From owner-svn-ports-all@freebsd.org Sun Mar 28 16:41:34 2021 Return-Path: Delivered-To: svn-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 C26E457F105; Sun, 28 Mar 2021 16:41:34 +0000 (UTC) (envelope-from yuri@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 4F7hLQ5BCZz4qJ8; Sun, 28 Mar 2021 16:41:34 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id A4F0523757; Sun, 28 Mar 2021 16:41:34 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 12SGfYfR041588; Sun, 28 Mar 2021 16:41:34 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 12SGfXcZ041585; Sun, 28 Mar 2021 16:41:33 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <202103281641.12SGfXcZ041585@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Sun, 28 Mar 2021 16:41:33 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r569400 - head/biology/igv X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: head/biology/igv X-SVN-Commit-Revision: 569400 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 28 Mar 2021 16:41:34 -0000 Author: yuri Date: Sun Mar 28 16:41:33 2021 New Revision: 569400 URL: https://svnweb.freebsd.org/changeset/ports/569400 Log: biology/igv: Update 2.8.13 -> 2.9.4 Modified: head/biology/igv/Makefile head/biology/igv/distinfo head/biology/igv/pkg-plist Modified: head/biology/igv/Makefile ============================================================================== --- head/biology/igv/Makefile Sun Mar 28 16:39:24 2021 (r569399) +++ head/biology/igv/Makefile Sun Mar 28 16:41:33 2021 (r569400) @@ -2,7 +2,7 @@ PORTNAME= igv DISTVERSIONPREFIX= v -DISTVERSION= 2.8.13 +DISTVERSION= 2.9.4 CATEGORIES= biology java MASTER_SITES= http://software.broadinstitute.org/software/igv/sites/cancerinformatics.org.igv/files/images/:img DISTFILES= tools.png:img @@ -33,7 +33,7 @@ MAKE_ENV+= GRADLE_USER_HOME=${WRKDIR} SUB_FILES= ${PORTNAME}.sh -DESKTOP_ENTRIES="IGV" "Integrative Genomics Viewer" "${PREFIX}/share/pixmaps/igv.xpm" "${PORTNAME}" \ +DESKTOP_ENTRIES="IGV" "Integrative Genomics Viewer" "${PREFIX}/share/pixmaps/igv.png" "${PORTNAME}" \ "Biology;Science;" true # to rebuild the deps archive: @@ -52,7 +52,7 @@ SUB_LIST= JAVA_HOME=${JAVA_HOME} .if (${DEV_UPDATE_MODE} == "yes") post-build: - @cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME} + @cd ${DEPS_CACHE_DIR} && ${TAR} czf ${DISTDIR}/${DIST_SUBDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX} gradle-${PORTNAME} @${ECHO} "(!!!) Please upload the deps archive: ${DISTDIR}/${DIST_SUBDIR}/${PORTNAME}-${DISTVERSION}-deps${EXTRACT_SUFX}" .else MASTER_SITES+= LOCAL/yuri/:deps Modified: head/biology/igv/distinfo ============================================================================== --- head/biology/igv/distinfo Sun Mar 28 16:39:24 2021 (r569399) +++ head/biology/igv/distinfo Sun Mar 28 16:41:33 2021 (r569400) @@ -1,7 +1,7 @@ -TIMESTAMP = 1606697368 -SHA256 (igv-2.8.13/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c -SIZE (igv-2.8.13/tools.png) = 