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AMR/tests/appveyor/travis_tool.sh

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#!/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 "$BOOTSTRAP_PANDOC" ]]; then
InstallPandoc 'mac'
fi
}
EnsureDevtools() {
if ! Rscript -e 'if (!("devtools" %in% rownames(installed.packages()))) q(status=1)' ; then
# Install devtools and testthat.
RBinaryInstall devtools testthat
fi
}
EnsureRemotes() {
if ! Rscript -e 'if (!("Rcpp" %in% rownames(installed.packages()))) q(status=1)' ; then
# Install remotes.
RBinaryInstall Rcpp
fi
if ! Rscript -e 'if (!("remotes" %in% rownames(installed.packages()))) q(status=1)' ; then
# Install remotes.
RBinaryInstall remotes
fi
if ! Rscript -e 'if (!("remotes" %in% rownames(installed.packages()))) q(status=1)' ; then
# Fallback: Install remotes from URL.
Rscript -e 'path <- file.path(tempdir(), "remotes_1.0.0.tar.gz"); download.file("https://cran.rstudio.com/src/contrib/Archive/remotes/remotes_1.0.0.tar.gz", path); install.packages(path, repos = NULL, type = "source")'
fi
}
AptGetInstall() {
if [[ "Linux" != "${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}"'")' "$@"
}
CleanLibrary() {
# removes all installed package so ensures a clean library
Rscript -e 'remove.packages(installed.packages()[is.na(installed.packages()[,"Priority"]), "Package"])'
}
InstallDeps() {
EnsureRemotes
echo "Installing dependencies"
Rscript -e 'options(repos = c(CRAN = "'"${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() {
Rscript -e 'sessionInfo()'
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 $COMMAND in
##
## Bootstrap a new core system
"bootstrap")
Bootstrap
;;
##
## Clean library
"clean_library")
CleanLibrary
;;
##
## Ensure devtools is loaded (implicitly called)
"install_devtools"|"devtools_install")
EnsureDevtools
;;
##
## Ensure remotes is loaded (implicitly called)
"install_remotes"|"remotes_install")
EnsureRemotes
;;
##
## Install a binary deb package via apt-get
"install_aptget"|"aptget_install")
AptGetInstall "$@"
;;
##
## 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
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