CVS commit: pkgsrc/biology/sra-tools

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology/sra-tools
From: "Jason Bacon" <bacon%netbsd.org@localhost>
Date: Sun, 2 Feb 2025 14:25:35 +0000

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sun Feb  2 14:25:35 UTC 2025

Modified Files:
        pkgsrc/biology/sra-tools: Makefile PLIST distinfo
        pkgsrc/biology/sra-tools/patches: patch-build_env.cmake
            patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c
            patch-ngs_ngs-java_CMakeLists.txt
            patch-ngs_ngs-python_examples_CMakeLists.txt
            patch-ngs_ngs-sdk_examples_CMakeLists.txt
            patch-tools_external_driver-tool_sratools.cpp
Added Files:
        pkgsrc/biology/sra-tools: patch-build_env.cmake

Log Message:
biology/sra-tools: Update to 3.2.0

Numerous fixes and enhancements
Changes: https://github.com/ncbi/sra-tools/commits/master/
Reported by: portscout


To generate a diff of this commit:
cvs rdiff -u -r1.9 -r1.10 pkgsrc/biology/sra-tools/Makefile
cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/sra-tools/PLIST \
    pkgsrc/biology/sra-tools/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/sra-tools/patch-build_env.cmake
cvs rdiff -u -r1.2 -r1.3 \
    pkgsrc/biology/sra-tools/patches/patch-build_env.cmake \
    pkgsrc/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c \
    pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt \
    pkgsrc/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp
cvs rdiff -u -r1.1 -r1.2 \
    pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt \
    pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt

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

Modified files:

Index: pkgsrc/biology/sra-tools/Makefile
diff -u pkgsrc/biology/sra-tools/Makefile:1.9 pkgsrc/biology/sra-tools/Makefile:1.10
--- pkgsrc/biology/sra-tools/Makefile:1.9       Tue Nov 19 20:22:31 2024
+++ pkgsrc/biology/sra-tools/Makefile   Sun Feb  2 14:25:34 2025
@@ -1,9 +1,9 @@
-# $NetBSD: Makefile,v 1.9 2024/11/19 20:22:31 bacon Exp $
+# $NetBSD: Makefile,v 1.10 2025/02/02 14:25:34 bacon Exp $
 
-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

Index: pkgsrc/biology/sra-tools/PLIST
diff -u pkgsrc/biology/sra-tools/PLIST:1.2 pkgsrc/biology/sra-tools/PLIST:1.3
--- pkgsrc/biology/sra-tools/PLIST:1.2  Tue Nov 19 20:22:32 2024
+++ pkgsrc/biology/sra-tools/PLIST      Sun Feb  2 14:25:34 2025
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.2 2024/11/19 20:22:32 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2025/02/02 14:25:34 bacon Exp $
 bin/abi-dump
 bin/abi-dump.3
 bin/abi-dump.${PKGVERSION}
Index: pkgsrc/biology/sra-tools/distinfo
diff -u pkgsrc/biology/sra-tools/distinfo:1.2 pkgsrc/biology/sra-tools/distinfo:1.3
--- pkgsrc/biology/sra-tools/distinfo:1.2       Tue Nov 19 20:22:32 2024
+++ pkgsrc/biology/sra-tools/distinfo   Sun Feb  2 14:25:34 2025
@@ -1,12 +1,12 @@
-$NetBSD: distinfo,v 1.2 2024/11/19 20:22:32 bacon Exp $
+$NetBSD: distinfo,v 1.3 2025/02/02 14:25:34 bacon Exp $
 
-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

Index: pkgsrc/biology/sra-tools/patches/patch-build_env.cmake
diff -u pkgsrc/biology/sra-tools/patches/patch-build_env.cmake:1.2 pkgsrc/biology/sra-tools/patches/patch-build_env.cmake:1.3
--- pkgsrc/biology/sra-tools/patches/patch-build_env.cmake:1.2  Tue Nov 19 20:22:32 2024
+++ pkgsrc/biology/sra-tools/patches/patch-build_env.cmake      Sun Feb  2 14:25:34 2025
@@ -1,15 +1,29 @@
-$NetBSD: patch-build_env.cmake,v 1.2 2024/11/19 20:22:32 bacon Exp $
+$NetBSD: patch-build_env.cmake,v 1.3 2025/02/02 14:25:34 bacon Exp $
 
