Bug#1017684: tiledb-r: ftbfs on riscv64("undefined symbol: __atomic_compare_exchange_1")

[Bo YU]

Hi,
On Sun, Aug 21, 2022 at 09:41:39AM -0500, Dirk Eddelbuettel wrote:

| Oh, yes, It is applied to debian/rules and I forget to mention it.:)

No worries :)   Do you have easy-enough access to the platform?  Could you
test this diff (and then also run 'autoconf' to regenerate 'configure'; else
I can send you a longer diff including it).  And of course remove what we had
added to src/Makevars.in 'by hand'.


| modified   configure.ac
@@ -153,6 +153,13 @@ if test x"${uname}" = x"Darwin" -a x"${machine}" = 
x"x86_64"; then
    AC_MSG_RESULT([${CXX17_MACOS}])
fi

+## Take care of riscv64 machines and need for -latomic
+if test x"${uname}" = x"riscv64"; then
+    AC_MSG_CHECKING([for riscv64 linker adjustment])
+    CXX17_MACOS="-mmacosx-version-min=10.14"
+    TILEDB_LIBS="${TILEDB_LIBS} -latomic"
+    AC_MSG_RESULT([${TILEDB_LIBS}])
+fi

It works except with word modifications:

--- a/configure.ac
+++ b/configure.ac
@@ -153,6 +153,14 @@
     AC_MSG_RESULT([${CXX17_MACOS}])
 fi

+## Take care of riscv64 machines and need for -latomic
+if test x"${machine}" = x"riscv64"; then
+    AC_MSG_CHECKING([for riscv64 linker adjustment])
+    #CXX17_MACOS="-mmacosx-version-min=10.14"
+    TILEDB_LIBS="${TILEDB_LIBS} -latomic"
+    AC_MSG_RESULT([${TILEDB_LIBS}])
+fi
+

And I tested it on real riscv64 hardware successfully.

here:


CXX17_MACOS should be redundant and can be safely deleted:
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-z,relro -o tiledb.so 
RcppExports.o arrowio.o batched.o deprecation.o durations.o libtiledb.o 
nullable.o shmem.o utilities.o -mmacosx-version-min=10.14 -ltiledb -latomic 
-L/usr/lib/R/lib -lR
g++: error: unrecognized command-line option ‘-mmacosx-version-min=10.14’
make[2]: *** [/usr/share/R/share/make/shlib.mk:10: tiledb.so] Error 1


--
Regards,
--
  Bo YU


--- a/configure.ac
+++ b/configure.ac
@@ -153,6 +153,14 @@
     AC_MSG_RESULT([${CXX17_MACOS}])
 fi
 
+## Take care of riscv64 machines and need for -latomic
+if test x"${machine}" = x"riscv64"; then
+    AC_MSG_CHECKING([for riscv64 linker adjustment])
+    #CXX17_MACOS="-mmacosx-version-min=10.14"
+    TILEDB_LIBS="${TILEDB_LIBS} -latomic"
+    AC_MSG_RESULT([${TILEDB_LIBS}])
+fi
+
 
 ## -- Part 3: Check for TileDB --------------------------------------------------
 ##

uname == linux

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