5139 -SHA256 (igv-2.8.13/igv-2.8.13-deps.tar.gz) = 0bea74c4e1934fba8273c91ed9a6c2e88540b96823a8b8d4cf5c3d82617f330a -SIZE (igv-2.8.13/igv-2.8.13-deps.tar.gz) = 54089812 -SHA256 (igv-2.8.13/igvteam-igv-v2.8.13_GH0.tar.gz) = 891d3874ab2bc75d54c8f3ae8bc1df6b0b4b8b3f371d8699b17c69cbace77e7c -SIZE (igv-2.8.13/igvteam-igv-v2.8.13_GH0.tar.gz) = 122357224 +TIMESTAMP = 1616904994 +SHA256 (igv-2.9.4/tools.png) = 7a619d7770da008d1bc23a60a07f416625ba3a404a3656b8d1bda0de97415d1c +SIZE (igv-2.9.4/tools.png) = 5139 +SHA256 (igv-2.9.4/igv-2.9.4-deps.tar.gz) = 034056e5d8f5ddbd4575fd337d81cfe7fdea172e1ae8a043103dae2aa74be070 +SIZE (igv-2.9.4/igv-2.9.4-deps.tar.gz) = 54460338 +SHA256 (igv-2.9.4/igvteam-igv-v2.9.4_GH0.tar.gz) = 1c40f286fd0baf62a8f1b813d535200f8829fc489ba40944b2c8483b66c3b4a1 +SIZE (igv-2.9.4/igvteam-igv-v2.9.4_GH0.tar.gz) = 121959982 Modified: head/biology/igv/pkg-plist ============================================================================== --- head/biology/igv/pkg-plist Sun Mar 28 16:39:24 2021 (r569399) +++ head/biology/igv/pkg-plist Sun Mar 28 16:41:33 2021 (r569400) @@ -1,12 +1,13 @@ bin/igv %%JAVAJARDIR%%/igv/AbsoluteLayout-RELEASE110.jar -%%JAVAJARDIR%%/igv/apache-client-2.15.9.jar -%%JAVAJARDIR%%/igv/arns-2.15.9.jar -%%JAVAJARDIR%%/igv/auth-2.15.9.jar -%%JAVAJARDIR%%/igv/aws-core-2.15.9.jar -%%JAVAJARDIR%%/igv/aws-json-protocol-2.15.9.jar -%%JAVAJARDIR%%/igv/aws-query-protocol-2.15.9.jar -%%JAVAJARDIR%%/igv/aws-xml-protocol-2.15.9.jar +%%JAVAJARDIR%%/igv/annotations-2.15.67.jar +%%JAVAJARDIR%%/igv/apache-client-2.15.67.jar +%%JAVAJARDIR%%/igv/arns-2.15.67.jar +%%JAVAJARDIR%%/igv/auth-2.15.67.jar +%%JAVAJARDIR%%/igv/aws-core-2.15.67.jar +%%JAVAJARDIR%%/igv/aws-json-protocol-2.15.67.jar +%%JAVAJARDIR%%/igv/aws-query-protocol-2.15.67.jar +%%JAVAJARDIR%%/igv/aws-xml-protocol-2.15.67.jar %%JAVAJARDIR%%/igv/batik-awt-util-1.11.jar %%JAVAJARDIR%%/igv/batik-codec-1.11.jar %%JAVAJARDIR%%/igv/batik-constants-1.11.jar @@ -17,7 +18,7 @@ bin/igv %%JAVAJARDIR%%/igv/batik-transcoder-1.11.jar %%JAVAJARDIR%%/igv/batik-util-1.11.jar %%JAVAJARDIR%%/igv/batik-xml-1.11.jar -%%JAVAJARDIR%%/igv/cognitoidentity-2.15.9.jar +%%JAVAJARDIR%%/igv/cognitoidentity-2.15.67.jar %%JAVAJARDIR%%/igv/commons-codec-1.11.jar %%JAVAJARDIR%%/igv/commons-collections-20040616.jar %%JAVAJARDIR%%/igv/commons-compress-1.19.jar @@ -116,6 +117,7 @@ bin/igv %%JAVAJARDIR%%/igv/genomes/ca21.chrom.sizes %%JAVAJARDIR%%/igv/genomes/canFam2.chrom.sizes %%JAVAJARDIR%%/igv/genomes/canFam3.chrom.sizes +%%JAVAJARDIR%%/igv/genomes/canFam4.chrom.sizes %%JAVAJARDIR%%/igv/genomes/candida.chrom.sizes %%JAVAJARDIR%%/igv/genomes/cavPor3.chrom.sizes %%JAVAJARDIR%%/igv/genomes/ce10.chrom.sizes @@ -216,46 +218,46 @@ bin/igv %%JAVAJARDIR%%/igv/gson-2.8.5.jar %%JAVAJARDIR%%/igv/guava-27.0.1-jre.jar %%JAVAJARDIR%%/igv/htsjdk-2.23.0.jar -%%JAVAJARDIR%%/igv/http-client-spi-2.15.9.jar -%%JAVAJARDIR%%/igv/httpclient-4.5.9.jar -%%JAVAJARDIR%%/igv/httpcore-4.4.11.jar +%%JAVAJARDIR%%/igv/http-client-spi-2.15.67.jar +%%JAVAJARDIR%%/igv/httpclient-4.5.13.jar +%%JAVAJARDIR%%/igv/httpcore-4.4.13.jar %%JAVAJARDIR%%/igv/icb-utils-2.0.2.jar %%JAVAJARDIR%%/igv/igv.jar %%JAVAJARDIR%%/igv/j2objc-annotations-1.1.jar -%%JAVAJARDIR%%/igv/jackson-annotations-2.10.4.jar -%%JAVAJARDIR%%/igv/jackson-core-2.10.4.jar -%%JAVAJARDIR%%/igv/jackson-databind-2.10.4.jar +%%JAVAJARDIR%%/igv/jackson-annotations-2.10.5.jar +%%JAVAJARDIR%%/igv/jackson-core-2.10.5.jar +%%JAVAJARDIR%%/igv/jackson-databind-2.10.5.1.jar %%JAVAJARDIR%%/igv/jide-common-3.7.3.jar %%JAVAJARDIR%%/igv/jsap-3.0.0.jar %%JAVAJARDIR%%/igv/log4j-1.2-api-2.11.0.jar %%JAVAJARDIR%%/igv/log4j-api-2.11.0.jar %%JAVAJARDIR%%/igv/log4j-core-2.11.0.jar -%%JAVAJARDIR%%/igv/metrics-spi-2.15.9.jar -%%JAVAJARDIR%%/igv/netty-buffer-4.1.46.Final.jar -%%JAVAJARDIR%%/igv/netty-codec-4.1.46.Final.jar -%%JAVAJARDIR%%/igv/netty-codec-http-4.1.46.Final.jar -%%JAVAJARDIR%%/igv/netty-common-4.1.46.Final.jar -%%JAVAJARDIR%%/igv/netty-handler-4.1.46.Final.jar -%%JAVAJARDIR%%/igv/netty-nio-client-2.15.9.jar +%%JAVAJARDIR%%/igv/metrics-spi-2.15.67.jar +%%JAVAJARDIR%%/igv/netty-buffer-4.1.53.Final.jar +%%JAVAJARDIR%%/igv/netty-codec-4.1.53.Final.jar +%%JAVAJARDIR%%/igv/netty-codec-http-4.1.53.Final.jar +%%JAVAJARDIR%%/igv/netty-common-4.1.53.Final.jar +%%JAVAJARDIR%%/igv/netty-handler-4.1.53.Final.jar +%%JAVAJARDIR%%/igv/netty-nio-client-2.15.67.jar %%JAVAJARDIR%%/igv/netty-reactive-streams-2.0.4.jar %%JAVAJARDIR%%/igv/netty-reactive-streams-http-2.0.4.jar -%%JAVAJARDIR%%/igv/netty-resolver-4.1.46.Final.jar -%%JAVAJARDIR%%/igv/netty-transport-4.1.46.Final.jar -%%JAVAJARDIR%%/igv/netty-transport-native-epoll-4.1.46.Final-linux-x86_64.jar -%%JAVAJARDIR%%/igv/netty-transport-native-unix-common-4.1.46.Final.jar +%%JAVAJARDIR%%/igv/netty-resolver-4.1.53.Final.jar +%%JAVAJARDIR%%/igv/netty-transport-4.1.53.Final.jar +%%JAVAJARDIR%%/igv/netty-transport-native-epoll-4.1.53.Final-linux-x86_64.jar +%%JAVAJARDIR%%/igv/netty-transport-native-unix-common-4.1.53.Final.jar %%JAVAJARDIR%%/igv/ngs-java-2.9.0.jar -%%JAVAJARDIR%%/igv/profiles-2.15.9.jar +%%JAVAJARDIR%%/igv/profiles-2.15.67.jar %%JAVAJARDIR%%/igv/protobuf-java-3.7.0-rc1.jar -%%JAVAJARDIR%%/igv/protocol-core-2.15.9.jar +%%JAVAJARDIR%%/igv/protocol-core-2.15.67.jar %%JAVAJARDIR%%/igv/reactive-streams-1.0.3.jar -%%JAVAJARDIR%%/igv/regions-2.15.9.jar -%%JAVAJARDIR%%/igv/s3-2.15.9.jar -%%JAVAJARDIR%%/igv/sdk-core-2.15.9.jar +%%JAVAJARDIR%%/igv/regions-2.15.67.jar +%%JAVAJARDIR%%/igv/s3-2.15.67.jar +%%JAVAJARDIR%%/igv/sdk-core-2.15.67.jar %%JAVAJARDIR%%/igv/slf4j-api-1.7.28.jar %%JAVAJARDIR%%/igv/slf4j-simple-1.7.26.jar %%JAVAJARDIR%%/igv/snappy-java-1.1.7.3.jar -%%JAVAJARDIR%%/igv/sts-2.15.9.jar +%%JAVAJARDIR%%/igv/sts-2.15.67.jar %%JAVAJARDIR%%/igv/swing-layout-1.0.3.jar -%%JAVAJARDIR%%/igv/utils-2.15.9.jar +%%JAVAJARDIR%%/igv/utils-2.15.67.jar %%JAVAJARDIR%%/igv/xmlgraphics-commons-2.3.jar share/pixmaps/igv.png