mirror of
https://github.com/msberends/AMR.git
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445 lines
14 KiB
Bash
445 lines
14 KiB
Bash
#!/bin/bash
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# -*- sh-basic-offset: 4; sh-indentation: 4 -*-
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# Bootstrap an R/travis environment.
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set -e
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# Comment out this line for quieter output:
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set -x
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CRAN=${CRAN:-"https://cran.rstudio.com"}
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BIOC=${BIOC:-"http://bioconductor.org/biocLite.R"}
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PKGTYPE=${PKGTYPE:-"win.binary"}
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BIOC_USE_DEVEL=${BIOC_USE_DEVEL:-"TRUE"}
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OS=$(uname -s)
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DOWNLOAD_FILE_METHOD=${DOWNLOAD_FILE_METHOD:-"auto"}
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PANDOC_VERSION='1.13.1'
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PANDOC_DIR="${HOME}/opt/pandoc"
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PANDOC_URL="https://s3.amazonaws.com/rstudio-buildtools/pandoc-${PANDOC_VERSION}.zip"
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# MacTeX installs in a new $PATH entry, and there's no way to force
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# the *parent* shell to source it from here. So we just manually add
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# all the entries to a location we already know to be on $PATH.
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#
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# TODO(craigcitro): Remove this once we can add `/usr/texbin` to the
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# root path.
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PATH="${PATH}:/usr/texbin"
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R_BUILD_ARGS=${R_BUILD_ARGS-"--no-manual"}
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R_CHECK_ARGS=${R_CHECK_ARGS-"--no-manual --as-cran"}
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R_VERSION_TEST="getRversion() >= '3.5.0'"
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R_USE_BIOC_INST="source('${BIOC}');"\
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" tryCatch(useDevel(${BIOC_USE_DEVEL}),"\
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" error=function(e) {if (!grepl('already in use', e$message)) {e}});"\
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" options(repos=biocinstallRepos())"
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R_USE_BIOC_MNGR="if (!requireNamespace('BiocManager', quietly=TRUE))"\
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" install.packages('BiocManager', repos=c(CRAN='${CRAN}'));"\
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" if (${BIOC_USE_DEVEL})"\
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" BiocManager::install(version = 'devel', ask = FALSE);"\
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" options(repos=BiocManager::repositories())"
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R_USE_BIOC_CMDS="if (${R_VERSION_TEST}) {${R_USE_BIOC_MNGR}} else {${R_USE_BIOC_INST}};"
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BIOC_INSTALL="{if (${R_VERSION_TEST}) BiocManager::install else BiocInstaller::biocLite}"
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Bootstrap() {
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if [[ "Darwin" == "${OS}" ]]; then
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BootstrapMac
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elif [[ "Linux" == "${OS}" ]]; then
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BootstrapLinux
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else
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echo "Unknown OS: ${OS}"
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exit 1
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fi
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if ! (test -e .Rbuildignore && grep -q 'travis_tool' .Rbuildignore); then
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echo '^travis_tool\.sh$' >>.Rbuildignore
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fi
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}
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InstallPandoc() {
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local os_path="$1"
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mkdir -p "${PANDOC_DIR}"
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curl -o /tmp/pandoc-${PANDOC_VERSION}.zip ${PANDOC_URL}
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unzip -j /tmp/pandoc-${PANDOC_VERSION}.zip "pandoc-${PANDOC_VERSION}/${os_path}/pandoc" -d "${PANDOC_DIR}"
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chmod +x "${PANDOC_DIR}/pandoc"
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sudo ln -s "${PANDOC_DIR}/pandoc" /usr/local/bin
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unzip -j /tmp/pandoc-${PANDOC_VERSION}.zip "pandoc-${PANDOC_VERSION}/${os_path}/pandoc-citeproc" -d "${PANDOC_DIR}"
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chmod +x "${PANDOC_DIR}/pandoc-citeproc"
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sudo ln -s "${PANDOC_DIR}/pandoc-citeproc" /usr/local/bin
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}
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BootstrapLinux() {
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# Set up our CRAN mirror.
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sudo add-apt-repository "deb ${CRAN}/bin/linux/ubuntu $(lsb_release -cs)/"
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sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
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# Add marutter's c2d4u repository.
