mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 20:41:58 +02:00
(v0.8.0.9017) keywords update
This commit is contained in:
193
tests/appveyor/appveyor_tool.ps1
Normal file
193
tests/appveyor/appveyor_tool.ps1
Normal file
@ -0,0 +1,193 @@
|
||||
if ( -not(Test-Path Env:\CRAN) ) {
|
||||
$CRAN = "https://cran.rstudio.com"
|
||||
}
|
||||
Else {
|
||||
$CRAN = $env:CRAN
|
||||
}
|
||||
|
||||
|
||||
# Found at http://zduck.com/2012/powershell-batch-files-exit-codes/
|
||||
Function Exec
|
||||
{
|
||||
[CmdletBinding()]
|
||||
param (
|
||||
[Parameter(Position=0, Mandatory=1)]
|
||||
[scriptblock]$Command,
|
||||
[Parameter(Position=1, Mandatory=0)]
|
||||
[string]$ErrorMessage = "Execution of command failed.`n$Command"
|
||||
)
|
||||
$ErrorActionPreference = "Continue"
|
||||
& $Command 2>&1 | %{ "$_" }
|
||||
if ($LastExitCode -ne 0) {
|
||||
throw "Exec: $ErrorMessage`nExit code: $LastExitCode"
|
||||
}
|
||||
}
|
||||
|
||||
Function Progress
|
||||
{
|
||||
[CmdletBinding()]
|
||||
param (
|
||||
[Parameter(Position=0, Mandatory=0)]
|
||||
[string]$Message = ""
|
||||
)
|
||||
|
||||
$ProgressMessage = '== ' + (Get-Date) + ': ' + $Message
|
||||
|
||||
Write-Host $ProgressMessage -ForegroundColor Magenta
|
||||
}
|
||||
|
||||
Function TravisTool
|
||||
{
|
||||
[CmdletBinding()]
|
||||
param (
|
||||
[Parameter(Position=0, Mandatory=1)]
|
||||
[string[]]$Params
|
||||
)
|
||||
|
||||
Exec { bash.exe ../travis_tool.sh $Params }
|
||||
}
|
||||
|
||||
Function InstallR {
|
||||
[CmdletBinding()]
|
||||
Param()
|
||||
|
||||
if ( -not(Test-Path Env:\R_VERSION) ) {
|
||||
$version = "patched"
|
||||
}
|
||||
Else {
|
||||
$version = $env:R_VERSION
|
||||
}
|
||||
|
||||
if ( -not(Test-Path Env:\R_ARCH) ) {
|
||||
$arch = "x64"
|
||||
}
|
||||
Else {
|
||||
$arch = $env:R_ARCH
|
||||
}
|
||||
|
||||
If ($arch -eq "i386") {
|
||||
$mingw_path = "mingw_32"
|
||||
}
|
||||
Else {
|
||||
$mingw_path = "mingw_64"
|
||||
}
|
||||
|
||||
Progress ("Version: " + $version)
|
||||
|
||||
If ($version -eq "devel") {
|
||||
$url_path = ""
|
||||
$version = "devel"
|
||||
}
|
||||
ElseIf (($version -eq "stable") -or ($version -eq "release")) {
|
||||
$url_path = ""
|
||||
$version = $(ConvertFrom-JSON $(Invoke-WebRequest http://rversions.r-pkg.org/r-release-win).Content).version
|
||||
If ($version -eq "3.2.4") {
|
||||
$version = "3.2.4revised"
|
||||
}
|
||||
}
|
||||
ElseIf ($version -eq "patched") {
|
||||
$url_path = ""
|
||||
$version = $(ConvertFrom-JSON $(Invoke-WebRequest http://rversions.r-pkg.org/r-release-win).Content).version + "patched"
|
||||
}
|
||||
ElseIf ($version -eq "oldrel") {
|
||||
$version = $(ConvertFrom-JSON $(Invoke-WebRequest http://rversions.r-pkg.org/r-oldrel).Content).version
