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subread: Begin work on 2.0.8 update

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <jtocino%gmx.com@localhost>
Pushed By:	outpaddling
Date:		Sun Jan 19 07:02:39 2025 -0600
Changeset:	7342127b691daa020efbc745482da5733f827255

Modified Files:
	subread/Makefile
	subread/distinfo
	subread/patches/patch-HelperFunctions.c
	subread/patches/patch-core-junction.c
	subread/patches/patch-gene-algorithms.c
	subread/patches/patch-input-files.c
	subread/patches/patch-long-hashtable.c
	subread/patches/patch-longread-one_LRMsorted-hashtable.c
	subread/patches/patch-longread-one_Makefile
	subread/patches/patch-longread-one_longread-mapping.c
	subread/patches/patch-read-repair.c
	subread/patches/patch-sambam-file.c
	subread/patches/patch-sorted-hashtable.c
	subread/patches/patch-subread.h

Log Message:
subread: Begin work on 2.0.8 update

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=7342127b691daa020efbc745482da5733f827255

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

diffstat:
 subread/Makefile                                   |  8 +--
 subread/distinfo                                   | 30 +++++-----
 subread/patches/patch-HelperFunctions.c            | 66 ++--------------------
 subread/patches/patch-core-junction.c              |  4 --
 subread/patches/patch-gene-algorithms.c            | 46 +--------------
 subread/patches/patch-input-files.c                | 10 +---
 subread/patches/patch-long-hashtable.c             | 12 +---
 .../patch-longread-one_LRMsorted-hashtable.c       |  4 --
 subread/patches/patch-longread-one_Makefile        | 20 +++----
 .../patches/patch-longread-one_longread-mapping.c  | 10 +---
 subread/patches/patch-read-repair.c                |  4 --
 subread/patches/patch-sambam-file.c                |  2 +-
 subread/patches/patch-sorted-hashtable.c           |  4 --
 subread/patches/patch-subread.h                    |  8 +--
 14 files changed, 50 insertions(+), 178 deletions(-)

diffs:
diff --git a/subread/Makefile b/subread/Makefile
index 73f07895ab..f3b088c6ad 100644
--- a/subread/Makefile
+++ b/subread/Makefile
@@ -7,19 +7,19 @@
 # The libsysinfo package is only for SunOS at the time of this writing.
 # FreeBSD has a libsysinfo port that may serve as a model for NetBSD.
 
-DISTNAME=	subread-2.0.2-source
-PKGNAME=	subread-2.0.2
+DISTNAME=	subread-2.0.8-source
+PKGNAME=	subread-2.0.8
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=subread/}
 
 MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://bioinf.wehi.edu.au/subread-package/
+HOMEPAGE=	https://subread.sourceforge.net/
 COMMENT=	High-performance read alignment, quantification and mutation discovery
 LICENSE=	gnu-gpl-v3
 
 USE_TOOLS+=	gmake
 
-WRKSRC=		${WRKDIR}/subread-2.0.2-source/src
+WRKSRC=		${WRKDIR}/subread-2.0.8-source/src
 
 CFLAGS+=	-fcommon
 MAKE_FILE=	${FILESDIR}/Makefile.pkg
diff --git a/subread/distinfo b/subread/distinfo
index 028c837054..90f2b4aa26 100644
--- a/subread/distinfo
+++ b/subread/distinfo
@@ -1,17 +1,17 @@
 $NetBSD$
 
