Remove non staged ports without pending PR from s*

svn path=/head/; revision=366980
2014-09-02 10:07:49 +00:00 · 2014-09-02 10:07:49 +00:00 · 38a0a80230 · 2021-03-31 03:12:20 +00:00
commit 38a0a80230
parent d081961986
372 changed files with 58 additions and 16287 deletions
--- a/6
+++ b/6
@ -25,7 +25,6 @@
 # ------------------------------------------------------------------------------
 *-for-1.4.tgz	net/dgd-lpmud			May not be used for monetary gain
 *_MegaCLI.zip		sysutils/megacli	Source recipient must acknowledge license. Reproduction or redistribution prohibited. See http://www.lsi.com/lookup/License.aspx
-ASpath-tree-*.tar.gz	net-mgmt/aspathtree	not redistributable, license agreement required
 26410-800.zip		audio/libaacplus	unclear legal status, probably need licenses from 3GPP, Via Licensing and Coding Technologies
 aacplusenc-*		audio/aacplusenc	unclear legal status, probably need licenses from 3GPP, Via Licensing and Coding Technologies
 acroread/AdbeRdr8.*	print/acroread8		Must fill out redistribution form at http://www.adobe.com/products/acrobat/distribute.html
@ -55,7 +54,6 @@ citrix_ica-*		net/citrix_ica		License prohibits redistribution
 arcconf-v*		sysutils/arcconf	May not be redistributed in binary form
 clustalw-*		biology/clustalw	No commercial use
 coldwar_demo*		games/linux-coldwar-demo	Redistribution is limited, see license
-contool-*		sysutils/contool	Do not incorporate the source code into a product which is subsequently sold
 cos-*			java/cos		Special conditions apply for commercial use
 cosmo/*			games/cosmo		Possible copyright infringement
 CrystalSVGforGnomeIcons* x11-themes/gnome-icons-crystal Themes may contain artwork not done by the author.  Keep FreeBSD safe if theme author violated copyrights.
@ -78,7 +76,6 @@ doom3-linux-*		games/linux-doom3-demo	Redistribution is limited, see license; Re
 doomsrc.zip		games/doom		Redistribution is limited, see license; Requested by id Software
 dr_freebsd_*.zip	sysutils/megarc		Must be downloaded directly from the manufacturer
 dsnake-*		games/dsnake		License prohibits any reselling
-dtiquery-*		science/dtiquery	License agreement is required
 eagle-lin-*.run		cad/linux-eagle5	Usage permitted for non-commercial purposes only
 eawpats*		audio/eawpats		Some of the patches are not for commercial use
 ecw_jpeg_2000_*.zip	graphics/libecwj2	Registration required to download sources, but sources no longer available on ERDAS website
@ -107,7 +104,6 @@ freqship/*		sysutils/freqsdwn	License agreement is required to download
 fretsonfire/FretsOnFire-*-linux* games/fretsonfire-data	Only Unreal Voodoo site is allowed to distribute the music
 fvcom/sourcecode1.tar.gz	science/fvcom	Requires (free) registration
 fvcom/sourcecode1.tar.gz	science/fvcom-mpi	Requires (free) registration
-gamess.*/gamess*	science/gamess		No Redistribution
 giac-*			math/giacxcas		The french documentation is for non commercial only use
 giftool*		graphics/giftool	Do not redistribute for profit
 gishdemo-*		games/gish-demo		(c) Copyright 2004 Chronic Logic All rights reserved
@ -156,7 +152,6 @@ kzip-*			archivers/kzip		License does not allow redistribution
 l0phtcrack/*		security/l0phtcrack	Parts are under GPL, so binaries should not be distributed.  Contains crypto code from OpenSSL
 ladder.tar		games/ladder		Possible copyright problems
 lame*			audio/lame		patent issues, see http://www.mp3licensing.com/
-lgrind/*		print/lgrind		Contains non-free code written by Van Jacobson
 lha-1.14i-ac*		archivers/lha-ac	No redistribution allowed
 libaacplus-*		audio/libaacplus	Unclear legal status
 libamrnb/26104-*.zip	audio/libamrnb		unclear legal status, probably need licenses from 3GPP and more
@ -242,7 +237,6 @@ taetgen-*		math/tetgen		Academic or personal use only
 tarsnap-*		sysutils/tarsnap	license restricts redistribution of source and binaries
 tcetest_*		games/linux-enemyterritory-tce	Redistribution limited
 teamspeak*		audio/teamspeak3-server	No redistribution
-TFMESS_BSP_FreeBSD_*	security/bsp_upektfmess	License prohibits redistribution
 thundercache		www/thundercache	Commercial software with shareware license to 50 threads
 tinker*			biology/tinker		Distribution is prohibited
 triangle-*/*		math/triangle		No commercial use without prior arrangement with the author
--- a/58
+++ b/58
@ -6863,3 +6863,61 @@ russian/prawda||2014-09-01|Not staged
 russian/pscyr||2014-09-01|Not staged
 russian/rux||2014-09-01|Not staged
 russian/tac+ia||2014-09-01|Not staged
+science/2dhf||2014-09-01|Not staged
+science/abinit||2014-09-01|Not staged
+science/dtiquery||2014-09-01|Not staged
+science/elmer-hutiter||2014-09-01|Not staged
+science/elmerpost||2014-09-01|Not staged
+science/g3data||2014-09-01|Not staged
+science/gamess||2014-09-01|Not staged
+science/mcstas||2014-09-01|Not staged
+science/minc||2014-09-01|Not staged
+science/psi3||2014-09-01|Not staged
+science/x11iraf||2014-09-01|Not staged
+science/xmds||2014-09-01|Not staged
+security/bioapi||2014-09-01|Not staged