|
||||
$url_path = ("old/" + $version + "/")
|
||||
}
|
||||
Else {
|
||||
$url_path = ("old/" + $version + "/")
|
||||
}
|
||||
|
||||
Progress ("URL path: " + $url_path)
|
||||
|
||||
$rurl = $CRAN + "/bin/windows/base/" + $url_path + "R-" + $version + "-win.exe"
|
||||
|
||||
Progress ("Downloading R from: " + $rurl)
|
||||
& "C:\Program Files\Git\mingw64\bin\curl.exe" -s -o ../R-win.exe -L $rurl
|
||||
|
||||
Progress "Running R installer"
|
||||
Start-Process -FilePath ..\R-win.exe -ArgumentList "/VERYSILENT /DIR=C:\R" -NoNewWindow -Wait
|
||||
|
||||
$RDrive = "C:"
|
||||
echo "R is now available on drive $RDrive"
|
||||
|
||||
Progress "Setting PATH"
|
||||
$env:PATH = $RDrive + '\R\bin\' + $arch + ';' + 'C:\Rtools\' + $mingw_path + '\bin;' + 'C:\MinGW\msys\1.0\bin;' + $env:PATH
|
||||
|
||||
Progress "Testing R installation"
|
||||
Rscript -e "sessionInfo()"
|
||||
}
|
||||
|
||||
Function InstallRtools {
|
||||
if ( -not(Test-Path Env:\RTOOLS_VERSION) ) {
|
||||
Progress "Determining Rtools version"
|
||||
$rtoolsver = $(Invoke-WebRequest ($CRAN + "/bin/windows/Rtools/VERSION.txt")).Content.Split(' ')[2].Split('.')[0..1] -Join ''
|
||||
}
|
||||
Else {
|
||||
$rtoolsver = $env:RTOOLS_VERSION
|
||||
}
|
||||
|
||||
$rtoolsurl = $CRAN + "/bin/windows/Rtools/Rtools$rtoolsver.exe"
|
||||
|
||||
Progress ("Downloading Rtools from: " + $rtoolsurl)
|
||||
& "C:\Program Files\Git\mingw64\bin\curl.exe" -s -o ../Rtools-current.exe -L $rtoolsurl
|
||||
|
||||
Progress "Running Rtools installer"
|
||||
Start-Process -FilePath ..\Rtools-current.exe -ArgumentList /VERYSILENT -NoNewWindow -Wait
|
||||
|
||||
$RtoolsDrive = "C:"
|
||||
echo "Rtools is now available on drive $RtoolsDrive"
|
||||
|
||||
Progress "Setting PATH"
|
||||
if ( -not(Test-Path Env:\GCC_PATH) ) {
|
||||
$gcc_path = "gcc-4.6.3"
|
||||
}
|
||||
Else {
|
||||
$gcc_path = $env:GCC_PATH
|
||||
}
|
||||
$env:PATH = $RtoolsDrive + '\Rtools\bin;' + $RtoolsDrive + '\Rtools\MinGW\bin;' + $RtoolsDrive + '\Rtools\' + $gcc_path + '\bin;' + $env:PATH
|
||||
$env:BINPREF=$RtoolsDrive + '/Rtools/mingw_$(WIN)/bin/'
|
||||
}
|
||||
|
||||
Function Bootstrap {
|
||||
[CmdletBinding()]
|
||||
Param()
|
||||
|
||||
Progress "Bootstrap: Start"
|
||||
|
||||
Progress "Adding GnuWin32 tools to PATH"
|
||||
$env:PATH = "C:\Program Files (x86)\Git\bin;" + $env:PATH
|
||||
|
||||
Progress "Setting time zone"
|
||||
tzutil /g
|
||||
tzutil /s "GMT Standard Time"
|
||||
tzutil /g
|
||||
|
||||
InstallR
|
||||
|
||||
if ((Test-Path "src") -or ($env:USE_RTOOLS -eq "true") -or ($env:USE_RTOOLS -eq "yes")) {
|
||||
InstallRtools
|
||||
}
|
||||
Else {
|
||||
Progress "Skipping download of Rtools because src/ directory is missing."
