Update internal S2 version and migrate dependency build to cmake

.Rbuildignore

@@ -12,3 +12,6 @@
 ^README\.Rmd$
 ^vignettes/articles$
 ^\.clang-format$
+^tools/build$
+^tools/dist$
+^compile_commands\.json$

.gitattributes

@@ -0,0 +1,2 @@
+tools/vendor/abseil-cpp linguist-vendored
+tools/vendor/s2-geometry linguist-vendored

.gitignore

@@ -4,3 +4,5 @@
 .vscode
 docs
 configure.log
+compile_commands.json
+.cache

configure

@@ -1,112 +1,74 @@
-# Anticonf (tm) script by Jeroen Ooms (2020)
-# 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'
-
-# Library settings
-PKG_CONFIG_NAME="openssl"
-PKG_DEB_NAME="libssl-dev"
-PKG_RPM_NAME="openssl-devel"
-PKG_CSW_NAME="libssl_dev"
-PKG_BREW_NAME="[email protected]"
-PKG_TEST_FILE="tools/version.c"
-PKG_LIBS="-lssl -lcrypto"
-PKG_CFLAGS=""
-
-# Use pkg-config if available
-pkg-config ${PKG_CONFIG_NAME} --atleast-version=1.0  2>/dev/null
-if [ $? -eq 0 ]; then
-  PKGCONFIG_CFLAGS=`pkg-config --cflags ${PKG_CONFIG_NAME}`
-  PKGCONFIG_LIBS=`pkg-config --libs ${PKG_CONFIG_NAME}`
-fi
 
-# 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 $PKG_LIBS"
-elif [ "$PKGCONFIG_CFLAGS" ] || [ "$PKGCONFIG_LIBS" ]; then
-  echo "Found pkg-config cflags and libs!"
-  PKG_CFLAGS=${PKGCONFIG_CFLAGS}
-  PKG_LIBS=${PKGCONFIG_LIBS}
-elif [ `uname` = "Darwin" ]; then
-  test ! "$CI" && brew --version 2>/dev/null
-  if [ $? -eq 0 ]; then
-    BREWDIR=`brew --prefix`
-    PKG_CFLAGS="-I$BREWDIR/opt/openssl/include -I$BREWDIR/opt/[email protected]/include"
-    PKG_LIBS="-L$BREWDIR/opt/openssl/lib -L$BREWDIR/opt/[email protected]/lib $PKG_LIBS"
-  else
-    curl -sfL "https://autobrew.github.io/scripts/$PKG_BREW_NAME" > autobrew
-    . ./autobrew
-  fi
+# https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-cmake
+
+if test -z "$CMAKE"; then CMAKE="`which cmake`"; fi
+if test -z "$CMAKE"; then CMAKE=/Applications/CMake.app/Contents/bin/cmake; fi
+if ${CMAKE} --version ; then
+  echo "Using CMAKE=$CMAKE"
+  echo "Using MAKE=$MAKE $MAKEVARS"
+else
+  echo "cmake not found"
 fi
 
-# Find compiler
-CC=`${R_HOME}/bin/R CMD config CC`
-CFLAGS=`${R_HOME}/bin/R CMD config CFLAGS`
-CPPFLAGS=`${R_HOME}/bin/R CMD config CPPFLAGS`
-
-# For debugging
-echo "Testing compiler using PKG_CFLAGS=$PKG_CFLAGS"
-
-# Test configuration
-${CC} ${CPPFLAGS} ${PKG_CFLAGS} ${CFLAGS} -E ${PKG_TEST_FILE} >/dev/null 2>configure.log
-
-# Customize the error
-if [ $? -ne 0 ]; then
-  echo "--------------------------- [ANTICONF] --------------------------------"
-  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 " * csw: $PKG_CSW_NAME (Solaris)"
-  echo " * brew: $PKG_BREW_NAME (Mac OSX)"
-  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 "-------------------------- [ERROR MESSAGE] ---------------------------"
-  cat configure.log
-  echo "--------------------------------------------------------------------"
+: ${R_HOME=`R RHOME`}
+if test -z "${R_HOME}"; then
+  echo "could not determine R_HOME"
   exit 1
 fi
 
