sra-tools: Successful install on Alma8

[Jason W. Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Sun Aug 13 08:50:38 2023 -0500
Changeset:	014be9d1f8bd3cf56176a278e928dd31ecc5ca57

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

Log Message:
sra-tools: Successful install on Alma8

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=014be9d1f8bd3cf56176a278e928dd31ecc5ca57

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

diffstat:
 sra-tools/Makefile                      |   9 +-
 sra-tools/PLIST                         | 267 ++++++++++++++++++++++++++++++++
 sra-tools/distinfo                      |   1 +
 sra-tools/patches/patch-build_env.cmake |  15 ++
 4 files changed, 288 insertions(+), 4 deletions(-)

diffs:
diff --git a/sra-tools/Makefile b/sra-tools/Makefile
index bee2fc8d5f..e875057c29 100644
--- a/sra-tools/Makefile
+++ b/sra-tools/Makefile
@@ -12,7 +12,6 @@
 #LICENSE_FILE_PD=	${WRKSRC}/LICENSE
 #LICENSE_DISTFILES_LGPL21+ =
 #USE_LDCONFIG=	${PREFIX}/lib64
-#USE_JAVA=	yes
 # Builds with earlier versions, but ngs-doc plist differs if jdk17 is present
 #JAVA_VERSION=	17+
 
@@ -37,6 +36,8 @@ ONLY_FOR_PLATFORM=	 *-*-aarch64 *-*-x86_64
 
 USE_LANGUAGES=	c c++
 USE_TOOLS+=	bash bison cmake
+USE_JAVA=	yes
+USE_JAVA2=	17
 
 # The config.c and file-path.posix.cpp reinplaces follow
 # static patches.  Run "make clean patch" before updating
@@ -64,12 +65,14 @@ REPLACE_BASH=	*/*.sh */*/*.sh */*/*/*.sh
 USE_CMAKE=	yes
 # Check this
 CMAKE_ARGS+=	-DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
+CMAKE_ARGS+=	-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
 
+# FIXME: Check for libstdc++-static on Linux
 pre-configure:
 	cd ${WRKSRC}/ncbi-vdb/build && cmake .. && make
 