|
||||
}
|
||||
|
||||
Progress "Downloading and installing travis_tool.sh"
|
||||
Invoke-WebRequest https://gitlab.com/msberends/AMR/raw/master/tests/appveyor/travis_tool.sh -OutFile "..\travis_tool.sh"
|
||||
echo '@bash.exe ../travis_tool.sh %*' | Out-File -Encoding ASCII .\travis_tool.sh.cmd
|
||||
cat .\travis_tool.sh.cmd
|
||||
bash -c "( echo; echo '^travis_tool\.sh\.cmd$' ) >> .Rbuildignore"
|
||||
cat .\.Rbuildignore
|
||||
|
||||
$env:PATH.Split(";")
|
||||
|
||||
Progress "Setting R_LIBS_USER"
|
||||
$env:R_LIBS_USER = 'c:\RLibrary'
|
||||
if ( -not(Test-Path $env:R_LIBS_USER) ) {
|
||||
mkdir $env:R_LIBS_USER
|
||||
}
|
||||
|
||||
Progress "Setting TAR to 'internal'"
|
||||
$env:TAR = 'internal'
|
||||
|
||||
Progress "Bootstrap: Done"
|
||||
}
|
||||
428
tests/appveyor/travis_tool.sh
Normal file
428
tests/appveyor/travis_tool.sh
Normal file
@ -0,0 +1,428 @@
|
||||
#!/bin/bash
|
||||
# -*- sh-basic-offset: 4; sh-indentation: 4 -*-
|
||||
# Bootstrap an R/travis environment.
|
||||
|
||||
set -e
|
||||
# Comment out this line for quieter output:
|
||||
set -x
|
||||
|
||||
CRAN=${CRAN:-"https://cran.rstudio.com"}
|
||||
BIOC=${BIOC:-"http://bioconductor.org/biocLite.R"}
|
||||
PKGTYPE=${PKGTYPE:-"win.binary"}
|
||||
BIOC_USE_DEVEL=${BIOC_USE_DEVEL:-"TRUE"}
|
||||
OS=$(uname -s)
|
||||
DOWNLOAD_FILE_METHOD=${DOWNLOAD_FILE_METHOD:-"auto"}
|
||||
|
||||
PANDOC_VERSION='1.13.1'
|
||||
PANDOC_DIR="${HOME}/opt/pandoc"
|
||||
PANDOC_URL="https://s3.amazonaws.com/rstudio-buildtools/pandoc-${PANDOC_VERSION}.zip"
|
||||
|
||||
# MacTeX installs in a new $PATH entry, and there's no way to force
|
||||
# the *parent* shell to source it from here. So we just manually add
|
||||
# all the entries to a location we already know to be on $PATH.
|
||||
#
|
||||
# TODO(craigcitro): Remove this once we can add `/usr/texbin` to the
|
||||
# root path.
|
||||
PATH="${PATH}:/usr/texbin"
|
||||
|
||||
R_BUILD_ARGS=${R_BUILD_ARGS-"--no-manual"}
|
||||
R_CHECK_ARGS=${R_CHECK_ARGS-"--no-manual --as-cran"}
|
||||
|
||||
R_VERSION_TEST="getRversion() >= '3.5.0'"
|
||||
|
||||
R_USE_BIOC_INST="source('${BIOC}');"\
|
||||
" tryCatch(useDevel(${BIOC_USE_DEVEL}),"\
|
||||
" error=function(e) {if (!grepl('already in use', e$message)) {e}});"\
|
||||
" options(repos=biocinstallRepos())"
|
||||
|
||||
R_USE_BIOC_MNGR="if (!requireNamespace('BiocManager', quietly=TRUE))"\
|
||||
" install.packages('BiocManager', repos=c(CRAN='${CRAN}'));"\
|
||||
" if (${BIOC_USE_DEVEL})"\
|
||||
" BiocManager::install(version = 'devel', ask = FALSE);"\
|
||||
" options(repos=BiocManager::repositories())"
|
||||
|
||||
R_USE_BIOC_CMDS="if (${R_VERSION_TEST}) {${R_USE_BIOC_MNGR}} else {${R_USE_BIOC_INST}};"
|
||||
|
||||
BIOC_INSTALL="{if (${R_VERSION_TEST}) BiocManager::install else BiocInstaller::biocLite}"
|
||||
|
||||
Bootstrap() {
|
||||
if [[ "Darwin" == "${OS}" ]]; then
|
||||
BootstrapMac
|
||||
elif [[ "Linux" == "${OS}" ]]; then
|
||||
BootstrapLinux
|
||||
else
|
||||
echo "Unknown OS: ${OS}"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
if ! (test -e .Rbuildignore && grep -q 'travis-tool' .Rbuildignore); then
|
||||
echo '^travis-tool\.sh$' >>.Rbuildignore
|
||||
fi
|
||||
}
|
||||
|
||||
InstallPandoc() {
|
||||
local os_path="$1"
|
||||
mkdir -p "${PANDOC_DIR}"
|
||||
curl -o /tmp/pandoc-${PANDOC_VERSION}.zip ${PANDOC_URL}
|
||||
unzip -j /tmp/pandoc-${PANDOC_VERSION}.zip "pandoc-${PANDOC_VERSION}/${os_path}/pandoc" -d "${PANDOC_DIR}"
|
||||
chmod +x "${PANDOC_DIR}/pandoc"
|
||||
sudo ln -s "${PANDOC_DIR}/pandoc" /usr/local/bin
|
||||
unzip -j /tmp/pandoc-${PANDOC_VERSION}.zip "pandoc-${PANDOC_VERSION}/${os_path}/pandoc-citeproc" -d "${PANDOC_DIR}"
|
||||
chmod +x "${PANDOC_DIR}/pandoc-citeproc"
