Skip to content

Commit

Permalink
Fix vignette entry (#6)
Browse files Browse the repository at this point in the history
* updated roxygen version

* fixing the name of the index entry - displayed when rendered in the Bioc landing page

* re-rendering manpages

* update github action workflow to that of iSEE

---------

Co-authored-by: Kevin Rue-Albrecht <[email protected]>
  • Loading branch information
federicomarini and kevinrue authored Sep 4, 2024
1 parent 8ebd71b commit 82c7093
Show file tree
Hide file tree
Showing 5 changed files with 43 additions and 26 deletions.
1 change: 1 addition & 0 deletions .Rbuildignore
Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,4 @@
^README\.Rmd$
^\.github$
^codecov\.yml$
^iSEEhex\.Rproj$
63 changes: 39 additions & 24 deletions .github/workflows/check-bioc.yml
Original file line number Diff line number Diff line change
Expand Up @@ -52,9 +52,9 @@ jobs:
fail-fast: false
matrix:
config:
- { os: ubuntu-latest, r: '4.2', bioc: '3.15', cont: "bioconductor/bioconductor_docker:RELEASE_3_15", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
- { os: macOS-latest, r: '4.2', bioc: '3.15'}
- { os: windows-latest, r: '4.2', bioc: '3.15'}
- { os: ubuntu-latest, r: 'devel', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
- { os: macOS-latest, r: 'devel', bioc: '3.20'}
- { os: windows-latest, r: 'devel', bioc: '3.20'}
## Check https://github.com/r-lib/actions/tree/master/examples
## for examples using the http-user-agent
env:
Expand All @@ -79,20 +79,20 @@ jobs:
## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
## If they update their steps, we will also need to update ours.
- name: Checkout Repository
uses: actions/checkout@v2
uses: actions/checkout@v3

## R is already included in the Bioconductor docker images
- name: Setup R from r-lib
if: runner.os != 'Linux'
uses: r-lib/actions/setup-r@master
uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}

## pandoc is already included in the Bioconductor docker images
- name: Setup pandoc from r-lib
if: runner.os != 'Linux'
uses: r-lib/actions/setup-pandoc@master
uses: r-lib/actions/setup-pandoc@v2

- name: Query dependencies
run: |
Expand All @@ -102,19 +102,19 @@ jobs:

- name: Restore R package cache
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-

- name: Cache R packages on Linux
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
uses: actions/cache@v2
uses: actions/cache@v3
with:
path: /home/runner/work/_temp/Library
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-

- name: Install Linux system dependencies
if: runner.os == 'Linux'
Expand All @@ -128,7 +128,7 @@ jobs:
run: |
## Enable installing XML from source if needed
brew install libxml2
echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
echo "XML_CONFIG=/opt/homebrew/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
## Required to install magick as noted at
## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
Expand All @@ -143,6 +143,21 @@ jobs:
## Required for tcltk
brew install xquartz --cask
## Required for terra
brew install gdal
## Temporary fix for freetype (https://github.com/r-lib/ragg/issues/170; Sep 2024)
#brew install --cask https://raw.githubusercontent.com/Homebrew/homebrew-core/d28afc3bfdb5d24eab02157bfffcc9e17ed6666c/Formula/f/freetype.rb
brew unlink freetype
curl -L https://raw.githubusercontent.com/Homebrew/homebrew-core/3db6dc6c4baf5a75e345f380cc4e8224c1ae5ae0/Formula/f/freetype.rb > freetype.rb && brew install freetype.rb
- name: Install binary units for macOS
if: matrix.config.os == 'macOS-latest'
run: |
## temporary fix due to issue in udunits (Sep 2024)
install.packages('https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/units_0.8-5.tgz')
shell: Rscript {0}

- name: Install Windows system dependencies
if: runner.os == 'Windows'
run: |
Expand Down Expand Up @@ -176,7 +191,7 @@ jobs:
gha_repos <- if(
.Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
) c(
"AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.15/bioc",
"AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.20/bioc",
BiocManager::repositories()
) else BiocManager::repositories()
Expand Down Expand Up @@ -210,13 +225,13 @@ jobs:
shell: Rscript {0}

- name: Install covr
if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
run: |
remotes::install_cran("covr")
shell: Rscript {0}

- name: Install pkgdown
if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
remotes::install_cran("pkgdown")
shell: Rscript {0}
Expand All @@ -237,7 +252,7 @@ jobs:
rcmdcheck::rcmdcheck(
args = c("--no-manual", "--no-vignettes", "--timings"),
build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
error_on = "error",
error_on = "warning",
check_dir = "check"
)
shell: Rscript {0}
Expand All @@ -259,28 +274,28 @@ jobs:
run: |
BiocCheck::BiocCheck(
dir('check', 'tar.gz$', full.names = TRUE),
`quit-with-status` = TRUE,
`quit-with-status` = FALSE,
`no-check-R-ver` = TRUE,
`no-check-bioc-help` = TRUE
)
shell: Rscript {0}

- name: Test coverage
if: github.ref == 'refs/heads/main' && env.run_covr == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
run: |
covr::codecov()
shell: Rscript {0}

- name: Install package
if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: R CMD INSTALL .

- name: Build and deploy pkgdown site
if: github.ref == 'refs/heads/main' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
git config --global user.name "$GITHUB_ACTOR"
git config --global user.email "[email protected]"
git config --global --add safe.directory /__w/iSEEhex/iSEEhex
git config --global --add safe.directory /__w/iSEE/iSEEhex
Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
shell: bash {0}
## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
Expand All @@ -292,15 +307,15 @@ jobs:
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-biocversion-RELEASE_3_15-r-4.2-results
name: ${{ runner.os }}-biocversion-devel-r-devel-results
path: check

- uses: docker/build-push-action@v1
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "
with:
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_PASSWORD }}
repository: iseedevelopers/iseehex
repository: isee/iseehex
tag_with_ref: true
tag_with_sha: true
tags: latest
2 changes: 1 addition & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ biocViews: Software,
Infrastructure
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.0
RoxygenNote: 7.3.2
Depends:
SummarizedExperiment,
iSEE
Expand Down
1 change: 1 addition & 0 deletions man/iSEEhex-pkg.Rd

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion vignettes/iSEEhex.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ date: "`r BiocStyle::doc_date()`"
package: iSEEhex
output: BiocStyle::html_document
vignette: >
%\VignetteIndexEntry{Panel universe}
%\VignetteIndexEntry{The iSEEhex package}
%\VignetteEncoding{UTF-8}
%\VignettePackage{iSEEhex}
%\VignetteKeywords{GeneExpression, RNASeq, Sequencing, Visualization, QualityControl, GUI}
Expand Down

0 comments on commit 82c7093

Please sign in to comment.