 post-install:
-	${STRIP} ${DESTDIR}${PREFIX}/bin/*.${DISTVERSION}
+	${STRIP} ${DESTDIR}${PREFIX}/bin/*.${PKGVERSION_NOREV}
 	${MV} ${DESTDIR}${PREFIX}/share/examples ${DESTDIR}${PREFIX}/share/examples-sratools
 	${MKDIR} ${DESTDIR}${EXAMPLESDIR}
 	${MV} ${DESTDIR}${PREFIX}/share/examples-sratools/* ${DESTDIR}${EXAMPLESDIR}
@@ -88,6 +91,4 @@ post-install:
 .include "../../devel/hdf5/buildlink3.mk"
 .include "../../archivers/zstd/buildlink3.mk"
 .include "../../devel/cmake/build.mk"
-# CentOS doesn't have zlib in the base, so uncomment if needed.
-# .include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/sra-tools/PLIST b/sra-tools/PLIST
index 48d96a5493..a7b500bdb7 100644
--- a/sra-tools/PLIST
+++ b/sra-tools/PLIST
@@ -1 +1,268 @@
 @comment $NetBSD$
+bin/abi-dump
+bin/abi-dump.3
+bin/abi-dump.${PKGVERSION}
+bin/align-info
+bin/align-info.3
+bin/align-info.${PKGVERSION}
+bin/cache-mgr
+bin/cache-mgr.3
+bin/cache-mgr.${PKGVERSION}
+bin/check-corrupt
+bin/check-corrupt.3
+bin/check-corrupt.${PKGVERSION}
+bin/fasterq-dump
+bin/fasterq-dump-orig.${PKGVERSION}
+bin/fasterq-dump.3
+bin/fasterq-dump.${PKGVERSION}
+bin/fastq-dump
+bin/fastq-dump-orig.${PKGVERSION}
+bin/fastq-dump.3
+bin/fastq-dump.${PKGVERSION}
+bin/illumina-dump
+bin/illumina-dump.3
+bin/illumina-dump.${PKGVERSION}
+bin/kdbmeta
+bin/kdbmeta.3
+bin/kdbmeta.${PKGVERSION}
+bin/ngs-pileup
+bin/ngs-pileup.3
+bin/ngs-pileup.${PKGVERSION}
+bin/prefetch
+bin/prefetch-orig.${PKGVERSION}
+bin/prefetch.3
+bin/prefetch.${PKGVERSION}
+bin/rcexplain
+bin/rcexplain.3
+bin/rcexplain.${PKGVERSION}
+bin/ref-variation
+bin/ref-variation.3
+bin/ref-variation.${PKGVERSION}
+bin/sam-dump
+bin/sam-dump-orig.${PKGVERSION}
+bin/sam-dump.3
+bin/sam-dump.${PKGVERSION}
+bin/sff-dump
+bin/sff-dump.3
+bin/sff-dump.${PKGVERSION}
+bin/sra-info
+bin/sra-info.3
+bin/sra-info.${PKGVERSION}
+bin/sra-pileup
+bin/sra-pileup-orig.${PKGVERSION}
+bin/sra-pileup.3
+bin/sra-pileup.${PKGVERSION}
+bin/sra-search
+bin/sra-search.3
+bin/sra-search.${PKGVERSION}
+bin/sra-stat
+bin/sra-stat.3
+bin/sra-stat.${PKGVERSION}
+bin/srapath
+bin/srapath-orig.${PKGVERSION}
+bin/srapath.3
+bin/srapath.${PKGVERSION}
+bin/sratools
+bin/sratools.3
+bin/sratools.${PKGVERSION}
+bin/test-sra
+bin/test-sra.3
+bin/test-sra.${PKGVERSION}
+bin/var-expand
+bin/var-expand.3
+bin/var-expand.${PKGVERSION}
+bin/vdb-config
+bin/vdb-config.3
+bin/vdb-config.${PKGVERSION}
+bin/vdb-decrypt
+bin/vdb-decrypt.3
+bin/vdb-decrypt.${PKGVERSION}
+bin/vdb-dump
+bin/vdb-dump-orig.${PKGVERSION}
+bin/vdb-dump.3
+bin/vdb-dump.${PKGVERSION}
+bin/vdb-encrypt
+bin/vdb-encrypt.3
+bin/vdb-encrypt.${PKGVERSION}
+bin/vdb-validate
+bin/vdb-validate.3
+bin/vdb-validate.${PKGVERSION}
+include/ncbi-vdb/NGS.hpp
+include/ngs/Alignment.hpp
+include/ngs/AlignmentIterator.hpp
+include/ngs/ErrorMsg.hpp
+include/ngs/Fragment.hpp
+include/ngs/FragmentIterator.hpp
+include/ngs/Package.hpp
+include/ngs/Pileup.hpp
+include/ngs/PileupEvent.hpp
+include/ngs/PileupEventIterator.hpp
+include/ngs/PileupIterator.hpp
+include/ngs/Read.hpp
+include/ngs/ReadCollection.hpp
+include/ngs/ReadGroup.hpp
+include/ngs/ReadGroupIterator.hpp
+include/ngs/ReadIterator.hpp
+include/ngs/Reference.hpp
+include/ngs/ReferenceIterator.hpp
+include/ngs/ReferenceSequence.hpp
+include/ngs/Statistics.hpp
+include/ngs/StringRef.hpp