+security/bsp_upektfmess||2014-09-01|Not staged
+security/distcache-devel||2014-09-01|Not staged
+security/mosref||2014-09-01|Not staged
+security/openvpn-beta||2014-09-01|Not staged
+security/pam_bsdbioapi||2014-09-01|Not staged
+security/php-Auth_OpenID2||2014-09-01|Not staged
+security/php-Auth_OpenID||2014-09-01|Not staged
+security/php-openid-ldap||2014-09-01|Not staged
+security/samhain-client||2014-09-01|Not staged
+security/samhain-server||2014-09-01|Not staged
+security/samhain||2014-09-01|Not staged
+security/scannedonly||2014-09-01|Not staged
+security/tinysu||2014-09-01|Not staged
+sysutils/asapm||2014-09-01|Not staged
+sysutils/asr-utils||2014-09-01|Not staged
+sysutils/be_agent||2014-09-01|Not staged
+sysutils/boxbackup-devel||2014-09-01|Not staged
+sysutils/bubblemon-dockapp||2014-09-01|Not staged
+sysutils/clockspeed-conf||2014-09-01|Not staged
+sysutils/comconsole||2014-09-01|Not staged
+sysutils/comiccron||2014-09-01|Not staged
+sysutils/contool||2014-09-01|Not staged
+sysutils/createrepo||2014-09-01|Not staged
+sysutils/cromwell||2014-09-01|Not staged
+sysutils/cvsweb-converters||2014-09-01|Not staged
+sysutils/eroaster||2014-09-01|Not staged
+sysutils/freqsdwn||2014-09-01|Not staged
+sysutils/ganglia-webfrontend||2014-09-01|Not staged
+sysutils/gnomebaker||2014-09-01|Not staged
+sysutils/ispman||2014-09-01|Not staged
+sysutils/jailadmin||2014-09-01|Not staged
+sysutils/jailuser||2014-09-01|Not staged
+sysutils/linux-afaapps||2014-09-01|Not staged
+sysutils/netident||2014-09-01|Not staged
+sysutils/news||2014-09-01|Not staged
+sysutils/nut22||2014-09-01|Not staged
+sysutils/nvtv||2014-09-01|Not staged
+sysutils/penv||2014-09-01|Not staged
+sysutils/pmap||2014-09-01|Not staged
+sysutils/py-zfs||2014-09-01|Not staged
+sysutils/replicant||2014-09-01|Not staged
+sysutils/sbniconfig||2014-09-01|Not staged
+sysutils/upsd||2014-09-01|Not staged
+sysutils/wmapm||2014-09-01|Not staged
+sysutils/xsi||2014-09-01|Not staged
--- a/science/2dhf/Makefile
+++ b/science/2dhf/Makefile
@ -1,86 +0,0 @@
-# Created by: NAKATA, Maho <maho@FreeBSD.org>
-# $FreeBSD$
-
-PORTNAME=	2dhf
-PORTVERSION=	2005.05
-PORTREVISION=	6
-CATEGORIES=	science
-MASTER_SITES=	http://www.fizyka.umk.pl/~jkob/2dhf/
-DISTNAME=	${PORTNAME}-05.05
-EXTRACT_SUFX=	.tgz
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Numerical Hartree-Fock Program for Diatomic Molecules
-
-BUILD_DEPENDS=	bash:${PORTSDIR}/shells/bash
-.if defined(WITH_INTEL)
-USES+=		fortran:ifort
-BUILD_DEPENDS+=  ${LOCALBASE}/intel_cc_80/bin/icc:${PORTSDIR}/lang/icc
-.else
-USES+=		fortran
-.endif
-
-.if exists(${LOCALBASE}/lib/libatlas.so) && !defined(WITH_BLAS)
-WITH_ATLAS=	yes
-.endif
-.if defined(WITH_ATLAS)
-LIB_DEPENDS+=	libatlas.so${PORTSDIR}/math/atlas
-BLAS=		-lf77blas
-.else
-LIB_DEPENDS+=	libblas.so:${PORTSDIR}/math/blas
-LIB_DEPENDS+=	liblapack.so:${PORTSDIR}/math/lapack
-BLAS=		-lblas
-.endif
-
-.if defined(WITH_OPTIMIZED_FLAGS)
-FFLAGS+=	-O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double
-.if (${MACHINE_ARCH} == "i386")
-FFLAGS+=	-mfancy-math-387
-.endif # i386
-.endif
-
-.if defined(WITH_INTEL)
-FC=		${LOCALBASE}/intel_fc_80/bin/ifort
-CC=		${LOCALBASE}/intel_cc_80/bin/icc
-FFLAGS=		-O3 -tpp7 -xKW -Vaxlib
-FFLAGS_ADD=	-w -132
-CFLAGS=		-O3 -tpp7 -xKW -Vaxlib
-BLAS+=		-lg2c -lm
-.else
-FFLAGS_ADD=	-w -ffixed-line-length-none
-.endif
-WRKSRC=		${WRKDIR}/${PORTNAME}
-USES+=		gmake
-ALL_TARGET=	all
-
-NO_STAGE=	yes
-pre-everything::
-	@${ECHO_CMD} "You can optimize by setting WITH_OPTIMIZED_FLAGS=yes."
-
-do-extract:
-	${MKDIR} ${WRKSRC}
-	@(cd ${WRKSRC} ;  ${TAR} xfz ${DISTDIR}/${DISTNAME}${EXTRACT_SUFX})
-
-post-patch:
-	@${REINPLACE_CMD} -e 's|%%FC%%|${FC}|g ; \
-	s|%%FFLAGS%%|${FFLAGS}|g ; \
-	s|%%FFLAGS_ADD%%|${FFLAGS_ADD}|g ; \
-	s|%%CC%%|${CC}|g ; \
-	s|%%CFLAGS%%|${CFLAGS}|g ; \
-	s|%%LOCALBASE%%|${LOCALBASE}|g ;\
-	s|%%BLAS%%|${BLAS}|g' \
-	 ${WRKSRC}/Makefile
-	@${REINPLACE_CMD} -e 's|%%PREFIX%%|${PREFIX}|g' \
-	 ${WRKSRC}/bin/xhf
-
-do-install:
-	@cd ${WRKSRC} ; ${INSTALL_PROGRAM} bin/x2dhf ${PREFIX}/bin/x2dhf
-	@cd ${WRKSRC} ; ${INSTALL_SCRIPT}  bin/xhf   ${PREFIX}/bin/xhf
-.if !defined(NOPORTDOCS)
-	@${MKDIR} ${DOCSDIR}
-	@cd ${WRKSRC}/doc ; ${INSTALL_DATA} 2dhf.pdf users-guide.pdf users-guide.html ${DOCSDIR}
-	@${MKDIR} ${EXAMPLESDIR}
-	@cd ${WRKSRC}/examples/ ; ${TAR} -chf - . | \
-		${TAR} -xf - -C ${EXAMPLESDIR}
-.endif
-.include <bsd.port.mk>
--- a/science/2dhf/distinfo
+++ b/science/2dhf/distinfo
@ -1,2 +0,0 @@
-SHA256 (2dhf-05.05.tgz) = ace9c6b96d7588cf72c331b0b52baaea76d125c86ea737d31d0b016e50b9354c
-SIZE (2dhf-05.05.tgz) = 1033962
--- a/science/2dhf/files/patch-Makefile
+++ b/science/2dhf/files/patch-Makefile
@ -1,50 +0,0 @@
--- Makefile.orig	Tue May 17 02:15:36 2005
-+++ Makefile	Tue Jan  9 17:36:22 2007
-@@ -45,21 +45,22 @@
- # of grid and orbital parameters according to expected range of input
- # data 
- 
-#MEMALLOC = main-static.inc
-+# MEMALLOC = main-static.inc
- 
- # For a Sun workstation with f77 or a PC with g77 compiler 
