epiRomics/.gitignore at main · Huising-Lab/epiRomics · GitHub

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# ---------------------------------------------------------------------------
# epiRomics/.gitignore
#
# Ships *only* package source to git. Anything built, cached, editor-local,
# OS-local, or regenerable lives outside the tarball and outside the repo.
# Matches .Rbuildignore intent where they overlap; see that file for the
# R CMD build exclusion list.
# ---------------------------------------------------------------------------

# R build artifacts ---------------------------------------------------------
*.tar.gz
*.Rcheck/
Meta/
inst/doc/
/doc/

# Compiled code -------------------------------------------------------------
src/*.o
src/*.so
src/*.dll

# Vignette build artifacts --------------------------------------------------
vignettes/**/*_cache/
vignettes/**/*_files/
vignettes/**/*.html
vignettes/**/*.pdf
vignettes/*.R
vignettes/preamble.tex
vignettes/built/

# Data files (fetched on demand via BiocFileCache) -- keep toy subset only --
inst/extdata/*
!inst/extdata/toy/
!inst/extdata/toy/**
!inst/extdata/example_epiRomics_BW_sheet.csv

# Test artifacts ------------------------------------------------------------
tests/testthat/expected_outputs/
tests/testthat/Rplots.pdf
tests/testthat/test-regression.R

# Generated files -----------------------------------------------------------
*.eps
*.timestamp
*.rdb
*.rdx

# BiocCheck output ----------------------------------------------------------
epiRomics.BiocCheck/

# pkgdown output (published to gh-pages, not main) --------------------------
docs/

# R session / user state ----------------------------------------------------
.Rhistory
.Rapp.history
.RData
.Ruserdata
.Rprofile
.Rproj.user/
*.Rproj

# Editor / IDE cruft --------------------------------------------------------
.vscode/
.idea/
*.swp
*.swo
*~
\#*\#
.\#*

# OS-specific junk ----------------------------------------------------------
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
ehthumbs.db
Thumbs.db
Desktop.ini

# Local tool caches / logs --------------------------------------------------
*.log
.cache/
node_modules/