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sudo add-apt-repository -y "ppa:marutter/rrutter"
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sudo add-apt-repository -y "ppa:marutter/c2d4u"
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# Update after adding all repositories. Retry several times to work around
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# flaky connection to Launchpad PPAs.
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Retry sudo apt-get update -qq
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# Install an R development environment. qpdf is also needed for
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# --as-cran checks:
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# https://stat.ethz.ch/pipermail/r-help//2012-September/335676.html
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Retry sudo apt-get install -y --no-install-recommends r-base-dev r-recommended qpdf
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# Change permissions for /usr/local/lib/R/site-library
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# This should really be via 'staff adduser travis staff'
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# but that may affect only the next shell
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sudo chmod 2777 /usr/local/lib/R /usr/local/lib/R/site-library
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# Process options
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BootstrapLinuxOptions
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}
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BootstrapLinuxOptions() {
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if [[ -n "$BOOTSTRAP_LATEX" ]]; then
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# We add a backports PPA for more recent TeX packages.
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sudo add-apt-repository -y "ppa:texlive-backports/ppa"
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Retry sudo apt-get install -y --no-install-recommends \
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texlive-base texlive-latex-base texlive-generic-recommended \
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texlive-fonts-recommended texlive-fonts-extra \
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texlive-extra-utils texlive-latex-recommended texlive-latex-extra \
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texinfo lmodern
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fi
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if [[ -n "$BOOTSTRAP_PANDOC" ]]; then
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InstallPandoc 'linux/debian/x86_64'
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fi
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}
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BootstrapMac() {
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# Install from latest CRAN binary build for OS X
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wget ${CRAN}/bin/macosx/R-latest.pkg -O /tmp/R-latest.pkg
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echo "Installing OS X binary package for R"
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sudo installer -pkg "/tmp/R-latest.pkg" -target /
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rm "/tmp/R-latest.pkg"
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# Process options
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BootstrapMacOptions
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}
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BootstrapMacOptions() {
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if [[ -n "$BOOTSTRAP_LATEX" ]]; then
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# TODO: Install MacTeX.pkg once there's enough disk space
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MACTEX=BasicTeX.pkg
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wget http://ctan.math.utah.edu/ctan/tex-archive/systems/mac/mactex/$MACTEX -O "/tmp/$MACTEX"
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echo "Installing OS X binary package for MacTeX"
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sudo installer -pkg "/tmp/$MACTEX" -target /
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rm "/tmp/$MACTEX"
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# We need a few more packages than the basic package provides; this
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# post saved me so much pain:
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# https://stat.ethz.ch/pipermail/r-sig-mac/2010-May/007399.html
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sudo tlmgr update --self
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sudo tlmgr install inconsolata upquote courier courier-scaled helvetic
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fi
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if [[ -n "$BOOTSTRAP_PANDOC" ]]; then
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InstallPandoc 'mac'
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fi
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}
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EnsureDevtools() {
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if ! Rscript -e 'if (!("devtools" %in% rownames(installed.packages()))) q(status=1)' ; then
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# Install devtools and testthat.
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RBinaryInstall devtools testthat
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fi
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}
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EnsureRemotes() {
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if ! Rscript -e 'if (!("Rcpp" %in% rownames(installed.packages()))) q(status=1)' ; then
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# Install remotes.
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RBinaryInstall Rcpp
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fi
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if ! Rscript -e 'if (!("remotes" %in% rownames(installed.packages()))) q(status=1)' ; then
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# Install remotes.
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RBinaryInstall remotes
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fi
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if ! Rscript -e 'if (!("remotes" %in% rownames(installed.packages()))) q(status=1)' ; then
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# Fallback: Install remotes from URL.