-MEMALLOC = main-dynamic-f77.inc
-+# MEMALLOC = main-dynamic-f77.inc
- 
- # For a DEC workstation and f77 compiler 
- # MEMALLOC = main-dynamic-f77-dec.inc
- 
- # For f90 compiler 
-# MEMALLOC = main-dynamic-f90.inc
-+MEMALLOC = main-dynamic-f90.inc
- 
- # set system type/compiler
- # available keywords are: cray, dec, ibm, lahey, linux, sgi, solaris
-+# and freebsd
- 
-SYSTEM = linux
-+SYSTEM = freebsd
- #SYSTEM = intel
- 
- # if BLAS library is available set the BLAS variable to yes
-@@ -189,6 +190,20 @@
- 	CC = cc
- 	CFLAGS = 
- endif
-+# FreeBSD 
-+ifeq ($(SYSTEM),freebsd)
-+	FC = %%FC%%
-+	FFLAGS = %%FFLAGS%%
-+#	-fstrength-reduce -funroll-loops
-+#	FFLAGS = -O1 -malign-double 
-+#       FFLAGS = -g -C 
-+	FFLAGS_ADD =  %%FFLAGS_ADD%%
-+	FLIB = -L%%LOCALBASE%%/lib %%BLAS%%
-+	BLAS = yes
-+
-+	CC = %%CC%%
-+	CFLAGS = %%CFLAGS%%
-+ endif	
- 
- 
- # nothing to be set below this line
--- a/science/2dhf/files/patch-bin+xhf
+++ b/science/2dhf/files/patch-bin+xhf
@ -1,11 +0,0 @@
--- bin/xhf.org	Thu Jul 24 18:25:05 2003
-+++ bin/xhf	Thu Jul 24 18:26:38 2003
-@@ -99,7 +99,7 @@
- 	endif
- 	echo '     '
- #  envoke x2dhf program
-	nice +19 ./x2dhf < $1.data  
-+	nice +19 %%PREFIX%%/bin/x2dhf < $1.data  
-     endif
- 
-     if ( $1 != 'remove' ) then
--- a/science/2dhf/files/patch-main-dynamic-f90.inc
+++ b/science/2dhf/files/patch-main-dynamic-f90.inc
@ -1,9 +0,0 @@
--- src/main-dynamic-f90.inc~	Tue May 17 02:22:50 2005
-+++ src/main-dynamic-f90.inc	Tue Jan  9 17:39:08 2007
-@@ -1,5 +1,5 @@
-       real*8,    dimension(:),allocatable :: cw_orb
-      real*8,    dimension(:),allocatable :
-+      real*8,    dimension(:),allocatable :: cw_coul
-       real*8,    dimension(:),allocatable :: cw_exch
-       real*8,    dimension(:),allocatable :: cw_suppl
-       real*8,    dimension(:),allocatable :: cw_sctch
--- a/science/2dhf/files/patch-src+fmalloc.c
+++ b/science/2dhf/files/patch-src+fmalloc.c
@ -1,14 +0,0 @@
--- src/fmalloc.c.orig	Thu Jul 24 17:32:52 2003
-+++ src/fmalloc.c	Thu Jul 24 17:33:22 2003
-@@ -15,7 +15,11 @@
- 
- #include <stdio.h>
- #include <sys/types.h>
-+#ifdef __FreeBSD__ 
-+#include <stdlib.h>
-+#else
- #include <malloc.h>
-+#endif
- 
- /*
-       bv:     is an integer to contain the address to the reserved
--- a/science/2dhf/files/patch-src+getusedcpu.c
+++ b/science/2dhf/files/patch-src+getusedcpu.c
@ -1,37 +0,0 @@
--- src/getusedcpu.c.orig	Sat Jan  4 21:21:37 2003
-+++ src/getusedcpu.c	Tue Aug  5 07:02:39 2003
-@@ -67,7 +67,6 @@
- #include <string.h>
- #include <ctype.h>
- 
-
- #include <sys/types.h>
- #include <sys/times.h>
- #include <sys/param.h>
-@@ -76,7 +75,7 @@
- #include <sys/acct.h>
- #endif
- 
-#if defined(ymp)
-+#if defined(ymp) || defined (__FreeBSD__)
- #include <time.h>
- #endif
- 
-@@ -106,7 +105,7 @@
- #if defined(dec)
-    start       = (float)(buffer.tms_utime  + buffer.tms_stime) / (float)(AHZ);
-    start_child = (float)(buffer.tms_cutime + buffer.tms_cstime)/ (float)(AHZ);
-#elif defined(ymp)
-+#elif defined(ymp) || defined(__FreeBSD__)
-    start       = (float)(buffer.tms_utime  + buffer.tms_stime)  / (float)(CLK_TCK);
-    start_child = (float)(buffer.tms_cutime + buffer.tms_cstime) / (float)(CLK_TCK);
- #else
-@@ -118,7 +117,7 @@
- #if defined(dec)
-    *Msecs = (float)(buffer.tms_utime  + buffer.tms_stime) / (float)(AHZ) - start_child;
-    *Csecs = (float)(buffer.tms_cutime + buffer.tms_cstime)/ (float)(AHZ) - start_child;
-#elif defined(ymp)
-+#elif defined(ymp) || defined(__FreeBSD__)
-    *Msecs = (float)(buffer.tms_utime  + buffer.tms_stime)  / (float)(CLK_TCK) - start;
-    *Csecs = (float)(buffer.tms_cutime + buffer.tms_cstime) / (float)(CLK_TCK) - start_child;
- #else
--- a/science/2dhf/files/patch-src+inihf.f
+++ b/science/2dhf/files/patch-src+inihf.f
@ -1,10 +0,0 @@
--- src/inihf.f~	Tue May 17 02:22:50 2005
-+++ src/inihf.f	Tue Jan  9 17:12:22 2007
-@@ -20,6 +20,7 @@
-       implicit integer*4 (i-n)
-       implicit real*8 (a-h,o-z)
-       character*8 atom1,term1,atom2,term2
-+      integer ouf2dhf1, ouf2dhf2
-       include 'commons8.inc'
-       dimension psi(*),pot(*),excp(*),f2(*),f4(*),wgt2(*),wk0(*)
-       dimension rhf1(9999),phf1(20,9999),ehf1(20),qc1(20),
--- a/science/2dhf/files/patch-src+setconst.f
+++ b/science/2dhf/files/patch-src+setconst.f
@ -1,11 +0,0 @@
--- src/setconst.f.org	Tue Jan  9 17:41:30 2007
-+++ src/setconst.f	Tue Jan  9 17:41:42 2007
-@@ -31,7 +31,7 @@
- 
- c     set default lengths of integer and real constants and variables used
- 
-      i8tmp1=2**31
-+      i8tmp1=2**30
-       i8tmp2=100000*i8tmp1
-       i4tmp1=i8tmp2
-       if (i4tmp1.eq.0) then
--- a/science/2dhf/pkg-descr
+++ b/science/2dhf/pkg-descr
@ -1,9 +0,0 @@
-A Numerical Hartree-Fock Program for Diatomic Molecules
-
-The program finds virtually exact solution of the Hartree-Fock
-and Hartree-Fock-Slater equations for diatomic molecules. The
-lowest eigenstates of a given irreducible representation and
-spin can be obtained. Distributed under GPL.
