revert to previous meryl version

ext/meryl/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "src/utility"]
+	path = src/utility
+	url = https://github.com/marbl/meryl-utility

ext/meryl/scripts/version_update.pl

@@ -39,7 +39,7 @@
 
 my $label    = "snapshot";      #  If not 'release' print this in the version output.
 my $major    = "1";             #  Bump before release.
-my $minor    = "2";             #  Bump before release.
+my $minor    = "0";             #  Bump before release.
 
 my $branch   = "master";
 my $version  = "v$major.$minor";
@@ -87,12 +87,7 @@
 
             $version = "v$major.$minor";
         } else {
-            $major   = "0";
-            $minor   = "0";
-            $commits = "0";
-            $hash1   = $_;
-
-            $version = "v$major.$minor";
+            die "Failed to parse describe string '$_'.\n";
         }
     }
     close(F);
@@ -168,12 +163,14 @@
 #  Report what we found.  This is really for the gmake output.
 
 if (defined($commits)) {
-    print "\$(info Building $label $version +$commits changes (r$revCount $hash1) ($dirty))\n";
+    print STDERR "Building $label $version +$commits changes (r$revCount $hash1) ($dirty)\n";
     foreach my $s (@submodules) {
-        print "\$(info \$(space)         $s)\n";
+        print STDERR "         $s\n";
     }
+    print STDERR "\n";
 } else {
-    print "\$(info Building $label $version)\n";
+    print STDERR "Building $label $version\n";
+    print STDERR "\n";
 }
 
 #  Dump a new file, but don't overwrite the original.

ext/meryl/src/Makefile

@@ -27,14 +27,7 @@
 #       instances of "$" within them need to be escaped with a second "$" to
 #       accomodate the double expansion that occurs when eval is invoked.
 
-#  Before doing ANYTHING, initialize submodules...if the version of
-#  git is compatible.
-gitv := $(shell git --version | cut -d\  -f 3 | cut -c 1)
-ifeq (1, $(gitv))
-  gitv := $(shell git --version | cut -d\  -f 3)
-  $(error git '$(shell which git)' version '$(gitv)' too old; at least version 2.12 is required)
-endif
-
+#  Before doing ANYTHING, initialize submodules.
 ifeq ($(wildcard utility/src/Makefile), )
   $(info $(shell git submodule update --init utility))
   $(info $(space))
@@ -350,9 +343,8 @@ DIR_STACK :=
 INCDIRS :=
 TGT_STACK :=
 
-# Discover our OS and architecture.  These were previously used to set
-# BUILD_DIR and TARGET_DIR to allow multi-platform builds.  DESTDIR will do
-# that for us too.
+# Discover our OS and architecture.  These are used to set the BUILD_DIR and TARGET_DIR to
+# something more useful than 'build' and '.'.
 
 OSTYPE      := $(shell echo `uname`)
 OSVERSION   := $(shell echo `uname -r`)
@@ -377,18 +369,6 @@ ifeq (${OSTYPE}, SunOS)
   endif
 endif
 
-#  Set paths for building and installing.  If DESTDIR doesn't exist, use the
-#  directory just above us.
-
-ifeq "$(strip ${DESTDIR})" ""
-  BUILD_DIR    := $(realpath ..)/build/obj
-  TARGET_DIR   := $(realpath ..)/build
-else
-  BUILD_DIR    := $(DESTDIR)/canu/build/obj
-  TARGET_DIR   := $(DESTDIR)/canu/build
-endif
-
-#
 #  Set compiler and flags based on discovered hardware
 #
 #  By default, debug symbols are included in all builds (even optimized).
@@ -405,6 +385,7 @@ endif
 #  BUILDJEMALLOC will enable jemalloc library support.
 #
 
+
 ifeq ($(origin CXXFLAGS), undefined)
   ifeq ($(BUILDOPTIMIZED), 1)
   else
@@ -456,27 +437,44 @@ endif
 #  So, we require gcc7 (from MacPorts) or gcc8 (from hommebrew).
 #
 #  If from MacPorts:
-#    port install gcc9
-#    port select gcc mp-gcc9
+#    port install gcc7
+#    port select gcc mp-gcc7
 #
 #  If CC is set to 'cc', the GNU make default, we'll automagically search for other
-#  versions and use those if found.
+#  versions and use those if found, preferring gcc7 over gcc8.
 #
+#  There' definitely a clever way to do this with 'foreach', but my Make is lacking.
+#
+ifeq (${OSTYPE}, Darwin)
+  ifeq ($(CC), cc)
+    CC7    := $(shell echo `which gcc-mp-7`)
+    CXX7   := $(shell echo `which g++-mp-7`)
 
-define TEST_COMPILER
-  ifeq ($${CC}, cc)
-    CCTEST  := $$(shell echo `which gcc-${1}`)
-    CXXTEST := $$(shell echo `which g++-${1}`)
+    ifdef CXX7
+      CC  := $(CC7)
+      CXX := $(CXX7)
+    endif
+  endif
+
+  ifeq ($(CC), cc)
+    CC8    := $(shell echo `which gcc-7`)
+	  CXX8   := $(shell echo `which g++-7`)
 
