kalibera/rchk:def

$ singularity pull shub://kalibera/rchk:def

Singularity Recipe

BootStrap: debootstrap
OSVersion: focal
MirrorURL: http://archive.ubuntu.com/ubuntu/

%post
  sed -i 's/main/main restricted universe/g' /etc/apt/sources.list
  sed -i 's/^# deb-src/deb-src/g' /etc/apt/sources.list
  test -z "`cat /etc/apt/sources.list | grep '^deb-src'`" && cat /etc/apt/sources.list | sed -e 's/^deb/deb-src/' >> /etc/apt/sources.list
  apt-get update

  # Install required R, Python, misc. utilities
  apt-get install -y libopenblas-dev libcurl4-openssl-dev libopenmpi-dev openmpi-bin openmpi-common openmpi-doc openssh-client openssh-server libssh-dev wget vim git cmake curl wget python autoconf bzip2 libtool libtool-bin python3-pip python-dev locales rsync
  apt-get build-dep -y r-base-core libpcre2-dev
  # LLVM
  apt-get install -y clang llvm-dev '^clang++$' llvm libllvm10 libc++-dev libc++abi-dev
  apt-get clean
  locale-gen en_US.UTF-8

  # wllvm
  pip3 install wllvm

  # rchk
  cd /opt
  git clone git://www.github.com/kalibera/rchk &&  \
    cd rchk && \
    cd src && \
    make -j `cat /proc/cpuinfo | grep "core id" | wc -l` \
        CXX=g++ BCHECK_MAX_STATES=3000000 CALLOCATORS_MAX_STATES=1000000 LLVM=/usr

  # download, build r-devel
  cd /opt
  wget -O - -q https://cran.r-project.org/src/base-prerelease/R-devel.tar.gz | tar zxvf -
  cd /opt/R-devel
  export WLLVM=/usr/local/bin
  export LLVM=/usr
  export RCHK=/opt/rchk
  export R_LIBS=
  export R_LIBS_SITE=
  export R_LIBS_USER=
  export R_MAKEVARS_USER=
  export R_MAKEVARS_SITE=
  export R_PROFILE=
  export R_PROFILE_USER=
  /opt/rchk/scripts/build_r.sh

  # fix up cmpconfig.inc to use user-defined PKG_BUILD, R_LIBS
  cat << EOF > /opt/rchk/scripts/cmpconfig.inc
# these options were tested on Ubuntu 16.04.2
#   they allow to build most but not all packages
export CFLAGS="-Wall -g -O0 -fPIC"
export CXXFLAGS="$CFLAGS -I/usr/include/libcxxabi"
export CC=$WLLVM/wllvm
export CXX="$WLLVM/wllvm++ -stdlib=libc++"
export PATH=$LLVM/bin:$PATH
export LLVM_COMPILER=clang
#  export PKG_BUILD_DIR=`pwd`/packages/build
#  export R_LIBS=`pwd`/packages/lib
export LD="clang++ -stdlib=libc++"
EOF

  # print usage message
  cat << EOF

Usage:
   singularity run <rchk_image> <package_tarball_full_path>
   singularity run <rchk_image> <package_name>
   singularity run <rchk_image> R [arguments]

Local package installation is performed when a package source path is
provided.  Otherwise, default CRAN and BIOC repositories are used.  Outputs
are placed in ${PKG_ROOT}/build, ${PKG_ROOT}/lib, and ${PKG_ROOT}/libsonly
directories, which are created if they do not exist.  If not set, the
PKG_ROOT shell variable is set to be the current working directory.