|
||||
sudo ln -s "${PANDOC_DIR}/pandoc-citeproc" /usr/local/bin
|
||||
}
|
||||
|
||||
BootstrapLinux() {
|
||||
# Set up our CRAN mirror.
|
||||
sudo add-apt-repository "deb ${CRAN}/bin/linux/ubuntu $(lsb_release -cs)/"
|
||||
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
|
||||
|
||||
# Add marutter's c2d4u repository.
|
||||
sudo add-apt-repository -y "ppa:marutter/rrutter"
|
||||
sudo add-apt-repository -y "ppa:marutter/c2d4u"
|
||||
|
||||
# Update after adding all repositories. Retry several times to work around
|
||||
# flaky connection to Launchpad PPAs.
|
||||
Retry sudo apt-get update -qq
|
||||
|
||||
# Install an R development environment. qpdf is also needed for
|
||||
# --as-cran checks:
|
||||
# https://stat.ethz.ch/pipermail/r-help//2012-September/335676.html
|
||||
Retry sudo apt-get install -y --no-install-recommends r-base-dev r-recommended qpdf
|
||||
|
||||
# Change permissions for /usr/local/lib/R/site-library
|
||||
# This should really be via 'staff adduser travis staff'
|
||||
# but that may affect only the next shell
|
||||
sudo chmod 2777 /usr/local/lib/R /usr/local/lib/R/site-library
|
||||
|
||||
# Process options
|
||||
BootstrapLinuxOptions
|
||||
}
|
||||
|
||||
BootstrapLinuxOptions() {
|
||||
if [[ -n "$BOOTSTRAP_LATEX" ]]; then
|
||||
# We add a backports PPA for more recent TeX packages.
|
||||
sudo add-apt-repository -y "ppa:texlive-backports/ppa"
|
||||
|
||||
Retry sudo apt-get install -y --no-install-recommends \
|
||||
texlive-base texlive-latex-base texlive-generic-recommended \
|
||||
texlive-fonts-recommended texlive-fonts-extra \
|
||||
texlive-extra-utils texlive-latex-recommended texlive-latex-extra \
|
||||
texinfo lmodern
|
||||
fi
|
||||
if [[ -n "$BOOTSTRAP_PANDOC" ]]; then
|
||||
InstallPandoc 'linux/debian/x86_64'
|
||||
fi
|
||||
}
|
||||
|
||||
BootstrapMac() {
|
||||
# Install from latest CRAN binary build for OS X
|
||||
wget ${CRAN}/bin/macosx/R-latest.pkg -O /tmp/R-latest.pkg
|
||||
|
||||
echo "Installing OS X binary package for R"
|
||||
sudo installer -pkg "/tmp/R-latest.pkg" -target /
|
||||
rm "/tmp/R-latest.pkg"
|
||||
|
||||
# Process options
|
||||
BootstrapMacOptions
|
||||
}
|
||||
|
||||
BootstrapMacOptions() {
|
||||
if [[ -n "$BOOTSTRAP_LATEX" ]]; then
|
||||
# TODO: Install MacTeX.pkg once there's enough disk space
|
||||
MACTEX=BasicTeX.pkg
|
||||
wget http://ctan.math.utah.edu/ctan/tex-archive/systems/mac/mactex/$MACTEX -O "/tmp/$MACTEX"
|
||||
|
||||
echo "Installing OS X binary package for MacTeX"
|
||||
sudo installer -pkg "/tmp/$MACTEX" -target /
|
||||
rm "/tmp/$MACTEX"
|
||||
# We need a few more packages than the basic package provides; this
|
||||
# post saved me so much pain:
|
||||
# https://stat.ethz.ch/pipermail/r-sig-mac/2010-May/007399.html
|
||||
sudo tlmgr update --self
|
||||
sudo tlmgr install inconsolata upquote courier courier-scaled helvetic
|
||||
fi
|
||||
if [[ -n "$BOOTSTRAP_PANDOC" ]]; then
|
||||
InstallPandoc 'mac'
|
||||
fi
|
||||
}
|
||||
|
||||
EnsureDevtools() {
|
||||
if ! Rscript -e 'if (!("devtools" %in% rownames(installed.packages()))) q(status=1)' ; then