-    ifdef CXXTEST
-      CC  := $${CCTEST}
-      CXX := $${CXXTEST}
+    ifdef CXX8
+      CC  := $(CC8)
+      CXX := $(CXX8)
     endif
   endif
-endef
 
-ifeq (${OSTYPE}, Darwin)
-  $(foreach suffix,mp-9 9  mp-8 8  mp-7 7,$(eval $(call TEST_COMPILER,${suffix})))
+  ifeq ($(CC), cc)
+    CC8    := $(shell echo `which gcc-8`)
+	  CXX8   := $(shell echo `which g++-8`)
+
+    ifdef CXX8
+      CC  := $(CC8)
+      CXX := $(CXX8)
+    endif
+  endif
 
   ifneq ($(shell echo `$(CXX) --version 2>&1 | grep -c clang`), 0)
      CPATH := $(shell echo `which $(CXX)`)
@@ -516,12 +514,9 @@ ifeq (${CANU_BUILD_ENV}, ports)
 
 else
 
-  # Ignore the gmake default 'c++' and force g++9.
-	ifeq ($(origin CXX), default)
-    CC    = gcc9
-    CXX   = g++9
-    CCLIB = -rpath /usr/local/lib/gcc9
-  endif
+  CC       ?= gcc6
+  CXX      ?= g++6
+  CCLIB    ?= -rpath /usr/local/lib/gcc6
 
   #  GCC
   CXXFLAGS  += -I/usr/local/include -pthread -fopenmp -fPIC
@@ -688,11 +683,11 @@ $(foreach TGT,${ALL_TGTS},\
 #  Makefile processed.  Regenerate the version number file, make some
 #  directories, and report that we're starting the build.
 
-$(eval $(shell ../scripts/version_update.pl meryl utility/src/utility/version.H))
+$(shell ../scripts/version_update.pl meryl utility/src/utility/version.H)
 
 $(shell mkdir -p ${TARGET_DIR}/bin)
 
-$(info For '${OSTYPE}' '${OSVERSION}' as '${MACHINETYPE}' into '${TARGET_DIR}/{bin,obj}'.)
+$(info For '${OSTYPE}' '${OSVERSION}' as '${MACHINETYPE}' into '${DESTDIR}${PREFIX}/$(OSTYPE)-$(MACHINETYPE)/{bin,obj}'.)
 $(info Using '$(shell which ${CXX})' version '${GXX_VV}'.)
 ifneq ($(origin CXXFLAGSUSER), undefined)
 $(info Using user-supplied CXXFLAGS '${CXXFLAGSUSER}'.)

ext/meryl/src/main.mk

@@ -1,5 +1,29 @@
-MODULE       :=    meryl
+
+#  If 'make' isn't run from the root directory, we need to set these to
+#  point to the upper level build directory.
+
+ifeq "$(strip ${DESTDIR})" ""
+  DESTDIR      :=
+endif
+
+ifeq "$(strip ${PREFIX})" ""
+  ifeq "$(strip ${DESTDIR})" ""
+    PREFIX     := $(realpath ..)
+  else
+    PREFIX     := /meryl
+  endif
+endif
+
+ifeq "$(strip ${BUILD_DIR})" ""
+  BUILD_DIR    := $(DESTDIR)$(PREFIX)/$(OSTYPE)-$(MACHINETYPE)/obj
+endif
+
+ifeq "$(strip ${TARGET_DIR})" ""
+  TARGET_DIR   := $(DESTDIR)$(PREFIX)/$(OSTYPE)-$(MACHINETYPE)
+endif
+
 TARGET       := libmeryl.a
+
 SOURCES      := utility/src/utility/edlib.C \
                 \
                 utility/src/utility/files.C \
@@ -28,11 +52,11 @@ SOURCES      := utility/src/utility/edlib.C \
                 utility/src/utility/kmers.C \
                 \
                 utility/src/utility/bits.C \
-                utility/src/utility/bits-wordArray.C \
                 \
                 utility/src/utility/hexDump.C \
                 utility/src/utility/md5.C \
                 utility/src/utility/mt19937ar.C \
+                utility/src/utility/objectStore.C \
                 utility/src/utility/speedCounter.C \
                 utility/src/utility/sweatShop.C \
                 \
@@ -59,12 +83,11 @@ SRC_INCDIRS  := . \
                 utility
 
 SUBMAKEFILES := meryl/meryl.mk \
-                meryl-analyze/meryl-analyze.mk \
                 meryl-simple/meryl-simple.mk \
                 meryl-import/meryl-import.mk \
-                meryl-lookup/meryl-lookup.mk
+                meryl-lookup/meryl-lookup.mk \
+                meryl-check/meryl-check.mk
 
 ifeq ($(BUILDTESTS), 1)
-SUBMAKEFILES += tests/merylCountArrayTest.mk \
-                tests/merylExactLookupTest.mk
+SUBMAKEFILES += tests/merylCountArrayTest.mk
 endif