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update R-CMD-Check workflow 4
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@pcastellanoescuder
pcastellanoescuder committed Feb 18, 2024
1 parent 89d6b4d commit cf69b92
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92 changes: 46 additions & 46 deletions .github/workflows/R-CMD-check.yaml
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Expand Up @@ -51,51 +51,51 @@ jobs:
with:
upload-snapshots: true

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:
needs: coverage

- name: Setup
run: |
R CMD INSTALL .
source shim_package.sh
- 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
# 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:
# needs: coverage
#
# - name: Setup
# run: |
# R CMD INSTALL .
# source shim_package.sh
#
# - 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


2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,6 +1,6 @@
Package: POMA
Title: Tools for Omics Data Analysis
Version: 1.13.20
Version: 1.13.21
Authors@R:
c(person(given = "Pol",
family = "Castellano-Escuder",
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2 changes: 1 addition & 1 deletion NEWS.md
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@@ -1,4 +1,4 @@
# POMA 1.13.20
# POMA 1.13.21

* New POMA theme and colorblind-friendly palette
* Available sample normalization (sum and quantile)
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2 changes: 1 addition & 1 deletion README.Rmd
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Expand Up @@ -16,7 +16,7 @@ output: github_document
| _BioC_ branch | Status | Version | Dependencies | Rank |
|- |- |- |- |- |
| [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) | [![Bioc release status](https://bioconductor.org/shields/build/release/bioc/POMA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) | [![BioC released version](https://img.shields.io/badge/release%20version-1.12.0-blue.svg)](https://www.bioconductor.org/packages/POMA) | [![Dependencies](http://bioconductor.org/shields/dependencies/release/POMA.svg)](http://bioconductor.org/packages/release/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/release/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |
| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.20-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |
| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.21-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |

<!-- badges: end -->

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -17,7 +17,7 @@ v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/li
| *BioC* branch | Status | Version | Dependencies | Rank |
|-------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------|
| [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) | [![Bioc release status](https://bioconductor.org/shields/build/release/bioc/POMA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) | [![BioC released version](https://img.shields.io/badge/release%20version-1.12.0-blue.svg)](https://www.bioconductor.org/packages/POMA) | [![Dependencies](http://bioconductor.org/shields/dependencies/release/POMA.svg)](http://bioconductor.org/packages/release/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/release/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |
| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.20-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |
| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.13.21-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |

<!-- badges: end -->

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