[r] Provide reference to libtiledbsoma source via soft-link

apis/r/.Rbuildignore

@@ -17,11 +17,14 @@
 
 # build artifacts with libtiledbsoma
 src/include
-src/libtiledbsoma
 tiledbsoma/libtiledbsoma.tar.gz.current
 tiledb.tar.gz
 tiledbsoma.tar.gz
 
+# subdirectories of soft-linked libtiledbsoma
+src/libtiledbsoma/build
+src/libtiledbsoma/test
+
 # vscode
 ^\.vscode$
 ^\.devcontainer$

apis/r/DESCRIPTION

@@ -4,7 +4,7 @@ Title: TileDB SOMA
 Description: Interface for working with 'TileDB'-based Stack of Matrices,
     Annotated ('SOMA'): an open data model for representing annotated matrices,
     like those commonly used for single cell data analysis.
-Version: 0.0.0.9023
+Version: 0.0.0.9024
 Authors@R: c(
     person(given = "Aaron",
            family = "Wolen",

apis/r/cleanup

@@ -12,6 +12,6 @@ rm -r -f \
    src/include/ \
    src/lib \
    src/cmake_log.txt \
-   src/build \
-   src/libtiledbsoma \
-   src/bin
+   src/libtiledbsoma/build-lib \
+   src/bin \
+   tools/build_libtiledbsoma.sh

apis/r/configure

@@ -26,11 +26,30 @@ if [ $? -eq 0 ]; then
             src/Makevars.in > src/Makevars
 
         echo "** updated src/Makevars for system library via pkg-config"
+
+        ## we can exit now as we have a working setup
         exit 0
     fi
 fi
 
 ## If we are still here `pkg-config` alone did not work.
-## So download tiledb (pre-made) and tiledbsoma (source, for now; then build)
-## This
-${R_HOME}/bin/Rscript tools/get_tarballs.R
+
+## Download tiledb pre-made
+${R_HOME}/bin/Rscript tools/get_tarball.R
+
+## Check for cmake and git
+${R_HOME}/bin/Rscript tools/check_cmake_and_git.R
+
+## Make libtiledbsoma library using cmake (and an added git dependency)
+tools/build_libtiledbsoma.sh
+
+pkgincl="-I../inst/tiledb/include -I../inst/tiledbsoma/include"
+pkglibs="-ltiledb -L../inst/tiledb/lib -ltiledbsoma -L../inst/tiledbsoma/lib"
+rpath="-Wl,-rpath,'\$\$ORIGIN/../tiledb/lib' -Wl,-rpath,'\$\$ORIGIN/../tiledbsoma/lib'"
+macosver=`${R_HOME}/bin/Rscript -e 'if (Sys.info()["machine"] == "x86_64" && Sys.info()["sysname"] == "Darwin") cat("-mmacosx-version-min=10.14") else cat("")'`
+
+sed -e "s|@tiledb_include@|$pkgincl |" \
+    -e "s|@tiledb_libs@|$pkglibs|" \
+    -e "s|@tiledb_rpath@|$rpath|" \
+    -e "s|@cxx17_macos@|$macosver|" \
+    src/Makevars.in > src/Makevars

apis/r/src/Makevars.in

@@ -4,16 +4,15 @@ CXX_STD = CXX17
 PKG_CPPFLAGS = -I. -I../inst/include/ @tiledb_include@ @cxx17_macos@ -Iinclude
 
 ## When this becomes a CRAN package we may have to remove this. For now it keeps the noise down
-PKG_CXX17FLAGS = -Wno-deprecated-declarations
+PKG_CXXFLAGS = -Wno-deprecated-declarations
 
 ## We also need the TileDB library
 PKG_LIBS = @cxx17_macos@ @tiledb_libs@ @tiledb_rpath@
 
 all: $(SHLIB)
-        # If we are:
-        #  - on macOS aka Darwin which needs this
-        #  - the library is present (implying non-system library use)
-        # then let us call install_name_tool
+        # On macOS aka Darwin we call install_name_tool
+        # Case one: If we had a downloaded TileDB Core artifact, adjust zlib path and add to @rpath
+        # Case two: If we see the system libraries (on macOS) ensure /usr/local/lib rpath is considered
 	if [ `uname -s` = 'Darwin' ] && [ -f tiledbsoma.so ]; then \
 	    if [ -f ../inst/tiledb/lib/libtiledb.dylib ] ; then \
 	        install_name_tool -change libz.1.dylib @rpath/libz.1.dylib ../inst/tiledb/lib/libtiledb.dylib; \

