Date: Tue, 13 May 2008 16:08:31 GMT From: Wen Heping <wenheping@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/123631: [NEW PORT] science/jmol : An Open-Source Java Viewer for Chemical Structures in 3D Message-ID: <200805131608.m4DG8V9I010182@www.freebsd.org> Resent-Message-ID: <200805131610.m4DGA2l2016540@freefall.freebsd.org>
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>Number: 123631 >Category: ports >Synopsis: [NEW PORT] science/jmol : An Open-Source Java Viewer for Chemical Structures in 3D >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Tue May 13 16:10:02 UTC 2008 >Closed-Date: >Last-Modified: >Originator: Wen Heping >Release: FreeBSD 7.0 release >Organization: ChangAn Middle School >Environment: FreeBSD fb7.wenjing.com 7.0-RELEASE FreeBSD 7.0-RELEASE #0: Sun Feb 24 19:59:52 UTC 2008 root@logan.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC i386 >Description: 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. WWW: http://sourceforge.net/projects/jmol/ >How-To-Repeat: >Fix: Patch attached with submission follows: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # /usr/ports/science/jmol # /usr/ports/science/jmol/Makefile # /usr/ports/science/jmol/pkg-descr # /usr/ports/science/jmol/distinfo # /usr/ports/science/jmol/pkg-plist # echo c - /usr/ports/science/jmol mkdir -p /usr/ports/science/jmol > /dev/null 2>&1 echo x - /usr/ports/science/jmol/Makefile sed 's/^X//' >/usr/ports/science/jmol/Makefile << 'END-of-/usr/ports/science/jmol/Makefile' X# Ports collection makefile for: jmol X# Date created: May 11, 2008 X# Whom: Wen heping <wenheping@gmail.com> X# X# $FreeBSD$ X# X XPORTNAME= jmol XPORTVERSION= 11.4.2 XCATEGORIES= science java XMASTER_SITES= SF:source1 \ X http://jmol.svn.sourceforge.net/viewvc/*checkout*/jmol/trunk/Jmol/selfSignedCertificate/:source2 XDISTFILES= ${PORTNAME}-${PORTVERSION}-full.tar.gz:source1 \ X selfSignedCertificate.cer:source2 \ X selfSignedCertificate.store:source2 XEXTRACT_ONLY= ${PORTNAME}-${PORTVERSION}-full.tar.gz X XMAINTAINER= wenheping@gmail.com XCOMMENT= An Open-Source Java Viewer for Chemical Structures in 3D X XUSE_JAVA= yes XJAVA_VERSION= 1.4+ XWRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} XJMOL_FILES= Jmol.jar JmolApplet.jar JmolApplet0.jar \ X JmolApplet0_Core.jar JmolApplet0_Jars.jar \ X JmolApplet0_Jvxl.jar JmolApplet0_Main.jar \ X JmolApplet0_Popup.jar JmolApplet0_Quantum.jar \ X JmolApplet0_ReadersCifPdb.jar JmolApplet0_ReadersMolXyz.jar \ X JmolApplet0_ReadersMore.jar JmolApplet0_ReadersXml.jar \ X JmolApplet0_ShapeBio.jar JmolApplet0_ShapeSpecial.jar \ X JmolApplet0_Smiles.jar JmolApplet0_Viewer.jar \ X JmolApplet0_i18n.jar XJMOL_FILES_EXT= Jmol.js XSIGN_DIR= ${WRKSRC}/selfSignedCertificate X X.if !defined(WITHOUT_COMPILE) XUSE_ANT= yes XALL_TARGET= all X.if !defined(NOPORTDOCS) XALL_TARGET= main X.endif X.else XNO_BUILD= yes X.endif X X.include <bsd.port.pre.mk> X Xpre-fetch: X @${ECHO_MSG} "" X @${ECHO_MSG} "You may use the following build options:" X @${ECHO_MSG} "" X @${ECHO_MSG} " WITHOUT_COMPILE=yes Install the pre-compiled .jar file" X @${ECHO_MSG} "" X Xpost-extract: X @${MKDIR} ${SIGN_DIR} X @${CP} ${DISTDIR}/selfSignedCertificate.cer ${SIGN_DIR} X @${CP} ${DISTDIR}/selfSignedCertificate.store ${SIGN_DIR} X Xdo-install: X.for j in ${JMOL_FILES_EXT} X ${INSTALL_DATA} ${WRKSRC}/${j} ${JAVAJARDIR} X.endfor X X.if !defined(WITHOUT_COMPILE) X.for j in ${JMOL_FILES} X ${INSTALL_DATA} ${WRKSRC}/build/${j} ${JAVAJARDIR} X.endfor X.else X.for j in ${JMOL_FILES} X ${INSTALL_DATA} ${WRKSRC}/${j} ${JAVAJARDIR} X.endfor X.endif X X.if !defined(NOPORTDOCS) X @${ECHO_MSG} -n ">> Installing documentation in ${DOCSDIR}..." X @cd ${WRKSRC}/doc && ${FIND} . -type d -exec ${MKDIR} ${DOCSDIR}/{} \; X @cd ${WRKSRC}/doc && ${FIND} . -type f -exec \ X ${INSTALL_DATA} {} ${DOCSDIR}/{} \; X @${ECHO_MSG} " [DONE]" X.endif X X.include <bsd.port.post.mk> END-of-/usr/ports/science/jmol/Makefile echo x - /usr/ports/science/jmol/pkg-descr sed 's/^X//' >/usr/ports/science/jmol/pkg-descr << 'END-of-/usr/ports/science/jmol/pkg-descr' XJmol is a Java molecular viewer for Xthree-dimensional chemical structures. XFeatures include reading a variety Xof file types and output from quantum Xchemistry programs, and animation of Xmulti-frame files and computed normal Xmodes from quantum programs. X XWWW: http://sourceforge.net/projects/jmol/ END-of-/usr/ports/science/jmol/pkg-descr echo x - /usr/ports/science/jmol/distinfo sed 's/^X//' >/usr/ports/science/jmol/distinfo << 'END-of-/usr/ports/science/jmol/distinfo' XMD5 (jmol-11.4.2-full.tar.gz) = 58b0cd6a38be0c94d4943c1e74a7d8b5 XSHA256 (jmol-11.4.2-full.tar.gz) = 8890805394a8d0d0260739e230b30bbd3eb6c915fd5c6c6fc21478be9e29ecaf XSIZE (jmol-11.4.2-full.tar.gz) = 15926387 XMD5 (selfSignedCertificate.cer) = ec6c4b413be88a8fab584399cc931d55 XSHA256 (selfSignedCertificate.cer) = 0fa14fd5f21593a328ba4439ac17b3b507969d71a2734e392239b83ae8ec2920 XSIZE (selfSignedCertificate.cer) = 735 XMD5 (selfSignedCertificate.store) = bf2be32212c831e4fa369809a639b75d XSHA256 (selfSignedCertificate.store) = 81b69722530d94dc599ce79382a3386cce518baa7ab79fbb530d13483b51bed5 XSIZE (selfSignedCertificate.store) = 1516 END-of-/usr/ports/science/jmol/distinfo echo x - /usr/ports/science/jmol/pkg-plist sed 's/^X//' >/usr/ports/science/jmol/pkg-plist << 'END-of-/usr/ports/science/jmol/pkg-plist' X%%DOCSDIR%%/JmolAppletGuide.html X%%DOCSDIR%%/JmolDevelopersGuide.html X%%DOCSDIR%%/JmolUserGuide/ch01.html X%%DOCSDIR%%/JmolUserGuide/ch02.html X%%DOCSDIR%%/JmolUserGuide/ch02s02.html X%%DOCSDIR%%/JmolUserGuide/ch02s03.html X%%DOCSDIR%%/JmolUserGuide/ch02s04.html X%%DOCSDIR%%/JmolUserGuide/ch02s05.html X%%DOCSDIR%%/JmolUserGuide/ch02s06.html X%%DOCSDIR%%/JmolUserGuide/ch02s07.html X%%DOCSDIR%%/JmolUserGuide/ch03.html X%%DOCSDIR%%/JmolUserGuide/ch03s02.html X%%DOCSDIR%%/JmolUserGuide/ch03s03.html X%%DOCSDIR%%/JmolUserGuide/ch03s04.html X%%DOCSDIR%%/JmolUserGuide/ch03s05.html X%%DOCSDIR%%/JmolUserGuide/ch04.html X%%DOCSDIR%%/JmolUserGuide/index.html X%%DOCSDIR%%/docbook-xml-4.4.zip X%%DOCSDIR%%/docbook-xsl-1.73.2.tar.gz X%%DOCSDIR%%/ibm.license.html X%%DOCSDIR%%/jcfl-1.2.6-source.tar.gz X%%DOCSDIR%%/jpegEncoder.license X%%DOCSDIR%%/lgpl.license X%%DOCSDIR%%/rasmol26.license X%%DOCSDIR%%/source/JmolAppletGuide.docbook.xml X%%DOCSDIR%%/source/JmolAppletGuide_de.docbook.xml