CVS commit: pkgsrc/biology/minimap2

["Nia Alarie" <nia%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   nia
Date:           Sat May 18 00:27:16 UTC 2024

Modified Files:
        pkgsrc/biology/minimap2: Makefile distinfo
        pkgsrc/biology/minimap2/patches: patch-Makefile.simde

Log Message:
minimap2: Honour LDFLAGS when linking


To generate a diff of this commit:
cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/minimap2/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/biology/minimap2/distinfo
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/minimap2/patches/patch-Makefile.simde

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

Modified files:

Index: pkgsrc/biology/minimap2/Makefile
diff -u pkgsrc/biology/minimap2/Makefile:1.6 pkgsrc/biology/minimap2/Makefile:1.7
--- pkgsrc/biology/minimap2/Makefile:1.6        Wed Apr 10 12:36:12 2024
+++ pkgsrc/biology/minimap2/Makefile    Sat May 18 00:27:16 2024
@@ -1,7 +1,8 @@
-# $NetBSD: Makefile,v 1.6 2024/04/10 12:36:12 bacon Exp $
+# $NetBSD: Makefile,v 1.7 2024/05/18 00:27:16 nia Exp $
 
 VERSION=       2.28
 DISTNAME=      minimap2-${VERSION}
+PKGREVISION=   1
 CATEGORIES=    biology python
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=lh3/}
 GITHUB_TAG=    v${VERSION}

Index: pkgsrc/biology/minimap2/distinfo
diff -u pkgsrc/biology/minimap2/distinfo:1.7 pkgsrc/biology/minimap2/distinfo:1.8
--- pkgsrc/biology/minimap2/distinfo:1.7        Wed Apr 10 12:36:12 2024
+++ pkgsrc/biology/minimap2/distinfo    Sat May 18 00:27:16 2024
@@ -1,7 +1,7 @@
-$NetBSD: distinfo,v 1.7 2024/04/10 12:36:12 bacon Exp $
+$NetBSD: distinfo,v 1.8 2024/05/18 00:27:16 nia Exp $
 
 BLAKE2s (minimap2-2.28.tar.gz) = 0a0afd89e588dd0d8a93a562264bb5fdfe50f88a18f5f057bf59be51e16bbe0b
 SHA512 (minimap2-2.28.tar.gz) = d8d4bb4381d6effb3eb3e1a66fac7a83bc00c3cf174d2e0537dd4790d0e4a3cc060b92e39ed2e2cafc6e5e713f6fdbee6bac1d279b6b77d4347f77f3e6d3c0d0
 Size (minimap2-2.28.tar.gz) = 260341 bytes
-SHA1 (patch-Makefile.simde) = 850a66c8843119f99bcd4a2b261cfd4bffa38551
+SHA1 (patch-Makefile.simde) = 10dc0a8a511c203611fb2fe65d4f73b17c6ebce6
 SHA1 (patch-example.c) = ccf0c4addfece2e11b90f5a558a6de324f255d7c

Index: pkgsrc/biology/minimap2/patches/patch-Makefile.simde
diff -u pkgsrc/biology/minimap2/patches/patch-Makefile.simde:1.2 pkgsrc/biology/minimap2/patches/patch-Makefile.simde:1.3
--- pkgsrc/biology/minimap2/patches/patch-Makefile.simde:1.2    Wed Apr 10 12:36:12 2024
+++ pkgsrc/biology/minimap2/patches/patch-Makefile.simde        Sat May 18 00:27:16 2024
@@ -1,10 +1,10 @@
-$NetBSD: patch-Makefile.simde,v 1.2 2024/04/10 12:36:12 bacon Exp $
+$NetBSD: patch-Makefile.simde,v 1.3 2024/05/18 00:27:16 nia Exp $
 
 # Respect standard env vars
 
---- Makefile.simde.orig        2021-11-18 22:11:48 UTC
+--- Makefile.simde.orig        2024-03-27 14:57:17.000000000 +0000
 +++ Makefile.simde
-@@ -1,13 +1,26 @@
+@@ -1,12 +1,25 @@
 -CFLAGS=               -g -Wall -O2 -Wc++-compat #-Wextra
 -CPPFLAGS=     -DHAVE_KALLOC -DUSE_SIMDE -DSIMDE_ENABLE_NATIVE_ALIASES
 -INCLUDES=     -Ilib/simde
@@ -27,15 +27,14 @@ $NetBSD: patch-Makefile.simde,v 1.2 2024
 +PREFIX?=      /usr/local
 +MAN1DIR?=     ${PREFIX}/man/man1
 +DATADIR?=     ${PREFIX}/share/minimap2
- 
++
 +MKDIR?=               mkdir
 +CP?=          cp      
 +INSTALL?=     install
 +STRIP?=               strip
-+
+ 
  ifneq ($(arm_neon),) # if arm_neon is defined
  ifeq ($(aarch64),)   #if aarch64 is not defined
-       CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char
 @@ -26,7 +39,7 @@ ifneq ($(tsan),)
        LIBS+=-fsanitize=thread
  endif
@@ -45,11 +44,23 @@ $NetBSD: patch-Makefile.simde,v 1.2 2024
  .SUFFIXES:.c .o
  
  .c.o:
-@@ -61,6 +74,22 @@ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2.h kalloc.h
-               $(CC) -c $(CFLAGS) -msse4.1 $(CPPFLAGS) $(INCLUDES) $< -o $@
+@@ -37,10 +50,10 @@ all:$(PROG)
+ extra:all $(PROG_EXTRA)
+ 
+ minimap2:main.o libminimap2.a
+-              $(CC) $(CFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
++              $(CC) $(LDFLAGS) main.o -o $@ -L. -lminimap2 $(LIBS)
+ 
+ minimap2-lite:example.o libminimap2.a
+-              $(CC) $(CFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
++              $(CC) $(LDFLAGS) $< -o $@ -L. -lminimap2 $(LIBS)
+ 
+ libminimap2.a:$(OBJS)
+               $(AR) -csru $@ $(OBJS)
+@@ -62,6 +75,22 @@ ksw2_exts2_simde.o:ksw2_exts2_sse.c ksw2
  
  # other non-file targets
-+
+ 
 +
 +install: all
 +      ${MKDIR} -p ${DESTDIR}${PREFIX}/bin
@@ -65,6 +76,7 @@ $NetBSD: patch-Makefile.simde,v 1.2 2024
 +      ${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2
 +      ${STRIP} ${DESTDIR}${PREFIX}/bin/minimap2-lite
 +      ${STRIP} ${DESTDIR}${PREFIX}/bin/sdust
- 
++
  clean:
                rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg*
+