sra-tools: Update to 3.1.1 and clean up

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: sra-tools: Update to 3.1.1 and clean up
From: Jason W. Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>
Date: Sun, 17 Nov 2024 14:57:30 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Nov 17 08:57:08 2024 -0600
Changeset:	c87e653f11600b919e4d76c146cb7ee74c936fc4

Modified Files:
	sra-tools/Makefile
	sra-tools/PLIST
	sra-tools/distinfo
Removed Files:
	sra-tools/patches/patch-ncbi-vdb_libs_kdbtext_path.hpp

Log Message:
sra-tools: Update to 3.1.1 and clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=c87e653f11600b919e4d76c146cb7ee74c936fc4

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

diffstat:
 sra-tools/Makefile                                 | 19 ++----
 sra-tools/PLIST                                    | 79 +++++++++++-----------
 sra-tools/distinfo                                 | 13 ++--
 .../patches/patch-ncbi-vdb_libs_kdbtext_path.hpp   | 14 ----
 4 files changed, 50 insertions(+), 75 deletions(-)

diffs:
diff --git a/sra-tools/Makefile b/sra-tools/Makefile
index 4345dfa7af..f6659eddf9 100644
--- a/sra-tools/Makefile
+++ b/sra-tools/Makefile
@@ -1,10 +1,9 @@
 # $NetBSD$
 
-DISTNAME=		sra-tools-3.0.10.133
+DISTNAME=		sra-tools-3.1.1
 CATEGORIES=		biology
 MASTER_SITES=		${MASTER_SITE_GITHUB:=ncbi/}
-GITHUB_TAG=		2a26be56758d6d6be3362f8c229f09ced4530873
-GITHUB_SUBMODULES+=	ncbi ncbi-vdb ff143ec1 ncbi-vdb
+GITHUB_SUBMODULES+=	ncbi ncbi-vdb 3.1.1 ncbi-vdb
 
 OWNER=		bacon%NetBSD.org@localhost
 HOMEPAGE=	https://github.com/ncbi/sra-tools
@@ -37,9 +36,8 @@ SUBST_FILES.submoddir+=	CMakeLists.txt
 
 REPLACE_BASH=	*/*.sh */*/*.sh */*/*/*.sh */*/*/*/*.sh
 
-USE_CMAKE=	yes
-CMAKE_CONFIGURE_ARGS+=	-DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
-CMAKE_CONFIGURE_ARGS+=	-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
+CMAKE_CONFIGURE_ARGS+=		-DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
+CMAKE_CONFIGURE_ARGS+=		-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
 BUILDLINK_TRANSFORM.NetBSD+=	rm:-ldl	# ncbi-vdb/CMakeLists.posix.txt
 
 EXAMPLESDIR=	${PREFIX}/share/examples/sra-tools
@@ -60,17 +58,10 @@ pre-configure:
 	${RM} -f ${WRKSRC}/ncbi-vdb/interfaces/cc/gcc/x86_64/byteswap.h
 .endif
 	cd ${WRKSRC}/ncbi-vdb/build && cmake -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON ..
-.if ${OPSYS} == Darwin
-	# Unsure how to prevent cmake from emitting @rpath in the first place
-	# No instances of @rpath or -install_name in any files before cmake
-	for f in ${WRKSRC}/ncbi-vdb/build/libs/ncbi-vdb/CMakeFiles/*/link.txt; do \
-		${SED} -e 's|@rpath|${PREFIX}/lib|g' $${f} > $${f}.tmp && ${MV} -f $${f}.tmp $${f}; \
-	done
-.endif
 	cd ${WRKSRC}/ncbi-vdb/build && ${MAKE}
 
