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Add rworkflows #48

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Add rworkflows #48

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340ff6b
Add rworkflows
bschilder Dec 22, 2022
b9ad734
retry with has_latex=T
bschilder Dec 22, 2022
3c3a8a1
update .Rbuildignore
bschilder Dec 23, 2022
d783d1d
implement changes suggested by @mtmorgan
bschilder Jan 5, 2023
b8797dd
Merge branch 'master' into master
bschilder Jan 5, 2023
0a19681
bump version to 2.16.1
bschilder Jan 5, 2023
07ae7b3
merge
bschilder Jan 5, 2023
732d45d
run without rcmdcheck
bschilder Jan 5, 2023
d6255b6
Update rworkflows
bschilder Sep 1, 2023
057b1cf
remove requested files
bschilder Sep 1, 2023
ebded47
address @hpages concerns
bschilder Sep 2, 2023
150db3f
address @hpages concerns
bschilder Sep 2, 2023
38fc65d
address @hpages concerns
bschilder Sep 2, 2023
892f84f
address @hpages concerns
bschilder Sep 2, 2023
7ef18c3
Add back .Rbuildignore. Adjust trigger branches
bschilder Sep 4, 2023
a048ce3
Merge branch 'devel' into master
bschilder Dec 28, 2023
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1 change: 1 addition & 0 deletions .Rbuildignore
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.github
48 changes: 48 additions & 0 deletions .github/workflows/rworkflows.yml
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name: rworkflows
'on':
push:
branches:
- devel
- RELEASE_**
pull_request:
branches:
- devel
- RELEASE_**
jobs:
rworkflows:
permissions:
contents: write
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
container: ${{ matrix.config.cont }}
strategy:
fail-fast: ${{ false }}
matrix:
config:
- os: ubuntu-latest
r: devel
bioc: devel
cont: bioconductor/bioconductor_docker:devel
rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release
- os: macOS-latest
r: latest
bioc: release
- os: windows-latest
r: latest
bioc: release
steps:
- uses: neurogenomics/rworkflows@master
with:
run_bioccheck: ${{ false }}
run_rcmdcheck: ${{ true }}
as_cran: ${{ false }}
run_vignettes: ${{ true }}
has_testthat: ${{ false }}
run_covr: ${{ true }}
run_pkgdown: ${{ true }}
has_runit: ${{ true }}
has_latex: ${{ true }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run_docker: ${{ false }}
runner_os: ${{ runner.os }}
cache_version: cache-master
2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -10,7 +10,7 @@ biocViews: DataImport, Sequencing, Coverage, Alignment, QualityControl
URL: https://bioconductor.org/packages/Rsamtools
Video: https://www.youtube.com/watch?v=Rfon-DQYbWA&list=UUqaMSQd_h-2EDGsU6WDiX0Q
BugReports: https://github.com/Bioconductor/Rsamtools/issues
Version: 2.19.2
Version: 2.19.3
License: Artistic-2.0 | file LICENSE
Encoding: UTF-8
Authors@R: c(
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6 changes: 6 additions & 0 deletions NEWS
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CHANGES IN VERSION 2.17.1

NEW FEATURES

o (v 2.17.1) Implemented rworkflows.

CHANGES IN VERSION 2.16
-----------------------

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2 changes: 2 additions & 0 deletions README.md
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[![R build status](https://github.com/Bioconductor/Rsamtools/workflows/rworkflows/badge.svg)](https://github.com/Bioconductor/Rsamtools/actions)

[<img src="https://www.bioconductor.org/images/logo/jpg/bioconductor_logo_rgb.jpg" width="200" align="right"/>](https://bioconductor.org/)

**Rsamtools** is an R/Bioconductor package that provides an interface to the `samtools`, `bcftools`, and `tabix` utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
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