Date: Wed, 13 Feb 2019 09:51:05 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r492840 - in head: . science science/jmol science/jmol/files Message-ID: <201902130951.x1D9p5nI086474@repo.freebsd.org>
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Author: yuri Date: Wed Feb 13 09:51:05 2019 New Revision: 492840 URL: https://svnweb.freebsd.org/changeset/ports/492840 Log: Re-add: science/jmol: Java 3D viewer for chemical structures Added: head/science/jmol/ - copied from r418056, head/science/jmol/ Deleted: head/science/jmol/pkg-plist Modified: head/MOVED head/science/Makefile head/science/jmol/Makefile head/science/jmol/distinfo head/science/jmol/files/jmol.in head/science/jmol/pkg-descr Modified: head/MOVED ============================================================================== --- head/MOVED Wed Feb 13 09:48:53 2019 (r492839) +++ head/MOVED Wed Feb 13 09:51:05 2019 (r492840) @@ -8355,7 +8355,6 @@ irc/slirc||2016-07-04|Has expired: Broken for more tha irc/qwebirc||2016-07-04|Has expired: Broken for more than 6 months biology/platon||2016-07-04|Has expired: Broken for more than 6 months news/slnr||2016-07-04|Has expired: Broken for more than 6 months -science/jmol||2016-07-04|Has expired: Broken for more than 6 months net/nstxd||2016-07-04|Has expired: Broken for more than 6 months net/sprinkle||2016-07-04|Has expired: Broken for more than 6 months editors/ssam||2016-07-04|Has expired: Broken for more than 6 months Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Wed Feb 13 09:48:53 2019 (r492839) +++ head/science/Makefile Wed Feb 13 09:51:05 2019 (r492840) @@ -107,6 +107,7 @@ SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jdftx + SUBDIR += jmol SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kst2 Modified: head/science/jmol/Makefile ============================================================================== --- head/science/jmol/Makefile Mon Jul 4 20:44:22 2016 (r418056) +++ head/science/jmol/Makefile Wed Feb 13 09:51:05 2019 (r492840) @@ -1,46 +1,58 @@ # Created by: Wen heping <wenheping@gmail.com> # $FreeBSD$ -PORTNAME= jmol -PORTVERSION= 13.2.3 +PORTNAME= Jmol +DISTVERSION= 14.29.31 CATEGORIES= science java -MASTER_SITES= SF/${PORTNAME}/Jmol/Version%2013.2/Version%20${PORTVERSION}:source1 \ - http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/selfSignedCertificate/:source2 -DISTFILES= Jmol-${PORTVERSION}-full.tar.gz:source1 \ - selfSignedCertificate.cer:source2 \ - selfSignedCertificate.store:source2 -EXTRACT_ONLY= Jmol-${PORTVERSION}-full.tar.gz +MASTER_SITES= SF/${PORTNAME:tl}/${PORTNAME}/Version%20${DISTVERSION:R}/Jmol%20${DISTVERSION}/:src \ + http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/selfSignedCertificate/:cert +DISTFILES= ${PORTNAME}-${DISTVERSION}-full${EXTRACT_SUFX}:src \ + selfSignedCertificate.cer:cert \ + selfSignedCertificate.store:cert +EXTRACT_ONLY= ${PORTNAME}-${PORTVERSION}-full${EXTRACT_SUFX} -MAINTAINER= ports@FreeBSD.org -COMMENT= Open-source Java viewer for chemical structures in 3D +MAINTAINER= yuri@FreeBSD.org +COMMENT= Java 3D viewer for chemical structures -BROKEN= unfetchable -DEPRECATED= Broken for more than 6 months -EXPIRATION_DATE= 2016-07-04 +LICENSE= LGPL21 +LICENSE_FILE= ${WRKSRC}/LICENSE.txt USE_JAVA= yes -JAVA_VERSION= 1.7+ USE_ANT= yes -ALL_TARGET= all -WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} +NO_ARCH= yes + +WRKSRC= ${WRKDIR}/${PORTNAME:tl}-${DISTVERSION} SIGN_DIR= ${WRKSRC}/selfSignedCertificate -SUB_FILES= ${PORTNAME} +SUB_FILES= ${PORTNAME:tl} +SUB_LIST= JAVA=${JAVA} +JARS= ${PORTNAME}.jar ${PORTNAME}Data.jar ${PORTNAME}Lib.jar + +PLIST_FILES= bin/${PORTNAME:tl} \ + ${JARS:S/^/${JAVAJARDIR}\//} + OPTIONS_DEFINE= DOCS -DESKTOP_ENTRIES="Jmol" "" "" "${PORTNAME}" "" false +PORTDOCS= * +DESKTOP_ENTRIES="${PORTNAME}" "" "" "${PORTNAME:tl}" "" false + post-extract: @${MKDIR} ${SIGN_DIR} @${CP} ${DISTDIR}/selfSignedCertificate.cer ${SIGN_DIR} @${CP} ${DISTDIR}/selfSignedCertificate.store ${SIGN_DIR} +post-patch: + @${REINPLACE_CMD} 's|<input message="private property file.