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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")'
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fi
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}
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AptGetInstall() {
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if [[ "Linux" != "${OS}" ]]; then
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echo "Wrong OS: ${OS}"
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exit 1
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fi
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if [[ "" == "$*" ]]; then
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echo "No arguments to aptget_install"
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exit 1
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fi
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echo "Installing apt package(s) $@"
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Retry sudo apt-get -y install "$@"
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}
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DpkgCurlInstall() {
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if [[ "Linux" != "${OS}" ]]; then
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echo "Wrong OS: ${OS}"
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exit 1
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fi
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if [[ "" == "$*" ]]; then
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echo "No arguments to dpkgcurl_install"
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exit 1
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fi
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echo "Installing remote package(s) $@"
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for rf in "$@"; do
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curl -OL ${rf}
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f=$(basename ${rf})
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sudo dpkg -i ${f}
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rm -v ${f}
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done
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}
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RInstall() {
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if [[ "" == "$*" ]]; then
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echo "No arguments to r_install"
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exit 1
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fi
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echo "Installing R package(s): $@"
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Rscript -e 'install.packages(commandArgs(TRUE), repos="'"${CRAN}"'", INSTALL_opts="", type="'"${PKGTYPE}"'")' "$@"
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}
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BiocInstall() {
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if [[ "" == "$*" ]]; then
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echo "No arguments to bioc_install"
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exit 1
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fi
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echo "Installing R Bioconductor package(s): $@"
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Rscript -e "${R_USE_BIOC_CMDS}"" ${BIOC_INSTALL}(commandArgs(TRUE))" "$@"
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}
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RBinaryInstall() {
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if [[ -z "$#" ]]; then
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echo "No arguments to r_binary_install"
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exit 1
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fi
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if [[ "Linux" != "${OS}" ]] || [[ -n "${FORCE_SOURCE_INSTALL}" ]]; then
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echo "Fallback: Installing from source"
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RInstall "$@"
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return
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fi
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echo "Installing *binary* R packages: $*"
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r_packages=$(echo $* | tr '[:upper:]' '[:lower:]')
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r_debs=$(for r_package in ${r_packages}; do echo -n "r-cran-${r_package} "; done)
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AptGetInstall ${r_debs}
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}
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InstallGithub() {
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EnsureRemotes
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echo "Installing GitHub packages: $@"
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# Install the package.
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Rscript -e 'options(repos = c(CRAN = "'"${CRAN}"'"), download.file.method = "'"${DOWNLOAD_FILE_METHOD}"'"); remotes::install_github(commandArgs(TRUE), type="'"${PKGTYPE}"'")' "$@"
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}
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CleanLibrary() {
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# removes all installed package so ensures a clean library
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Rscript -e 'remove.packages(installed.packages()[is.na(installed.packages()[,"Priority"]), "Package"])'
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}
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InstallDeps() {
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EnsureRemotes
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echo "Installing dependencies"
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Rscript -e 'options(repos = c(CRAN = "'"${CRAN}"'"), download.file.method = "'"${DOWNLOAD_FILE_METHOD}"'"); remotes::install_deps(dependencies = TRUE, type="'"${PKGTYPE}"'")'
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}
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InstallBiocDeps() {
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EnsureDevtools
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Rscript -e "${R_USE_BIOC_CMDS}"' library(devtools); install_deps(dependencies = TRUE, type="'"${PKGTYPE}"'")'
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}
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DumpSysinfo() {
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echo "Dumping system information."
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R -e '.libPaths(); sessionInfo(); installed.packages()'
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}
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DumpLogsByExtension() {
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if [[ -z "$1" ]]; then
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echo "dump_logs_by_extension requires exactly one argument, got: $@"
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exit 1
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fi
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extension=$1
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shift
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package=$(find . -maxdepth 1 -name "*.Rcheck" -type d)
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if [[ ${#package[@]} -ne 1 ]]; then
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echo "Could not find package Rcheck directory, skipping log dump."
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exit 0
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fi
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for name in $(find "${package}" -type f -name "*${extension}"); do
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echo ">>> Filename: ${name} <<<"
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cat ${name}
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done
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}
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DumpLogs() {
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echo "Dumping test execution logs."
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DumpLogsByExtension "out"
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DumpLogsByExtension "log"
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DumpLogsByExtension "fail"
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}
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RunTests() {
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Rscript -e 'sessionInfo()'
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echo "Building with: R CMD build ${R_BUILD_ARGS}"
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if [[ "${KEEP_VIGNETTES}" == "" ]]; then
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if [[ "${OS:0:5}" == "MINGW" || "${OS:0:4}" == "MSYS" ]]; then
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if [[ -d vignettes ]]; then
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rm -rf vignettes
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Rscript -e "d <- read.dcf('DESCRIPTION'); d[, colnames(d) == 'VignetteBuilder'] <- NA; write.dcf(d, 'DESCRIPTION')"
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fi
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fi
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fi
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R CMD build ${R_BUILD_ARGS} .
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# We want to grab the version we just built.
