Build enhancement for Conda (#722)

* Build enhancement for Conda

* Turn window build matrix CI back to r-rel and r-dev

* Roll micro version, update NEWS [ci skip]

* Correct DYLIB_EXT on Darwin aka macOS

* Another refinement

.github/workflows/windows.yaml

@@ -11,11 +11,8 @@ jobs:
       fail-fast: false
       matrix:
         include: [
-          #{ windows: windows-latest, r: release    },
-          #{ windows: windows-latest, r: devel      }
-          #
-          # for now just r-release
-          { windows: windows-latest, r: release    }
+          { windows: windows-latest, r: release    },
+          { windows: windows-latest, r: devel      }
         ]
     steps:
       - run: git config --global core.autocrlf false

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tiledb
 Type: Package
-Version: 0.28.0.1
+Version: 0.28.0.2
 Title: Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays
 Authors@R: c(person("TileDB, Inc.", role = c("aut", "cph")),
   person("Dirk", "Eddelbuettel", email = "dirk@tiledb.com", role = "cre"))

NEWS.md

@@ -4,6 +4,12 @@
 
 * When creating arrays with `fromDataFrame`, start and/or end timestamps can now be specified (#719)
 
+## Build and Test Systems
+
+* The nighly continuous integration matrix now included Core release 2.24.0 and 2.22.0 is dropped (#721)
+
+* The Conda build is now accomodating the change from #710 (#722)
+
 
 # tiledb 0.28.0
 

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for TileDB-R 0.26.0.
+# Generated by GNU Autoconf 2.71 for TileDB-R 0.28.0.
 #
 #
 # Copyright (C) 1992-1996, 1998-2017, 2020-2021 Free Software Foundation,
@@ -607,8 +607,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='TileDB-R'
 PACKAGE_TARNAME='tiledb-r'
-PACKAGE_VERSION='0.26.0'
-PACKAGE_STRING='TileDB-R 0.26.0'
+PACKAGE_VERSION='0.28.0'
+PACKAGE_STRING='TileDB-R 0.28.0'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -646,6 +646,7 @@ ac_includes_default="\
 ac_header_cxx_list=
 ac_subst_vars='LTLIBOBJS
 LIBOBJS
+DYLIB_EXT
 FILESYSTEM_HEADER_MISSSING
 CXX17_MACOS
 have_git
@@ -1270,7 +1271,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures TileDB-R 0.26.0 to adapt to many kinds of systems.
+\`configure' configures TileDB-R 0.28.0 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1332,7 +1333,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of TileDB-R 0.26.0:";;
+     short | recursive ) echo "Configuration of TileDB-R 0.28.0:";;
    esac
   cat <<\_ACEOF
 
@@ -1425,7 +1426,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-TileDB-R configure 0.26.0
+TileDB-R configure 0.28.0
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -1572,7 +1573,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by TileDB-R $as_me 0.26.0, which was
+It was created by TileDB-R $as_me 0.28.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -2155,6 +2156,8 @@ CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
 CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
 CXX11FLAGS=`"${R_HOME}/bin/R" CMD config CXX11FLAGS`
 CXX17FLAGS=`"${R_HOME}/bin/R" CMD config CXX17FLAGS`
+DYLIB_EXT=`"${R_HOME}/bin/R" CMD config DYLIB_EXT`
+
 ac_ext=cpp
 ac_cpp='$CXXCPP $CPPFLAGS'
 ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -6055,6 +6058,10 @@ printf %s "checking for Darwin use minimum version override... " >&6; }
     CXX17_MACOS="-mmacosx-version-min=11"
     { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: ${CXX17_MACOS}" >&5
 printf "%s\n" "${CXX17_MACOS}" >&6; }
+    ## Obscure but important override: we may have gotten .dylib, but we prefer .so -- unless it is Conda
+    if test x"${CONDA_BUILD}" != x"1"; then
+       DYLIB_EXT=".so"
+    fi
 fi
 
 ## Take care of riscv64 machines and need for -latomic
@@ -6375,6 +6382,8 @@ fi
 
 
 
+
+
 ac_config_files="$ac_config_files src/Makevars"
 
 cat >confcache <<\_ACEOF
@@ -6912,7 +6921,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by TileDB-R $as_me 0.26.0, which was
+This file was extended by TileDB-R $as_me 0.28.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -6967,7 +6976,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-TileDB-R config.status 0.26.0
+TileDB-R config.status 0.28.0
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -24,7 +24,7 @@
 
 ## require at least autoconf 2.69
 AC_PREREQ([2.69])
-AC_INIT([TileDB-R],[0.26.0])
+AC_INIT([TileDB-R],[0.28.0])
 
 ## -- Part 1: Setup -------------------------------------------------------------
 ##
@@ -43,6 +43,8 @@ CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXXFLAGS`
 CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
 CXX11FLAGS=`"${R_HOME}/bin/R" CMD config CXX11FLAGS`
 CXX17FLAGS=`"${R_HOME}/bin/R" CMD config CXX17FLAGS`
+DYLIB_EXT=`"${R_HOME}/bin/R" CMD config DYLIB_EXT`
+
 AC_LANG(C++)
 AC_REQUIRE_CPP
 AC_PROG_CXX
@@ -166,6 +168,10 @@ if test x"${uname}" = x"Darwin"; then
     AC_MSG_CHECKING([for Darwin use minimum version override])
     CXX17_MACOS="-mmacosx-version-min=11"
     AC_MSG_RESULT([${CXX17_MACOS}])
+    ## Obscure but important override: we may have gotten .dylib, but we prefer .so -- unless it is Conda
+    if test x"${CONDA_BUILD}" != x"1"; then
+       DYLIB_EXT=".so"
+    fi
 fi
 
 ## Take care of riscv64 machines and need for -latomic
@@ -286,8 +292,10 @@ if test x"${have_tiledb}" = x"no"; then
 
 fi
 
+
 AC_SUBST([CXX17_MACOS])
 AC_SUBST([FILESYSTEM_HEADER_MISSSING])
+AC_SUBST([DYLIB_EXT])
 
 AC_CONFIG_FILES([src/Makevars])
 AC_OUTPUT

src/Makevars.in

@@ -8,14 +8,14 @@ PKG_CPPFLAGS = -I. -I../inst/include/ @CXX17_MACOS@ @TILEDB_INCLUDE@ @TILEDB_SIL
 PKG_LIBS = @CXX17_MACOS@ @TILEDB_LIBS@ @TILEDB_RPATH@
 
 LIB_CON_DIR = ../inst/lib$(R_ARCH)
-LIB_CON = $(LIB_CON_DIR)/libconnection.so
+LIB_CON = $(LIB_CON_DIR)/libconnection@DYLIB_EXT@
 
 all: $(OBJECTS) $(LIB_CON) $(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
-	@if [ `uname -s` = 'Darwin' ]; then \
+	@if [ `uname -s` = 'Darwin' ] && [ -f ../inst/tiledb/lib/libtiledb.dylib ] && [ -f tiledb.so ]; then \
 	    install_name_tool -change libz.1.dylib @rpath/libz.1.dylib ../inst/tiledb/lib/libtiledb.dylib; \
 	    install_name_tool -add_rpath @loader_path/../tiledb/lib tiledb.so; \
 	    install_name_tool -add_rpath @loader_path/../tiledb/lib $(LIB_CON); \