 # 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
Index: pkgsrc/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c
diff -u pkgsrc/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c:1.2 pkgsrc/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c:1.3
--- pkgsrc/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c:1.2 Tue Nov 19 20:22:32 2024
+++ pkgsrc/biology/sra-tools/patches/patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c     Sun Feb  2 14:25:34 2025
@@ -1,4 +1,4 @@
-$NetBSD: patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c,v 1.2 2024/11/19 20:22:32 bacon Exp $
+$NetBSD: patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c,v 1.3 2025/02/02 14:25:34 bacon Exp $
 
 # Add NetBSD pthread_main_np() stand-in
 
Index: pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt
diff -u pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt:1.2 pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt:1.3
--- pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt:1.2      Tue Nov 19 20:22:32 2024
+++ pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-java_CMakeLists.txt  Sun Feb  2 14:25:34 2025
@@ -1,4 +1,4 @@
-$NetBSD: patch-ngs_ngs-java_CMakeLists.txt,v 1.2 2024/11/19 20:22:32 bacon Exp $
+$NetBSD: patch-ngs_ngs-java_CMakeLists.txt,v 1.3 2025/02/02 14:25:34 bacon Exp $
 
 # Disable java
 
Index: pkgsrc/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp
diff -u pkgsrc/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp:1.2 pkgsrc/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp:1.3
--- pkgsrc/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp:1.2  Tue Nov 19 20:22:32 2024
+++ pkgsrc/biology/sra-tools/patches/patch-tools_external_driver-tool_sratools.cpp      Sun Feb  2 14:25:35 2025
@@ -1,4 +1,4 @@
-$NetBSD: patch-tools_external_driver-tool_sratools.cpp,v 1.2 2024/11/19 20:22:32 bacon Exp $
+$NetBSD: patch-tools_external_driver-tool_sratools.cpp,v 1.3 2025/02/02 14:25:35 bacon Exp $
 
 # Add NetBSD pthread_main_np() stand-in
 

Index: pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt
diff -u pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt:1.1 pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt:1.2
--- pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt:1.1   Tue Nov 19 20:22:32 2024
+++ pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-python_examples_CMakeLists.txt       Sun Feb  2 14:25:34 2025
@@ -1,4 +1,4 @@
-$NetBSD: patch-ngs_ngs-python_examples_CMakeLists.txt,v 1.1 2024/11/19 20:22:32 bacon Exp $
+$NetBSD: patch-ngs_ngs-python_examples_CMakeLists.txt,v 1.2 2025/02/02 14:25:34 bacon Exp $
 
 # Canonicalize python examples dir
 
Index: pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt
diff -u pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt:1.1 pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt:1.2
--- pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt:1.1      Tue Nov 19 20:22:32 2024
+++ pkgsrc/biology/sra-tools/patches/patch-ngs_ngs-sdk_examples_CMakeLists.txt  Sun Feb  2 14:25:35 2025
@@ -1,4 +1,4 @@
-$NetBSD: patch-ngs_ngs-sdk_examples_CMakeLists.txt,v 1.1 2024/11/19 20:22:32 bacon Exp $
+$NetBSD: patch-ngs_ngs-sdk_examples_CMakeLists.txt,v 1.2 2025/02/02 14:25:35 bacon Exp $
 
 # Canonicalize examples dir
 

Added files:

Index: pkgsrc/biology/sra-tools/patch-build_env.cmake
diff -u /dev/null pkgsrc/biology/sra-tools/patch-build_env.cmake:1.1
--- /dev/null   Sun Feb  2 14:25:35 2025
+++ pkgsrc/biology/sra-tools/patch-build_env.cmake      Sun Feb  2 14:25:34 2025
@@ -0,0 +1,15 @@
+$NetBSD: patch-build_env.cmake,v 1.1 2025/02/02 14:25:34 bacon Exp $
+
+# 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
+@@ -555,7 +555,7 @@ endfunction()
+ function(MakeLinksExe target install_via_driver)
+ 
+     if ( "GNU" STREQUAL "${CMAKE_C_COMPILER_ID}" )
+-        target_link_options( ${target} PRIVATE -static-libgcc -static-libstdc++ )
++        target_link_options( ${target} PRIVATE )
+     endif()
+ 
+ # creates dependency loops

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