 post-install:
-	${STRIP} ${DESTDIR}${PREFIX}/bin/*.3.1.0
+	${STRIP} ${DESTDIR}${PREFIX}/bin/*.${PKGVERSION}
 	${MV} ${DESTDIR}${PREFIX}/share/examples ${DESTDIR}${PREFIX}/share/examples-sratools
 	${MKDIR} ${DESTDIR}${EXAMPLESDIR}
 	${MV} ${DESTDIR}${PREFIX}/share/examples-sratools/* ${DESTDIR}${EXAMPLESDIR}
diff --git a/sra-tools/PLIST b/sra-tools/PLIST
index 8f401b8463..b6a6bb584c 100644
--- a/sra-tools/PLIST
+++ b/sra-tools/PLIST
@@ -1,92 +1,92 @@
 @comment $NetBSD$
 bin/abi-dump
 bin/abi-dump.3
-bin/abi-dump.3.1.0
+bin/abi-dump.${PKGVERSION}
 bin/align-info
 bin/align-info.3
-bin/align-info.3.1.0
+bin/align-info.${PKGVERSION}
 bin/cache-mgr
 bin/cache-mgr.3
-bin/cache-mgr.3.1.0
+bin/cache-mgr.${PKGVERSION}
 bin/check-corrupt
 bin/check-corrupt.3
-bin/check-corrupt.3.1.0
+bin/check-corrupt.${PKGVERSION}
 bin/fasterq-dump
-bin/fasterq-dump-orig.3.1.0
+bin/fasterq-dump-orig.${PKGVERSION}
 bin/fasterq-dump.3
-bin/fasterq-dump.3.1.0
+bin/fasterq-dump.${PKGVERSION}
 bin/fastq-dump
-bin/fastq-dump-orig.3.1.0
+bin/fastq-dump-orig.${PKGVERSION}
 bin/fastq-dump.3
-bin/fastq-dump.3.1.0
+bin/fastq-dump.${PKGVERSION}
 bin/illumina-dump
 bin/illumina-dump.3
-bin/illumina-dump.3.1.0
+bin/illumina-dump.${PKGVERSION}
 bin/kdbmeta
 bin/kdbmeta.3
-bin/kdbmeta.3.1.0
+bin/kdbmeta.${PKGVERSION}
 bin/ngs-pileup
 bin/ngs-pileup.3
-bin/ngs-pileup.3.1.0
+bin/ngs-pileup.${PKGVERSION}
 bin/prefetch
-bin/prefetch-orig.3.1.0
+bin/prefetch-orig.${PKGVERSION}
 bin/prefetch.3
-bin/prefetch.3.1.0
+bin/prefetch.${PKGVERSION}
 bin/rcexplain
 bin/rcexplain.3
-bin/rcexplain.3.1.0
+bin/rcexplain.${PKGVERSION}
 bin/ref-variation
 bin/ref-variation.3
-bin/ref-variation.3.1.0
+bin/ref-variation.${PKGVERSION}
 bin/sam-dump
-bin/sam-dump-orig.3.1.0
+bin/sam-dump-orig.${PKGVERSION}
 bin/sam-dump.3
-bin/sam-dump.3.1.0
+bin/sam-dump.${PKGVERSION}
 bin/sff-dump
 bin/sff-dump.3
-bin/sff-dump.3.1.0
+bin/sff-dump.${PKGVERSION}
 bin/sra-info
 bin/sra-info.3
-bin/sra-info.3.1.0
+bin/sra-info.${PKGVERSION}
 bin/sra-pileup
-bin/sra-pileup-orig.3.1.0
+bin/sra-pileup-orig.${PKGVERSION}
 bin/sra-pileup.3
-bin/sra-pileup.3.1.0
+bin/sra-pileup.${PKGVERSION}
 bin/sra-search
 bin/sra-search.3
-bin/sra-search.3.1.0
+bin/sra-search.${PKGVERSION}
 bin/sra-stat
 bin/sra-stat.3
-bin/sra-stat.3.1.0
+bin/sra-stat.${PKGVERSION}
 bin/srapath
-bin/srapath-orig.3.1.0
+bin/srapath-orig.${PKGVERSION}
 bin/srapath.3
-bin/srapath.3.1.0
+bin/srapath.${PKGVERSION}
 bin/sratools
 bin/sratools.3
-bin/sratools.3.1.0
+bin/sratools.${PKGVERSION}
 bin/test-sra
 bin/test-sra.3
-bin/test-sra.3.1.0
+bin/test-sra.${PKGVERSION}
 bin/var-expand
 bin/var-expand.3
-bin/var-expand.3.1.0
+bin/var-expand.${PKGVERSION}
 bin/vdb-config
 bin/vdb-config.3
-bin/vdb-config.3.1.0
+bin/vdb-config.${PKGVERSION}
 bin/vdb-decrypt
 bin/vdb-decrypt.3
-bin/vdb-decrypt.3.1.0
+bin/vdb-decrypt.${PKGVERSION}
 bin/vdb-dump
-bin/vdb-dump-orig.3.1.0
+bin/vdb-dump-orig.${PKGVERSION}
 bin/vdb-dump.3
-bin/vdb-dump.3.1.0
+bin/vdb-dump.${PKGVERSION}
 bin/vdb-encrypt
 bin/vdb-encrypt.3
-bin/vdb-encrypt.3.1.0
+bin/vdb-encrypt.${PKGVERSION}
 bin/vdb-validate
 bin/vdb-validate.3
-bin/vdb-validate.3.1.0
+bin/vdb-validate.${PKGVERSION}
 include/ncbi-vdb/NGS.hpp
 include/ngs/Alignment.hpp
 include/ngs/AlignmentIterator.hpp
@@ -181,21 +181,21 @@ include/ngs/win/stdbool.h
 lib/libncbi-ngs-c++-static.a
 lib/libncbi-ngs-c++.a
 lib/libncbi-ngs-c++.a.3
-lib/libncbi-ngs-c++.a.3.1.0
+lib/libncbi-ngs-c++.a.${PKGVERSION}
 lib/libncbi-ngs-static.a
 lib/libncbi-ngs.a
 lib/libncbi-ngs.a.3
-lib/libncbi-ngs.a.3.1.0
+lib/libncbi-ngs.a.${PKGVERSION}
 lib/libncbi-ngs.so
 lib/libncbi-ngs.so.3
-lib/libncbi-ngs.so.3.1.0
+lib/libncbi-ngs.so.${PKGVERSION}
 lib/libngs-c++-static.a
 lib/libngs-c++.a
 lib/libngs-c++.a.3
-lib/libngs-c++.a.3.1.0
+lib/libngs-c++.a.${PKGVERSION}
 lib/libngs-c++.so
 lib/libngs-c++.so.3
-lib/libngs-c++.so.3.1.0
+lib/libngs-c++.so.${PKGVERSION}
 share/examples/sra-tools/AlignSliceTest.cpp
 share/examples/sra-tools/AlignTest.cpp
 share/examples/sra-tools/DumpReferenceFASTA.cpp
@@ -213,4 +213,3 @@ share/examples/sra-tools/python/PileupTest.py
 share/examples/sra-tools/python/README.txt
 share/examples/sra-tools/python/RefTest.py
 share/examples/sra-tools/python/expected.txt
-
diff --git a/sra-tools/distinfo b/sra-tools/distinfo
index 2a36ad645a..8a5cc185d5 100644
--- a/sra-tools/distinfo
+++ b/sra-tools/distinfo
@@ -1,13 +1,12 @@
 $NetBSD$
 
