rainbow: Clean up, eliminate gmake dep

[root <root%centosdev.ceas.uwm.edu@localhost>]

Module Name:	pkgsrc-wip
Committed By:	root <root%centosdev.ceas.uwm.edu@localhost>
Pushed By:	outpaddling
Date:		Thu Mar 22 16:39:36 2018 -0500
Changeset:	4976a510a737e765fb39491545bfa988819b69f2

Modified Files:
	rainbow/Makefile
	rainbow/distinfo
	rainbow/patches/patch-Makefile

Log Message:
rainbow: Clean up, eliminate gmake dep

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=4976a510a737e765fb39491545bfa988819b69f2

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 rainbow/Makefile               |  5 -----
 rainbow/distinfo               |  2 +-
 rainbow/patches/patch-Makefile | 34 +++++++++++++++++++++++++++++++---
 3 files changed, 32 insertions(+), 9 deletions(-)

diffs:
diff --git a/rainbow/Makefile b/rainbow/Makefile
index 6d19035611..a4c1bead59 100644
--- a/rainbow/Makefile
+++ b/rainbow/Makefile
@@ -7,7 +7,6 @@
 DISTNAME=	rainbow_${PORTVERSION}
 PKGNAME=	rainbow-${PORTVERSION}
 CATEGORIES=	biology
-# FreeBSD MASTER_SITES: SF/bio-rainbow
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=bio-rainbow/}
 
 MAINTAINER=	bacon%NetBSD.org@localhost
@@ -15,10 +14,6 @@ HOMEPAGE=	http://sourceforge.net/projects/bio-rainbow/
 COMMENT=	Short reads clustering and local assembly
 LICENSE=	gnu-gpl-v3
 
-# Just assuming C and C++: Adjust this!
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	gmake
-
 PORTVERSION=	2.0.4
 
 INSTALLATION_DIRS=	bin
diff --git a/rainbow/distinfo b/rainbow/distinfo
index 0d503896ff..45df7b8923 100644
--- a/rainbow/distinfo
+++ b/rainbow/distinfo
@@ -4,4 +4,4 @@ SHA1 (rainbow_2.0.4.tar.gz) = c8a8458892873f59136176a3960f337ee7bea376
 RMD160 (rainbow_2.0.4.tar.gz) = bec9fa59563a06fd274b531acd33060b7c5c6a21
 SHA512 (rainbow_2.0.4.tar.gz) = 4308b618cc87811f3fcaabe508304a3df80de3c0c7b667d235db1ed336531517c9764a1af402cfe7dc3339ec903f9fb868d0a7f092c27fa579e74a635694cae9
 Size (rainbow_2.0.4.tar.gz) = 77111 bytes
-SHA1 (patch-Makefile) = a489782c89f2b3eff6e2dbf3a7186ab3ec72dac4
+SHA1 (patch-Makefile) = 0d812a8caf8efc0742046199e3674b1eb30b1275
diff --git a/rainbow/patches/patch-Makefile b/rainbow/patches/patch-Makefile
index 1f4a957fc3..bcc88ca24f 100644
--- a/rainbow/patches/patch-Makefile
+++ b/rainbow/patches/patch-Makefile
@@ -1,9 +1,10 @@
 $NetBSD$
 
-Allow environment to specify CC & CFLAGS.
---- Makefile.orig	2015-07-27 18:28:54 UTC
+# Respect env, eliminate gmake dep
+
+--- Makefile.orig	2015-07-27 18:28:54.000000000 +0000
 +++ Makefile
-@@ -1,5 +1,5 @@
+@@ -1,9 +1,12 @@
 -CC=gcc
 -CFLAGS= -W -O2 -Wall -Wno-self-assign -Wno-unused-function
 +CC?=gcc
@@ -11,3 +12,30 @@ Allow environment to specify CC & CFLAGS.
  DFLAGS= -D_FILE_OFFSET_BITS=64
  GLIBS=-lm
  GENERIC_SRC= string.h bitvec.h file_reader.h hashset.h sort.h list.h dna.h heap.h stdaln.h vector.h
+ 
++RAINBOW_OBJS=	main.o  divide.o file_reader.o asm_R2.o mergectg.o cluster.o
++RBASM_OBJS=	asm_R2.o rbasm_main.o file_reader.o
++
+ .SUFFIXES:.c .o
+ 
+ .c.o:
+@@ -12,14 +15,14 @@ GENERIC_SRC= string.h bitvec.h file_read
+ #all: rainbow rbasm rbmergetag ezmsim 
+ all: rainbow ezmsim rbasm
+ 
+-rainbow: main.o  divide.o file_reader.o asm_R2.o mergectg.o cluster.o
+-	$(CC) $(CFLAGS) -o $@ $^ $(GLIBS) 
++rainbow: $(RAINBOW_OBJS)
++	$(CC) $(CFLAGS) -o $@ $(RAINBOW_OBJS) $(GLIBS) 
+ 
+-rbasm: asm_R2.o rbasm_main.o file_reader.o
+-	$(CC) $(CFLAGS) -o $@ $^ $(GLIBS)
++rbasm: $(RBASM_OBJS)
++	$(CC) $(CFLAGS) -o $@ $(RBASM_OBJS) $(GLIBS)
+ 
+ ezmsim: ezmsim.o
+-	$(CC) $(CFLAGS) -o $@ $^ $(GLIBS)
++	$(CC) $(CFLAGS) -o $@ ezmsim.o $(GLIBS)
+ 
+ asm_R2.o: asm_R2.c asm_R2.h string.h vector.h hashset.h file_reader.h \
+   dna.h