-RMD160 (subread-2.0.2-source.tar.gz) = 2cfa127a7bea963d67330edee2ca226f9d6dde49
-SHA512 (subread-2.0.2-source.tar.gz) = 549164aadcd1e05cd1f941a4c10d6e19f904d2d75dae8391bbf3003a26e13f6a14cc22618662c2baf804b4d020a58e7ba0b0be9b4ff1181ad981a24270ffb64e
-Size (subread-2.0.2-source.tar.gz) = 23295764 bytes
-SHA1 (patch-HelperFunctions.c) = 88d0bc9955d14d62551aa7eed277f3742eb7f4b9
-SHA1 (patch-core-junction.c) = 481cd069aa42d673bbc10c80bb9548547e808b0c
-SHA1 (patch-gene-algorithms.c) = 27f8c0314ac2afcd676aa104a47e342ad74e0e0b
-SHA1 (patch-input-files.c) = 0e79ba9453dd150e7f4aac3be6beb8555880e082
-SHA1 (patch-long-hashtable.c) = 4d0d1a04e4306517151a5081aca507a822db4f8a
-SHA1 (patch-longread-one_LRMsorted-hashtable.c) = f08066fab9cb83da77a289b269395693ab80393a
-SHA1 (patch-longread-one_Makefile) = 48e06a0d3987aa47aefa17fcfdb395f647bc4141
-SHA1 (patch-longread-one_longread-mapping.c) = cd164a8268d73e78c3760529ec475172a8ea54ec
-SHA1 (patch-read-repair.c) = 4d7085ec8558647c7d92f5d0697b04b526496a75
-SHA1 (patch-sambam-file.c) = 007489e7140c8e22116a0748b734c636adc40896
-SHA1 (patch-sorted-hashtable.c) = 691dc605c2c5451eb7857366df4386de9813bace
-SHA1 (patch-subread.h) = 182016760358f56a845cdf49899a5c7ccfe84aef
+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) = e3cc55a2844ad8fbc415fa6e3f112f39bd83b276
+SHA1 (patch-core-junction.c) = f05d63e7949e30b4d40160858823369be675ae59
+SHA1 (patch-gene-algorithms.c) = 37b1334ed733f7cd6e1b905f4bb065e8f003207c
+SHA1 (patch-input-files.c) = 278661cee86525d258b6a1109c82c7cc0e1990e4
+SHA1 (patch-long-hashtable.c) = 24046bcb0a2f3e1157d3922c4f50ffb4404089df
+SHA1 (patch-longread-one_LRMsorted-hashtable.c) = 434bf36fa170ed51409e51b2e037c5ec722e9305
+SHA1 (patch-longread-one_Makefile) = 0855b1a0cc81b50e0e621bd3f4c86d227f7623c0
+SHA1 (patch-longread-one_longread-mapping.c) = e2a2f3170063fc7d6e1e1af6f2f04c4c6bb601db
+SHA1 (patch-read-repair.c) = 91b67022053738e0e669f176a42dca51d7bb1bf2
+SHA1 (patch-sambam-file.c) = 16d3bf05718db64518cfd94e6574b2c3a0794c79
+SHA1 (patch-sorted-hashtable.c) = 563f376063159387f2411286d5c4f145541148aa
+SHA1 (patch-subread.h) = b3d27a6f964ffece4b51ec59d5fd95fbd6ead160
diff --git a/subread/patches/patch-HelperFunctions.c b/subread/patches/patch-HelperFunctions.c
index 62671bb7d3..e10e44273b 100644
--- a/subread/patches/patch-HelperFunctions.c
+++ b/subread/patches/patch-HelperFunctions.c
@@ -1,31 +1,6 @@
-$NetBSD$
-
-# Use predefined macros, guard sysinfo
-
---- HelperFunctions.c.orig	2021-03-27 07:38:08.000000000 +0000
+--- HelperFunctions.c.orig	2020-06-04 23:58:40 UTC
 +++ HelperFunctions.c
-@@ -26,7 +26,7 @@
- #include <pthread.h>
- 
- 
--#ifdef MACOS
-+#ifdef __APPLE__
- 
- #include <sys/types.h>
- #include <sys/socket.h>
-@@ -47,8 +47,11 @@
- #include <sys/ioctl.h>
- #include <netinet/in.h>
- #include <net/if.h>
-+// Add other platforms that lack native or pkgsrc libsysinfo
-+#if !defined(__FreeBSD__) && !defined(__NetBSD__)
- #include <sys/sysinfo.h>
- #endif
-+#endif
- #include <sys/types.h>
- #endif
- 
-@@ -846,10 +849,10 @@ int strcmp_number(char * s1, char * s2)
+@@ -845,7 +845,7 @@ int strcmp_number(char * s1, char * s2)
  
  int mac_str(char * str_buff)
  {
@@ -33,44 +8,13 @@ $NetBSD$
 +#if defined(__FreeBSD__) || defined(__MINGW32__)
  	return 1;
  #else
--#ifdef MACOS
-+#ifdef __APPLE__
-     int         mib[6], x1, ret = 1;
- 	size_t		len;
-     char            *buf;
-@@ -2702,22 +2705,20 @@ void main(){
- #include <windows.h>
- #endif
+ #ifdef MACOS
+@@ -2703,7 +2703,7 @@ void main(){
  