-BLAKE2s (ncbi-ncbi-vdb-ff143ec1.tar.gz) = 66163ec0c658d03ed085425448ebbfebe23a67d28776d928384cdeb39d1bb4d1
-SHA512 (ncbi-ncbi-vdb-ff143ec1.tar.gz) = bf35ad78623f90fd8f9ddf30f33c8b8febb44a40fee1abad215fd8f1a986725593a2c94c7da82b5b8362fe9308cbf3ee026d14eb9921dac2e090a7710b93d202
-Size (ncbi-ncbi-vdb-ff143ec1.tar.gz) = 19057498 bytes
-BLAKE2s (sra-tools-3.0.10.133-2a26be56758d6d6be3362f8c229f09ced4530873.tar.gz) = 5a0f368e997114b00fd38c9bd05bc1d01565bb14e46a85e007f1535b0501b799
-SHA512 (sra-tools-3.0.10.133-2a26be56758d6d6be3362f8c229f09ced4530873.tar.gz) = f39bdd5036de1a1afec8c36badd5193ce4ce106202638f8e16e05518394c19241935aa6d8537d6554637663828ca44caaffd93f4ecbe0b731af67de7e868edce
-Size (sra-tools-3.0.10.133-2a26be56758d6d6be3362f8c229f09ced4530873.tar.gz) = 45451112 bytes
+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
-SHA1 (patch-ncbi-vdb_libs_kdbtext_path.hpp) = 78ec06ed7aa60fd2bded6129ddf25172c104ad77
 SHA1 (patch-ncbi-vdb_libs_kproc_bsd_sysmgr.c) = f49eb28f8bfeb528c1d7c2e9d184502b9eba273c
 SHA1 (patch-ngs_ngs-java_CMakeLists.txt) = 44b822381fd564d045406cc926f807adae9fbe59
 SHA1 (patch-tools_external_driver-tool_sratools.cpp) = c490d83f03471e6e8e34b8e88534469ed45b2886
diff --git a/sra-tools/patches/patch-ncbi-vdb_libs_kdbtext_path.hpp b/sra-tools/patches/patch-ncbi-vdb_libs_kdbtext_path.hpp
deleted file mode 100644
index 17f9a0b598..0000000000
--- a/sra-tools/patches/patch-ncbi-vdb_libs_kdbtext_path.hpp
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-# va_list
-
---- ncbi-vdb/libs/kdbtext/path.hpp.orig	2024-03-21 22:06:49.815904250 +0000
-+++ ncbi-vdb/libs/kdbtext/path.hpp
-@@ -28,6 +28,7 @@
- 
- #include <string>
- #include <queue>
-+#include <cstdarg>
- 
- #include <klib/rc.h>
-
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