-
-WWW: http://scarecrow.1g.fi/2d/admin/getit.html
-
--- a/science/2dhf/pkg-plist
+++ b/science/2dhf/pkg-plist
@ -1,92 +0,0 @@
-bin/xhf
-bin/x2dhf
-%%PORTDOCS%%%%DOCSDIR%%/2dhf.pdf
-%%PORTDOCS%%%%DOCSDIR%%/users-guide.pdf
-%%PORTDOCS%%%%DOCSDIR%%/users-guide.html
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94la.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94l.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94la.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94lb.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf.inp
-%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94.pun
-%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94lb.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/bf/bf_g94.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/n2/n2.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/n2/n2.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/th89/th89_2s.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/th89/th89_1s.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/th89/th89_1s.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/th89/th89_2s.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/h2/h2.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/h2/h2.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/h2/h2a.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/h2/h2b.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/h2+/h2+.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/h2+/h2+.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/h2+/h2plus.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/h2+/h2plus.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/c/c.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/c/cplus.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/c/c.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/c/cplus.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/c/c1d2.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/c/c3p1.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/c/c1d2.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/c/c3p1.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/be/be.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/be/be.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/be/be-1.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/be/be-1.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/bef/bef.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/bef/bef.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/c2/c2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/c2/c2a.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/c2/c2.pun
-%%PORTDOCS%%%%EXAMPLESDIR%%/c2/c2b.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/c2/c2c.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/c2/c2a.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/bo/bo.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/bo/bo.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/bo/bo.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/bo/bo.pun
-%%PORTDOCS%%%%EXAMPLESDIR%%/bo/bo.inp
-%%PORTDOCS%%%%EXAMPLESDIR%%/f2/f2.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/f2/f2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/f2/f2.pun
-%%PORTDOCS%%%%EXAMPLESDIR%%/f2/f2.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/gaf/gaf.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/gaf/gaf.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/li2/li2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/li2/li2.pun
-%%PORTDOCS%%%%EXAMPLESDIR%%/li2/li2.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/li2/li2.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-223-150-0-1.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-223-150-m1-1.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/fh/Run_FH
-%%PORTDOCS%%%%EXAMPLESDIR%%/fh/Run_elprop.pl
-%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-223-150-m2-1.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-223-150-p1-1.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-223-150-p2-1.output
-%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-m2.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-p2.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-m1.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-0.data
-%%PORTDOCS%%%%EXAMPLESDIR%%/fh/fh-p1.data
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/bf
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/n2
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/th89
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/h2+
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/h2
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/c
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/be
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/bef
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/c2
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/bo
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/f2
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/gaf
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/li2
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/fh
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
--- a/science/Makefile
+++ b/science/Makefile
@ -4,7 +4,6 @@
    COMMENT = Scientific ports

    SUBDIR += 2d-rewriter
-    SUBDIR += 2dhf
    SUBDIR += InsightToolkit
    SUBDIR += R-cran-AMORE
    SUBDIR += R-cran-DCluster
@ -15,7 +14,6 @@
    SUBDIR += R-cran-epicalc
    SUBDIR += R-cran-snow
    SUBDIR += R-cran-som
-    SUBDIR += abinit
    SUBDIR += afni
    SUBDIR += avogadro
    SUBDIR += bddsolve
@ -38,14 +36,11 @@
    SUBDIR += dcl
    SUBDIR += devisor
    SUBDIR += dlpoly-classic
-    SUBDIR += dtiquery
    SUBDIR += ecs
    SUBDIR += elmer-eio
-    SUBDIR += elmer-hutiter
    SUBDIR += elmer-matc
    SUBDIR += elmer-meshgen2d
    SUBDIR += elmergrid
-    SUBDIR += elmerpost
    SUBDIR += epte
    SUBDIR += fastcap
    SUBDIR += fasthenry
@ -53,8 +48,6 @@
    SUBDIR += fvcom
    SUBDIR += fvcom-mpi
    SUBDIR += fvm
-    SUBDIR += g3data
-    SUBDIR += gamess
    SUBDIR += gchemutils
    SUBDIR += getdp
    SUBDIR += ghemical
@ -90,12 +83,10 @@
    SUBDIR += linsmith
    SUBDIR += massxpert
    SUBDIR += mbdyn
-    SUBDIR += mcstas
    SUBDIR += medit
    SUBDIR += meep
    SUBDIR += mei
    SUBDIR += metaf2xml
-    SUBDIR += minc
    SUBDIR += minc2
    SUBDIR += mol2ps
    SUBDIR += mpb
@ -141,7 +132,6 @@
    SUBDIR += paje
    SUBDIR += paraview
    SUBDIR += pnetcdf
-    SUBDIR += psi3
    SUBDIR += psychopy
    SUBDIR += pulseview