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FILE=$(ls -1t *.tar.gz | head -n 1)
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# Create binary package (currently Windows only)
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if [[ "${OS:0:5}" == "MINGW" || "${OS:0:4}" == "MSYS" ]]; then
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R_CHECK_INSTALL_ARGS="--install-args=--build"
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fi
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echo "Testing with: R CMD check \"${FILE}\" ${R_CHECK_ARGS} ${R_CHECK_INSTALL_ARGS}"
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_R_CHECK_CRAN_INCOMING_=${_R_CHECK_CRAN_INCOMING_:-FALSE}
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if [[ "$_R_CHECK_CRAN_INCOMING_" == "FALSE" ]]; then
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echo "(CRAN incoming checks are off)"
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fi
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_R_CHECK_CRAN_INCOMING_=${_R_CHECK_CRAN_INCOMING_} R_QPDF=true R CMD check "${FILE}" ${R_CHECK_ARGS} ${R_CHECK_INSTALL_ARGS}
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# Check reverse dependencies
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if [[ -n "$R_CHECK_REVDEP" ]]; then
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echo "Checking reverse dependencies"
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EnsureDevtools
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Rscript -e 'library(devtools); checkOutput <- unlist(revdep_check(as.package(".")$package));if (!is.null(checkOutput)) {print(data.frame(pkg = names(checkOutput), error = checkOutput));for(i in seq_along(checkOutput)){;cat("\n", names(checkOutput)[i], " Check Output:\n ", paste(readLines(regmatches(checkOutput[i], regexec("/.*\\.out", checkOutput[i]))[[1]]), collapse = "\n ", sep = ""), "\n", sep = "")};q(status = 1, save = "no")}'
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fi
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if [[ -n "${WARNINGS_ARE_ERRORS}" ]]; then
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if DumpLogsByExtension "00check.log" | grep -q WARNING; then
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echo "Found warnings, treated as errors."
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echo "Clear or unset the WARNINGS_ARE_ERRORS environment variable to ignore warnings."
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exit 1
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fi
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fi
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}
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Retry() {
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if "$@"; then
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return 0
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fi
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for wait_time in 5 20 30 60; do
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echo "Command failed, retrying in ${wait_time} ..."
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sleep ${wait_time}
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if "$@"; then
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return 0
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fi
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done
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echo "Failed all retries!"
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exit 1
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}
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COMMAND=$1
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echo "Running command: ${COMMAND}"
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shift
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case $COMMAND in
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##
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## Bootstrap a new core system
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"bootstrap")
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Bootstrap
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;;
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##
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## Clean library
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"clean_library")
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CleanLibrary
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;;
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##
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## Ensure devtools is loaded (implicitly called)
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"install_devtools"|"devtools_install")
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EnsureDevtools
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;;
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##
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## Ensure remotes is loaded (implicitly called)
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"install_remotes"|"remotes_install")
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EnsureRemotes
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;;
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##
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## Install a binary deb package via apt-get
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"install_aptget"|"aptget_install")
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AptGetInstall "$@"
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;;
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##
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## Install a binary deb package via a curl call and local dpkg -i
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"install_dpkgcurl"|"dpkgcurl_install")
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DpkgCurlInstall "$@"
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;;
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##
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## Install an R dependency from CRAN
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"install_r"|"r_install")
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RInstall "$@"
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;;
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##
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## Install an R dependency from Bioconductor
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"install_bioc"|"bioc_install")
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BiocInstall "$@"
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;;
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##
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## Install an R dependency as a binary (via c2d4u PPA)
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"install_r_binary"|"r_binary_install")
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RBinaryInstall "$@"
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;;
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##
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## Install a package from github sources (needs remotes)
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"install_github"|"github_package")
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InstallGithub "$@"
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;;
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##
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## Install package dependencies from CRAN (needs remotes)
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"install_deps")
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InstallDeps
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;;
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##
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## Install package dependencies from Bioconductor and CRAN (needs devtools)
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"install_bioc_deps")
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InstallBiocDeps
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;;
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##
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## Run the actual tests, ie R CMD check
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"run_tests")
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RunTests
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;;
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##
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## Dump information about installed packages
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"dump_sysinfo")
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DumpSysinfo
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;;
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##
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## Dump build or check logs
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"dump_logs")
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DumpLogs
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;;
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##
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## Dump selected build or check logs
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"dump_logs_by_extension")
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DumpLogsByExtension "$@"
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;;
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esac
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