sra-tools: Upstream most patches to my github fork

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: sra-tools: Upstream most patches to my github fork
From: Jason W. Bacon <bacon%NetBSD.org@localhost>
Date: Tue, 15 Aug 2023 13:08:46 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Tue Aug 15 08:08:46 2023 -0500
Changeset:	8bfb01e2be6c3d044f39c7c6b69ac198b73ad2ae

Modified Files:
	sra-tools/Makefile
	sra-tools/distinfo
	sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c
	sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp
Removed 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-tools_external_driver-tool_build-version.cpp
	sra-tools/patches/patch-tools_external_driver-tool_build-version.hpp

Log Message:
sra-tools: Upstream most patches to my github fork

Pull request pending

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=8bfb01e2be6c3d044f39c7c6b69ac198b73ad2ae

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

diffstat:
 sra-tools/Makefile                                 |  4 +--
 sra-tools/distinfo                                 | 20 ++++++---------
 .../patch-ncbi-vdb_interfaces_os_bsd_byteswap.h    | 29 ----------------------
 .../patch-ncbi-vdb_interfaces_os_bsd_endian.h      | 13 ----------
 .../patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c |  8 +++---
 ...ch-tools_external_driver-tool_build-version.cpp | 15 -----------
 ...ch-tools_external_driver-tool_build-version.hpp | 23 -----------------
 .../patch-tools_external_driver-tool_sratools.cpp  | 17 +++++++------
 8 files changed, 23 insertions(+), 106 deletions(-)

diffs:
diff --git a/sra-tools/Makefile b/sra-tools/Makefile
index 312061ba15..9027a8ab20 100644
--- a/sra-tools/Makefile
+++ b/sra-tools/Makefile
@@ -8,8 +8,8 @@
 DISTNAME=		sra-tools-3.0.6
 CATEGORIES=		biology
 MASTER_SITES=		${MASTER_SITE_GITHUB:=outpaddling/}
-GITHUB_TAG=		de3d50d111874171766fd017c8cbcf92a9009263
-GITHUB_SUBMODULES+=	outpaddling ncbi-vdb 802ae6e ncbi-vdb
+GITHUB_TAG=		984f1493e8612cd59a269569bf8c06e25e4e604c
+GITHUB_SUBMODULES+=	outpaddling ncbi-vdb 38972fc ncbi-vdb
 
 OWNER=		bacon%NetBSD.org@localhost
 HOMEPAGE=	https://github.com/ncbi/sra-tools
diff --git a/sra-tools/distinfo b/sra-tools/distinfo
index 7ce43ae94e..b128fcc200 100644
--- a/sra-tools/distinfo
+++ b/sra-tools/distinfo
@@ -1,16 +1,12 @@
 $NetBSD$
 
-BLAKE2s (outpaddling-ncbi-vdb-802ae6e.tar.gz) = bfdf236363008fb286611002e3997a9f8ac9277375de22dd0ec40222bbd117a3
-SHA512 (outpaddling-ncbi-vdb-802ae6e.tar.gz) = 5cb1f2c17fda873ba6c5fe24424dda72d596452ec15baf85870b9dad969a63448218551a637aa72313cf51543a2a89bdc55aa4066534f84fc9f7246f7cf0b6f3
-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
+BLAKE2s (outpaddling-ncbi-vdb-38972fc.tar.gz) = 600ac8ff4f2fbea9d2f06edc0277087e1559636226756eae415826dfbdb1fb5a
+SHA512 (outpaddling-ncbi-vdb-38972fc.tar.gz) = 0cda01bf2faf59aa16c4a402bcc132d4a2fc948240f6e13b2f1d3d93c4f900a837ebf8c24ee8089e88ed4de90a8ab441a4176f8193052fd7b538e27384bcb118
+Size (outpaddling-ncbi-vdb-38972fc.tar.gz) = 18978410 bytes
+BLAKE2s (sra-tools-3.0.6-984f1493e8612cd59a269569bf8c06e25e4e604c.tar.gz) = 2a13546011d4ea0a000a7e1e5fdfdf1d915b6adbac8fd818967ebf4c1670dba5
+SHA512 (sra-tools-3.0.6-984f1493e8612cd59a269569bf8c06e25e4e604c.tar.gz) = 9b1e671c92ba1006392160258c5b6fba85ba7dba59a23e9ed8b534ca31b46ed9e6cf2c92ea69dc2897f5a4aa9da31f5c8981cebb442236d11bcef76b854dbec9
+Size (sra-tools-3.0.6-984f1493e8612cd59a269569bf8c06e25e4e604c.tar.gz) = 44961381 bytes
 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) = 453533319677ccb1004d0b851016f410bfb60422
+SHA1 (patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c) = f49eb28f8bfeb528c1d7c2e9d184502b9eba273c
 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) = ca8fe3882ae36fb076e3be9bddbfca7493b6afd5
+SHA1 (patch-tools_external_driver-tool_sratools.cpp) = c490d83f03471e6e8e34b8e88534469ed45b2886
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
deleted file mode 100644
index 01453e5465..0000000000
--- a/sra-tools/patches/patch-ncbi-vdb_interfaces_os_bsd_byteswap.h
+++ /dev/null
@@ -1,29 +0,0 @@
-$NetBSD$
-
-# Add NetBSD support
-
---- 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_
- #define _bsd_byteswap_h_
- 
--#if defined(__FreeBSD__)
-+#if defined(__FreeBSD__) || defined(__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_interfaces_os_bsd_endian.h b/sra-tools/patches/patch-ncbi-vdb_interfaces_os_bsd_endian.h
deleted file mode 100644
index 5460b30c0d..0000000000
--- a/sra-tools/patches/patch-ncbi-vdb_interfaces_os_bsd_endian.h
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD$
-
-# 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_kproc_bsd_sysmgr.c b/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c
index aeb05e09f9..f66cc198c6 100644
--- a/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c
+++ b/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c
@@ -1,8 +1,8 @@
 $NetBSD$
 
