sra-tools: Work on NetBSD patches

[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 10:21:24 2023 -0500
Changeset:	bbf7a93b7d164e7322d0c423d99a9bff18821647

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

Log Message:
sra-tools: Work on NetBSD patches

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=bbf7a93b7d164e7322d0c423d99a9bff18821647

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

diffstat:
 sra-tools/Makefile                                   |  2 +-
 sra-tools/distinfo                                   |  3 +++
 .../patch-ncbi-vdb_interfaces_os_bsd_byteswap.h      | 15 +++++++++++++++
 .../patch-ncbi-vdb_interfaces_os_bsd_endian.h        | 13 +++++++++++++
 sra-tools/patches/patch-ncbi-vdb_libs_align_bam.c    | 20 ++++++++++++++++++++
 5 files changed, 52 insertions(+), 1 deletion(-)

diffs:
diff --git a/sra-tools/Makefile b/sra-tools/Makefile
index c68ae192ad..3ca7453c7f 100644
--- a/sra-tools/Makefile
+++ b/sra-tools/Makefile
@@ -71,7 +71,7 @@ EXAMPLESDIR=	${PREFIX}/share/examples/sra-tools
 
 # FIXME: Check for libstdc++-static on Linux
 pre-configure:
-	cd ${WRKSRC}/ncbi-vdb/build && cmake .. && make
+	cd ${WRKSRC}/ncbi-vdb/build && cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON .. && make
 
 post-install:
 	${STRIP} ${DESTDIR}${PREFIX}/bin/*.${PKGVERSION_NOREV}
diff --git a/sra-tools/distinfo b/sra-tools/distinfo
index b06158a46a..1c5887f52c 100644
--- a/sra-tools/distinfo
+++ b/sra-tools/distinfo
@@ -7,3 +7,6 @@ BLAKE2s (sra-tools-3.0.6-de3d50d111874171766fd017c8cbcf92a9009263.tar.gz) = b1d0
 SHA512 (sra-tools-3.0.6-de3d50d111874171766fd017c8cbcf92a9009263.tar.gz) = 1286b69d45b111155152f2431e0bfa358519bb00fa0d1f78b437f16d8ea35d3d8ef7fb43280246c3142511a2b9118f3591aca7753648d8b22f375427adccf34c
 Size (sra-tools-3.0.6-de3d50d111874171766fd017c8cbcf92a9009263.tar.gz) = 44963316 bytes
 SHA1 (patch-build_env.cmake) = f4dc781bb59aeb3d5c4377f741679069e80fe896
+SHA1 (patch-ncbi-vdb_interfaces_os_bsd_byteswap.h) = 9c923136941fe7a79657e81c1b97f593e31e6bc3
+SHA1 (patch-ncbi-vdb_interfaces_os_bsd_endian.h) = fa522758b0a122f5da8b3ddc2b98fff1c1d82e33
+SHA1 (patch-ncbi-vdb_libs_align_bam.c) = 00e45c00dac9ba6ae245dd274f87c5572ff892ab
diff --git a/sra-tools/patches/patch-ncbi-vdb_interfaces_os_bsd_byteswap.h b/sra-tools/patches/patch-ncbi-vdb_interfaces_os_bsd_byteswap.h
new file mode 100644
index 0000000000..51d1a3e467
--- /dev/null
+++ b/sra-tools/patches/patch-ncbi-vdb_interfaces_os_bsd_byteswap.h
@@ -0,0 +1,15 @@
+$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
+@@ -2,7 +2,7 @@
+ #ifndef _bsd_byteswap_h_
+ #define _bsd_byteswap_h_
+ 
+-#if defined(__FreeBSD__)
++#if defined(__FreeBSD__) || defined(__NetBSD__)
+ 
+ #include <sys/endian.h>
+ 
diff --git a/sra-tools/patches/patch-ncbi-vdb_interfaces_os_bsd_endian.h b/sra-tools/patches/patch-ncbi-vdb_interfaces_os_bsd_endian.h
new file mode 100644
index 0000000000..5460b30c0d
--- /dev/null
+++ b/sra-tools/patches/patch-ncbi-vdb_interfaces_os_bsd_endian.h
@@ -0,0 +1,13 @@
+$NetBSD$
+
+# Add NetBSD support
+
+--- ncbi-vdb/interfaces/os/bsd/endian.h.orig	2023-08-13 15:20:29.641640461 +0000
++++ ncbi-vdb/interfaces/os/bsd/endian.h
+@@ -1,5 +1,5 @@
+ 
+-#if defined(__FreeBSD__)
++#if defined(__FreeBSD__) || defined(__NetBSD__)
+ 
+ #include <sys/endian.h>
+ 
diff --git a/sra-tools/patches/patch-ncbi-vdb_libs_align_bam.c b/sra-tools/patches/patch-ncbi-vdb_libs_align_bam.c
new file mode 100644
index 0000000000..6cc135312b
--- /dev/null
+++ b/sra-tools/patches/patch-ncbi-vdb_libs_align_bam.c
@@ -0,0 +1,20 @@
+$NetBSD$
+
+--- 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; }