--
-+/* FIXME: Should this always return 0, or send back -1 as an error code? */
  int get_free_total_mem(size_t * total, size_t * free_mem){
  
 -#ifdef FREEBSD
-+// Add other platforms that lack native or pkgsrc libsysinfo
-+#if defined(__FreeBSD__) || defined(__NetBSD__)
++#ifdef __FreeBSD__
      return -1;
--#endif
--
--#ifdef __MINGW32__
-+#elif defined(__MINGW32__)
- 	MEMORYSTATUSEX statex;
- 	statex.dwLength = sizeof (statex);
- 	GlobalMemoryStatusEx (&statex);
- 	(*total) = statex.ullTotalPhys;
- 	(*free_mem) = statex.ullAvailPhys;
- 	return 0;
--#else
--#ifdef MACOS
-+#elif defined(__APPLE__)
-     mach_msg_type_number_t count = HOST_VM_INFO_COUNT;
-     vm_statistics_data_t vmstat;
-     int page_size = getpagesize();
-@@ -2737,7 +2738,6 @@ int get_free_total_mem(size_t * total, s
-     *total = sinf.totalram;
-     return 0;
  #endif
--#endif
- }
  
- void worker_master_mutex_init(worker_master_mutex_t * wmt, int all_workers){
diff --git a/subread/patches/patch-core-junction.c b/subread/patches/patch-core-junction.c
index 408f848df7..44567984a1 100644
--- a/subread/patches/patch-core-junction.c
+++ b/subread/patches/patch-core-junction.c
@@ -1,7 +1,3 @@
-$NetBSD$
-
-# Portability
-
 --- core-junction.c.orig	2018-11-08 15:19:02 UTC
 +++ core-junction.c
 @@ -22,6 +22,7 @@
diff --git a/subread/patches/patch-gene-algorithms.c b/subread/patches/patch-gene-algorithms.c
index 46310a1308..d8bfc0d449 100644
--- a/subread/patches/patch-gene-algorithms.c
+++ b/subread/patches/patch-gene-algorithms.c
@@ -1,8 +1,4 @@
-$NetBSD$
-
-# Use predefined macros, getttimeofday()
-
---- gene-algorithms.c.orig	2021-03-27 07:38:08.000000000 +0000
+--- gene-algorithms.c.orig	2021-03-30 13:51:05 UTC
 +++ gene-algorithms.c
 @@ -29,7 +29,7 @@
  #include <sys/stat.h>
@@ -13,48 +9,12 @@ $NetBSD$
  #include <sys/timeb.h>
  #endif
  
-@@ -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);
-@@ -1568,7 +1568,7 @@ int load_offsets(gene_offset_t* offsets 
+@@ -1568,7 +1568,7 @@ int load_offsets(gene_offset_t* offsets , const char i
  
  double miltime(){
  	double ret;
 -	#ifdef FREEBSD
-+	#if defined(__FreeBSD__) || defined(__NetBSD__)
++	#ifdef __FreeBSD__
  		struct timeval tp;
  		struct timezone tz;
  		tz.tz_minuteswest=0;
diff --git a/subread/patches/patch-input-files.c b/subread/patches/patch-input-files.c
index b1247835c4..37eca1d9e7 100644
--- a/subread/patches/patch-input-files.c
+++ b/subread/patches/patch-input-files.c
@@ -1,15 +1,11 @@
-$NetBSD$
-
-# Use predefined macros
-
---- input-files.c.orig	2021-03-27 07:38:08.000000000 +0000
+--- input-files.c.orig	2020-06-05 00:33:03 UTC
 +++ input-files.c
-@@ -48,7 +48,7 @@ FILE * f_subr_open(const char * fname, c
+@@ -48,7 +48,7 @@ FILE * f_subr_open(const char * fname, const char * mo
  #ifdef __MINGW32__
  		return fopen64(fname, mode);
  #else
 -#if defined(__LP64__) || defined(_LP64) || defined(MACOS) 
-+#if defined(__LP64__) || defined(_LP64) || defined(__APPLE__) || defined(__FreeBSD__)
++#if defined(__LP64__) || defined(_LP64) || defined(MACOS) || 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 8edf9fa456..cfb9557fa6 100644
--- a/subread/patches/patch-long-hashtable.c
+++ b/subread/patches/patch-long-hashtable.c
@@ -1,16 +1,10 @@
-$NetBSD$
-
-# Use predefined macros
-
---- long-hashtable.c.orig	2021-03-31 00:35:27.202818216 +0000
+--- long-hashtable.c.orig	2020-06-04 23:59:33 UTC
 +++ long-hashtable.c
-@@ -21,8 +21,8 @@
- #include <stdlib.h>
+@@ -22,7 +22,7 @@
  #include <string.h>
  