-# pthread_main_np() for NetBSD
+# Add NetBSD pthread_main_np() stand-in
 
---- ncbi-vdb/libs/kproc/bsd/sysmgr.c.orig	2023-08-12 23:35:46.000000000 +0000
+--- ncbi-vdb/libs/kproc/bsd/sysmgr.c.orig	2023-08-15 12:41:59.000000000 +0000
 +++ ncbi-vdb/libs/kproc/bsd/sysmgr.c
 @@ -30,6 +30,23 @@
  #include <pthread.h>
@@ -16,12 +16,12 @@ $NetBSD$
 +
 +// This should be initialized to pthread_self() at the start of main()
 +// If the thread ID of this thread is the same, then this is the main thread
-+pthread_t _thr_main;
++pthread_t _ncbi_thr_main;
 +
 +int	pthread_main_np(void)
 +
 +{
-+    return pthread_equal(pthread_self(), _thr_main);
++    return pthread_equal(pthread_self(), _ncbi_thr_main);
 +}
 +#endif
 +
diff --git a/sra-tools/patches/patch-tools_external_driver-tool_build-version.cpp b/sra-tools/patches/patch-tools_external_driver-tool_build-version.cpp
deleted file mode 100644
index b3eb6f3b3d..0000000000
--- a/sra-tools/patches/patch-tools_external_driver-tool_build-version.cpp
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-# Resolve collision on NetBSD
-
---- tools/external/driver-tool/build-version.cpp.orig	2023-08-13 20:53:11.943803445 +0000
-+++ tools/external/driver-tool/build-version.cpp
-@@ -60,7 +60,7 @@ public:
-     }
- 
-     VersionBuffer(sratools::Version const &vers) noexcept {
--        begin = utoa(vers.major(), '.', utoa(vers.minor(), '.', utoa(vers.revision(), '\0', end())));
-+        begin = utoa(vers.ncbi_major(), '.', utoa(vers.ncbi_minor(), '.', utoa(vers.revision(), '\0', end())));
-     }
- };
- 
diff --git a/sra-tools/patches/patch-tools_external_driver-tool_build-version.hpp b/sra-tools/patches/patch-tools_external_driver-tool_build-version.hpp
deleted file mode 100644
index 87bf699e25..0000000000
--- a/sra-tools/patches/patch-tools_external_driver-tool_build-version.hpp
+++ /dev/null
@@ -1,23 +0,0 @@
-$NetBSD$
-
-# Resolve collision on NetBSD
-
---- tools/external/driver-tool/build-version.hpp.orig	2023-08-13 20:51:13.494470918 +0000
-+++ tools/external/driver-tool/build-version.hpp
-@@ -77,12 +77,12 @@ struct Version {
-     : packed((((uint32_t)major) << 24) | (((uint32_t)minor) << 16) | ((uint32_t)revision))
-     {}
- 
--    unsigned major() const noexcept { return packed >> 24; }
--    unsigned minor() const noexcept { return (packed >> 16) & 0xFF; }
-+    unsigned ncbi_major() const noexcept { return packed >> 24; }
-+    unsigned ncbi_minor() const noexcept { return (packed >> 16) & 0xFF; }
-     unsigned revision() const noexcept { return packed & 0xFFFF; }
- 
--    Version nextMinor() const noexcept { return Version(uint8_t(major()), uint8_t(minor() + 1), 0); }
--    Version nextMajor() const noexcept { return Version(uint8_t(major() + 1), 0, 0); }
-+    Version nextMinor() const noexcept { return Version(uint8_t(ncbi_major()), uint8_t(ncbi_minor() + 1), 0); }
-+    Version nextMajor() const noexcept { return Version(uint8_t(ncbi_major() + 1), 0, 0); }
- 
-     /// \brief Scan the name for a version string; if found, remove it.
-     /// \Returns The found version or `Version()`.
diff --git a/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp b/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp
index d96bf03fd8..325976371d 100644
--- a/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp
+++ b/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp
@@ -1,26 +1,27 @@
 $NetBSD$
 
-# pthread_main_np() for NetBSD
+# Add NetBSD pthread_main_np() stand-in
 
---- tools/external/driver-tool/sratools.cpp.orig	2023-08-12 23:35:22.000000000 +0000
+--- tools/external/driver-tool/sratools.cpp.orig	2023-08-15 12:51:29.845642918 +0000
 +++ tools/external/driver-tool/sratools.cpp
-@@ -578,9 +578,18 @@ static int main(CommandLine const &argv)
+@@ -578,11 +578,20 @@ static int main(CommandLine const &argv)
  
  } // namespace sratools
  
--#if BSD
 +#ifdef __NetBSD__
 +// Defined in sysmgr.c
-+extern pthread_t	_thr_main;
++extern pthread_t       _ncbi_thr_main;
 +#endif
 +
-+#if BSD && ! MAC
+ // BSD is defined when compiling on Mac
+ // Use the MAC case below, not this one
+ #if BSD && !MAC
  int main(int argc, char *argv[], char *envp[])
  {
 +#ifdef __NetBSD__
-+    _thr_main = pthread_self();
++    _ncbi_thr_main = pthread_self();
 +#endif
-+    
++
      auto const invocation = CommandLine(argc, argv, envp, nullptr);
      return sratools::main(invocation);
  }
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