hisat2: Unbreak build on Darwin

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: hisat2: Unbreak build on Darwin
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Thu, 17 Mar 2022 14:01:37 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu Mar 17 09:01:37 2022 -0500
Changeset:	4452e819d7b04166d65d0952346420406326c534

Modified Files:
	hisat2/Makefile
	hisat2/distinfo
	hisat2/patches/patch-Makefile

Log Message:
hisat2: Unbreak build on Darwin

"VERSION" file picked up by #include <version> in xcode headers

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=4452e819d7b04166d65d0952346420406326c534

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

diffstat:
 hisat2/Makefile               |  4 +++
 hisat2/distinfo               |  2 +-
 hisat2/patches/patch-Makefile | 79 ++++++++++++++++++++++++++++++++++++++-----
 3 files changed, 75 insertions(+), 10 deletions(-)

diffs:
diff --git a/hisat2/Makefile b/hisat2/Makefile
index e07dba25ee..b23125be6e 100644
--- a/hisat2/Makefile
+++ b/hisat2/Makefile
@@ -23,6 +23,10 @@ REPLACE_PYTHON=		*.py scripts/*.py hisat2-build hisat2-inspect
 PTHREAD_AUTO_VARS=	yes
 WRKSRC=			${WRKDIR}/hisat2-2.2.1
 
+# Unbreak #include <version> on case-insensitive file systems
+post-patch:
+	${MV} ${WRKSRC}/VERSION ${WRKSRC}/HISAT2_VERSION
+
 .include "../../wip/simde/buildlink3.mk"
 .include "../../lang/python/application.mk"
 .include "../../mk/pthread.buildlink3.mk"
diff --git a/hisat2/distinfo b/hisat2/distinfo
index 0d4944bf69..0f331bc61f 100644
--- a/hisat2/distinfo
+++ b/hisat2/distinfo
@@ -3,7 +3,7 @@ $NetBSD$
 BLAKE2s (hisat2-2.2.1.tar.gz) = 1cc424a10f1fcf25c70294bef3b21e67b07cebcb7b73e36c0176a2dfdec51bdb
 SHA512 (hisat2-2.2.1.tar.gz) = a5a688ad0ccfaf326b3ec6dc97206995306aa6f5b6e58223c2113adbca2745f1e8205b436fdf8e01f42da7a38718f9f3bf214b951fb5360d53247d99a0bdbf46
 Size (hisat2-2.2.1.tar.gz) = 6761242 bytes
-SHA1 (patch-Makefile) = e002806f8daa4e5c45b95b5f173de818a8737b43
+SHA1 (patch-Makefile) = 067b766ecebacd840db4a287bba25d2d2264b339
 SHA1 (patch-aligner__sw.h) = 628c14bfd6b26185eada73013175e35de2b38227
 SHA1 (patch-hisat2) = 6010f5fcc1e7dfcb383a4defc4e3d9f06322370d
 SHA1 (patch-processor__support.h) = 56d9cd4ba18e37879acba521a0f431fe2b4290af
diff --git a/hisat2/patches/patch-Makefile b/hisat2/patches/patch-Makefile
index b3e62f2180..5615e72d99 100644
--- a/hisat2/patches/patch-Makefile
+++ b/hisat2/patches/patch-Makefile
@@ -2,7 +2,7 @@ $NetBSD$
 
 # Respect env
 
---- Makefile.orig	2020-07-24 20:07:54 UTC
+--- Makefile.orig	2020-07-24 20:07:54.000000000 +0000
 +++ Makefile
 @@ -23,9 +23,11 @@
  INC =
@@ -19,7 +19,7 @@ $NetBSD$
  HEADERS = $(wildcard *.h)
  BOWTIE_MM = 1
  BOWTIE_SHARED_MEM = 0
-@@ -55,7 +57,7 @@ ifneq (,$(findstring Darwin,$(shell uname)))
+@@ -55,7 +57,7 @@ ifneq (,$(findstring Darwin,$(shell unam
  	MACOS = 1
  endif
  
@@ -28,10 +28,12 @@ $NetBSD$
  INC += -I. -I third_party 
  
  MM_DEF = 
-@@ -152,31 +154,9 @@ HISAT2_REPEAT_CPPS_MAIN = $(REPEAT_CPPS) $(BUILD_CPPS)
- SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
- VERSION = $(shell cat VERSION)
+@@ -150,33 +152,11 @@ HISAT2_BUILD_CPPS_MAIN = $(BUILD_CPPS) h
+ HISAT2_REPEAT_CPPS_MAIN = $(REPEAT_CPPS) $(BUILD_CPPS) hisat2_repeat_main.cpp
  
+ SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c)
+-VERSION = $(shell cat VERSION)
+-
 -# Convert BITS=?? to a -m flag
 -BITS=32
 -ifeq (x86_64,$(shell uname -m))
@@ -53,7 +55,8 @@ $NetBSD$
 -	BITS_FLAG = -m64
 -endif
 -SSE_FLAG=-msse2
--
++HISAT2_VERSION = $(shell cat HISAT2_VERSION)
+ 
  DEBUG_FLAGS    = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
  DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
 -RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
@@ -61,11 +64,68 @@ $NetBSD$
  RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
  NOASSERT_FLAGS = -DNDEBUG
  FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
-@@ -553,6 +533,20 @@ doc/manual.inc.html: MANUAL.markdown
+@@ -251,7 +231,7 @@ GENERAL_LIST = $(wildcard scripts/*.sh) 
+ 	MANUAL \
+ 	MANUAL.markdown \
+ 	TUTORIAL \
+-	VERSION
++	HISAT2_VERSION
+ 
+ ifeq (1,$(WINDOWS))
+ 	HISAT2_BIN_LIST := $(HISAT2_BIN_LIST) hisat2.bat hisat2-build.bat hisat2-inspect.bat 
+@@ -287,7 +267,7 @@ repeat: hisat2-repeat
+ repeat-debug: hisat2-repeat-debug
  
+ DEFS=-fno-strict-aliasing \
+-     -DHISAT2_VERSION="\"`cat VERSION`\"" \
++     -DHISAT2_VERSION="\"`cat HISAT2_VERSION`\"" \
+      -DBUILD_HOST="\"`hostname`\"" \
+      -DBUILD_TIME="\"`date`\"" \
+      -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
+@@ -517,12 +497,12 @@ hisat2-inspect.bat:
+ hisat2-src: $(SRC_PKG_LIST)
+ 	chmod a+x scripts/*.sh scripts/*.pl
+ 	mkdir .src.tmp
+-	mkdir .src.tmp/hisat2-$(VERSION)
++	mkdir .src.tmp/hisat2-$(HISAT2_VERSION)
+ 	zip tmp.zip $(SRC_PKG_LIST)
+-	mv tmp.zip .src.tmp/hisat2-$(VERSION)
+-	cd .src.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
+-	cd .src.tmp ; zip -r hisat2-$(VERSION)-source.zip hisat2-$(VERSION)
+-	cp .src.tmp/hisat2-$(VERSION)-source.zip .
++	mv tmp.zip .src.tmp/hisat2-$(HISAT2_VERSION)
++	cd .src.tmp/hisat2-$(HISAT2_VERSION) ; unzip tmp.zip ; rm -f tmp.zip
++	cd .src.tmp ; zip -r hisat2-$(HISAT2_VERSION)-source.zip hisat2-$(HISAT2_VERSION)
++	cp .src.tmp/hisat2-$(HISAT2_VERSION)-source.zip .
+ 	rm -rf .src.tmp
+ 
+ .PHONY: hisat2-bin
+@@ -530,16 +510,16 @@ hisat2-bin: $(BIN_PKG_LIST) $(HISAT2_BIN
+ 	chmod a+x scripts/*.sh scripts/*.pl
+ 	rm -rf .bin.tmp
+ 	mkdir .bin.tmp
+-	mkdir .bin.tmp/hisat2-$(VERSION)
++	mkdir .bin.tmp/hisat2-$(HISAT2_VERSION)
+ 	if [ -f hisat2.exe ] ; then \
+ 		zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)) ; \
+ 	else \
+ 		zip tmp.zip $(BIN_PKG_LIST) $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) ; \
+ 	fi
+-	mv tmp.zip .bin.tmp/hisat2-$(VERSION)
+-	cd .bin.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip
+-	cd .bin.tmp ; zip -r hisat2-$(VERSION)-$(BITS).zip hisat2-$(VERSION)
+-	cp .bin.tmp/hisat2-$(VERSION)-$(BITS).zip .
++	mv tmp.zip .bin.tmp/hisat2-$(HISAT2_VERSION)
++	cd .bin.tmp/hisat2-$(HISAT2_VERSION) ; unzip tmp.zip ; rm -f tmp.zip
++	cd .bin.tmp ; zip -r hisat2-$(HISAT2_VERSION)-$(BITS).zip hisat2-$(HISAT2_VERSION)
++	cp .bin.tmp/hisat2-$(HISAT2_VERSION)-$(BITS).zip .
+ 	rm -rf .bin.tmp
+ 
+ .PHONY: doc
+@@ -554,6 +534,20 @@ doc/manual.inc.html: MANUAL.markdown
  MANUAL: MANUAL.markdown
  	perl doc/strip_markdown.pl < $^ > $@
-+
+ 
 +# Install per filesystem hierarchy standard:
 +# https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard
 +
@@ -79,6 +139,7 @@ $NetBSD$
 +	mkdir -p ${DESTDIR}${PREFIX}/libexec/hisat2
 +	${INSTALL} -c scripts/*.sh scripts/*.pl scripts/*.py *.py \
 +		${DESTDIR}${PREFIX}/libexec/hisat2
- 
++
  .PHONY: clean
  clean:
+ 	rm -f $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) \
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