Usage examples:

# Install curl from CRAN and check:
singularity run rchk.img curl

# Local package install
wget https://cran.r-project.org/src/contrib/irlba_2.3.1.tar.gz
singularity run rchk.img $(pwd)/irlba_2.3.1.tar.gz

# Set the output directory to /tmp
PKG_ROOT=/tmp singularity run rchk.img curl

EOF



%runscript
  if test -z "$1"; then
    echo
    echo "Usage: singularity run <rchk_image> <package_tarball_full_path>"
    echo "       singularity run <rchk_image> <package_name>"
    echo "       singularity run <rchk_image> R"
    # for compatibility with older version, also <package_name> <package_tarball_full_path>
    echo
    exit 1
  fi
  if test -n "$2"; then
    PKG_NAME="$1"
    PKG_PATH="$2"
  else
    PKG_PATH="$1"
    if echo "$1" | grep -q "tar\.gz$" ; then
      PKG_NAME=`echo $1 | sed -e 's/.*\///g' | sed -e 's/\(.*\)_.*/\1/g'`
    else
      PKG_NAME="$1"
    fi
  fi
  if test -z "$PKG_ROOT"; then
    export PKG_ROOT=`pwd`
    echo
    echo "Note: Setting PKG_ROOT variable to the current directory."
    echo "Output will be in ./lib, ./build and ./libsonly subdirectories."
    echo "If it is not, maybe your local singularity configuration does"
    echo "not allow singularity container to access your current directory;"
    echo "it may help to try with PKG_ROOT=/tmp or check the configurarion."
    echo
  fi
  export LLVM=/usr
  export WLLVM=/usr/local/bin
  export RCHK=/opt/rchk
  export CFLAGS="-Wall -g -O0 -fpic"  
  export CXXFLAGS="$CFLAGS -I/usr/include/libcxxabi"
  export CC=$WLLVM/wllvm
  export CXX="$WLLVM/wllvm++ -stdlib=libc++"
  export PATH=$LLVM/bin:$PATH
  export LLVM_COMPILER=clang
  export PKG_BUILD_DIR="${PKG_ROOT}/build"
  export R_LIBS="${PKG_ROOT}/lib"
  export R_LIBSONLY="${PKG_ROOT}/libsonly"
  export R_LIBS_USER="${PKG_ROOT}/lib"
  export R_LIBS_SITE=
  export R_MAKEVARS_USER=
  export R_MAKEVARS_SITE=
  export R_PROFILE=
  export R_PROFILE_USER=
  export LD="clang++ -stdlib=libc++"  
  mkdir -p "${PKG_BUILD_DIR}"
  mkdir -p "${R_LIBS}"
  mkdir -p "${R_LIBSONLY}"
  if test "$PKG_NAME" = R ; then
    cd /tmp
    shift
    /opt/R-devel/bin/R --vanilla $*
    exit
  fi
  cd /opt/R-devel
  if test "$PKG_PATH" != "$PKG_NAME" ; then
    if [ ! -r "$PKG_PATH" ] ; then
      echo
      echo "The container cannot access package tarball $PKG_PATH."
      echo "Please specify it as full path."
      echo
      exit 2
    fi
  fi
  echo "source(\"${RCHK}/scripts/utils.r\"); install_package_libs(\"${PKG_PATH}\")"
  echo "source(\"${RCHK}/scripts/utils.r\"); install_package_libs(\"${PKG_PATH}\")" | ./bin/R --vanilla --no-echo
  find "${PKG_ROOT}/libsonly/${PKG_NAME}/libs" \( -name "*.bcheck" -o -name "*.maacheck" -o -name "*.fficheck" \) -exec rm {} \;
  /opt/rchk/scripts/check_package.sh "$PKG_NAME"
  echo
  find "${PKG_ROOT}/libsonly/${PKG_NAME}/libs" \( -name "*.bcheck" -o -name "*.maacheck" -o -name "*.fficheck" \) -exec cat {} \;
  echo
  echo "Rchk version: "`cd /opt/rchk && git rev-parse HEAD`
  echo "R version: "`echo 'cat(paste(R.version$svn, R.version$version.string, sep="/"))'  | ./bin/R --vanilla --no-echo`
  echo "LLVM version: "`/usr/bin/llvm-config --version`
  exit

Collection

• Name: kalibera/rchk
• License: None

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