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biology/sra-tools: lib64 -> lib

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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
This commit is contained in:
Jason W. Bacon
2026-05-29 16:48:39 -05:00
parent ff0628cc99
commit b1346a4080
5 changed files with 46 additions and 27 deletions
Download Patch File Download Diff File Expand all files Collapse all files
biology/sra-tools/Makefile
+3 -3
View File
@@ -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}
biology/sra-tools/distinfo
+1 -1
View File
@@ -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
biology/sra-tools/files/patch-build_env.cmake
+10 -1
View File
@@ -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 ${CMAKE_INSTALL_PREFIX}/lib )
endif()
function( ExportStatic name install )
biology/sra-tools/files/patch-ncbi-vdb_libs_kfg_CMakeLists.txt
+10
View File
@@ -0,0 +1,10 @@
--- ncbi-vdb/libs/kfg/CMakeLists.txt.orig 2026-05-13 00:05:30 UTC
+++ ncbi-vdb/libs/kfg/CMakeLists.txt
@@ -58,6 +58,6 @@ if ( SINGLE_CONFIG AND NOT _NCBIVDB_CFG_PACKAGING)
if ( SINGLE_CONFIG AND NOT _NCBIVDB_CFG_PACKAGING)
install( SCRIPT CODE
- "execute_process(COMMAND /bin/bash -c \"${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()
biology/sra-tools/pkg-plist
+22 -22
View File
@@ -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.cpp