
repo-token: ${{ secrets.GITHUB_TOKEN }}

- uses: r-lib/actions/setup-r@v2

- name: Install dependencies
run: install.packages("styler")
shell: Rscript {0}

- name: Style
run: styler::style_pkg()
shell: Rscript {0}

- name: commit
run: |
git config --local user.name "$GITHUB_ACTOR"
git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
git add \*.R
git commit -m 'Style'
- uses: r-lib/actions/pr-push@v2
with:
repo-token: ${{ secrets.GITHUB_TOKEN }}
50 changes: 50 additions & 0 deletions .github/workflows/test-coverage.yaml
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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
on:
push:
branches: [main, master]
pull_request:
branches: [main, master]

name: test-coverage

jobs:
test-coverage:
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

steps:
- uses: actions/checkout@v3

- uses: r-lib/actions/setup-r@v2
with:
use-public-rspm: true

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::covr
needs: coverage

- name: Test coverage
run: |
covr::codecov(
quiet = FALSE,
clean = FALSE,
install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
)
shell: Rscript {0}

- name: Show testthat output
if: always()
run: |
## --------------------------------------------------------------------
find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash

- name: Upload test results
if: failure()
uses: actions/upload-artifact@v3
with:
name: coverage-test-failures
path: ${{ runner.temp }}/package
4 changes: 4 additions & 0 deletions NEWS.md
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# selection.index 1.2.0
* add new function `meanPerformance()` for calculating the mean performance in randomized block design data
* remove some typos from the documentation

# selection.index 1.1.4
* removed two functions `sel.index()` and `sel.score.rank()` for easy implementation of `comb.indices()`

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16 changes: 5 additions & 11 deletions README.Rmd
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Expand Up @@ -21,21 +21,15 @@ knitr::opts_chunk$set(
<!-- badges: start -->

[![R-CMD-check](https://github.com/zankrut20/selection.index/workflows/R-CMD-check/badge.svg)](https://github.com/zankrut20/selection.index/actions)
[![AppVeyor build
status](https://ci.appveyor.com/api/projects/status/github/zankrut20/selection.index?branch=master&svg=true)](https://ci.appveyor.com/project/zankrut20/selection.index)
[![CRAN
checks](https://cranchecks.info/badges/summary/selection.index)](https://cran.r-project.org/web/checks/check_results_selection.index.html)
[![CRAN checks](https://cranchecks.info/badges/summary/selection.index)](https://cran.r-project.org/web/checks/check_results_selection.index.html)
[![status](https://www.r-pkg.org/badges/version/selection.index)](https://CRAN.R-project.org/package=selection.index)
[![Dependencies](https://tinyverse.netlify.com/badge/selection.index)](https://cran.r-project.org/package=selection.index)
[![Total
downloads](http://cranlogs.r-pkg.org/badges/grand-total/selection.index?color=blue)](https://cran.r-project.org/package=selection.index)
[![Last-Month
downloads](http://cranlogs.r-pkg.org/badges/last-month/selection.index?color=green)](https://cran.r-project.org/package=selection.index)
[![Last-Week
downloads](http://cranlogs.r-pkg.org/badges/last-week/selection.index?color=green)](https://cran.r-project.org/package=selection.index)
[![Total downloads](http://cranlogs.r-pkg.org/badges/grand-total/selection.index?color=blue)](https://cran.r-project.org/package=selection.index)
[![Last-Month downloads](http://cranlogs.r-pkg.org/badges/last-month/selection.index?color=green)](https://cran.r-project.org/package=selection.index)
[![Last-Week downloads](http://cranlogs.r-pkg.org/badges/last-week/selection.index?color=green)](https://cran.r-project.org/package=selection.index)
[![CodeFactor](https://www.codefactor.io/repository/github/zankrut20/selection.index/badge)](https://www.codefactor.io/repository/github/zankrut20/selection.index)
[![R-CMD-check](https://github.com/zankrut20/selection.index/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/zankrut20/selection.index/actions/workflows/R-CMD-check.yaml)

[![Codecov test coverage](https://codecov.io/gh/zankrut20/selection.index/branch/master/graph/badge.svg)](https://app.codecov.io/gh/zankrut20/selection.index?branch=master)
<!-- badges: end -->

The goal of selection.index is to easily construct the selection index
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4 changes: 1 addition & 3 deletions README.md
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Expand Up @@ -6,8 +6,6 @@
<!-- badges: start -->

[![R-CMD-check](https://github.com/zankrut20/selection.index/workflows/R-CMD-check/badge.svg)](https://github.com/zankrut20/selection.index/actions)
[![AppVeyor build
status](https://ci.appveyor.com/api/projects/status/github/zankrut20/selection.index?branch=master&svg=true)](https://ci.appveyor.com/project/zankrut20/selection.index)
[![CRAN
checks](https://cranchecks.info/badges/summary/selection.index)](https://cran.r-project.org/web/checks/check_results_selection.index.html)
[![status](https://www.r-pkg.org/badges/version/selection.index)](https://CRAN.R-project.org/package=selection.index)
Expand Down Expand Up @@ -106,7 +104,7 @@ weightMat
#> [7,] 1 0.5226
```

- Genetic gain of Yield
- Genetic gain of Yield

``` r
GAY<- gen.advance(phen_mat = phenMat[1,1], gen_mat = genMat[1,1],
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52 changes: 0 additions & 52 deletions appveyor.yml

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14 changes: 14 additions & 0 deletions codecov.yml
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comment: false

coverage:
status:
project:
default:
target: auto
threshold: 1%
informational: true
patch:
default:
target: auto
threshold: 1%
informational: true
3 changes: 0 additions & 3 deletions cran-comments.md
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+ Windows R release
+ ubuntu R devel
+ ubuntu R release

* AppVeyor
+ Windows R release

## R CMD check results

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12 changes: 0 additions & 12 deletions docs/articles/Examples_files/header-attrs-2.7/header-attrs.js

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60 changes: 0 additions & 60 deletions docs/bootstrap-toc.css

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