apis/r/src/libtiledbsoma

@@ -0,0 +1 @@
+../../../libtiledbsoma/

apis/r/tools/build_libtiledbsoma.sh.in

@@ -0,0 +1,28 @@
+#!/bin/sh
+
+if [ ! -d src/libtiledbsoma ]; then
+    echo "No 'src/libtiledbsoma' directory. Exiting."
+    exit 1
+fi
+
+if [ ! -d src/libtiledbsoma/build-lib ]; then
+    mkdir src/libtiledbsoma/build-lib
+fi
+
+cwd=`pwd`
+
+cd src/libtiledbsoma/build-lib
+
+## The placeholder is filled in by check_cmake_and_git.R
+@cmake@ \
+      -DDOWNLOAD_TILEDB_PREBUILT=ON \
+      -DTILEDBSOMA_BUILD_CLI=OFF \
+      -DTILEDBSOMA_ENABLE_TESTING=OFF \
+      -DOVERRIDE_INSTALL_PREFIX=OFF \
+      -DCMAKE_INSTALL_PREFIX=${cwd}/inst/tiledbsoma ..
+
+make
+
+make install-libtiledbsoma
+
+rm -rf src/libtiledbsoma/build-lib

apis/r/tools/check_cmake_and_git.R

@@ -0,0 +1,19 @@
+
+
+cmake_bin <- Sys.which("cmake")
+if (cmake_bin == "" && file.exists("/Applications/CMake.app/Contents/bin/cmake"))
+    cmake_bin <- "/Applications/CMake.app/Contents/bin/cmake"
+
+if (cmake_bin == "") {
+    stop("No 'cmake' binary found", call. = FALSE)
+}
+
+git_bin <- Sys.which("git")
+if (git_bin == "") {
+    stop("No 'git' binary found", call. = FALSE)
+}
+
+lines <- readLines("tools/build_libtiledbsoma.sh.in")
+lines <- gsub("@cmake@", cmake_bin, lines)
+writeLines(lines, "tools/build_libtiledbsoma.sh")
+Sys.chmod("tools/build_libtiledbsoma.sh", mode="0755")

apis/r/tools/get_tarball.R

@@ -0,0 +1,31 @@
+#!/usr/bin/env Rscript
+
+## version pinning info
+tiledb_core_version <- "2.15.2"
+tiledb_core_sha1 <- "90f30eb"
+
+if ( ! dir.exists("inst/") ) {
+    stop("No 'inst/' directory. Exiting.", call. = FALSE)
+}
+
+makeUrl <- function(arch, ver=tiledb_core_version, sha1=tiledb_core_sha1) {
+    sprintf("https://github.com/TileDB-Inc/TileDB/releases/download/%s/tiledb-%s-%s-%s.tar.gz", ver, arch, ver, sha1)
+}
+
+isX86 <- Sys.info()["machine"] == "x86_64"
+isMac <- Sys.info()["sysname"] == "Darwin"
+isLinux <- Sys.info()["sysname"] == "Linux"
+
+if (isMac && isX86) {
+    url <- makeUrl("macos-x86_64")
+} else if (isMac && !isX86) {
+    url <- makeUrl("macos-arm64")
+} else if (isLinux) {
+    url <- makeUrl("linux-x86_64")
+} else {
+    stop("Unsupported platform for downloading artifacts. Please have TileDB Core installed locally.")
+}
+
+tarball <- "tiledb.tar.gz"
+if (!file.exists(tarball)) download.file(url, tarball, quiet=TRUE)
+if (!dir.exists("inst/tiledb")) untar(tarball, exdir="inst/tiledb")

apis/r/tools/r-ci.sh

@@ -195,6 +195,7 @@ BootstrapLinuxOptions() {
     #    InstallPandoc 'linux/debian/x86_64'
     #fi
     if [[ "${USE_BSPM}" != "FALSE" ]]; then
+        echo "options(bspm.sudo = TRUE)" | sudo tee --append /etc/R/Rprofile.site >/dev/null
         echo "suppressMessages(bspm::enable())" | sudo tee --append /etc/R/Rprofile.site >/dev/null
         echo "options(bspm.version.check=FALSE)" | sudo tee --append /etc/R/Rprofile.site >/dev/null
     fi