From owner-dev-commits-ports-all@freebsd.org Sun Apr 25 23:04:33 2021 Return-Path: Delivered-To: dev-commits-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 23D385EF683; Sun, 25 Apr 2021 23:04:33 +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 "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4FT3WP0Vnlz4jhc; Sun, 25 Apr 2021 23:04:33 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (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 did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 03DF31CC22; Sun, 25 Apr 2021 23:04:33 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 13PN4Wb6084011; Sun, 25 Apr 2021 23:04:32 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 13PN4WSg084010; Sun, 25 Apr 2021 23:04:32 GMT (envelope-from git) Date: Sun, 25 Apr 2021 23:04:32 GMT Message-Id: <202104252304.13PN4WSg084010@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: af49fbec4f0f - main - biology/jalview: Update 2.07 -> 2.11.1.4 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: af49fbec4f0f6453b4b3dfe522107ed2918ae8f7 Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 25 Apr 2021 23:04:33 -0000 The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=af49fbec4f0f6453b4b3dfe522107ed2918ae8f7 commit af49fbec4f0f6453b4b3dfe522107ed2918ae8f7 Author: Yuri Victorovich AuthorDate: 2021-04-25 23:00:36 +0000 Commit: Yuri Victorovich CommitDate: 2021-04-25 23:00:36 +0000 biology/jalview: Update 2.07 -> 2.11.1.4 Take maintainership. --- biology/jalview/Makefile | 64 ++++++++++++++++++++++++++++++----- biology/jalview/distinfo | 7 ++-- biology/jalview/files/jalview.sh.in | 3 +- biology/jalview/files/patch-build.xml | 50 --------------------------- biology/jalview/pkg-descr | 2 +- biology/jalview/pkg-plist | 16 --------- 6 files changed, 62 insertions(+), 80 deletions(-) diff --git a/biology/jalview/Makefile b/biology/jalview/Makefile index 33341bd764c1..f99bd8d81676 100644 --- a/biology/jalview/Makefile +++ b/biology/jalview/Makefile @@ -1,27 +1,73 @@ # Created by: Fernan Aguero PORTNAME= jalview -PORTVERSION= 2.07 -PORTREVISION= 3 +DISTVERSION= 2.11.1.4 CATEGORIES= biology java -MASTER_SITES= http://www.jalview.org/source/ -DISTNAME= ${PORTNAME}_${PORTVERSION:S/./_/} +MASTER_SITES= https://www.jalview.org/source/ +DISTNAME= ${PORTNAME}_${DISTVERSION:S/./_/g} +DISTFILES= ${DISTNAME}${EXTRACT_SUFX} +EXTRACT_ONLY= ${PORTNAME}_${DISTVERSION:S/./_/g}${EXTRACT_SUFX} -MAINTAINER= ports@FreeBSD.org +EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} + +MAINTAINER= yuri@FreeBSD.org COMMENT= Viewer and editor for multiple sequence alignments +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= gradle:devel/gradle + USE_JAVA= yes -JAVA_VERSION= 8 -USE_ANT= yes -ALL_TARGET= makejars +JAVA_VERSION= 11 + WRKSRC= ${WRKDIR}/${PORTNAME} +USE_LOCALE= en_US.UTF-8 + DATADIR= ${JAVASHAREDIR}/${PORTNAME} SUB_FILES= jalview.sh +SUB_LIST= JAVA=${JAVA} + +NO_ARCH= yes + +# to rebuild the deps archive: +# 1. set DEV_UPDATE_MODE=yes +# 2. make makesum build +# 3. upload the *-deps archive +# 4. set DEV_UPDATE_MODE=no +# 5. make clean makesum + +DEV_UPDATE_MODE= no + +DEPS_CACHE_DIR= ${WRKDIR} + +.if (${DEV_UPDATE_MODE} == "yes") +post-build: + @cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME} + @${ECHO} "(!!!) Please upload the deps archive: ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}" +.else +MASTER_SITES+= LOCAL/yuri/:deps +DISTFILES+= ${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}:deps +GRADLE_ARGS= --offline + +post-extract: # need a separate extract step because the cache is in /tmp, and not under work/ like with maven + @cd ${DEPS_CACHE_DIR} && ${TAR} xzf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} +.endif + +BINARY_ALIAS= git=false java=${JAVA} + +PLIST_FILES= bin/jalview \ + ${DATADIR}/jalview.jar + +do-build: + @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} gradle \ + --gradle-user-home ${DEPS_CACHE_DIR}/gradle-${PORTNAME} --project-cache-dir ${DEPS_CACHE_DIR}/gradle-${PORTNAME} \ + ${GRADLE_ARGS} --build-cache shadowJar do-install: ${INSTALL_SCRIPT} ${WRKDIR}/jalview.sh ${STAGEDIR}${PREFIX}/bin/jalview @${MKDIR} ${STAGEDIR}${DATADIR} - ${INSTALL_DATA} ${WRKSRC}/dist/* ${STAGEDIR}${DATADIR} + ${INSTALL_DATA} ${WRKSRC}/build/libs/jalview-all-${DISTVERSION}-j${JAVA_VERSION}.jar ${STAGEDIR}${DATADIR}/jalview.jar .include diff --git a/biology/jalview/distinfo b/biology/jalview/distinfo index a92579a7f909..1a5fba7ea4d9 100644 --- a/biology/jalview/distinfo +++ b/biology/jalview/distinfo @@ -1,2 +1,5 @@ -SHA256 (jalview_2_07.tar.gz) = 2cc6b5ec40cf45b0e8e8048b98eacb14af230db6ed6929b95bec4ce0792a51f7 -SIZE (jalview_2_07.tar.gz) = 8439780 +TIMESTAMP = 1619390838 +SHA256 (jalview_2_11_1_4.tar.gz) = 30c0a89bbaf58bc5fd15fd7b167768d21cda1431676f28e22669fd5a342396eb +SIZE (jalview_2_11_1_4.tar.gz) = 103154170 +SHA256 (jalview-2.11.1.4-deps.tar.gz) = 93e88557841d295146aa5f9144e22a8774c9699c9a6a43a4a25673148d91c7d9 +SIZE (jalview-2.11.1.4-deps.tar.gz) = 21061379 diff --git a/biology/jalview/files/jalview.sh.in b/biology/jalview/files/jalview.sh.in index 33b1a7e75195..eb25b886f2de 100644 --- a/biology/jalview/files/jalview.sh.in +++ b/biology/jalview/files/jalview.sh.in @@ -1,4 +1,3 @@ #!/bin/sh -# Shell script to launch jalview using our javavm wrapper -"%%LOCALBASE%%/bin/java" -Djava.ext.dirs="%%DATADIR%%" -cp "%%DATADIR%%/jalview.jar" jalview.bin.Jalview +%%JAVA%% -classpath %%DATADIR%% -jar %%DATADIR%%/jalview.jar jalview.bin.Jalview diff --git a/biology/jalview/files/patch-build.xml b/biology/jalview/files/patch-build.xml deleted file mode 100644 index 7d6449347ba4..000000000000 --- a/biology/jalview/files/patch-build.xml +++ /dev/null @@ -1,50 +0,0 @@ -This patch removes the webstart support. - ---- build.xml.orig Mon Dec 12 14:57:02 2005 -+++ build.xml Fri Jan 27 12:20:52 2006 -@@ -180,6 +180,10 @@ - - - -+ - -+ - -+ - - - diff --git a/biology/jalview/pkg-descr b/biology/jalview/pkg-descr index dd89d5cac1a6..4fae9fde95ba 100644 --- a/biology/jalview/pkg-descr +++ b/biology/jalview/pkg-descr @@ -22,4 +22,4 @@ o Output alignments as HTML pages, images (PNG) or postscript (EPS). If you use Jalview in your work, please quote this publication. Clamp, M., et al. (2004), The Jalview Java Alignment Editor. Bioinformatics, 12, 426-7 -WWW: http://www.jalview.org +WWW: https://www.jalview.org diff --git a/biology/jalview/pkg-plist b/biology/jalview/pkg-plist deleted file mode 100644 index 763d29468ed4..000000000000 --- a/biology/jalview/pkg-plist +++ /dev/null @@ -1,16 +0,0 @@ -bin/jalview -%%DATADIR%%/activation.jar -%%DATADIR%%/xercesImpl.jar -%%DATADIR%%/wsdl4j.jar -%%DATADIR%%/saaj.jar -%%DATADIR%%/regex.jar -%%DATADIR%%/mail.jar -%%DATADIR%%/log4j-1.2.8.jar -%%DATADIR%%/jhall.jar -%%DATADIR%%/jaxrpc.jar -%%DATADIR%%/jalview.jar -%%DATADIR%%/commons-logging.jar -%%DATADIR%%/commons-discovery.jar -%%DATADIR%%/castor-0.9.6-xml.jar -%%DATADIR%%/axis.jar -%%DATADIR%%/xml-apis.jar