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Fix GHA #11

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merged 2 commits into from
Aug 1, 2024
Merged

Fix GHA #11

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10f93bf
docs: fix token for codecov
jorainer Jul 31, 2024
8b7f431
ci: remove manual library install on macOS and add codevov token
jorainer Aug 1, 2024
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28 changes: 2 additions & 26 deletions .github/workflows/check-bioc.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -123,31 +123,7 @@ jobs:
- name: Install macOS system dependencies
if: matrix.config.os == 'macOS-latest'
run: |
## Enable installing XML from source if needed
brew install libxml2
echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV

## Required to install magick as noted at
## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
brew install imagemagick@6

## For textshaping, required by ragg, and required by pkgdown
brew install harfbuzz fribidi

## For installing usethis's dependency gert
brew install libgit2

## required for ncdf4 - can not use the homebrew one because that uses GCC
## Use pre-compiled libraries from https://mac.r-project.org/libs-4/
curl -O https://mac.r-project.org/libs-4/netcdf-4.7.4-darwin.17-x86_64.tar.gz
tar fvxzm netcdf-4.7.4-darwin.17-x86_64.tar.gz -C /
rm netcdf-4.7.4-darwin.17-x86_64.tar.gz
curl -O https://mac.r-project.org/libs-4/hdf5-1.12.0-darwin.17-x86_64.tar.gz
tar fvxzm hdf5-1.12.0-darwin.17-x86_64.tar.gz -C /
rm hdf5-1.12.0-darwin.17-x86_64.tar.gz
curl -O https://mac.r-project.org/libs-4/szip-2.1.1-darwin.17-x86_64.tar.gz
tar fvxzm szip-2.1.1-darwin.17-x86_64.tar.gz -C /
rm szip-2.1.1-darwin.17-x86_64.tar.gz
shell: Rscript {0}

- name: Install Windows system dependencies
if: runner.os == 'Windows'
Expand Down Expand Up @@ -264,7 +240,7 @@ jobs:
- name: Test coverage
if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
run: |
covr::codecov()
covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")
shell: Rscript {0}

- name: Install package
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2 changes: 1 addition & 1 deletion README.md
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@@ -1,7 +1,7 @@
# MsIO

[![R-CMD-check-bioc](https://github.com/RforMassSpectrometry/MsIO/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/RforMassSpectrometry/MsIO/actions?query=workflow%3AR-CMD-check-bioc)
[![codecov](https://codecov.io/gh/rformassspectrometry/MsIO/branch/main/graph/badge.svg?token=jy0Mid9gKn)](https://codecov.io/gh/rformassspectrometry/MsIO)
[![codecov](https://codecov.io/gh/rformassspectrometry/MsIO/branch/main/graph/badge.svg?token=M4yYzef5mK)](https://codecov.io/gh/rformassspectrometry/MsIO)
[![license](https://img.shields.io/badge/license-Artistic--2.0-brightgreen.svg)](https://opensource.org/licenses/Artistic-2.0)


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