|
||||
# Install devtools and testthat.
|
||||
RBinaryInstall devtools testthat
|
||||
fi
|
||||
}
|
||||
|
||||
EnsureRemotes() {
|
||||
if ! Rscript -e 'if (!("remotes" %in% rownames(installed.packages()))) q(status=1)' ; then
|
||||
# Install remotes.
|
||||
RBinaryInstall remotes
|
||||
fi
|
||||
if ! Rscript -e 'if (!("remotes" %in% rownames(installed.packages()))) q(status=1)' ; then
|
||||
# Fallback: Install remotes from URL.
|
||||
Rscript -e 'path <- file.path(tempdir(), "remotes_1.0.0.tar.gz"); download.file("https://cran.rstudio.com/src/contrib/Archive/remotes/remotes_1.0.0.tar.gz", path); install.packages(path, repos = NULL, type = "source")'
|
||||
fi
|
||||
}
|
||||
|
||||
AptGetInstall() {
|
||||
if [[ "Linux" != "${OS}" ]]; then
|
||||
echo "Wrong OS: ${OS}"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
if [[ "" == "$*" ]]; then
|
||||
echo "No arguments to aptget_install"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "Installing apt package(s) $@"
|
||||
Retry sudo apt-get -y install "$@"
|
||||
}
|
||||
|
||||
DpkgCurlInstall() {
|
||||
if [[ "Linux" != "${OS}" ]]; then
|
||||
echo "Wrong OS: ${OS}"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
if [[ "" == "$*" ]]; then
|
||||
echo "No arguments to dpkgcurl_install"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "Installing remote package(s) $@"
|
||||
for rf in "$@"; do
|
||||
curl -OL ${rf}
|
||||
f=$(basename ${rf})
|
||||
sudo dpkg -i ${f}
|
||||
rm -v ${f}
|
||||
done
|
||||
}
|
||||
|
||||
RInstall() {
|
||||
if [[ "" == "$*" ]]; then
|
||||
echo "No arguments to r_install"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "Installing R package(s): $@"
|
||||
Rscript -e 'install.packages(commandArgs(TRUE), repos="'"${CRAN}"'", INSTALL_opts="", type="'"${PKGTYPE}"'")' "$@"
|
||||
}
|
||||
|
||||
BiocInstall() {
|
||||
if [[ "" == "$*" ]]; then
|
||||
echo "No arguments to bioc_install"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
echo "Installing R Bioconductor package(s): $@"
|
||||
Rscript -e "${R_USE_BIOC_CMDS}"" ${BIOC_INSTALL}(commandArgs(TRUE))" "$@"
|
||||
}
|
||||
|
||||
RBinaryInstall() {
|
||||
if [[ -z "$#" ]]; then
|
||||
echo "No arguments to r_binary_install"
|
||||
exit 1
|
||||
fi
|
||||
|
||||
if [[ "Linux" != "${OS}" ]] || [[ -n "${FORCE_SOURCE_INSTALL}" ]]; then
|
||||
echo "Fallback: Installing from source"
|
||||
RInstall "$@"
|
||||
return
|
||||
fi
|
||||
|
||||
echo "Installing *binary* R packages: $*"
|
||||
r_packages=$(echo $* | tr '[:upper:]' '[:lower:]')
|
||||
r_debs=$(for r_package in ${r_packages}; do echo -n "r-cran-${r_package} "; done)
|
||||
|
||||
AptGetInstall ${r_debs}
|
||||
}
|
||||
|
||||
InstallGithub() {
|
||||
EnsureRemotes
|
||||
|
||||
echo "Installing GitHub packages: $@"