+include/ngs/adapter/AlignmentItf.hpp
+include/ngs/adapter/ErrorMsg.hpp
+include/ngs/adapter/FragmentItf.hpp
+include/ngs/adapter/PileupEventItf.hpp
+include/ngs/adapter/PileupItf.hpp
+include/ngs/adapter/ReadCollectionItf.hpp
+include/ngs/adapter/ReadGroupItf.hpp
+include/ngs/adapter/ReadItf.hpp
+include/ngs/adapter/Refcount.hpp
+include/ngs/adapter/ReferenceItf.hpp
+include/ngs/adapter/ReferenceSequenceItf.hpp
+include/ngs/adapter/StatisticsItf.hpp
+include/ngs/adapter/StringItf.hpp
+include/ngs/adapter/defs.h
+include/ngs/inl/Alignment.hpp
+include/ngs/inl/AlignmentIterator.hpp
+include/ngs/inl/Fragment.hpp
+include/ngs/inl/FragmentIterator.hpp
+include/ngs/inl/Package.hpp
+include/ngs/inl/Pileup.hpp
+include/ngs/inl/PileupEvent.hpp
+include/ngs/inl/PileupEventIterator.hpp
+include/ngs/inl/PileupIterator.hpp
+include/ngs/inl/Read.hpp
+include/ngs/inl/ReadCollection.hpp
+include/ngs/inl/ReadGroup.hpp
+include/ngs/inl/ReadGroupIterator.hpp
+include/ngs/inl/ReadIterator.hpp
+include/ngs/inl/Reference.hpp
+include/ngs/inl/ReferenceIterator.hpp
+include/ngs/inl/ReferenceSequence.hpp
+include/ngs/inl/Statistics.hpp
+include/ngs/inl/StringRef.hpp
+include/ngs/itf/AlignmentItf.h
+include/ngs/itf/AlignmentItf.hpp
+include/ngs/itf/ErrBlock.h
+include/ngs/itf/ErrBlock.hpp
+include/ngs/itf/ErrorMsg.hpp
+include/ngs/itf/FragmentItf.h
+include/ngs/itf/FragmentItf.hpp
+include/ngs/itf/PackageItf.hpp
+include/ngs/itf/PileupEventItf.h
+include/ngs/itf/PileupEventItf.hpp
+include/ngs/itf/PileupItf.h
+include/ngs/itf/PileupItf.hpp
+include/ngs/itf/ReadCollectionItf.h
+include/ngs/itf/ReadCollectionItf.hpp
+include/ngs/itf/ReadGroupItf.h
+include/ngs/itf/ReadGroupItf.hpp
+include/ngs/itf/ReadItf.h
+include/ngs/itf/ReadItf.hpp
+include/ngs/itf/Refcount.h
+include/ngs/itf/Refcount.hpp
+include/ngs/itf/ReferenceItf.h
+include/ngs/itf/ReferenceItf.hpp
+include/ngs/itf/ReferenceSequenceItf.h
+include/ngs/itf/ReferenceSequenceItf.hpp
+include/ngs/itf/StatisticsItf.h
+include/ngs/itf/StatisticsItf.hpp
+include/ngs/itf/StringItf.h
+include/ngs/itf/StringItf.hpp
+include/ngs/itf/VTable.h
+include/ngs/itf/VTable.hpp
+include/ngs/itf/defs.h
+include/ngs/unix/arm64/atomic32.h
+include/ngs/unix/fat86/atomic32.h
+include/ngs/unix/i386/atomic32.h
+include/ngs/unix/x86_64/atomic32.h
+include/ngs/win/atomic32.h
+include/ngs/win/stdbool.h
+jar/ngs-doc.jar
+jar/ngs-examples.jar
+jar/ngs-java.jar
+jar/ngs-src.jar
+lib/libncbi-ngs-c++-static.a
+lib/libncbi-ngs-c++.a
+lib/libncbi-ngs-c++.a.3
+lib/libncbi-ngs-c++.a.${PKGVERSION}
+lib/libncbi-ngs-static.a
+lib/libncbi-ngs.a
+lib/libncbi-ngs.a.3
+lib/libncbi-ngs.a.${PKGVERSION}
+lib/libncbi-ngs.so
+lib/libncbi-ngs.so.3
+lib/libncbi-ngs.so.${PKGVERSION}
+lib/libngs-c++-static.a
+lib/libngs-c++.a
+lib/libngs-c++.a.3
+lib/libngs-c++.a.${PKGVERSION}
+lib/libngs-c++.so
+lib/libngs-c++.so.3
+lib/libngs-c++.so.${PKGVERSION}
+share/javadoc/ngs-doc/allclasses-index.html
+share/javadoc/ngs-doc/allclasses.html
+share/javadoc/ngs-doc/allpackages-index.html
+share/javadoc/ngs-doc/constant-values.html
+share/javadoc/ngs-doc/deprecated-list.html
+share/javadoc/ngs-doc/element-list
+share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/LibDependencies.html
+share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/NGS.html
+share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-summary.html