-# Try to link against the correct OpenSSL version
-if [ -z "$AUTOBREW" ]; then
-SONAME=`${CC} -E ${PKG_CFLAGS} src/tests/soname.h | sh | xargs`
-if [ "$SONAME" ]; then
-if [ `uname` = "Darwin" ]; then
-  PKG_LIBS_VERSIONED=`echo "${PKG_LIBS}" | sed "s/-lssl/-lssl.${SONAME}/" | sed "s/-lcrypto/-lcrypto.${SONAME}/"`
-else
-  PKG_LIBS_VERSIONED=`echo "${PKG_LIBS}" | sed "s/-lssl/-l:libssl.so.${SONAME}/" | sed "s/-lcrypto/-l:libcrypto.so.${SONAME}/"`
-fi
+CC=`"${R_HOME}/bin/R" CMD config CC`
+CXX=`${R_HOME}/bin/R CMD config CXX14`
+CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
+CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
+CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXX14FLAGS`
+LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
 
-# Test if versioned linking works
-${CC} ${PKG_CFLAGS} src/tests/main.c ${PKG_LIBS_VERSIONED} -o src/main.exe 2>/dev/null
-if [ $? -eq 0 ]; then PKG_LIBS="${PKG_LIBS_VERSIONED}"; fi
-rm src/main.exe || true
+CMAKE_INSTALL_PREFIX="`pwd`/tools/dist"
+CMAKE_PREFIX_PATH="`pwd`/tools/dist/lib/cmake"
 
-# Suppress opensslv3 warnings for now
-if [ "$SONAME" = "3" ]; then
-PKG_CFLAGS="$PKG_CFLAGS -DOPENSSL_SUPPRESS_DEPRECATED"
-fi
+build_cmake () {
+  if [ ! -d "tools/build/$1" ]; then
+    mkdir -p "tools/build/$1"
+  fi
 
-fi #SONAME
-fi #AUTOBREW
-
-# Define system endianness (compile-time endianness using system/compiler
-# defines isn't detected on Solaris)
-# based on endian detection from the feather package by @hadley
-R_ENDIAN=`${R_HOME}/bin/Rscript -e 'cat(.Platform$endian)'`
-# Trim off any warning messages that Rscript appends in front of the platform endianness
-R_ENDIAN=`expr "$R_ENDIAN" : '.*\(little\)$'`
-SYS_ENDIAN=""
-if [ "$R_ENDIAN" = "little" ]; then
-    PKG_CFLAGS="$PKG_CFLAGS -DIS_LITTLE_ENDIAN"
-else
-    PKG_CFLAGS="$PKG_CFLAGS -DIS_BIG_ENDIAN"
+  cd "tools/build/$1"
+
+  ${CMAKE} \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DBUILD_SHARED_LIBS=OFF \
+    -DCMAKE_POSITION_INDEPENDENT_CODE=ON \
+    -DCMAKE_INSTALL_PREFIX="${CMAKE_INSTALL_PREFIX}" \
+    -DCMAKE_PREFIX_PATH="${CMAKE_PREFIX_PATH}" \
+    -DCMAKE_OSX_DEPLOYMENT_TARGET=11.3 \
+    -DCMAKE_CXX_STANDARD=14 "${@:2}" \
+    "../../vendor/$1" &&
+    ${MAKE} ${MAKEVARS} &&
+    ${CMAKE} --install .
+
+  cd ../../..
+}
+
+# Consider doing this in a separate CMakeLists.txt?
+
+if [ -d tools/build ] || [ ! -d tools/dist ]; then
+  build_cmake abseil-cpp -DABSL_PROPAGATE_CXX_STD=ON &&
+    build_cmake s2geometry &&
+    build_cmake s2geography -DS2_ROOT_DIR="`pwd`/tools/dist" &&
+    cp tools/build/s2geography/OPENSSL* tools/dist/ &&
+    rm -rf tools/build
 fi
 
