diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..87b476d --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,2 @@ +^\.github$ +^LICENSE\.md$ diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 0000000..2d19fc7 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..a3ac618 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,49 @@ +# 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: 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 + + 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 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..b9f349d --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,18 @@ +Package: lymphomaSurvivalPipeline +Title: R tools for a pipeline to analyze lymphoma survival data based on RNAseq +Version: 0.0.0.9000 +Authors@R: + person("Lukas", "Gessl", , "lukas.gessl@icloud.com", role = c("aut", "cre")) +Description: This package provides tools to train classifiers predicting + progression-free survival for lymphoma patients. It makes integrating + new data sets, new classes of models and new features easy. It prepares + data (which is expected to have a certain format) for training models + and assesses each model, most importantly in terms of prevalence versus + precision. +License: MIT + file LICENSE +Encoding: UTF-8 +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.2.3 +Suggests: + testthat (>= 3.0.0) +Config/testthat/edition: 3 diff --git a/LICENSE b/LICENSE index 153ada8..e8e848a 100644 --- a/LICENSE +++ b/LICENSE @@ -1,21 +1,2 @@ -MIT License - -Copyright (c) 2023 lgessl - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. +YEAR: 2023 +COPYRIGHT HOLDER: lymphomaSurvivalPipeline authors diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..7d19795 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,21 @@ +# MIT License + +Copyright (c) 2023 lymphomaSurvivalPipeline authors + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..6ae9268 --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,2 @@ +# Generated by roxygen2: do not edit by hand + diff --git a/README.md b/README.md index ffb5f6d..5b56536 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,6 @@ # lymphomaSurvivalPipeline An R pipeline for RNAseq-based lymphoma survival analysis + + + [![R-CMD-check](https://github.com/lgessl/lymphomaSurvivalPipeline/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/lgessl/lymphomaSurvivalPipeline/actions/workflows/R-CMD-check.yaml) + \ No newline at end of file diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000..52fdc6e --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,12 @@ +# This file is part of the standard setup for testthat. +# It is recommended that you do not modify it. +# +# Where should you do additional test configuration? +# Learn more about the roles of various files in: +# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview +# * https://testthat.r-lib.org/articles/special-files.html + +library(testthat) +library(lymphomaSurvivalPipeline) + +test_check("lymphomaSurvivalPipeline") diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R new file mode 100644 index 0000000..c701a66 --- /dev/null +++ b/tests/testthat/helper.R @@ -0,0 +1 @@ +# You can later put helper functions for tests here \ No newline at end of file