+share/javadoc/ngs-doc/gov/nih/nlm/ncbi/ngs/package-tree.html
+share/javadoc/ngs-doc/help-doc.html
+share/javadoc/ngs-doc/index-all.html
+share/javadoc/ngs-doc/index.html
+share/javadoc/ngs-doc/jquery-ui.overrides.css
+share/javadoc/ngs-doc/jquery/external/jquery/jquery.js
+share/javadoc/ngs-doc/jquery/jquery-3.6.1.min.js
+share/javadoc/ngs-doc/jquery/jquery-ui.min.css
+share/javadoc/ngs-doc/jquery/jquery-ui.min.js
+share/javadoc/ngs-doc/jquery/jszip-utils/dist/jszip-utils-ie.js
+share/javadoc/ngs-doc/jquery/jszip-utils/dist/jszip-utils-ie.min.js
+share/javadoc/ngs-doc/jquery/jszip-utils/dist/jszip-utils.js
+share/javadoc/ngs-doc/jquery/jszip-utils/dist/jszip-utils.min.js
+share/javadoc/ngs-doc/jquery/jszip/dist/jszip.js
+share/javadoc/ngs-doc/jquery/jszip/dist/jszip.min.js
+share/javadoc/ngs-doc/legal/ADDITIONAL_LICENSE_INFO
+share/javadoc/ngs-doc/legal/ASSEMBLY_EXCEPTION
+share/javadoc/ngs-doc/legal/LICENSE
+share/javadoc/ngs-doc/legal/jquery.md
+share/javadoc/ngs-doc/legal/jqueryUI.md
+share/javadoc/ngs-doc/legal/jszip.md
+share/javadoc/ngs-doc/legal/pako.md
+share/javadoc/ngs-doc/member-search-index.js
+share/javadoc/ngs-doc/member-search-index.zip
+share/javadoc/ngs-doc/ngs/Alignment.html
+share/javadoc/ngs-doc/ngs/AlignmentIterator.html
+share/javadoc/ngs-doc/ngs/ErrorMsg.html
+share/javadoc/ngs-doc/ngs/Fragment.html
+share/javadoc/ngs-doc/ngs/FragmentIterator.html
+share/javadoc/ngs-doc/ngs/Package.html
+share/javadoc/ngs-doc/ngs/Pileup.html
+share/javadoc/ngs-doc/ngs/PileupEvent.html
+share/javadoc/ngs-doc/ngs/PileupEventIterator.html
+share/javadoc/ngs-doc/ngs/PileupIterator.html
+share/javadoc/ngs-doc/ngs/Read.html
+share/javadoc/ngs-doc/ngs/ReadCollection.html
+share/javadoc/ngs-doc/ngs/ReadGroup.html
+share/javadoc/ngs-doc/ngs/ReadGroupIterator.html
+share/javadoc/ngs-doc/ngs/ReadIterator.html
+share/javadoc/ngs-doc/ngs/Reference.html
+share/javadoc/ngs-doc/ngs/ReferenceIterator.html
+share/javadoc/ngs-doc/ngs/ReferenceSequence.html
+share/javadoc/ngs-doc/ngs/Statistics.html
+share/javadoc/ngs-doc/ngs/package-summary.html
+share/javadoc/ngs-doc/ngs/package-tree.html
+share/javadoc/ngs-doc/overview-summary.html
+share/javadoc/ngs-doc/overview-tree.html
+share/javadoc/ngs-doc/package-search-index.js
+share/javadoc/ngs-doc/package-search-index.zip
+share/javadoc/ngs-doc/resources/glass.png
+share/javadoc/ngs-doc/resources/x.png
+share/javadoc/ngs-doc/script.js
+share/javadoc/ngs-doc/search.js
+share/javadoc/ngs-doc/serialized-form.html
+share/javadoc/ngs-doc/stylesheet.css
+share/javadoc/ngs-doc/type-search-index.js
+share/javadoc/ngs-doc/type-search-index.zip
diff --git a/sra-tools/distinfo b/sra-tools/distinfo
index a5ef546e1a..b06158a46a 100644
--- a/sra-tools/distinfo
+++ b/sra-tools/distinfo
@@ -6,3 +6,4 @@ 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
+SHA1 (patch-build_env.cmake) = f4dc781bb59aeb3d5c4377f741679069e80fe896
diff --git a/sra-tools/patches/patch-build_env.cmake b/sra-tools/patches/patch-build_env.cmake
new file mode 100644
index 0000000000..e3db199688
--- /dev/null
+++ b/sra-tools/patches/patch-build_env.cmake
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# libstdc++-static is not standard nor easy to install on Alma Linux
+
+--- build/env.cmake.orig	2023-08-13 13:33:25.870195377 +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