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update docs

update docs #142

Workflow file for this run

# 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, nhmm]
pull_request:
branches: [main, nhmm]
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'}
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes
# this sets the env variable to true or false depending on whether the
# commit message contains text 'run-extended'
SEQHMM_EXTENDED_TESTS: ${{contains(github.event.head_commit.message, 'run-extended')}}
steps:
- uses: actions/checkout@v3
- uses: r-lib/actions/setup-pandoc@v2
- uses: r-lib/actions/setup-tinytex@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
with:
extra-packages:
any::rcmdcheck
any::tinytex
- name: Install dependencies
run: |
tinytex::parse_install(text = "! LaTeX Error: File `ae.sty' not found.")
tinytex::parse_install(text = "! LaTeX Error: File `grfext.sty' not found.")
tinytex::tlmgr_install("babel-english")
shell: Rscript {0}
- uses: r-lib/actions/check-r-package@v2
with:
upload-snapshots: true
args: 'c("--as-cran", "--no-manual", "--no-vignettes", "--no-build-vignettes", "--ignore-vignettes")'
build_args: 'c("--no-build-vignettes")'