From nobody Fri May 29 21:53:54 2026 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4gRxvR0tZqz6g92d for ; Fri, 29 May 2026 21:53:55 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R13" (not verified)) by mx1.freebsd.org (Postfix) with ESMTPS id 4gRxvQ72Zcz4DHY for ; Fri, 29 May 2026 21:53:54 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1780091635; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=Yn/Js3VA2sPWWUSmzuUalOC+nOfix9khZwzjjnWSxPc=; b=Rtkj1K+KcUUabgAXwf+A8/NEYnhrcJ68SgQspSwH27hFHwE0qUT9OzVlOlKYwAuD/LiwQJ eegQegn5OsV38RM/3LUUtFvao+CTtVRF0O/4V0JzBZ1jMIzB5ymZJ4Ryr+5H5c/zZNrvaa G9nBCnY6YJWh7jQMAXPbbJXOL1jTFU59CnnNi96RJ6Vg06dTQJlYfoNtzUrOU5BOj6XztB /alM/e+il1lPTiblSb3ZSg5yLpiaovurqvrHnyZx71rXhM6TtgHhCVQ1ssrgjmaKs7aOPS SodyMClhq65G9qyi+LSxN6AUwHG1M2eksrKRfmvjbPYjP8Tp2n05YE2sSUncTQ== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1780091635; a=rsa-sha256; cv=none; b=kZb7XZoKwrnH2Q4OXzaqn6quPxyqQdPjnw8C3a7Ovcoyhmi3dasIEUYkThGNBxZEpRHp6H 4c1K9EHBzvvBYVR9EerWFNKYAQApts3yIKh9YIbowy8lpVC+O6e263x4HroJ9JYTcw8tsY 5uslGLLeJdIHkmj72D0sbWC2h+wlzGtw/iETOSgUZWOvF4U1gw6zVKdH2KIjuXWjiLdk8D fPuKJiAylxmJKeBzWPkTg3Xwrp0Qlw4IKxuNQsAwpZhCzfmJmzDizaGxjJl71MtvgXjAEa TAHjIUv0HpbMTC+l5qlNw6sIpWClLhktsM7Z/BIeOtc9K94N4YskplT5qFw9hA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1780091635; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=Yn/Js3VA2sPWWUSmzuUalOC+nOfix9khZwzjjnWSxPc=; b=B+Nd/k7IIfsW1czjra1B0mNm5O1fLtw6Cvy8tBnyLFJZ7ugyRmWWanUmydUTk1EJE4a6NI y2to2ZO7Xr5KWsXVzS6WTtsu5+p1oDQywMdUQ/4LvK13qi8KeGWM4JVQXLzlvp1GCiEZPM xaKcACX95LffQQwLxNz0Wk26XX2ytVkuZsBnjdydsuMaboz2Nm5BBI2uygtIjD6egh3JIn OfAPESOwmBBcym2E42/x70q9NAw0Yc+ygbFp1mX7z5OvjSYwzLI3aP4Qv4aYSpgA5HGuip CUih0mhm1PJ4MYl397CfERssfIC0QMxqY+cwBnoEw8/E9bHTIOA+hYPdzFhcNg== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4gRxvQ6KvpzrTh for ; Fri, 29 May 2026 21:53:54 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from git (uid 1279) (envelope-from git@FreeBSD.org) id 3be1d by gitrepo.freebsd.org (DragonFly Mail Agent v0.13+ on gitrepo.freebsd.org); Fri, 29 May 2026 21:53:54 +0000 To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Jason W. Bacon Subject: git: b1346a408014 - main - biology/sra-tools: lib64 -> lib List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@FreeBSD.org List-Id: List-Post: List-Help: List-Subscribe: List-Unsubscribe: List-Owner: Precedence: list MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: b1346a408014d2319a633622a2099c3fa1275d90 Auto-Submitted: auto-generated Date: Fri, 29 May 2026 21:53:54 +0000 Message-Id: <6a1a0af2.3be1d.4363a494@gitrepo.freebsd.org> The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=b1346a408014d2319a633622a2099c3fa1275d90 commit b1346a408014d2319a633622a2099c3fa1275d90 Author: Jason W. Bacon AuthorDate: 2026-05-29 21:48:39 +0000 Commit: Jason W. Bacon 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.cpp