+# Assemble bulit libraries
+CMAKE_LIBS="-labsl_base -labsl_city -labsl_cord -labsl_cord_internal -labsl_cordz_functions -labsl_cordz_handle -labsl_cordz_info -labsl_hash -labsl_hashtablez_sampler -labsl_int128 -labsl_kernel_timeout_internal -labsl_low_level_hash -labsl_malloc_internal -labsl_raw_hash_set -labsl_raw_logging_internal -labsl_spinlock_wait -labsl_stacktrace -labsl_str_format_internal -labsl_strerror -labsl_string_view -labsl_strings -labsl_strings_internal -labsl_synchronization -labsl_throw_delegate -labsl_time -labsl_time_zone -ls2 -ls2geography"
+
+#CMAKE_LIBS=`ls tools/dist/lib | grep -e "lib" | sed -e "s/^lib/-l/" -e "s/.a$//" | tr '\n' ' '`
+OPENSSL_INCLUDE_DIR=`cat tools/dist/OPENSSL_INCLUDE_DIR`
+OPENSSL_CRYPTO_LIBRARY=`cat tools/dist/OPENSSL_CRYPTO_LIBRARY`
+OPENSSSL_LIB_DIR=`dirname $OPENSSL_CRYPTO_LIBRARY`
+
+PKG_LIBS="-L`pwd`/tools/dist/lib $CMAKE_LIBS -L$OPENSSSL_LIB_DIR -lcrypto"
+PKG_CFLAGS="-I`pwd`/tools/dist/include -I$OPENSSL_INCLUDE_DIR"
+
 # From apache/arrow/r/configure:
 # If on Raspberry Pi, need to manually link against latomic
 # See: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81358 for similar example
@@ -117,7 +79,6 @@ fi
 echo "Using PKG_LIBS=$PKG_LIBS"
 echo "Using PKG_CFLAGS=$PKG_CFLAGS"
 
-
 # Write to Makevars
 sed -e "s|@cflags@|$PKG_CFLAGS|" -e "s|@libs@|$PKG_LIBS|" src/Makevars.in > src/Makevars
 

data-raw/update-absl.R

@@ -1,166 +1,28 @@
 
 library(tidyverse)
-tag <- "20220623.1"
+tag <- "20230802.1"
 