    SUBDIR += py-DendroPy
@ -188,9 +178,7 @@
    SUBDIR += veusz
    SUBDIR += vmd
    SUBDIR += voro++
-    SUBDIR += x11iraf
    SUBDIR += xfce4-equake-plugin
    SUBDIR += xmakemol
-    SUBDIR += xmds

 .include <bsd.port.subdir.mk>
--- a/science/abinit/Makefile
+++ b/science/abinit/Makefile
@ -1,88 +0,0 @@
-# Created by: NAKATA Maho <maho@FreeBSD.org>
-# $FreeBSD$
-
-PORTNAME=	abinit
-PORTVERSION=	5.7.3
-PORTREVISION=	16
-CATEGORIES=	science
-MASTER_SITES=	ftp://ftp.abinit.org/pub/abinitio/ABINIT_v${PORTVERSION}/
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Abinit calculates electronic structure of systems
-
-BUILD_DEPENDS=	python:${PORTSDIR}/lang/python \
-		${PYTHON_SITELIBDIR}/numarray/__init__.py:${PORTSDIR}/math/py-numarray
-LIB_DEPENDS=	libnetcdff.so:${PORTSDIR}/science/netcdf-fortran \
-		libgsl.so:${PORTSDIR}/math/gsl
-
-USES=		fortran gmake perl5
-USE_PYTHON=	yes
-USE_PERL5=	build
-USE_AUTOTOOLS=	autoconf automake
-CONFIGURE_ENV=	WGET=${TRUE}
-CONFIGURE_ARGS=	--disable-wannier90 --disable-bigdft --disable-etsf-io	\
-		--with-plugins-tardir=/dev/null				\
-		--with-netcdf-includes="-I${LOCALBASE}/include"		\
-		--enable-bindings --enable-gsl				\
-		--with-netcdf-libs="-L${LOCALBASE}/lib -lnetcdff -lnetcdf"
-CPPFLAGS+=	-I${LOCALBASE}/include
-LDFLAGS+=	-L${LOCALBASE}/lib
-
-OPTIONS_DEFINE=	DOCS EXAMPLES
-
-NO_STAGE=	yes
-.include <bsd.port.options.mk>
-
-.if ${PORT_OPTIONS:MDOCS}
-USE_TEX=	latex:build dvipsk:build
-BUILD_DEPENDS+= gm4:${PORTSDIR}/devel/m4		\
-		markdown:${PORTSDIR}/textproc/markdown
-USE_GHOSTSCRIPT_BUILD=	yes
-.endif
-
-.if ${ARCH} == "ia64" || ${ARCH} == "powerpc" || ${ARCH} == "sparc64"
-MANUAL_PACKAGE_BUILD=	takes a tremendous amount of time to build on pointyhat nodes
-.endif
-
-.if exists(${LOCALBASE}/lib/libatlas.so) && !defined(WITH_BLAS)
-WITH_ATLAS=	yes
-.endif
-.if defined(WITH_ATLAS)
-LIB_DEPENDS+=	libatlas.so:${PORTSDIR}/math/atlas
-BLAS=		-lf77blas
-LAPACK=		-lalapack -lcblas
-.else
-LIB_DEPENDS+=	libblas.so:${PORTSDIR}/math/blas
-LIB_DEPENDS+=	liblapack.so:${PORTSDIR}/math/lapack
-BLAS=		-lblas
-LAPACK=		-llapack
-.endif
-
-pre-configure:
-.if ! ${PORT_OPTIONS:MDOCS}
-	${REINPLACE_CMD} -e '/^abinit_top_subdirs =/s| doc||' ${WRKSRC}/config/specs/other.cf
-.endif
-.if ! ${PORT_OPTIONS:MEXAMPLES}
-	${REINPLACE_CMD} -e '/^abinit_top_subdirs =/s| tests||' ${WRKSRC}/config/specs/other.cf
-.endif
-	(cd ${WRKSRC} && ./config/scripts/makemake)
-	${CHMOD} a+x ${WRKSRC}/bindings/parser/*.py
-
-post-build:
-	@(cd ${BUILD_WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} \
-		${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} libabinit)
-
-post-install:
-	${MKDIR} ${PREFIX}/include ${PREFIX}/lib
-.for lf in libabinip.a libabinis.a
-	${INSTALL_DATA} ${WRKSRC}/${lf} ${PREFIX}/lib
-.endfor
-.for lf in ab_dtset_c.h dtset_c.h dtset_c.static.h dtset_f90.inc dtset_py.h	\
-	ab_dtset_f90_get.f90
-	${INSTALL_DATA} ${WRKSRC}/bindings/parser/${lf} ${PREFIX}/include
-.endfor
-
-regression-test:
-	cd ${WRKSRC}/tests ; ${MAKE_CMD} tests_min
-
-.include <bsd.port.mk>
--- a/science/abinit/distinfo
+++ b/science/abinit/distinfo
@ -1,2 +0,0 @@
-SHA256 (abinit-5.7.3.tar.gz) = caac56530ceaa5e16326fd4407adcd0b1aede07ded51017f3eb6a6a3696c2867
-SIZE (abinit-5.7.3.tar.gz) = 31683174
--- a/science/abinit/files/makefile_macros
+++ b/science/abinit/files/makefile_macros
@ -1,50 +0,0 @@
-# This file contains the definitions needed for every possible script
-# to be used with the ABINIT makefiles.  It is very much machine-dependent.
-# It is read by makemake and makearch.
-
-# This file for cernunnos (Pentium 4, Slackware Linux) at the Institute for
-# Materials Physics, University of Vienna, by Wolfgang Pichl
-# with the Intel compiler, Version 7.1
-# see http://www.intel.com/software/products/compilers/flin/noncom.htm
-
-# In this file, the blas library is linked in the same way as the other
-# libraries (lapack, ffts, numrecip).
-
-# Explanations about this file can be found in the  help.makefile_macros file,
-# in the Infos subdirectory
-
-####################################################################
-# Only for the sequential version 
-
-# Machine type
-MACHINE=P6
-# Fortran optimized compilation
-FC=%%FC%%
-FFLAGS=%%FFLAGS%%
-FFLAGS_LIBS=%%FFLAGS_LIBS%%
-
-# C preprocessor, used to preprocess the fortran source.
-CPP=%%CPP%%
-CPP_FLAGS=-P -traditional -D__IFC
-# The cpp directive CHGSTDIO changes the standard I/O definition
-# Uncomment the next line for this to happen.
-#CPP_FLAGS=-P -DCHGSTDIO 
-
-# C optimized compilation.
-CC=%%CC%%
-CFLAGS=%%CFLAGS%%
-
-# Location of perl . Used to generate the script fldiff, in ~ABINIT/Utilities .
-PERL=%%PERL%%
-
-# List of machine-dependent routines
-MACHINE_DEP_C_SEQ_SUBS_LIST=etime.o
-
-# Create BLAS library from abinis source
-# The following lines should be redundant, since this is the default
-# however, we got troubles when they where missing
-BLAS=%%BLAS%%
-LAPACK=%%LAPACK%%
-LIBS=$(LAPACK) $(BLAS)
-
-# This is a last line in makefile_macros ----------
--- a/science/abinit/files/patch-bindings_parser_ab_dtset_c.c
+++ b/science/abinit/files/patch-bindings_parser_ab_dtset_c.c
@ -1,11 +0,0 @@
--- bindings/parser/ab_dtset_c.c.orig	2009-02-22 07:08:32.000000000 +0100
-+++ bindings/parser/ab_dtset_c.c	2009-03-26 22:21:33.000000000 +0100
-@@ -7,6 +7,8 @@
- /* g95 : #define FC_MOD_NAME(A) ab_dtset_MP_ ## A */
- #define FC_MOD_CALL(A,...) FC_MOD_NAME(A)(__VA_ARGS__)
- 
-+typedef unsigned int uint;
-+
- /* Fortran interface. */
- void FC_MOD_NAME(ab_dtset_new)(int *dt, const char *filename, int *len);
- void FC_MOD_NAME(ab_dtset_new_from_string)(int *dt, const char *string, int *len);
--- a/science/abinit/files/patch-bindings_parser_parser.mk
+++ b/science/abinit/files/patch-bindings_parser_parser.mk
@ -1,11 +0,0 @@
--- bindings/parser/parser.mk~	2009-03-11 14:12:20.000000000 +0900
-+++ bindings/parser/parser.mk	2009-04-13 11:53:44.000000000 +0900
-@@ -25,7 +25,7 @@
- 	$(RANLIB) libbindings.a
- 
- ab_dtset_py.o: dtset_py.h ab_dtset_c.h
-	$(CC) $(CPPFLAGS) $(PYTHON_CPPFLAGS) -I. $(CFLAGS) -c $(abinit_srcdir)/bindings/parser/ab_dtset_py.c
-+	$(CC) $(CPPFLAGS) $(CFLAGS_EXTRA) $(PYTHON_CPPFLAGS) -I. $(CFLAGS) -c $(abinit_srcdir)/bindings/parser/ab_dtset_py.c
- 
- 
- python: ab_dtset_py.o
--- a/science/abinit/files/patch-config+m4+init.m4
+++ b/science/abinit/files/patch-config+m4+init.m4
@ -1,129 +0,0 @@
--- ./config/m4/init.m4.orig	2009-03-11 06:12:22.000000000 +0100
-+++ ./config/m4/init.m4	2009-03-28 16:29:06.000000000 +0100
-@@ -231,6 +231,101 @@
-    abi_cpu_bits="64"
-    ;;
- 
-+  i386-*freebsd*)
-+  dnl Pentium 3 ?
