subread: Patch for Darwin

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: subread: Patch for Darwin
From: Jason Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>
Date: Mon, 20 Jan 2025 17:10:32 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Mon Jan 20 11:10:12 2025 -0600
Changeset:	317ffc25f0a6e78b656cc43e246aa4a3e96bf7c2

Modified Files:
	subread/distinfo
	subread/patches/patch-HelperFunctions.c
	subread/patches/patch-gene-algorithms.c
	subread/patches/patch-input-files.c
	subread/patches/patch-long-hashtable.c

Log Message:
subread: Patch for Darwin

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=317ffc25f0a6e78b656cc43e246aa4a3e96bf7c2

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

diffstat:
 subread/distinfo                        |  8 +++----
 subread/patches/patch-HelperFunctions.c | 41 +++++++++++++++++++++++++++++----
 subread/patches/patch-gene-algorithms.c | 40 ++++++++++++++++++++++++++++++--
 subread/patches/patch-input-files.c     |  8 +++----
 subread/patches/patch-long-hashtable.c  |  8 ++++---
 5 files changed, 88 insertions(+), 17 deletions(-)

diffs:
diff --git a/subread/distinfo b/subread/distinfo
index 5fd8e09618..48c75089c8 100644
--- a/subread/distinfo
+++ b/subread/distinfo
@@ -3,11 +3,11 @@ $NetBSD$
 BLAKE2s (subread-2.0.8-source.tar.gz) = ddf9b8e627210aa133e019496deb90fdba8a387585ca9403fa630192f44211ee
 SHA512 (subread-2.0.8-source.tar.gz) = 740c14243fbf24ccd7316966788575f8f310a442acd8bb978e330797805b9568fb719cde28afb9e747170c92835b1661c12ce045e3bf1452a71e0286d73a0ad7
 Size (subread-2.0.8-source.tar.gz) = 26074498 bytes
-SHA1 (patch-HelperFunctions.c) = d54debdba0a3a71cced2463aeef65bfe05dc9dfe
+SHA1 (patch-HelperFunctions.c) = fac250be541ec76fef1cb439a4849050fd8be420
 SHA1 (patch-core-junction.c) = 481cd069aa42d673bbc10c80bb9548547e808b0c
-SHA1 (patch-gene-algorithms.c) = 42e879e95bd22eb34973ec5f87105c18dcac82b7
-SHA1 (patch-input-files.c) = 5fbaf9c38d7fdff74b9227b79db82865c03abcd6
-SHA1 (patch-long-hashtable.c) = 3fcc2e0b7c8564b329a9d4582caaed025e7832b2
+SHA1 (patch-gene-algorithms.c) = 35667746d92a3060a70229d69cdefd862da1a4c1
+SHA1 (patch-input-files.c) = 5058ff5d00b2afb57ff4127a7ba737753cb47c58
+SHA1 (patch-long-hashtable.c) = 794139ee464a313a424ca929e3009df99d57dbf6
 SHA1 (patch-longread-one_LRMsorted-hashtable.c) = d46ea9b73dee4f0531a002c22099865e3cce1034
 SHA1 (patch-longread-one_Makefile) = 138e6cf370a1b566738eb98793d40a61b4837320
 SHA1 (patch-longread-one_longread-mapping.c) = de09092da544f2286f4a5fee7a70c08135e44b40
diff --git a/subread/patches/patch-HelperFunctions.c b/subread/patches/patch-HelperFunctions.c
index d8f0cfe584..3a1cc2068a 100644
--- a/subread/patches/patch-HelperFunctions.c
+++ b/subread/patches/patch-HelperFunctions.c
@@ -2,9 +2,29 @@ $NetBSD$
 
 # Use standard compiler macros
 
---- HelperFunctions.c.orig	2020-06-04 23:58:40 UTC
+--- HelperFunctions.c.orig	2024-07-25 00:30:10.000000000 +0000
 +++ HelperFunctions.c
-@@ -845,7 +845,7 @@ int strcmp_number(char * s1, char * s2)
+@@ -26,7 +26,7 @@
+ #include <pthread.h>
+ 
+ 
+-#ifdef MACOS
++#ifdef __APPLE__
+ 
+ #include <sys/types.h>
+ #include <sys/socket.h>
+@@ -47,8 +47,10 @@
+ #include <sys/ioctl.h>
+ #include <netinet/in.h>
+ #include <net/if.h>
++#ifndef __APPLE__
+ #include <sys/sysinfo.h>
+ #endif
++#endif
+ #include <sys/types.h>
+ #endif
+ 
+@@ -860,10 +862,10 @@ int strcmp_number(char * s1, char * s2)
  
  int mac_str(char * str_buff)
  {
@@ -12,8 +32,12 @@ $NetBSD$
 +#if defined(__FreeBSD__) || defined(__MINGW32__)
  	return 1;
  #else
- #ifdef MACOS
-@@ -2703,7 +2703,7 @@ void main(){
+-#ifdef MACOS
++#ifdef __APPLE__
+     int         mib[6], x1, ret = 1;
+ 	size_t		len;
+     char            *buf;
+@@ -2719,7 +2721,7 @@ void main(){
  