|
||||
# Install the package.
|
||||
Rscript -e 'options(repos = c(CRAN = "'"${CRAN}"'"), download.file.method = "'"${DOWNLOAD_FILE_METHOD}"'"); remotes::install_github(commandArgs(TRUE), type="'"${PKGTYPE}"'")' "$@"
|
||||
}
|
||||
|
||||
InstallDeps() {
|
||||
EnsureRemotes
|
||||
|
||||
echo "Installing dependencies"
|
||||
Rscript -e 'options(repos = c(CRAN = "'"${CRAN}"'"), download.file.method = "'"${DOWNLOAD_FILE_METHOD}"'"); remotes::install_deps(dependencies = TRUE, type="'"${PKGTYPE}"'")'
|
||||
}
|
||||
|
||||
InstallBiocDeps() {
|
||||
EnsureDevtools
|
||||
Rscript -e "${R_USE_BIOC_CMDS}"' library(devtools); install_deps(dependencies = TRUE, type="'"${PKGTYPE}"'")'
|
||||
}
|
||||
|
||||
DumpSysinfo() {
|
||||
echo "Dumping system information."
|
||||
R -e '.libPaths(); sessionInfo(); installed.packages()'
|
||||
}
|
||||
|
||||
DumpLogsByExtension() {
|
||||
if [[ -z "$1" ]]; then
|
||||
echo "dump_logs_by_extension requires exactly one argument, got: $@"
|
||||
exit 1
|
||||
fi
|
||||
extension=$1
|
||||
shift
|
||||
package=$(find . -maxdepth 1 -name "*.Rcheck" -type d)
|
||||
if [[ ${#package[@]} -ne 1 ]]; then
|
||||
echo "Could not find package Rcheck directory, skipping log dump."
|
||||
exit 0
|
||||
fi
|
||||
for name in $(find "${package}" -type f -name "*${extension}"); do
|
||||
echo ">>> Filename: ${name} <<<"
|
||||
cat ${name}
|
||||
done
|
||||
}
|
||||
|
||||
DumpLogs() {
|
||||
echo "Dumping test execution logs."
|
||||
DumpLogsByExtension "out"
|
||||
DumpLogsByExtension "log"
|
||||
DumpLogsByExtension "fail"
|
||||
}
|
||||
|
||||
RunTests() {
|
||||
echo "Building with: R CMD build ${R_BUILD_ARGS}"
|
||||
if [[ "${KEEP_VIGNETTES}" == "" ]]; then
|
||||
if [[ "${OS:0:5}" == "MINGW" || "${OS:0:4}" == "MSYS" ]]; then
|
||||
if [[ -d vignettes ]]; then
|
||||
rm -rf vignettes
|
||||
Rscript -e "d <- read.dcf('DESCRIPTION'); d[, colnames(d) == 'VignetteBuilder'] <- NA; write.dcf(d, 'DESCRIPTION')"
|
||||
fi
|
||||
fi
|
||||
fi
|
||||
R CMD build ${R_BUILD_ARGS} .
|
||||
# We want to grab the version we just built.
|
||||
FILE=$(ls -1t *.tar.gz | head -n 1)
|
||||
|
||||
# Create binary package (currently Windows only)
|
||||
if [[ "${OS:0:5}" == "MINGW" || "${OS:0:4}" == "MSYS" ]]; then
|
||||
R_CHECK_INSTALL_ARGS="--install-args=--build"
|
||||
fi
|
||||
|
||||
echo "Testing with: R CMD check \"${FILE}\" ${R_CHECK_ARGS} ${R_CHECK_INSTALL_ARGS}"
|
||||
_R_CHECK_CRAN_INCOMING_=${_R_CHECK_CRAN_INCOMING_:-FALSE}
|
||||
if [[ "$_R_CHECK_CRAN_INCOMING_" == "FALSE" ]]; then
|
||||
echo "(CRAN incoming checks are off)"
|
||||
fi
|
||||
_R_CHECK_CRAN_INCOMING_=${_R_CHECK_CRAN_INCOMING_} R_QPDF=true R CMD check "${FILE}" ${R_CHECK_ARGS} ${R_CHECK_INSTALL_ARGS}
|
||||
|
||||
# Check reverse dependencies
|
||||
if [[ -n "$R_CHECK_REVDEP" ]]; then
|
||||
echo "Checking reverse dependencies"
|
||||
EnsureDevtools
|
||||
Rscript -e 'library(devtools); checkOutput <- unlist(revdep_check(as.package(".")$package));if (!is.null(checkOutput)) {print(data.frame(pkg = names(checkOutput), error = checkOutput));for(i in seq_along(checkOutput)){;cat("\n", names(checkOutput)[i], " Check Output:\n ", paste(readLines(regmatches(checkOutput[i], regexec("/.*\\.out", checkOutput[i]))[[1]]), collapse = "\n ", sep = ""), "\n", sep = "")};q(status = 1, save = "no")}'
|
||||
fi
|
||||
|
||||
if [[ -n "${WARNINGS_ARE_ERRORS}" ]]; then
|
||||
if DumpLogsByExtension "00check.log" | grep -q WARNING; then
|
||||
echo "Found warnings, treated as errors."
