Date: Fri, 29 May 2026 21:53:54 +0000 From: Jason W. Bacon <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: b1346a408014 - main - biology/sra-tools: lib64 -> lib Message-ID: <6a1a0af2.3be1d.4363a494@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=b1346a408014d2319a633622a2099c3fa1275d90 commit b1346a408014d2319a633622a2099c3fa1275d90 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2026-05-29 21:48:39 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2026-05-29 21:48:39 +0000 biology/sra-tools: lib64 -> lib Patch to better respect filesystem hierarchy. The lib64 default was left alone originally because the old esoteric build system was difficult to patch. The new system is much simpler. Reporter indicated that the presence of ${PREFIX}/lib64 causes build failures in some other ports. PR: 294837 Reported by: milios@ccsys.com --- biology/sra-tools/Makefile | 6 +-- biology/sra-tools/distinfo | 2 +- biology/sra-tools/files/patch-build_env.cmake | 11 +++++- .../files/patch-ncbi-vdb_libs_kfg_CMakeLists.txt | 10 +++++ biology/sra-tools/pkg-plist | 44 +++++++++++----------- 5 files changed, 46 insertions(+), 27 deletions(-) diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile index ae9900e9a08b..6349393f5493 100644 --- a/biology/sra-tools/Makefile +++ b/biology/sra-tools/Makefile @@ -1,6 +1,6 @@ PORTNAME= sra-tools DISTVERSION= 3.4.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology java MAINTAINER= jwb@FreeBSD.org @@ -21,7 +21,7 @@ RUN_DEPENDS= hdf5>0:science/hdf5 USES= bison cmake java shebangfix USE_GITHUB= yes -USE_LDCONFIG= ${PREFIX}/lib64 +USE_LDCONFIG= yes # Builds with earlier versions, but ngs-doc plist differs if jdk17 is present JAVA_VERSION= 17 @@ -57,7 +57,7 @@ pre-configure: # Just hack the version out for now. Not sure we even need javadoc installed. post-stage: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.${DISTVERSION} - ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib64/*.${DISTVERSION} + ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.${DISTVERSION} post-stage-EXAMPLES-off: ${RM} -r ${STAGEDIR}${EXAMPLESDIR} diff --git a/biology/sra-tools/distinfo b/biology/sra-tools/distinfo index b1e90b984179..b25432518e22 100644 --- a/biology/sra-tools/distinfo +++ b/biology/sra-tools/distinfo @@ -1,4 +1,4 @@ -TIMESTAMP = 1774483084 +TIMESTAMP = 1778630814 SHA256 (ncbi-sra-tools-3.4.1_GH0.tar.gz) = 874dcbb28b7ebffb5554839254e777b1137b0f0430815bab175068decfe96e98 SIZE (ncbi-sra-tools-3.4.1_GH0.tar.gz) = 66796004 SHA256 (ncbi-ncbi-vdb-3.4.1_GH0.tar.gz) = 2fa0919b2842641ead93eeeb45047e87ca480a543b6e4eda15f94d5187e91c85 diff --git a/biology/sra-tools/files/patch-build_env.cmake b/biology/sra-tools/files/patch-build_env.cmake index b23966de6be0..c99cf6af041b 100644 --- a/biology/sra-tools/files/patch-build_env.cmake +++ b/biology/sra-tools/files/patch-build_env.cmake @@ -1,4 +1,4 @@ ---- build/env.cmake.orig 2026-05-12 21:39:17 UTC +--- build/env.cmake.orig 2026-03-25 20:33:21 UTC +++ build/env.cmake @@ -470,8 +470,8 @@ if( Python3_EXECUTABLE ) find_package( Python3 