Migrate zlib to zlib-ng

Author: brainstorm

recipes/bwa-mem2/meta.yaml

@@ -11,9 +11,10 @@ source:
       - Makefile.patch # [ not aarch64 and not arm64 ]
       - safestr-makefile.patch  # [ not aarch64 and not arm64 ] 
       - sse2neon.patch # [ aarch64 or arm64 ]
+      - zlib_to_zlib-ng.patch
 
 build:
-  number: 8
+  number: 11
   run_exports:
     - {{ pin_subpackage("bwa-mem2", max_pin="x") }}
 
@@ -25,7 +26,7 @@ requirements:
     - {{ compiler('cxx') }}
     - git
   host:
-    - zlib
+    - zlib-ng
 
 test:
   commands:

recipes/bwa-mem2/zlib_to_zlib-ng.patch

@@ -0,0 +1,126 @@
+diff --git a/src/bntseq.cpp b/src/bntseq.cpp
+index 13aceb4..b1dca18 100644
+--- a/src/bntseq.cpp
++++ b/src/bntseq.cpp
+@@ -31,7 +31,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <string.h>
+-#include <zlib.h>
++#include <zlib-ng.h>
+ #include <unistd.h>
+ #include <errno.h>
+ #include <limits.h>
+diff --git a/src/bntseq.h b/src/bntseq.h
+index b241a3a..a50fcb2 100644
+--- a/src/bntseq.h
++++ b/src/bntseq.h
+@@ -31,7 +31,7 @@
+ #include <assert.h>
+ #include <stdint.h>
+ #include <stdio.h>
+-#include <zlib.h>
++#include <zlib-ng.h>
+ 
+ #ifndef BWA_UBYTE
+ #define BWA_UBYTE
+diff --git a/src/bwa.cpp b/src/bwa.cpp
+index b764381..260fabb 100644
+--- a/src/bwa.cpp
++++ b/src/bwa.cpp
+@@ -30,7 +30,7 @@ Authors: Vasimuddin Md <[email protected]>; Sanchit Misra <sanchit.misra@i
+ 
+ #include <string.h>
+ #include <stdio.h>
+-#include <zlib.h>
++#include <zlib-ng.h>
+ #include <assert.h>
+ #include "bntseq.h"
+ #include "bwa.h"
+diff --git a/src/bwa.h b/src/bwa.h
+index 877f00c..97b2220 100644
+--- a/src/bwa.h
++++ b/src/bwa.h
+@@ -32,7 +32,7 @@ Authors: Vasimuddin Md <[email protected]>; Sanchit Misra <sanchit.misra@i
+ #define BWA_H_
+ 
+ #include <stdint.h>
+-#include <zlib.h>
++#include <zlib-ng.h>
+ #include "bntseq.h"
+ #include "bwt.h"
+ #include "macro.h"
+diff --git a/src/bwtindex.cpp b/src/bwtindex.cpp
+index 4a48b20..8d94050 100644
+--- a/src/bwtindex.cpp
++++ b/src/bwtindex.cpp
+@@ -33,7 +33,7 @@
+ #include <string.h>
+ #include <unistd.h>
+ #include <time.h>
+-#include <zlib.h>
++#include <zlib-ng.h>
+ #include "bntseq.h"
+ #include "bwa.h"
+ #include "bwt.h"
+diff --git a/src/fastmap.h b/src/fastmap.h
+index e94022f..c1ee9d5 100644
+--- a/src/fastmap.h
++++ b/src/fastmap.h
+@@ -32,7 +32,7 @@ Authors: Vasimuddin Md <[email protected]>; Sanchit Misra <sanchit.misra@i
+ #define FASTMAP_HPP
+ 
+ #include <ctype.h>
+-#include <zlib.h>
++#include <zlib-ng.h>
+ #include <stdio.h>
+ #include <unistd.h>
+ #include <stdlib.h>
+diff --git a/src/ksw.cpp b/src/ksw.cpp
+index 4b93b8a..03397bd 100644
+--- a/src/ksw.cpp
++++ b/src/ksw.cpp
+@@ -684,7 +684,7 @@ int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
+ 
+ #include <unistd.h>
+ #include <stdio.h>
+-#include <zlib.h>
++#include <zlib-ng.h>
+ #include "kseq.h"
+ KSEQ_INIT(gzFile, err_gzread)
+ 
+diff --git a/src/utils.cpp b/src/utils.cpp
+index d90d4f7..54c2940 100644
+--- a/src/utils.cpp
++++ b/src/utils.cpp
+@@ -30,7 +30,7 @@
+ #include <stdarg.h>
+ #include <stdlib.h>
+ #include <string.h>
+-#include <zlib.h>
++#include <zlib-ng.h>
+ #include <errno.h>
+ #ifdef FSYNC_ON_FLUSH
+ #include <sys/types.h>
+@@ -77,7 +77,7 @@ gzFile err_xzopen_core(const char *func, const char *fn, const char *mode)
+ 	gzFile fp;
+ 	if (strcmp(fn, "-") == 0) {
+ 		fp = gzdopen(fileno((strstr(mode, "r"))? stdin : stdout), mode);
+-		/* According to zlib.h, this is the only reason gzdopen can fail */
++		/* According to zlib-ng.h, this is the only reason gzdopen can fail */
+ 		if (!fp) err_fatal(func, "Out of memory");
+ 		return fp;
+ 	}
+diff --git a/src/utils.h b/src/utils.h
+index d26209d..55049d5 100644
+--- a/src/utils.h
++++ b/src/utils.h
+@@ -30,7 +30,7 @@
+ 
+ #include <stdint.h>
+ #include <stdio.h>
+-#include <zlib.h>
++#include <zlib-ng.h>
+ 
+ #ifdef __GNUC__
+ // Tell GCC to validate printf format string and args