 # download Abseil
 source_url <- glue::glue("https://github.com/abseil/abseil-cpp/archive/refs/tags/{tag}.zip")
 curl::curl_download(source_url, "data-raw/abseil-cpp-source.zip")
-unzip("data-raw/abseil-cpp-source.zip", exdir = "data-raw")
-
-
-absl_copy <- function(src, dst) {
-  src_files <- list.files(src, "\\.(cc|h|inc)$", recursive = TRUE) %>%
-    str_subset("_test(ing)?\\.(cc|h)$", negate = TRUE) %>%
-    str_subset("test_", negate = TRUE) %>%
-    str_subset("_benchmark", negate = TRUE)
-
-  dst_files <- file.path(dst, src_files)
-  dst_dirs <- unique(dirname(dst_files))
-  for (d in sort(dst_dirs)) {
-    if (!dir.exists(d)) dir.create(d, recursive = TRUE)
-  }
-
-  stopifnot(all(file.copy(file.path(src, src_files), dst_files)))
-}
-
-unlink("src/absl", recursive = TRUE)
-
-absl_copy(
-  glue::glue("data-raw/abseil-cpp-{tag}/absl/container"),
-  "src/absl/container"
-)
-
-absl_copy(
-  glue::glue("data-raw/abseil-cpp-{tag}/absl/base"),
-  "src/absl/base"
-)
-
-absl_copy(
-  glue::glue("data-raw/abseil-cpp-{tag}/absl/meta"),
-  "src/absl/meta"
-)
-
-absl_copy(
-  glue::glue("data-raw/abseil-cpp-{tag}/absl/synchronization"),
-  "src/absl/synchronization"
-)
-
-absl_copy(
-  glue::glue("data-raw/abseil-cpp-{tag}/absl/time"),
-  "src/absl/time"
-)
-
-absl_copy(
-  glue::glue("data-raw/abseil-cpp-{tag}/absl/strings"),
-  "src/absl/strings"
-)
-
-absl_copy(
-  glue::glue("data-raw/abseil-cpp-{tag}/absl/utility"),
-  "src/absl/utility"
-)
-
-absl_copy(
-  glue::glue("data-raw/abseil-cpp-{tag}/absl/debugging"),
-  "src/absl/debugging"
-)
-
-absl_copy(
-  glue::glue("data-raw/abseil-cpp-{tag}/absl/memory"),
-  "src/absl/memory"
-)
-
-absl_copy(
-  glue::glue("data-raw/abseil-cpp-{tag}/absl/types"),
-  "src/absl/types"
+unzip("data-raw/abseil-cpp-source.zip", exdir = "tools/vendor")
+file.rename(glue::glue("tools/vendor/abseil-cpp-{tag}"), "tools/vendor/abseil-cpp")
+
+# prune unused components
+unlink("tools/vendor/abseil-cpp/.github", recursive = TRUE)
+unlink("tools/vendor/abseil-cpp/ci", recursive = TRUE)
+unlink(list.files("tools/vendor/abseil-cpp", "\\.py$", full.names = TRUE))
+unlink(
+  list.files(
+    "tools/vendor/abseil-cpp/absl", "_test.cc$",
+    full.names = TRUE,
+    recursive = TRUE
+  )
+)
+unlink(
+  list.files(
+    "tools/vendor/abseil-cpp/absl", "_benchmark.cc$",
+    full.names = TRUE,
+    recursive = TRUE
+  )
 )
-
-absl_copy(
-  glue::glue("data-raw/abseil-cpp-{tag}/absl/numeric"),
-  "src/absl/numeric"
-)
-
-absl_copy(
-  glue::glue("data-raw/abseil-cpp-{tag}/absl/algorithm"),
-  "src/absl/algorithm"
-)
-
-absl_copy(
-  glue::glue("data-raw/abseil-cpp-{tag}/absl/functional"),
-  "src/absl/functional"
-)
-
-absl_copy(
-  glue::glue("data-raw/abseil-cpp-{tag}/absl/profiling"),
-  "src/absl/profiling"
-)
-
-absl_objects <- list.files("src/absl", ".cc$", recursive = TRUE) %>%
-  file.path("absl", .) %>%
-  str_subset("\\.cc$") %>%
-  str_replace("\\.cc$", ".o") %>%
-  paste0(collapse = " \\\n    ") %>%
-  paste0("ABSL_LIBS = ", .)
-
-clipr::write_clip(absl_objects)
-usethis::edit_file("src/Makevars.win")
-usethis::edit_file("src/Makevars.in")
-
-# Edits needed to make CMD check happy
-
-# Pragmas
-fix_pragmas <- function(f) {
-  content <- readr::read_file(f)
-  content <- stringr::str_replace_all(content, "\n#pragma", "\n// #pragma")
-  readr::write_file(content, f)
-}
-
-fix_pragmas("src/absl/base/internal/invoke.h")
-fix_pragmas("src/absl/container/inlined_vector.h")
-fix_pragmas("src/absl/container/internal/inlined_vector.h")
-fix_pragmas("src/absl/functional/internal/any_invocable.h")
-fix_pragmas("src/absl/types/internal/optional.h")
-fix_pragmas("src/absl/container/internal/counting_allocator.h")
-
-# Aborts
-fix_aborts <- function(f) {
-  content <- readr::read_file(f)
-  content <- stringr::str_replace_all(content, fixed("abort()"), "throw std::runtime_error(\"abort()\")")
-  readr::write_file(content, f)
-}
-
-fix_aborts("src/absl/base/internal/raw_logging.cc")
-fix_aborts("src/absl/base/internal/sysinfo.cc")
-fix_aborts("src/absl/debugging/symbolize_elf.inc")
-
-# Manual updates
-
-# The symbolizer implementation causes some trouble. We don't use this feature here
-# and there seems to be a way to turn it off completely. Do this.
-usethis::edit_file("src/absl/debugging/symbolize.cc")
-
-# On Windows, R.h defines a macro 'Free', which we have to undefine
-usethis::edit_file("src/absl/base/internal/low_level_alloc.h")
-
-# On Windows with rtools35 (i.e., very old GCC with incomplete C++11), a reference
-# to std::get_time() causes compilation error. We don't need strptime here, so just
-# return nullptr in this function.
-usethis::edit_file("src/absl/time/internal/cctz/src/time_zone_format.cc")
-
-# Windows builds have some additional issues with format strings. These are all within
-# absl logger functions...just remove the definition of ABSL_RAW_LOG(...).
-usethis::edit_file("src/absl/base/internal/raw_logging.h")
-
-# Fix a workaround for older gcc that causes a check warning. The bug that the
-# workaround is addressing only applies to old gcc, so only use that bit of code
-# for old gcc
-usethis::edit_file("src/absl/container/internal/raw_hash_set.h")
-
-# CRAN compiles with -Wpedantic, so we can't use the __int128 intrinsic type
-# undefine ABSL_HAVE_INTRINSIC_INT128 here:
-usethis::edit_file("src/absl/base/config.h")
-
-# The use of ABSL_HAVE_CPP_ATTRIBUTE() with ABSL_FALLTHROUGH_INTENDED
-# here uses C++17 attributes even if -std=c++17 is not set,
-# which causes CRAN warnings with -Wpedantic
-usethis::edit_file("src/absl/base/attributes.h")