COMPONENTS Interpreter Development ) @@ -11,3 +11,12 @@ endif() endif() +@@ -485,7 +485,7 @@ if ( NOT CMAKE_INSTALL_LIBDIR ) + endif() + + if ( NOT CMAKE_INSTALL_LIBDIR ) +- set( CMAKE_INSTALL_LIBDIR ${CMAKE_INSTALL_PREFIX}/lib64 ) ++ set( CMAKE_INSTALL_LIBDIR ${CMAKE_INSTALL_PREFIX}/lib ) + endif() + + function( ExportStatic name install ) diff --git a/biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_CMakeLists.txt b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_CMakeLists.txt new file mode 100644 index 000000000000..57d8d6af7b16 --- /dev/null +++ b/biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_CMakeLists.txt @@ -0,0 +1,10 @@ +--- ncbi-vdb/libs/kfg/CMakeLists.txt.orig 2026-05-13 00:05:30 UTC ++++ ncbi-vdb/libs/kfg/CMakeLists.txt +@@ -58,6 +58,6 @@ if ( SINGLE_CONFIG AND NOT _NCBIVDB_CFG_PACKAGING) + + if ( SINGLE_CONFIG AND NOT _NCBIVDB_CFG_PACKAGING) + install( SCRIPT CODE +- "execute_process(COMMAND /bin/bash -c \"${CMAKE_CURRENT_SOURCE_DIR}/install.sh ${CMAKE_SOURCE_DIR}/interfaces/kfg/ncbi ${CMAKE_INSTALL_PREFIX}/lib64/ncbi /etc/ncbi ${CMAKE_SOURCE_DIR}/interfaces/kfg/ncbi/kfgsums \" )" ++ "execute_process(COMMAND /bin/bash -c \"${CMAKE_CURRENT_SOURCE_DIR}/install.sh ${CMAKE_SOURCE_DIR}/interfaces/kfg/ncbi ${CMAKE_INSTALL_PREFIX}/lib/ncbi /etc/ncbi ${CMAKE_SOURCE_DIR}/interfaces/kfg/ncbi/kfgsums \" )" + ) + endif() diff --git a/biology/sra-tools/pkg-plist b/biology/sra-tools/pkg-plist index b140de4f836a..1360b711e40f 100644 --- a/biology/sra-tools/pkg-plist +++ b/biology/sra-tools/pkg-plist @@ -177,28 +177,28 @@ include/ngs/win/stdbool.h jar/ngs-examples.jar jar/ngs-java.jar jar/ngs-src.jar -lib64/libkapp-static.a -lib64/libkapp.a -lib64/libkapp.a.3 -lib64/libkapp.a.%%PORTVERSION%% -lib64/libncbi-ngs-c++-static.a -lib64/libncbi-ngs-c++.a -lib64/libncbi-ngs-c++.a.3 -lib64/libncbi-ngs-c++.a.%%PORTVERSION%% -lib64/libncbi-ngs-static.a -lib64/libncbi-ngs.a -lib64/libncbi-ngs.a.3 -lib64/libncbi-ngs.a.%%PORTVERSION%% -lib64/libncbi-ngs.so -lib64/libncbi-ngs.so.3 -lib64/libncbi-ngs.so.%%PORTVERSION%% -lib64/libngs-c++-static.a -lib64/libngs-c++.a -lib64/libngs-c++.a.3 -lib64/libngs-c++.a.%%PORTVERSION%% -lib64/libngs-c++.so -lib64/libngs-c++.so.3 -lib64/libngs-c++.so.%%PORTVERSION%% +lib/libkapp-static.a +lib/libkapp.a +lib/libkapp.a.3 +lib/libkapp.a.%%PORTVERSION%% +lib/libncbi-ngs-c++-static.a +lib/libncbi-ngs-c++.a +lib/libncbi-ngs-c++.a.3 +lib/libncbi-ngs-c++.a.%%PORTVERSION%% +lib/libncbi-ngs-static.a +lib/libncbi-ngs.a +lib/libncbi-ngs.a.3 +lib/libncbi-ngs.a.%%PORTVERSION%% +lib/libncbi-ngs.so +lib/libncbi-ngs.so.3 +lib/libncbi-ngs.so.%%PORTVERSION%% +lib/libngs-c++-static.a +lib/libngs-c++.a +lib/libngs-c++.a.3 +lib/libngs-c++.a.%%PORTVERSION%% +lib/libngs-c++.so +lib/libngs-c++.so.3 +lib/libngs-c++.so.%%PORTVERSION%% %%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignSliceTest.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/AlignTest.cpp %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DumpReferenceFASTA.cpphome | help
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