configure

#!/bin/sh
# Anticonf (tm) script originally by Jeroen Ooms (2015) from rlib/xml2
# Modified by James Eapen (2024)
# This script will query 'pkg-config' for the required cflags and ldflags.
# If pkg-config is unavailable or does not find the library, try setting
# INCLUDE_DIR and LIB_DIR manually via e.g:
# R CMD INSTALL --configure-vars='INCLUDE_DIR=/.../include LIB_DIR=/.../lib'

echo ""
echo "Configuring for package installation..."

# Library settings
PKG_CONFIG_NAME="htslib"
PKG_DEB_NAME="libhts-dev"
PKG_RPM_NAME="htslib-devel"
PKG_TEST_HEADER="<htslib/hts.h>"
PKG_LIBS="-lhts"

# Note that cflags may be empty in case of success
if [ "$INCLUDE_DIR" ] || [ "$LIB_DIR" ]; then
  echo "Found INCLUDE_DIR and/or LIB_DIR!"
  PKG_CFLAGS="-I$INCLUDE_DIR $PKG_CFLAGS"
  PKG_LIBS="-L$LIB_DIR $PKG_LIBS"
else
  pkg-config --version >/dev/null 2>&1
  if [ $? -eq 0 ]; then
    PKGCONFIG_CFLAGS=$(pkg-config --cflags $PKG_CONFIG_NAME)
    PKGCONFIG_LIBS=$(pkg-config --libs $PKG_CONFIG_NAME)
  fi

  if [ "$PKGCONFIG_CFLAGS" ] || [ "$PKGCONFIG_LIBS" ]; then
    echo "Found pkg-config cflags and libs for ${PKG_CONFIG_NAME}!"
    PKG_CFLAGS=${PKGCONFIG_CFLAGS}
    PKG_LIBS=${PKGCONFIG_LIBS}
  else
      echo "------------------------- ANTICONF ERROR ---------------------------"
      echo "Configuration failed because $PKG_CONFIG_NAME was not found. Try installing:"
      echo " * deb: $PKG_DEB_NAME (Debian, Ubuntu, etc)"
      echo " * rpm: $PKG_RPM_NAME (Fedora, CentOS, RHEL)"
      echo "If $PKG_CONFIG_NAME is already installed, check that 'pkg-config' is in your"
      echo "PATH and PKG_CONFIG_PATH contains a $PKG_CONFIG_NAME.pc file. If pkg-config"
      echo "is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:"
      echo "R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'"
      echo "--------------------------------------------------------------------"
      exit 1;
  fi
fi

# Find compiler
CC=`${R_HOME}/bin/R CMD config CC`
CFLAGS=`${R_HOME}/bin/R CMD config CFLAGS`
CPPFLAGS=`${R_HOME}/bin/R CMD config CPPFLAGS`

# For debugging
echo "Using PKG_CFLAGS=$PKG_CFLAGS"
echo "Using PKG_LIBS=$PKG_LIBS"

# Test configuration
echo "#include $PKG_TEST_HEADER" | ${CC} ${CPPFLAGS} ${PKG_CFLAGS} ${CFLAGS} -E -xc - >/dev/null 2>&1 || R_CONFIG_ERROR=1;

if [ $R_CONFIG_ERROR ]; then
  echo "------------------------- ANTICONF ERROR ---------------------------"
  echo "Could not test config by compiling $PKG_TEST_HEADER with this command:"
  echo "echo #include $PKG_TEST_HEADER | ${CC} ${CPPFLAGS} ${PKG_CFLAGS} ${CFLAGS} -E -xc -"
  echo "--------------------------------------------------------------------"
  exit 1;
fi

# Write to Makevars
sed -e "s|@cflags@|$PKG_CFLAGS|" -e "s|@libs@|$PKG_LIBS|" src/Makevars.in > src/Makevars

# Success
echo "Success!"
echo ""
exit 0