-+  if test "${abi_cpu_model}" = ""; then
-+   abi_cpu_model=`sysctl hw.model | grep 'Pentium III'`
-+   if test "${abi_cpu_model}" != ""; then
-+    abi_cpu_model="pentium3"
-+    abi_cpu_64bits="no"
-+    abi_cpu_bits="32"
-+   fi
-+  fi
-+  dnl Pentium 4 ?
-+  if test "${abi_cpu_model}" = ""; then
-+   abi_cpu_model=`sysctl hw.model | grep 'Intel(R) Pentium(R) 4'`
-+   if test "${abi_cpu_model}" != ""; then
-+    abi_cpu_model="pentium4"
-+    abi_cpu_64bits="no"
-+    abi_cpu_bits="32"
-+   fi
-+  fi
-+  dnl Pentium 4M ?
-+  if test "${abi_cpu_model}" = ""; then
-+   abi_cpu_model=`sysctl hw.model | grep 'Intel(R) Pentium(R) M'`
-+   if test "${abi_cpu_model}" != ""; then
-+    abi_cpu_model="pentium4"
-+    abi_cpu_64bits="no"
-+    abi_cpu_bits="32"
-+   fi
-+  fi
-+  dnl Unknown
-+  if test "${abi_cpu_model}" = ""; then
-+   abi_cpu_model="unknown"
-+  fi
-+  dnl The processor is anyway 32-bit
-+  abi_cpu_64bits="no"
-+  abi_cpu_bits="32"
-+  ;;
-+
-+  amd64-*freebsd*)
-+  dnl Opteron ?
-+  if test "${abi_cpu_model}" = ""; then
-+   abi_cpu_model=`sysctl hw.model | grep 'Opteron'`
-+   if test "${abi_cpu_model}" != ""; then
-+    abi_cpu_model="opteron"
-+    abi_cpu_64bits="yes"
-+    abi_cpu_bits="64"
-+   fi
-+  fi
-+  dnl Xeon ?
-+  if test "${abi_cpu_model}" = ""; then
-+   abi_cpu_model=`sysctl hw.model | grep 'Intel(R) XEON(TM)'`
-+   if test "${abi_cpu_model}" != ""; then
-+    abi_cpu_model="xeon"
-+    abi_cpu_64bits="yes"
-+    abi_cpu_bits="64"
-+   fi
-+  fi
-+  dnl Unknown
-+  if test "${abi_cpu_model}" = ""; then
-+   abi_cpu_model="unknown"
-+  fi
-+  dnl The processor is anyway 64-bit
-+  abi_cpu_64bits="yes"
-+  abi_cpu_bits="64"
-+  ;;
-+
-+  ia64-*freebsd*)
-+  dnl Itanium 1 ?
-+  if test "${abi_cpu_model}" = ""; then
-+   abi_cpu_model=`sysctl hw.model | grep 'Itanium 1'`
-+   if test "${abi_cpu_model}" = ""; then
-+    abi_cpu_model="itanium1"
-+   fi
-+  fi
-+  dnl Itanium 2 ?
-+  if test "${abi_cpu_model}" = ""; then
-+   abi_cpu_model=`sysctl hw.model | grep 'Itanium 2'`
-+   if test "${abi_cpu_model}" != ""; then
-+    abi_cpu_model="itanium2"
-+   fi
-+  fi
-+  dnl Unknown
-+  if test "${abi_cpu_model}" = ""; then
-+   abi_cpu_model="unknown"
-+  fi
-+  dnl The processor is anyway 64-bit
-+  abi_cpu_64bits="yes"
-+  abi_cpu_bits="64"
-+  ;;
-+
-+  sparc64-*freebsd*)
-+   abi_cpu_model="unknown"
-+   abi_cpu_64bits="yes"
-+   abi_cpu_bits="64"
-+  ;;
-+
-  esac
- 
-  AC_SUBST(abi_cpu_vendor)
-@@ -289,15 +384,15 @@
-  fi
- 
-  dnl Set-up all directory names
- abinit_bindir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/bin"
- abinit_chkdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/tests"
- abinit_datdir="${abinit_prefix}/abinit"
- abinit_docdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/doc"
- abinit_incdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/include"
- abinit_libdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/lib"
- abinit_mandir="${abinit_prefix}/abinit/man"
- abinit_rundir="${abinit_prefix}/abinit/bin"
- abinit_wwwdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/www"
-+ abinit_bindir="${abinit_prefix}/bin"
-+ abinit_chkdir="${abinit_prefix}/share/examples/abinit/tests"
-+ abinit_datdir="${abinit_prefix}/share/abinit"
-+ abinit_docdir="${abinit_prefix}/share/doc/abinit/"
-+ abinit_incdir="${abinit_prefix}/include/abinit"
-+ abinit_libdir="${abinit_prefix}/lib"
-+ abinit_mandir="${abinit_prefix}/man"
-+ abinit_rundir="${abinit_prefix}/bin"
-+ abinit_wwwdir="${abinit_prefix}/www/abinit"
- 
-  dnl Substitute all variables
-  AC_SUBST(abinit_prefix)
--- a/science/abinit/files/patch-config+optflags
+++ b/science/abinit/files/patch-config+optflags
@ -1,14 +0,0 @@
--- /dev/null	Wed Jan 17 11:53:59 2007
-+++ config/optflags/gnu_fc/all/opteron	Wed Jan 17 11:53:27 2007
-@@ -0,0 +1 @@
-+FCFLAGS_OPT="-O2 -fforce-addr -ffast-math -mmmx -msse -msse2"
-
--- /dev/null	Wed Jan 17 11:55:01 2007
-+++ config/optflags/gnu_cc/all/opteron	Wed Jan 17 11:54:40 2007
-@@ -0,0 +1 @@
-+CFLAGS_OPT="-O2 -fforce-addr -ffast-math -mmmx -msse -msse2"
-
--- /dev/null	Wed Jan 17 11:55:01 2007
-+++ config/optflags/gnu_cxx/all/opteron	Wed Jan 17 11:54:40 2007
-@@ -0,0 +1 @@
-+CFLAGS_OPT="-O2 -fforce-addr -ffast-math -mmmx -msse -msse2"
--- a/science/abinit/files/patch-config.mk.in
+++ b/science/abinit/files/patch-config.mk.in
@ -1,11 +0,0 @@
--- config.mk.in.orig	2009-02-22 07:08:32.000000000 +0100