X%%DOCSDIR%%/source/JmolAppletGuide_fr.docbook.xml X%%DOCSDIR%%/source/JmolDevelopersGuide.docbook.xml X%%DOCSDIR%%/source/JmolDevelopersGuide_de.docbook.xml X%%DOCSDIR%%/source/JmolDevelopersGuide_fr.docbook.xml X%%DOCSDIR%%/source/JmolGuide.docbook.xml X%%DOCSDIR%%/source/JmolGuide_de.docbook.xml X%%DOCSDIR%%/source/JmolGuide_fr.docbook.xml X%%DOCSDIR%%/source/JmolHistory.xml X%%DOCSDIR%%/source/JmolHistoryToHtml.xsl X%%DOCSDIR%%/source/JmolHistory_fr.xml X%%DOCSDIR%%/source/JmolHistory_nl.xml X%%DOCSDIR%%/source/applet/browsers.docbook.xml X%%DOCSDIR%%/source/applet/browsers_fr.docbook.xml X%%DOCSDIR%%/source/applet/hardware.docbook.xml X%%DOCSDIR%%/source/applet/hardware_fr.docbook.xml X%%DOCSDIR%%/source/applet/intro.docbook.xml X%%DOCSDIR%%/source/applet/intro_fr.docbook.xml X%%DOCSDIR%%/source/applet/serverconfig.docbook.xml X%%DOCSDIR%%/source/applet/serverconfig_fr.docbook.xml X%%DOCSDIR%%/source/applet/usage.docbook.xml X%%DOCSDIR%%/source/applet/usage_fr.docbook.xml X%%DOCSDIR%%/source/guide/commandline.docbook.xml X%%DOCSDIR%%/source/guide/commandline_fr.docbook.xml X%%DOCSDIR%%/source/guide/intro.docbook.xml X%%DOCSDIR%%/source/guide/intro_fr.docbook.xml X%%DOCSDIR%%/source/guide/menus.docbook.xml X%%DOCSDIR%%/source/guide/menus_fr.docbook.xml X%%DOCSDIR%%/source/guide/scriptCommands.docbook.xml X%%DOCSDIR%%/source/guide/scripts.docbook.xml X%%DOCSDIR%%/source/guide/scripts_fr.docbook.xml X%%DOCSDIR%%/source/history/changes.xml X%%DOCSDIR%%/source/history/changes_fr.xml X%%DOCSDIR%%/source/history/changes_nl.xml X%%DOCSDIR%%/source/history/contributors.xml X%%DOCSDIR%%/source/po/JmolAppletGuide.de.po X%%DOCSDIR%%/source/po/JmolAppletGuide.pot X%%DOCSDIR%%/source/po/JmolDevelopersGuide.de.po X%%DOCSDIR%%/source/po/JmolDevelopersGuide.pot X%%DOCSDIR%%/source/po/JmolGuide.de.po X%%DOCSDIR%%/source/po/JmolGuide.pot X%%DOCSDIR%%/source/xml2po-modes/docbook.py X%%DOCSDIR%%/source/xml2po-modes/empty.py X%%DOCSDIR%%/source/xml2po-modes/gs.py X%%DOCSDIR%%/source/xml2po.bat X%%DOCSDIR%%/source/xml2po.py X%%DOCSDIR%%/source/xml2po.sh X%%DOCSDIR%%/splash.ai X%%JAVAJARDIR%%/Jmol.jar X%%JAVAJARDIR%%/Jmol.js X%%JAVAJARDIR%%/JmolApplet.jar X%%JAVAJARDIR%%/JmolApplet0.jar X%%JAVAJARDIR%%/JmolApplet0_Core.jar X%%JAVAJARDIR%%/JmolApplet0_Jars.jar X%%JAVAJARDIR%%/JmolApplet0_Jvxl.jar X%%JAVAJARDIR%%/JmolApplet0_Main.jar X%%JAVAJARDIR%%/JmolApplet0_Popup.jar X%%JAVAJARDIR%%/JmolApplet0_Quantum.jar X%%JAVAJARDIR%%/JmolApplet0_ReadersCifPdb.jar X%%JAVAJARDIR%%/JmolApplet0_ReadersMolXyz.jar X%%JAVAJARDIR%%/JmolApplet0_ReadersMore.jar X%%JAVAJARDIR%%/JmolApplet0_ReadersXml.jar X%%JAVAJARDIR%%/JmolApplet0_ShapeBio.jar X%%JAVAJARDIR%%/JmolApplet0_ShapeSpecial.jar X%%JAVAJARDIR%%/JmolApplet0_Smiles.jar X%%JAVAJARDIR%%/JmolApplet0_Viewer.jar X%%JAVAJARDIR%%/JmolApplet0_i18n.jar X@dirrm %%DOCSDIR%%/source/xml2po-modes X@dirrm %%DOCSDIR%%/source/po X@dirrm %%DOCSDIR%%/source/history X@dirrm %%DOCSDIR%%/source/guide X@dirrm %%DOCSDIR%%/source/applet X@dirrm %%DOCSDIR%%/source X@dirrm %%DOCSDIR%%/JmolUserGuide X@dirrm %%DOCSDIR%% END-of-/usr/ports/science/jmol/pkg-plist exit >Release-Note: >Audit-Trail: >Unformatted:
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