sra-tools: Update to 3.2.0

[Jason W. Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <jtocino%gmx.com@localhost>
Pushed By:	outpaddling
Date:		Wed Jan 29 14:33:25 2025 -0600
Changeset:	a0a26eb2a7cd39ee33d11dfd22b266afcff0b7bd

Modified Files:
	sra-tools/Makefile
	sra-tools/distinfo
	sra-tools/patches/patch-build_env.cmake

Log Message:
sra-tools: Update to 3.2.0

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=a0a26eb2a7cd39ee33d11dfd22b266afcff0b7bd

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                      | 14 +++++++-------
 sra-tools/patches/patch-build_env.cmake | 26 ++++++++++++++++++++------
 3 files changed, 29 insertions(+), 15 deletions(-)

diffs:
diff --git a/sra-tools/Makefile b/sra-tools/Makefile
index 52ef319cc1..4a8b39850c 100644
--- a/sra-tools/Makefile
+++ b/sra-tools/Makefile
@@ -1,9 +1,9 @@
 # $NetBSD$
 
-DISTNAME=		sra-tools-3.1.1
+DISTNAME=		sra-tools-3.2.0
 CATEGORIES=		biology
 MASTER_SITES=		${MASTER_SITE_GITHUB:=ncbi/}
-GITHUB_SUBMODULES+=	ncbi ncbi-vdb 3.1.1 ncbi-vdb
+GITHUB_SUBMODULES+=	ncbi ncbi-vdb ${PKGVERSION_NOREV} 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 6b3c4f1642..b167b5dedf 100644
--- a/sra-tools/distinfo
+++ b/sra-tools/distinfo
@@ -1,12 +1,12 @@
 $NetBSD$
 
-BLAKE2s (ncbi-ncbi-vdb-3.1.1.tar.gz) = 60e10ac43b3bfbeac580fa1680ba86291b7f2656c950e6f13d0f2021a6894029
-SHA512 (ncbi-ncbi-vdb-3.1.1.tar.gz) = ccfeb38abf8eb80d54394b4a32d851e78408d9019d1ca4b53c71681e2e9ffec904d222b2d0d32fc98fe527f66c84764ae73a8d63dada7f3b5a33c51dc3f84462
-Size (ncbi-ncbi-vdb-3.1.1.tar.gz) = 19055901 bytes
-BLAKE2s (sra-tools-3.1.1.tar.gz) = de0665b9ec114fad64b052eda29e521612ea6dddaf5555a6ed32078222834553
-SHA512 (sra-tools-3.1.1.tar.gz) = df8ae5fca3761712306db6a98074d1b1e1a02a78c09c861852a16a9bc576fc39dd6e5afe0f1572e4901786fd3a757675fe0af7e79bb85d9eac021e69e88c48f1
-Size (sra-tools-3.1.1.tar.gz) = 45754110 bytes
-SHA1 (patch-build_env.cmake) = 14add56e66e5578fd0d51ce55329285e0981ac4e
+BLAKE2s (ncbi-ncbi-vdb-3.2.0.tar.gz) = eb3a98cb754ea78869adfc3651afce3f8e961e1f512e1f77427e9de85924ace2
+SHA512 (ncbi-ncbi-vdb-3.2.0.tar.gz) = badd63525eaaaeedb4de8bb0ab88b40cbeb388e0a0f93ac934c1af716da6f0fb2425eb2e1e95c198496a32fd9c04dfb8badf43b9b6f686b970411b18afec9ea2
+Size (ncbi-ncbi-vdb-3.2.0.tar.gz) = 19061110 bytes
+BLAKE2s (sra-tools-3.2.0.tar.gz) = 6afccc13740b972d483303db5040b0475484ebc6e62fb61f8e56e38f4946789c
+SHA512 (sra-tools-3.2.0.tar.gz) = ceddc5a2fd97c16ad56d130dc4469c6c8dd0f550825718b4fdd4c50d19e182bc42bc4c1681790ab3ea8912812fddb11dff03aca254999fc5b9e2c3fd39d42402
+Size (sra-tools-3.2.0.tar.gz) = 60313243 bytes
+SHA1 (patch-build_env.cmake) = 7c95dbe65c818ac638754ba6165eab1e613fe0eb
 SHA1 (patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c) = f49eb28f8bfeb528c1d7c2e9d184502b9eba273c
 SHA1 (patch-ngs_ngs-java_CMakeLists.txt) = 44b822381fd564d045406cc926f807adae9fbe59
 SHA1 (patch-ngs_ngs-python_examples_CMakeLists.txt) = a8a01d17a27c060c08311ab8571ae10af265781d
diff --git a/sra-tools/patches/patch-build_env.cmake b/sra-tools/patches/patch-build_env.cmake
index 4b7c4c08af..d0854ac90a 100644
--- a/sra-tools/patches/patch-build_env.cmake
+++ b/sra-tools/patches/patch-build_env.cmake
@@ -2,14 +2,28 @@ $NetBSD$
 
 # static standard libs are not standard nor easy to install on Alma Linux
 
---- build/env.cmake.orig	2023-08-13 18:06:02.445968665 +0000
+--- build/env.cmake.orig	2025-01-29 20:24:37.167226512 +0000
 +++ build/env.cmake
-@@ -555,7 +555,7 @@ endfunction()
- function(MakeLinksExe target install_via_driver)
+@@ -574,9 +574,7 @@ include(CheckCXXSourceRuns)
+ 
+ if ( "GNU" STREQUAL "${CMAKE_C_COMPILER_ID}" )
+     # check for the presence of static C/C++ runtime libraries
+-    set(CMAKE_REQUIRED_LINK_OPTIONS -static-libgcc)
+     check_cxx_source_runs("int main(int argc, char *argv[]) { return 0; }" HAVE_STATIC_LIBGCC)
+-    set(CMAKE_REQUIRED_LINK_OPTIONS -static-libstdc++)
+     check_cxx_source_runs("int main(int argc, char *argv[]) { return 0; }" HAVE_STATIC_LIBSTDCXX)
+ endif()
+ 
+@@ -584,10 +582,10 @@ function(MakeLinksExe target install_via
  
      if ( "GNU" STREQUAL "${CMAKE_C_COMPILER_ID}" )
--        target_link_options( ${target} PRIVATE -static-libgcc -static-libstdc++ )
-+        target_link_options( ${target} PRIVATE )
+         if ( HAVE_STATIC_LIBGCC )
+-            target_link_options( ${target} PRIVATE -static-libgcc )
++            target_link_options( ${target} PRIVATE )
+         endif()
+         if ( HAVE_STATIC_LIBSTDCXX )
+-            target_link_options( ${target} PRIVATE -static-libstdc++ )
++            target_link_options( ${target} PRIVATE )
+         endif()
      endif()
  
- # creates dependency loops