-+++ config.mk.in	2009-03-08 09:54:35.000000000 +0100
-@@ -41,7 +41,7 @@
- PYTHON  = @PYTHON@
- LN_S    = @LN_S@
- EGREP   = @EGREP@
-MKDIR_P = @MKDIR_P@
-+MKDIR_P = @abinit_builddir@/@MKDIR_P@
- 
- # Architecture
- target          = @target@
--- a/science/abinit/files/patch-config_scripts_make-macros-autotools
+++ b/science/abinit/files/patch-config_scripts_make-macros-autotools
@ -1,11 +0,0 @@
--- ./config/scripts/make-macros-autotools.orig	2009-02-22 07:08:33.000000000 +0100
-+++ ./config/scripts/make-macros-autotools	2009-03-25 22:34:01.000000000 +0100
-@@ -413,7 +413,7 @@
- now = strftime("%Y/%m/%d %H:%M:%S +0000",gmtime())
- 
- # Get Autotools versions
-(m4_ret,m4_version) = commands.getstatusoutput("m4 --version")
-+(m4_ret,m4_version) = commands.getstatusoutput("gm4 --version")
- (ac_ret,ac_version) = commands.getstatusoutput("autoconf --version")
- (am_ret,am_version) = commands.getstatusoutput("automake --version")
- (lt_ret,lt_version) = commands.getstatusoutput("libtool  --version")
--- a/science/abinit/files/patch-configure
+++ b/science/abinit/files/patch-configure
@ -1,27 +0,0 @@
--- configure.orig	2009-02-22 08:32:10.000000000 +0100
-+++ configure	2009-03-09 20:01:48.000000000 +0100
-@@ -5151,15 +5151,15 @@
-   abinit_prefix="${prefix}"
-  fi
- 
-  abinit_bindir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/bin"
- abinit_chkdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/tests"
- abinit_datdir="${abinit_prefix}/abinit"
- abinit_docdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/doc"
- abinit_incdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/include"
- abinit_libdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/lib"
- abinit_mandir="${abinit_prefix}/abinit/man"
- abinit_rundir="${abinit_prefix}/abinit/bin"
- abinit_wwwdir="${abinit_prefix}/abinit/${ABINIT_VERSION_BASE}/www"
-+ abinit_bindir="${abinit_prefix}/bin"
-+ abinit_chkdir="${abinit_prefix}/share/examples/abinit/tests"
-+ abinit_datdir="${abinit_prefix}/share/abinit"
-+ abinit_docdir="${abinit_prefix}/share/doc/abinit/"
-+ abinit_incdir="${abinit_prefix}/include/abinit"
-+ abinit_libdir="${abinit_prefix}/lib"
-+ abinit_mandir="${abinit_prefix}/man"
-+ abinit_rundir="${abinit_prefix}/bin"
-+ abinit_wwwdir="${abinit_prefix}/www/abinit"
- 
- 
- 
--- a/science/abinit/files/patch-prereqs+linalg+linalg.mk
+++ b/science/abinit/files/patch-prereqs+linalg+linalg.mk
@ -1,11 +0,0 @@
--- prereqs/linalg/linalg.mk~	2009-03-11 14:12:18.000000000 +0900
-+++ prereqs/linalg/linalg.mk	2009-04-13 11:39:18.000000000 +0900
-@@ -32,7 +32,7 @@
- 	touch build-stamp
- 
- install-stamp: build
-	$(MKDIR_P) tmp/lib
-+	mkdir -p tmp/lib
- 	cp blas/libblas.a lapack/liblapack.a tmp/lib
- 	touch install-stamp
- 
--- a/science/abinit/pkg-descr
+++ b/science/abinit/pkg-descr
@ -1,7 +0,0 @@
-ABINIT is a package whose main program allows one to find
-the total energy, charge density and electronic structure of
-systems made of electrons and nulcei (molecules and periodic
-solids) within Density Functional Theory (DFT), using pseudo-
-potentials and a planewave basis.
-
-WWW: http://www.abinit.org/
--- a/science/abinit/pkg-plist
+++ b/science/abinit/pkg-plist
--- a/science/dtiquery/Makefile
+++ b/science/dtiquery/Makefile
@ -1,61 +0,0 @@
-# Created by: Jason W. Bacon <jwbacon@tds.net>
-# $FreeBSD$
-
-PORTNAME=	dtiquery
-PORTVERSION=	1.1
-PORTREVISION=	5
-CATEGORIES=	science biology
-MASTER_SITES=	http://graphics.stanford.edu/projects/dti/
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Stanford DTI Visualization tool
-
-BUILD_DEPENDS=	${LOCALBASE}/include/tnt/tnt.h:${PORTSDIR}/devel/tnt \
-		${LOCALBASE}/include/tnt/jama_cholesky.h:${PORTSDIR}/math/jama \
-		${LOCALBASE}/lib/libRAPID.a:${PORTSDIR}/math/rapid
-EXTRACT_DEPENDS=	dos2unix:${PORTSDIR}/converters/unix2dos
-LIB_DEPENDS=	libwx_gtk2_core-2.8.so:${PORTSDIR}/x11-toolkits/wxgtk28 \
-		libvtkCommon.so:${PORTSDIR}/math/vtk5
-
-CONFLICTS=	dtiquery-1.0*
-
-RESTRICTED=	Must register to download at http://graphics.stanford.edu/projects/dti/
-
-SUB_FILES=	pkg-message
-PKGMESSAGE=	${WRKDIR}/pkg-message
-
-USES=		gmake
-
-PLIST_FILES=	bin/dtiquery \
-		bin/dtiprecompute_cmd \
-		bin/dtiprecompute_gui
-
-ALL_TARGET=
-
-MAN1=		dtiquery.1 \
-		dtiprecompute_cmd.1 \
-		dtiprecompute_gui.1
-
-NO_STAGE=	yes
-.include <bsd.port.pre.mk>
-
-.if !exists(${DISTDIR}/${DISTNAME}.tar.gz)
-IGNORE=	you must manually fetch ${DISTNAME}.tar.gz from http://graphics.stanford.edu/projects/dti/, place it in ${DISTDIR}, and then run make again
