sra-tools: Progress toward NetBSD build

[Jason W. Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Aug 13 11:54:36 2023 -0500
Changeset:	d6539bdfecf2f1f277166fb54f4d82e2edd66ae5

Modified Files:
	sra-tools/Makefile
	sra-tools/distinfo
	sra-tools/patches/patch-ncbi-vdb_interfaces_os_bsd_byteswap.h
Removed Files:
	sra-tools/patches/patch-ncbi-vdb_libs_align_bam.c

Log Message:
sra-tools: Progress toward NetBSD build

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=d6539bdfecf2f1f277166fb54f4d82e2edd66ae5

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

diffstat:
 sra-tools/Makefile                                   |  7 +++++--
 sra-tools/distinfo                                   |  5 ++---
 .../patch-ncbi-vdb_interfaces_os_bsd_byteswap.h      | 16 +++++++++++++++-
 sra-tools/patches/patch-ncbi-vdb_libs_align_bam.c    | 20 --------------------
 4 files changed, 22 insertions(+), 26 deletions(-)

diffs:
diff --git a/sra-tools/Makefile b/sra-tools/Makefile
index 3ca7453c7f..387e83fe4e 100644
--- a/sra-tools/Makefile
+++ b/sra-tools/Makefile
@@ -69,8 +69,13 @@ CMAKE_ARGS+=	-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
 
 EXAMPLESDIR=	${PREFIX}/share/examples/sra-tools
 
+.include "../../mk/bsd.prefs.mk"
+
 # FIXME: Check for libstdc++-static on Linux
 pre-configure:
+.if ${OPSYS} == NetBSD
+	${RM} ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/x86_64/byteswap.h
+.endif
 	cd ${WRKSRC}/ncbi-vdb/build && cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON .. && make
 
 post-install:
@@ -82,8 +87,6 @@ post-install:
 	${MV} ${DESTDIR}${PREFIX}/share/examples-java ${DESTDIR}${EXAMPLESDIR}/java
 	${MV} ${DESTDIR}${PREFIX}/share/examples-python ${DESTDIR}${EXAMPLESDIR}/python
 
-.include "../../mk/bsd.prefs.mk"
-
 # Shouldn't epoll bl3 check this?
 .if ${OPSYS} != Linux
 .include "../../devel/libepoll-shim/buildlink3.mk"
diff --git a/sra-tools/distinfo b/sra-tools/distinfo
index 1c5887f52c..3263b218d1 100644
--- a/sra-tools/distinfo
+++ b/sra-tools/distinfo
@@ -6,7 +6,6 @@ Size (outpaddling-ncbi-vdb-802ae6e.tar.gz) = 18977582 bytes
 BLAKE2s (sra-tools-3.0.6-de3d50d111874171766fd017c8cbcf92a9009263.tar.gz) = b1d07bd7eedb1ca76f18e2715570ad52ac93af4999f48629f65a837566b7ead8
 SHA512 (sra-tools-3.0.6-de3d50d111874171766fd017c8cbcf92a9009263.tar.gz) = 1286b69d45b111155152f2431e0bfa358519bb00fa0d1f78b437f16d8ea35d3d8ef7fb43280246c3142511a2b9118f3591aca7753648d8b22f375427adccf34c
 Size (sra-tools-3.0.6-de3d50d111874171766fd017c8cbcf92a9009263.tar.gz) = 44963316 bytes
-SHA1 (patch-build_env.cmake) = f4dc781bb59aeb3d5c4377f741679069e80fe896
-SHA1 (patch-ncbi-vdb_interfaces_os_bsd_byteswap.h) = 9c923136941fe7a79657e81c1b97f593e31e6bc3
+SHA1 (patch-build_env.cmake) = 95cd352d4d75122c1125fa87be152d0f847e38af
+SHA1 (patch-ncbi-vdb_interfaces_os_bsd_byteswap.h) = 2ecc80bca4dd3b0c28b20d1a82c2a315d29bb02c
 SHA1 (patch-ncbi-vdb_interfaces_os_bsd_endian.h) = fa522758b0a122f5da8b3ddc2b98fff1c1d82e33
-SHA1 (patch-ncbi-vdb_libs_align_bam.c) = 00e45c00dac9ba6ae245dd274f87c5572ff892ab
diff --git a/sra-tools/patches/patch-ncbi-vdb_interfaces_os_bsd_byteswap.h b/sra-tools/patches/patch-ncbi-vdb_interfaces_os_bsd_byteswap.h
index 51d1a3e467..01453e5465 100644
--- a/sra-tools/patches/patch-ncbi-vdb_interfaces_os_bsd_byteswap.h
+++ b/sra-tools/patches/patch-ncbi-vdb_interfaces_os_bsd_byteswap.h
@@ -2,7 +2,7 @@ $NetBSD$
 
 # Add NetBSD support
 
---- ncbi-vdb/interfaces/os/bsd/byteswap.h.orig	2023-08-13 14:38:57.514168395 +0000
+--- ncbi-vdb/interfaces/os/bsd/byteswap.h.orig	2023-08-12 23:35:46.000000000 +0000
 +++ ncbi-vdb/interfaces/os/bsd/byteswap.h
 @@ -2,7 +2,7 @@
  #ifndef _bsd_byteswap_h_
@@ -13,3 +13,17 @@ $NetBSD$
  
  #include <sys/endian.h>
  
+@@ -14,6 +14,13 @@
+ #define bswap_32(x) bswap32 (x)
+ #define bswap_64(x) bswap64 (x)
+ 
++// #define XSTR(x) STR(x)
++// #define STR(x)  #x
++
++// #pragma message "_BYTE_ORDER = " XSTR(_BYTE_ORDER)
++// #pragma message "__BYTE_ORDER = " XSTR(__BYTE_ORDER)
++// #pragma message "__LITTLE_ENDIAN = " XSTR(__LITTLE_ENDIAN)
++
+ #else
+ 
+ #error "You must define macros for this BSD variant."
diff --git a/sra-tools/patches/patch-ncbi-vdb_libs_align_bam.c b/sra-tools/patches/patch-ncbi-vdb_libs_align_bam.c
deleted file mode 100644
index 6cc135312b..0000000000
--- a/sra-tools/patches/patch-ncbi-vdb_libs_align_bam.c
+++ /dev/null
@@ -1,20 +0,0 @@
-$NetBSD$
-
---- ncbi-vdb/libs/align/bam.c.orig	2023-08-13 15:08:20.104984546 +0000
-+++ ncbi-vdb/libs/align/bam.c
-@@ -64,6 +64,15 @@
- 
- #include <os-native.h>
- 
-+#define	__BYTE_ORDER _BYTE_ORDER
-+
-+#define XSTR(x) STR(x)
-+#define STR(x)  #x
-+
-+#pragma message "_BYTE_ORDER = " XSTR(_BYTE_ORDER)
-+#pragma message "__BYTE_ORDER = " XSTR(__BYTE_ORDER)
-+#pragma message "__LITTLE_ENDIAN = " XSTR(__LITTLE_ENDIAN)
-+
- #if __BYTE_ORDER == __LITTLE_ENDIAN
- static uint16_t LE2HUI16(void const *X) { uint16_t y; memmove(&y, X, sizeof(y)); return y; }
- static uint32_t LE2HUI32(void const *X) { uint32_t y; memmove(&y, X, sizeof(y)); return y; }