*||' ${WRKSRC}/build.xml + do-install: - ${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME} ${STAGEDIR}${PREFIX}/bin - (cd ${WRKSRC}/build && ${INSTALL_DATA} Jmol.jar JmolData.jar \ - JmolLib.jar ${STAGEDIR}${JAVAJARDIR}) - (cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR}) + ${INSTALL_SCRIPT} ${WRKDIR}/${PORTNAME:tl} ${STAGEDIR}${PREFIX}/bin +.for jar in ${JARS} + ${INSTALL_DATA} ${WRKSRC}/build/${jar} ${STAGEDIR}${JAVAJARDIR} +.endfor +do-install-DOCS-on: + cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR} + .include <bsd.port.mk> -.undef MAKE_ARGS Modified: head/science/jmol/distinfo ============================================================================== --- head/science/jmol/distinfo Mon Jul 4 20:44:22 2016 (r418056) +++ head/science/jmol/distinfo Wed Feb 13 09:51:05 2019 (r492840) @@ -1,5 +1,6 @@ -SHA256 (Jmol-13.2.3-full.tar.gz) = c5835015ddaebd90c286fbfd55938b6995046481c117a0cd20c7f369f61ba70f -SIZE (Jmol-13.2.3-full.tar.gz) = 116255368 +TIMESTAMP = 1550050423 +SHA256 (Jmol-14.29.31-full.tar.gz) = 359c7b664109e671b441cc1a37ef0d2a446f8dd37a48df46cb72e512cdf65e2e +SIZE (Jmol-14.29.31-full.tar.gz) = 143253985 SHA256 (selfSignedCertificate.cer) = 0fa14fd5f21593a328ba4439ac17b3b507969d71a2734e392239b83ae8ec2920 SIZE (selfSignedCertificate.cer) = 735 SHA256 (selfSignedCertificate.store) = 81b69722530d94dc599ce79382a3386cce518baa7ab79fbb530d13483b51bed5 Modified: head/science/jmol/files/jmol.in ============================================================================== --- head/science/jmol/files/jmol.in Mon Jul 4 20:44:22 2016 (r418056) +++ head/science/jmol/files/jmol.in Wed Feb 13 09:51:05 2019 (r492840) @@ -1,3 +1,3 @@ #!/bin/sh -exec java -Djmol.home="%%JAVAJARDIR%%" -jar "%%JAVAJARDIR%%/Jmol.jar" "$@" +exec %%JAVA%% -Djmol.home="%%JAVAJARDIR%%" -jar "%%JAVAJARDIR%%/Jmol.jar" "$@" Modified: head/science/jmol/pkg-descr ============================================================================== --- head/science/jmol/pkg-descr Mon Jul 4 20:44:22 2016 (r418056) +++ head/science/jmol/pkg-descr Wed Feb 13 09:51:05 2019 (r492840) @@ -1,9 +1,15 @@ -Jmol is a Java molecular viewer for -three-dimensional chemical structures. -Features include reading a variety -of file types and output from quantum -chemistry programs, and animation of -multi-frame files and computed normal -modes from quantum programs. +Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four +independent modes: an HTML5-only web application utilizing jQuery, a Java +applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side +component (JmolData.jar). Jmol can read many file types, including PDB, CIF, +SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, +GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other +quantum chemistry programs. Files can be transferred directly from several +databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple +files can be loaded and compared. A rich scripting language and a well-developed +web API allow easy customization of the user interface. Features include +interactive animation and linear morphing. Jmol interfaces well with JSpecView +for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD +programs for 3D printing (VRML export). -WWW: http://sourceforge.net/projects/jmol/ +WWW: https://sourceforge.net/projects/jmol/
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