--#ifndef MACOS
+ #ifndef MACOS
 -#ifndef FREEBSD
-+#ifndef __APPLE__
 +#ifndef __FreeBSD__
  #include <malloc.h>
  #endif
diff --git a/subread/patches/patch-longread-one_LRMsorted-hashtable.c b/subread/patches/patch-longread-one_LRMsorted-hashtable.c
index 08486388ec..f5cfe3d3cb 100644
--- a/subread/patches/patch-longread-one_LRMsorted-hashtable.c
+++ b/subread/patches/patch-longread-one_LRMsorted-hashtable.c
@@ -1,7 +1,3 @@
-$NetBSD$
-
-# Use predefined macros
-
 --- longread-one/LRMsorted-hashtable.c.orig	2018-11-08 14:47:43 UTC
 +++ longread-one/LRMsorted-hashtable.c
 @@ -22,11 +22,9 @@
diff --git a/subread/patches/patch-longread-one_Makefile b/subread/patches/patch-longread-one_Makefile
index 3ef12e5c27..41a2a468ea 100644
--- a/subread/patches/patch-longread-one_Makefile
+++ b/subread/patches/patch-longread-one_Makefile
@@ -1,8 +1,4 @@
-$NetBSD$
-
-# Respect env
-
---- longread-one/Makefile.orig	2019-09-04 04:22:49 UTC
+--- longread-one/Makefile.orig	2024-07-25 00:35:55 UTC
 +++ longread-one/Makefile
 @@ -1,12 +1,12 @@
 -CC_EXEC = gcc
@@ -11,24 +7,26 @@ $NetBSD$
  include ../makefile.version
  include make.version
  
--CCFLAGS = -mtune=core2 ${MACOS} -O${OPT_LEVEL} -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE  -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32}
+-CCFLAGS =  ${MACOS} -O${OPT_LEVEL} -Wall  -DMAKE_FOR_EXON  -D MAKE_STANDALONE  -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32}
 -LDFLAGS =  -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
 -CC = ${CC_EXEC}  ${CCFLAGS}  -fmessage-length=0  -ggdb
 +CC ?= gcc
-+CFLAGS += -DMAKE_FOR_EXON  -D MAKE_STANDALONE  -D_FILE_OFFSET_BITS=64 \
-+	-DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32}
++CCFLAGS += -DMAKE_FOR_EXON  -D MAKE_STANDALONE  -D_FILE_OFFSET_BITS=64 \
++	    -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32}
 +LDFLAGS +=  -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST
  
  ALL_LIBS=LRMsorted-hashtable LRMbase-index LRMchro-event LRMhelper LRMseek-zlib LRMfile-io LRMhashtable
  ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS})
-@@ -20,8 +20,8 @@ clean:
+@@ -19,9 +19,8 @@ clean:
+ clean:
  	rm -f *.o LRM
  
- LRM: longread-mapping.c  ${ALL_OBJECTS} 
+-LRM: longread-mapping.c  ${ALL_OBJECTS} 
 -	${CC} -o LRM longread-mapping.c   ${ALL_OBJECTS}  ${LDFLAGS}
++LRM: longread-mapping.c  ${ALL_OBJECTS}
 +	${CC} -o LRM ${CFLAGS} longread-mapping.c   ${ALL_OBJECTS}  ${LDFLAGS}
  
