CVS commit: pkgsrc/biology/minimap2

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

Module Name:    pkgsrc
Committed By:   nia
Date:           Sun Jul  9 08:37:39 UTC 2023

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

Log Message:
minimap2: Honour CFLAGS/LDFLAGS. Hopefully fixes build on platforms
where zlib is installed from pkgsrc.


To generate a diff of this commit:
cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/minimap2/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/minimap2/patches/patch-Makefile

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/distinfo
diff -u pkgsrc/biology/minimap2/distinfo:1.4 pkgsrc/biology/minimap2/distinfo:1.5
--- pkgsrc/biology/minimap2/distinfo:1.4        Sun Mar 13 08:05:07 2022
+++ pkgsrc/biology/minimap2/distinfo    Sun Jul  9 08:37:39 2023
@@ -1,5 +1,6 @@
-$NetBSD: distinfo,v 1.4 2022/03/13 08:05:07 mef Exp $
+$NetBSD: distinfo,v 1.5 2023/07/09 08:37:39 nia Exp $
 
 BLAKE2s (minimap2-2.24.tar.gz) = fad5bbbfd6563f32ffe046528758eca23b071386847b1a93d3388f5be205de5b
 SHA512 (minimap2-2.24.tar.gz) = f53a28ce5cd8624fbc5e964dc58edfa27ecea5f253cd49cb7b57396a40810b673392ebf323f0fb5d3b6ef82d4a9a96b025581aee10246e3c8d59e954819876e7
 Size (minimap2-2.24.tar.gz) = 253050 bytes
+SHA1 (patch-Makefile) = ae4be7748e5ec1e8ed1ff235be5ac6eeeeb0d3b3

Added files:

Index: pkgsrc/biology/minimap2/patches/patch-Makefile
diff -u /dev/null pkgsrc/biology/minimap2/patches/patch-Makefile:1.1
--- /dev/null   Sun Jul  9 08:37:39 2023
+++ pkgsrc/biology/minimap2/patches/patch-Makefile      Sun Jul  9 08:37:39 2023
@@ -0,0 +1,26 @@
+$NetBSD: patch-Makefile,v 1.1 2023/07/09 08:37:39 nia Exp $
+
+Honour CFLAGS/LDFLAGS. Hopefully fixes building on platforms where zlib
+is installed from pkgsrc.
+
+--- Makefile.orig      2021-12-26 20:14:54.000000000 +0000
++++ Makefile
+@@ -1,4 +1,4 @@
+-CFLAGS=               -g -Wall -O2 -Wc++-compat #-Wextra
++CFLAGS+=      -Wall -Wc++-compat #-Wextra
+ CPPFLAGS=     -DHAVE_KALLOC
+ INCLUDES=
+ OBJS=         kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o \
+@@ -45,10 +45,10 @@ 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)