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Misc fixes found when running package checks on newer releases of R #5283

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Misc fixes found when running package checks on newer releases of R

Misc fixes found when running package checks on newer releases of R #5283

Workflow file for this run

.github/workflows/ci.yml at 29b7108
name: CI
on:
push:
branches:
- master
- develop
tags:
- '*'
pull_request:
merge_group:
issue_comment:
types:
- created
env:
R_LIBS_USER: /usr/local/lib/R/site-library
LC_ALL: en_US.UTF-8
NCPUS: 2
PGHOST: postgres
CI: true
jobs:
# ----------------------------------------------------------------------
# R TEST
# ----------------------------------------------------------------------
test:
if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build')
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
strategy:
fail-fast: false
matrix:
R:
- "4.2"
- "4.1"
services:
postgres:
image: mdillon/postgis:9.5
options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
container:
image: pecan/depends:R${{ matrix.R }}
steps:
# checkout source code
- name: work around https://github.com/actions/checkout/issues/766
run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
- uses: actions/checkout@v4
with:
set-safe-directory: false
# install additional tools needed
- name: install utils
run: apt-get update && apt-get install -y postgresql-client qpdf
- name: update dependency lists
run: Rscript scripts/generate_dependencies.R
- name: check for out-of-date dependencies files
uses: infotroph/tree-is-clean@v1
- name: install newly-added dependencies
working-directory: docker/depends
run: Rscript pecan.depends.R
# initialize database
- name: db setup
uses: docker://pecan/db:ci
- name: add models to db
run: ./scripts/add.models.sh
# run PEcAn tests
- name: test
run: make -j1 test
- name: check for out-of-date files
uses: infotroph/tree-is-clean@v1
# ----------------------------------------------------------------------
# R CHECK
# ----------------------------------------------------------------------
check:
if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build')
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
package: [check_base, check_modules, check_models]
R:
- "4.2"
- "4.1"
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
_R_CHECK_LENGTH_1_CONDITION_: true
_R_CHECK_LENGTH_1_LOGIC2_: true
# Avoid compilation check warnings that come from the system Makevars
# See https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003898.html
_R_CHECK_COMPILATION_FLAGS_KNOWN_: -Wformat -Werror=format-security -Wdate-time
# Keep R checks from trying to consult the very flaky worldclockapi.com
_R_CHECK_SYSTEM_CLOCK_: 0
container:
image: pecan/depends:R${{ matrix.R }}
steps:
# checkout source code
- name: work around https://github.com/actions/checkout/issues/766
run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
- uses: actions/checkout@v4
with:
set-safe-directory: false
# Forbid spaces in names. Yes, *we* know it's not 1980 anymore, but Make doesn't.
- name: check for filenames that would confuse Make
run: |
SPACENAMES=`find . -name '* *'`
if [ -n "$SPACENAMES" ]; then
echo "::error file=${SPACENAMES}::Spaces in filename(s): ${SPACENAMES}. Please rename these files by converting spaces to underscores."
exit 1
fi
# install additional tools needed
- name: install utils
run: apt-get update && apt-get install -y postgresql-client qpdf
- name: install new dependencies
run: Rscript scripts/generate_dependencies.R && cd docker/depends/ && Rscript pecan.depends.R
# run PEcAn checks
# The package names of base, modules, and models are passed as matrix variables to avoid repeatability of code
- name: check
run: make -j1 ${{ matrix.package }}
env:
REBUILD_DOCS: "FALSE"
RUN_TESTS: "FALSE"
- name: check for out-of-date files
uses: infotroph/tree-is-clean@v1
# ----------------------------------------------------------------------
# SIPNET TESTS
# ----------------------------------------------------------------------
sipnet:
if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build')
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
strategy:
fail-fast: false
matrix:
R:
- "4.2"
- "4.1"
services:
postgres:
image: mdillon/postgis:9.5
options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
container:
image: pecan/depends:R${{ matrix.R }}
steps:
# checkout source code
- name: work around https://github.com/actions/checkout/issues/766
run: git config --global --add safe.directory "$GITHUB_WORKSPACE"
- uses: actions/checkout@v4
with:
set-safe-directory: false
# install additional tools needed
- name: install utils
run: apt-get update && apt-get install -y postgresql-client qpdf
- name: install new dependencies
run: Rscript scripts/generate_dependencies.R && cd docker/depends/ && Rscript pecan.depends.R
# initialize database
- name: db setup
uses: docker://pecan/db:ci
- name: add models to db
run: ./scripts/add.models.sh
# install sipnet
- name: Check out SIPNET
uses: actions/checkout@v4
with:
repository: PecanProject/sipnet
path: sipnet
set-safe-directory: false
- name: install sipnet
run: |
cd ${GITHUB_WORKSPACE}/sipnet
make
# compile PEcAn code
- name: build
run: make -j1
# run SIPNET test
- name: integration test
run: ./tests/integration.sh ghaction