  $(ALL_OBJECTS): $(ALL_C) $(ALL_H)
 -	$(CC) -o $@ -c $(subst .o,.c,$@)
+-	
 +	$(CC) -o $@ -c ${CFLAGS} $(subst .o,.c,$@)
- 	
diff --git a/subread/patches/patch-longread-one_longread-mapping.c b/subread/patches/patch-longread-one_longread-mapping.c
index c74f211dbf..4db4bfa499 100644
--- a/subread/patches/patch-longread-one_longread-mapping.c
+++ b/subread/patches/patch-longread-one_longread-mapping.c
@@ -1,8 +1,4 @@
-$NetBSD$
-
-# Use gettimeofday() on BSD
-
---- longread-one/longread-mapping.c.orig	2021-03-25 01:56:09.000000000 +0000
+--- longread-one/longread-mapping.c.orig	2021-03-30 13:58:29 UTC
 +++ longread-one/longread-mapping.c
 @@ -30,7 +30,9 @@
  #ifndef __MINGW32__
@@ -14,11 +10,11 @@ $NetBSD$
  #include <sys/stat.h>
  #include <locale.h>
  #include <ctype.h>
-@@ -225,6 +227,17 @@ int LRMvalidate_and_init_context(LRMcont
+@@ -225,6 +227,17 @@ int LRMvalidate_and_init_context(LRMcontext_t ** conte
  #endif
  double LRMmiltime(){
  	double ret;
-+#if defined(__FreeBSD__) || defined(__NetBSD__)
++#ifdef __FreeBSD__
 +
 +	struct timeval tp;
 +	struct timezone tz;
diff --git a/subread/patches/patch-read-repair.c b/subread/patches/patch-read-repair.c
index df2dbf8afb..aebf9c9449 100644
--- a/subread/patches/patch-read-repair.c
+++ b/subread/patches/patch-read-repair.c
@@ -1,7 +1,3 @@
-$NetBSD$
-
-# Portability
-
 --- read-repair.c.orig	2018-11-08 15:20:06 UTC
 +++ read-repair.c
 @@ -3,6 +3,7 @@
diff --git a/subread/patches/patch-sambam-file.c b/subread/patches/patch-sambam-file.c
index a3cddf1959..66da68c2fe 100644
--- a/subread/patches/patch-sambam-file.c
+++ b/subread/patches/patch-sambam-file.c
@@ -2,7 +2,7 @@ $NetBSD$
 
 # Portability
 
---- sambam-file.c.orig	2021-03-27 07:38:08.000000000 +0000
+--- sambam-file.c.orig	2024-07-25 00:30:10.000000000 +0000
 +++ sambam-file.c
 @@ -30,6 +30,7 @@
  #include <string.h>
diff --git a/subread/patches/patch-sorted-hashtable.c b/subread/patches/patch-sorted-hashtable.c
index a61e58cb77..9a3637e942 100644
--- a/subread/patches/patch-sorted-hashtable.c
+++ b/subread/patches/patch-sorted-hashtable.c
@@ -1,7 +1,3 @@
-$NetBSD$
-
-# Portability
-
 --- sorted-hashtable.c.orig	2018-11-08 03:33:50 UTC
 +++ sorted-hashtable.c
 @@ -23,11 +23,9 @@
diff --git a/subread/patches/patch-subread.h b/subread/patches/patch-subread.h
index c5e179bfab..99eb5c0bbf 100644
--- a/subread/patches/patch-subread.h
+++ b/subread/patches/patch-subread.h
@@ -1,12 +1,12 @@
 $NetBSD$
 
-# Use predefined macros
+# Use standard compiler macros
 
---- subread.h.orig	2018-11-08 14:46:06 UTC
+--- subread.h.orig	2024-07-25 00:30:10.000000000 +0000
 +++ subread.h
-@@ -102,7 +102,7 @@
- 
+@@ -114,7 +114,7 @@
  #define USE_POSIX_MUTEX_LOCK
+ #endif
  
 -#if defined(MACOS) || defined(FREEBSD) || defined(USE_POSIX_MUTEX_LOCK)
 +#if defined(__APPLE__) || defined(__FreeBSD__) || defined(USE_POSIX_MUTEX_LOCK)
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