sra-tools: Successful build on Darwin with Java disabled

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Aug 13 16:51:33 2023 -0500
Changeset:	f9f96e45ee511c04fbb99fe131884a8c79ed4af6

Modified Files:
	sra-tools/Makefile
	sra-tools/distinfo
Added Files:
	sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt
	sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp

Log Message:
sra-tools: Successful build on Darwin with Java disabled

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f9f96e45ee511c04fbb99fe131884a8c79ed4af6

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                                        |  2 ++
 sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt       | 15 +++++++++++++++
 .../patches/patch-tools_external_driver-tool_sratools.cpp | 15 +++++++++++++++
 4 files changed, 35 insertions(+), 4 deletions(-)

diffs:
diff --git a/sra-tools/Makefile b/sra-tools/Makefile
index 82d3d03d51..ceb227a5db 100644
--- a/sra-tools/Makefile
+++ b/sra-tools/Makefile
@@ -12,8 +12,6 @@
 #LICENSE_FILE_PD=	${WRKSRC}/LICENSE
 #LICENSE_DISTFILES_LGPL21+ =
 #USE_LDCONFIG=		${PREFIX}/lib64
-# Builds with earlier versions, but ngs-doc plist differs if jdk17 is present
-#JAVA_VERSION=		17+
 
 DISTNAME=		sra-tools-3.0.6
 CATEGORIES=		biology
@@ -36,8 +34,9 @@ ONLY_FOR_PLATFORM=	*-*-aarch64 *-*-x86_64
 
 USE_LANGUAGES=	c c++
 USE_TOOLS+=	bash bison cmake
-USE_JAVA=	yes
-USE_JAVA2=	17
+# USE_JAVA=	yes
+# Builds with earlier versions, but ngs-doc plist differs if jdk17 is present
+# USE_JAVA2=	17
 
 # The config.c and file-path.posix.cpp reinplaces follow
 # static patches.  Run "make clean patch" before updating
diff --git a/sra-tools/distinfo b/sra-tools/distinfo
index 6d42259bd0..addd2bfaed 100644
--- a/sra-tools/distinfo
+++ b/sra-tools/distinfo
@@ -10,5 +10,7 @@ SHA1 (patch-build_env.cmake) = 14add56e66e5578fd0d51ce55329285e0981ac4e
 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_kproc_bsd_sysmgr.c) = 00fc8af348db6a6fe213c4023fc6e8e46c34cf2c
+SHA1 (patch-ngs_ngs-java_CMakeLists.txt) = 44b822381fd564d045406cc926f807adae9fbe59
 SHA1 (patch-tools_external_driver-tool_build-version.cpp) = ec194aad65c86035c1fee0fe42722faf06af17fe
 SHA1 (patch-tools_external_driver-tool_build-version.hpp) = 0d50aba6b3fe1086cf0562c935f114bb117ac195
+SHA1 (patch-tools_external_driver-tool_sratools.cpp) = 2d097a61b01dca48dbefdf51369252b2f8a2ca10
diff --git a/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt b/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt
new file mode 100644
index 0000000000..01010dbda6
--- /dev/null
+++ b/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Disable java
+
+--- ngs/ngs-java/CMakeLists.txt.orig	2023-08-13 21:46:05.343038455 +0000
++++ ngs/ngs-java/CMakeLists.txt
+@@ -99,7 +99,7 @@ if ( Java_FOUND )
+         gov/nih/nlm/ncbi/ngs/error/cause/UnsupportedArchCause.java
+     )
+ 
+-    find_package(JNI)
++    # find_package(JNI)
+ 
+     if ( JNI_FOUND )
+         add_jar( ngs-java
diff --git a/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp b/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp
new file mode 100644
index 0000000000..e5cdfeb1de
--- /dev/null
+++ b/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Resolve conflict
+
+--- tools/external/driver-tool/sratools.cpp.orig	2023-08-13 21:49:06.139091507 +0000
++++ tools/external/driver-tool/sratools.cpp
+@@ -578,7 +578,7 @@ static int main(CommandLine const &argv)
+ 
+ } // namespace sratools
+ 
+-#if BSD
++#if BSD && ! MAC
+ int main(int argc, char *argv[], char *envp[])
+ {
+     auto const invocation = CommandLine(argc, argv, envp, nullptr);