  int get_free_total_mem(size_t * total, size_t * free_mem){
  
@@ -22,3 +46,12 @@ $NetBSD$
      return -1;
  #endif
  
+@@ -2731,7 +2733,7 @@ int get_free_total_mem(size_t * total, s
+ 	(*free_mem) = statex.ullAvailPhys;
+ 	return 0;
+ #else
+-#ifdef MACOS
++#ifdef __APPLE__
+     mach_msg_type_number_t count = HOST_VM_INFO_COUNT;
+     vm_statistics_data_t vmstat;
+     int page_size = getpagesize();
diff --git a/subread/patches/patch-gene-algorithms.c b/subread/patches/patch-gene-algorithms.c
index 0d2ae0ea1f..de536646ee 100644
--- a/subread/patches/patch-gene-algorithms.c
+++ b/subread/patches/patch-gene-algorithms.c
@@ -2,7 +2,7 @@ $NetBSD$
 
 # Use standard compiler macros
 
---- gene-algorithms.c.orig	2021-03-30 13:51:05 UTC
+--- gene-algorithms.c.orig	2024-07-25 00:30:10.000000000 +0000
 +++ gene-algorithms.c
 @@ -29,7 +29,7 @@
  #include <sys/stat.h>
@@ -13,7 +13,43 @@ $NetBSD$
  #include <sys/timeb.h>
  #endif
  
-@@ -1568,7 +1568,7 @@ int load_offsets(gene_offset_t* offsets , const char i
+@@ -45,7 +45,7 @@ void non_func(const char * fmt, ...)
+ 
+ void subread_lock_release(subread_lock_t * lock)
+ {
+-	#ifdef MACOS
++	#ifdef __APPLE__
+ 	pthread_mutex_unlock(lock);
+ 	#else
+ 	pthread_spin_unlock(lock);
+@@ -54,7 +54,7 @@ void subread_lock_release(subread_lock_t
+ void subread_lock_occupy(subread_lock_t * lock)
+ {
+ 
+-	#ifdef MACOS
++	#ifdef __APPLE__
+ 	pthread_mutex_lock(lock);
+ 	#else
+ 	pthread_spin_lock(lock);
+@@ -62,7 +62,7 @@ void subread_lock_occupy(subread_lock_t
+ }
+ 
+ void subread_destroy_lock(subread_lock_t * lock) {
+-	#ifdef MACOS
++	#ifdef __APPLE__
+ 	pthread_mutex_destroy(lock);
+ 	#else
+ 	pthread_spin_destroy(lock);
+@@ -71,7 +71,7 @@ void subread_destroy_lock(subread_lock_t
+ 
+ void subread_init_lock(subread_lock_t * lock)
+ {
+-	#ifdef MACOS
++	#ifdef __APPLE__
+ 	pthread_mutex_init(lock, NULL);
+ 	#else
+ 	pthread_spin_init(lock, PTHREAD_PROCESS_PRIVATE);
+@@ -1378,7 +1378,7 @@ int load_offsets(gene_offset_t* offsets
  
  double miltime(){
  	double ret;
diff --git a/subread/patches/patch-input-files.c b/subread/patches/patch-input-files.c
index ea69f9adef..9afc38b39a 100644
--- a/subread/patches/patch-input-files.c
+++ b/subread/patches/patch-input-files.c
@@ -1,15 +1,15 @@
 $NetBSD$
 
-# Add FreeBSD support
+# Use standard compiler macros
 
---- input-files.c.orig	2020-06-05 00:33:03 UTC
+--- input-files.c.orig	2024-07-26 04:36:04.000000000 +0000
 +++ input-files.c
-@@ -48,7 +48,7 @@ FILE * f_subr_open(const char * fname, const char * mo
+@@ -48,7 +48,7 @@ FILE * f_subr_open(const char * fname, c
  #ifdef __MINGW32__
  		return fopen64(fname, mode);
  #else
 -#if defined(__LP64__) || defined(_LP64) || defined(MACOS) 
-+#if defined(__LP64__) || defined(_LP64) || defined(MACOS) || defined(__FreeBSD__)
++#if defined(__LP64__) || defined(_LP64) || defined(__APPLE__) || defined(__FreeBSD__)
  		return fopen(fname, mode);
  #else
  		return fopen64(fname, mode);
diff --git a/subread/patches/patch-long-hashtable.c b/subread/patches/patch-long-hashtable.c
index d3ef8788a1..ffe04eb98d 100644
--- a/subread/patches/patch-long-hashtable.c
+++ b/subread/patches/patch-long-hashtable.c
@@ -2,13 +2,15 @@ $NetBSD$
 
 # Use standard compiler macros
 
---- long-hashtable.c.orig	2020-06-04 23:59:33 UTC
+--- long-hashtable.c.orig	2024-07-25 00:30:10.000000000 +0000
 +++ long-hashtable.c
-@@ -22,7 +22,7 @@
+@@ -21,8 +21,8 @@
+ #include <stdlib.h>
  #include <string.h>
  
- #ifndef MACOS
+-#ifndef MACOS
 -#ifndef FREEBSD
++#ifndef __APPLE__
 +#ifndef __FreeBSD__
  #include <malloc.h>
  #endif
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