Skip to content

Update stan submodule #657

Update stan submodule

Update stan submodule #657

Workflow file for this run

---
# Github Actions workflow to check and build StanHeaders and RStan
# yamllint disable rule:line-length
name: R-CMD-check
'on':
push:
branches:
- develop
- experimental
- StanHeaders_*
pull_request:
branches:
- develop
- experimental
- StanHeaders_*
jobs:
R-CMD-check:
if: "! contains(github.event.head_commit.message, '[ci skip]')"
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
strategy:
fail-fast: true
matrix:
config:
- {os: macOS-latest, r: 'release'}
- {os: macOS-latest, r: 'oldrel'}
- {os: windows-latest, r: 'release'}
- {os: windows-latest, r: 'oldrel'}
- {os: ubuntu-20.04, r: 'devel'}
- {os: ubuntu-20.04, r: 'release'}
- {os: ubuntu-20.04, r: 'oldrel'}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
- uses: r-lib/actions/setup-pandoc@v2
- name: Query dependencies
run: |
options(install.packages.check.source = "no")
options(pkgType = ifelse(grepl("linux", R.version$os), "source", "binary"))
install.packages('remotes')
install.packages('V8')
saveRDS(remotes::dev_package_deps(pkg = "./rstan/rstan", dependencies = TRUE), ".github/depends.Rds", version = 2)
writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
shell: Rscript {0}
- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
- name: Install system dependencies
if: runner.os == 'Linux'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
Rscript -e "remotes::install_github('r-hub/sysreqs')"
sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('./rstan/rstan/DESCRIPTION'))")
sudo -s eval "$sysreqs"
shell: bash
- name: Install dependencies
run: |
remotes::install_deps(pkg = "./rstan/rstan", dependencies = TRUE)
remotes::install_cran("rcmdcheck")
remotes::install_cran("rstantools", type = "source")
remotes::install_cran("sessioninfo")
if (utils::packageVersion("sessioninfo") >= "1.2.1") {
sessioninfo::session_info(pkgs = "installed", include_base = TRUE)
} else {
options(width = 200)
sessioninfo::session_info(rownames(installed.packages()), include_base = TRUE)
}
shell: Rscript {0}
- name: Install StanHeaders
run: |
try(system("sh sh_b.sh --no-build-vignettes --no-manual"))
shell: Rscript {0}
- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}
- name: Verify Math Version
run: |
readLines(system.file("include","stan","math","version.hpp", package="StanHeaders"))
shell: Rscript {0}
- name: Check
env:
_R_CHECK_CRAN_INCOMING_: false
run: |
if (R.version$major < 4 && isTRUE(.Platform$OS.type == "windows")) {
dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
path_makevars <- ifelse(.Platform$OS.type == "windows", "Makevars.win", "Makevars")
M <- file.path(dotR, path_makevars)
if (!file.exists(M)) file.create(M)
cat("\nCXX14FLAGS=-O3",
"CXX14 = $(BINPREF)g++ -m$(WIN) -std=c++1y",
"CXX11FLAGS=-O3",
file = M, sep = "\n", append = TRUE)
}
rcmdcheck::rcmdcheck(path = "./rstan/rstan", args = c("--no-manual", "--as-cran", "--ignore-vignettes"), build_args = c("--no-build-vignettes"), error_on = "warning", check_dir = "check")
shell: Rscript {0}
- name: Show testthat output
if: always()
run: |
rm -rf check/rstan.Rcheck/rstan check/rstan.Rcheck/*pkg_src
find check -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash
- name: Upload check results
if: failure()
uses: actions/upload-artifact@v2
with:
name: ${{ runner.os }}-r${{ matrix.config.r }}-results
path: check
- name: Extract version and check StanHeaders source package
run: |
set -x
echo "STANHEADERS_VERSION=$(grep '^Version' StanHeaders/DESCRIPTION | sed 's/.*: *//')" >> $GITHUB_ENV
echo "RSTAN_VERSION=$(grep '^Version' rstan/rstan/DESCRIPTION | sed 's/.*: *//')" >> $GITHUB_ENV
if [[ ! -f StanHeaders_*.tar.gz ]]; then
sh sh_b.sh --no-build-vignettes --no-manual || true
fi
mkdir -p build || true
cp -v StanHeaders_*.tar.gz build/ || true
ls -R build/
shell: bash
- name: Build RStan source package
if: matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'devel'
run: |
src_rstan <- pkgbuild::build("./rstan/rstan", dest_path = tempdir(), vignettes = FALSE, manual = FALSE)
file.copy(src_rstan, "build")
shell: Rscript {0}
- name: Build binary packages
run: |
bin1 <- pkgbuild::build("./build/StanHeaders_${{ env.STANHEADERS_VERSION }}.tar.gz", dest_path = tempdir(), vignettes = FALSE, manual = FALSE, binary = TRUE)
bin2 <- pkgbuild::build("./rstan/rstan", dest_path = tempdir(), vignettes = FALSE, manual = FALSE, binary = TRUE)
dir.create("build_bin")
file.copy(c(bin1, bin2), "build_bin")
shell: Rscript {0}
- name: Upload StanHeaders source package
if: matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'devel'
uses: actions/upload-artifact@v2
with:
name: StanHeaders_${{ env.STANHEADERS_VERSION }}.tar.gz
path: build/StanHeaders_${{ env.STANHEADERS_VERSION }}.tar.gz
- name: Upload RStan source package
if: matrix.config.os == 'ubuntu-20.04' && matrix.config.r == 'devel'
uses: actions/upload-artifact@v2
with:
name: rstan_${{ env.RSTAN_VERSION }}.tar.gz
path: build/rstan_${{ env.RSTAN_VERSION }}.tar.gz
- name: Upload binary packages
uses: actions/upload-artifact@v2
with:
name: R-${{ matrix.config.r }}_${{ matrix.config.os }}
path: build_bin