Patch htslib 1.10 to fix build with autoconf 2.70+

details in: samtools/htslib#1198

Author: ihnorton

libtiledbvcf/cmake/Modules/FindHTSlib_EP.cmake

@@ -89,6 +89,8 @@ if (NOT HTSLIB_FOUND)
         $(MAKE)
       INSTALL_COMMAND
         $(MAKE) install
+      PATCH_COMMAND
+        patch -N -p1 < ${CMAKE_CURRENT_SOURCE_DIR}/cmake/patches/htslib-1.10-config.patch
       BUILD_IN_SOURCE TRUE
       LOG_DOWNLOAD TRUE
       LOG_CONFIGURE TRUE
@@ -114,4 +116,4 @@ endif()
 if (EP_HTSLIB_BUILT AND TARGET HTSlib::HTSlib)
   include(TileDBCommon)
   install_target_libs(HTSlib::HTSlib)
-endif()
+endif()

libtiledbvcf/cmake/patches/htslib-1.10-config.patch

@@ -0,0 +1,31 @@
+From 6821fc8ed88706e9282b561e74dfa45dac4d74c8 Mon Sep 17 00:00:00 2001
+From: John Marshall <[email protected]>
+Date: Fri, 1 Jan 2021 10:37:22 +0000
+Subject: [PATCH] Don't set $host_alias as that confuses autoconf 2.70
+
+Autoconf 2.70 is more careful about cross compilation, so with this
+version using AC_FUNC_MMAP implies AC_CANONICAL_HOST and hence computes
+$build/build_alias/host/host_alias/etc. Setting $host_alias ourselves
+interferes with that. Hat tip Matthias Klose (via debbug#978835).
+
+As autoconf 2.70 implicitly uses AC_CANONICAL_HOST, it requires (and its
+autoreconf --install installs) config.guess and config.sub. Ignore those,
+and ignore install-sh as well for good measure.
+---
+diff --git a/configure.ac b/configure.ac
+index 9bd1642d7..f473c97e5 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -137,9 +137,9 @@ AC_ARG_ENABLE([s3],
+                   [support Amazon AWS S3 URLs])],
+   [], [enable_s3=check])
+ 
+-test -n "$host_alias" || host_alias=unknown-`uname -s`
+-AC_MSG_CHECKING([shared library type for $host_alias])
+-case $host_alias in
++basic_host=${host_alias:-unknown-`uname -s`}
++AC_MSG_CHECKING([shared library type for $basic_host])
++case $basic_host in
+   *-cygwin* | *-CYGWIN*)
+     host_result="Cygwin DLL"
+     PLATFORM=CYGWIN