|
||||
echo "Clear or unset the WARNINGS_ARE_ERRORS environment variable to ignore warnings."
|
||||
exit 1
|
||||
fi
|
||||
fi
|
||||
}
|
||||
|
||||
Retry() {
|
||||
if "$@"; then
|
||||
return 0
|
||||
fi
|
||||
for wait_time in 5 20 30 60; do
|
||||
echo "Command failed, retrying in ${wait_time} ..."
|
||||
sleep ${wait_time}
|
||||
if "$@"; then
|
||||
return 0
|
||||
fi
|
||||
done
|
||||
echo "Failed all retries!"
|
||||
exit 1
|
||||
}
|
||||
|
||||
COMMAND=$1
|
||||
echo "Running command: ${COMMAND}"
|
||||
shift
|
||||
case $COMMAND in
|
||||
##
|
||||
## Bootstrap a new core system
|
||||
"bootstrap")
|
||||
Bootstrap
|
||||
;;
|
||||
##
|
||||
## Ensure devtools is loaded (implicitly called)
|
||||
"install_devtools"|"devtools_install")
|
||||
EnsureDevtools
|
||||
;;
|
||||
##
|
||||
## Ensure remotes is loaded (implicitly called)
|
||||
"install_remotes"|"remotes_install")
|
||||
EnsureRemotes
|
||||
;;
|
||||
##
|
||||
## Install a binary deb package via apt-get
|
||||
"install_aptget"|"aptget_install")
|
||||
AptGetInstall "$@"
|
||||
;;
|
||||
##
|
||||
## Install a binary deb package via a curl call and local dpkg -i
|
||||
"install_dpkgcurl"|"dpkgcurl_install")
|
||||
DpkgCurlInstall "$@"
|
||||
;;
|
||||
##
|
||||
## Install an R dependency from CRAN
|
||||
"install_r"|"r_install")
|
||||
RInstall "$@"
|
||||
;;
|
||||
##
|
||||
## Install an R dependency from Bioconductor
|
||||
"install_bioc"|"bioc_install")
|
||||
BiocInstall "$@"
|
||||
;;
|
||||
##
|
||||
## Install an R dependency as a binary (via c2d4u PPA)
|
||||
"install_r_binary"|"r_binary_install")
|
||||
RBinaryInstall "$@"
|
||||
;;
|
||||
##
|
||||
## Install a package from github sources (needs remotes)
|
||||
"install_github"|"github_package")
|
||||
InstallGithub "$@"
|
||||
;;
|
||||
##
|
||||
## Install package dependencies from CRAN (needs remotes)
|
||||
"install_deps")
|
||||
InstallDeps
|
||||
;;
|
||||
##
|
||||
## Install package dependencies from Bioconductor and CRAN (needs devtools)
|
||||
"install_bioc_deps")
|
||||
InstallBiocDeps
|
||||
;;
|
||||
##
|
||||
## Run the actual tests, ie R CMD check
|
||||
"run_tests")
|
||||
RunTests
|
||||
;;
|
||||
##
|
||||
## Dump information about installed packages
|
||||
"dump_sysinfo")
|
||||
DumpSysinfo
|
||||
;;
|
||||
##
|
||||
## Dump build or check logs
|
||||
"dump_logs")
|
||||
DumpLogs
|
||||
;;
|
||||
##
|
||||
## Dump selected build or check logs
|
||||
"dump_logs_by_extension")
|
||||
DumpLogsByExtension "$@"
|
||||
;;
|
||||
esac
|
||||
Reference in New Issue
Block a user