svn commit: r492840 - in head: . science science/jmol science/jmol/files
Yuri Victorovich
yuri at FreeBSD.org
Wed Feb 13 09:51:07 UTC 2019
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 at 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 at FreeBSD.org
-COMMENT= Open-source Java viewer for chemical structures in 3D
+MAINTAINER= yuri at 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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