-.endif
-
-post-extract:
-	dos2unix ${WRKSRC}/*/Makefile ${WRKSRC}/Makefile*
-	${REINPLACE_CMD} "s/zlib-1.2.2 RAPID201//g" ${WRKSRC}/Makefile
-
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/DTIQuery/dtiquery ${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/precompute/dtiprecompute_cmd ${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/precompute/dtiprecompute_gui ${PREFIX}/bin
-	${INSTALL_MAN} ${FILESDIR}/dtiquery.1 ${MAN1PREFIX}/man/man1
-	${INSTALL_MAN} ${FILESDIR}/dtiquery.1 ${MAN1PREFIX}/man/man1/dtiprecompute_cmd.1
-	${INSTALL_MAN} ${FILESDIR}/dtiquery.1 ${MAN1PREFIX}/man/man1/dtiprecompute_gui.1
-
-post-install:
-	@${CAT} ${PKGMESSAGE}
-
-.include <bsd.port.post.mk>
--- a/science/dtiquery/distinfo
+++ b/science/dtiquery/distinfo
@ -1,2 +0,0 @@
-SHA256 (dtiquery-1.1.tar.gz) = c59f5911e633f1f364cfd03ed18c296f99963184e2c2ddea937109f45f4b456e
-SIZE (dtiquery-1.1.tar.gz) = 285780
--- a/science/dtiquery/files/dtiquery.1
+++ b/science/dtiquery/files/dtiquery.1
@ -1,35 +0,0 @@
-.TH DTIQUERY 1
-.SH NAME    \" Section header
-.PP
-
-DTIQuery - DTI Visualization Software
-
-.SH SYNOPSIS
-.PP
-.nf 
-.na 
-dtiquery
-dtiprecompute_cmd [args]
-dtiprecompute_gui
-
-.ad
-.fi
-
-.SH "DESCRIPTION"
-
-DTIQuery is a software suite for analyzing DTI (Diffusion Tensor Imaging)
-data obtained via MRI (Magnetic Resonence Imaging).  For full documentation,
-please visit 
-
-http://graphics.stanford.edu/projects/dti/software/.
-
-.SH "SEE ALSO"
-
-afni(1), caret(1), freesurfer(1), fsl(1)
-
-.SH AUTHOR
-.nf
-.na
-David Akers
-Stanford University
-
--- a/science/dtiquery/files/patch-DTIQuery-Makefile
+++ b/science/dtiquery/files/patch-DTIQuery-Makefile
@ -1,13 +0,0 @@
--- DTIQuery/Makefile.orig	Thu Dec  6 13:48:54 2007
-+++ DTIQuery/Makefile	Thu Dec  6 13:49:24 2007
-@@ -12,8 +12,8 @@
- 
- VTK_LIBS = -lvtkIO \
-         -lvtkRendering -lvtkGraphics -lvtkImaging \
-        -lvtkFiltering -lvtkCommon -lvtkHybrid -lvtkpng -lvtkzlib \
-        -lvtkftgl -lvtkfreetype -lvtkjpeg -lvtkDICOMParser \
-+        -lvtkFiltering -lvtkCommon -lvtkHybrid -lpng -lz \
-+        -lvtkftgl -lvtkfreetype -ljpeg -lvtkDICOMParser \
- 
- # for FreeBSD, need -lpng -ljpeg -lz instead of -lvtkpng -lvtkzlib -lvtkjpeg
- 
--- a/science/dtiquery/files/patch-Makefile.definitions
+++ b/science/dtiquery/files/patch-Makefile.definitions
@ -1,34 +0,0 @@
--- Makefile.definitions.orig	Wed Dec 19 10:50:50 2007
-+++ Makefile.definitions	Wed Dec 19 10:51:13 2007
-@@ -1,6 +1,6 @@
-CYGWIN = 1
-+# CYGWIN = 1
- # mac = 1
-# FreeBSD = 1
-+FreeBSD = 1
- # linux = 1
- 
- # Uncomment the line above corresponding to your system. Then find the 
-@@ -46,18 +46,19 @@
- 
- ifdef FreeBSD
- 
-WX_CONFIG_BIN		?= /usr/X11R6/bin/wxgtk2-2.8-config
-+WX_CONFIG_BIN		?= ${LOCALBASE}/bin/wxgtk2-2.8-config
- VTK_INCLUDE_PATHS	?= -I/usr/local/include/vtk-5.4/
- VTK_LIB_PATHS		?= -L/usr/local/lib/vtk-5.4/
- WX_INCLUDE_PATHS	?= `$(WX_CONFIG_BIN) --cxxflags`
- WX_LIB_PATHS		?= `$(WX_CONFIG_BIN) --libs` `$(WX_CONFIG_BIN) \
- 				--gl-libs`
-RAPID_INCLUDE_PATH	?= -I/usr/local/include
-+RAPID_INCLUDE_PATH	?= -I/usr/local/include/RAPID
- RAPID_LIB_PATH		?= -L/usr/local/lib
- TNT_INCLUDE_PATH	?= -I/usr/local/include/tnt/
- JAMA_INCLUDE_PATH	?= -I/usr/local/include/
- ZLIB_INCLUDE_PATH	?= -I/usr/include
-SYS_INCLUDE_PATHS	?= -I/usr/include -I/usr/X11R6/include -I/usr/local/include/gtk-2.0 -I/usr/X11R6/include/gtk-2.0 -I/usr/local/include/glib-2.0 -I/usr/local/include/cairo -I/usr/local/include/pango-1.0 -I/usr/X11R6/include/pango-1.0 -I/usr/local/include/atk-1.0 
-+SYS_INCLUDE_PATHS	?= -I/usr/include -I${LOCALBASE}/include -I/usr/local/include/gtk-2.0 -I${LOCALBASE}/include/gtk-2.0 -I/usr/local/include/glib-2.0 -I/usr/local/include/cairo -I/usr/local/include/pango-1.0 -I${LOCALBASE}/include/pango-1.0 -I/usr/local/include/atk-1.0 
-+SYS_CXXFLAGS 		?= -g
- SYS_LIBS		?= -L/usr/local/lib -lXt -lGL -lpng
- 
- else
--- a/science/dtiquery/files/patch-precompute-Makefile
+++ b/science/dtiquery/files/patch-precompute-Makefile
@ -1,13 +0,0 @@
--- precompute/Makefile.orig	Thu Dec  6 13:51:44 2007
-+++ precompute/Makefile	Thu Dec  6 13:52:16 2007
-@@ -21,8 +21,8 @@
- 
- VTK_LIBS = -lvtkIO \
-         -lvtkRendering -lvtkGraphics -lvtkImaging \
-        -lvtkFiltering -lvtkCommon -lvtkHybrid -lvtkpng -lvtkzlib \
-        -lvtkftgl -lvtkfreetype -lvtkjpeg -lvtkDICOMParser \
-+        -lvtkFiltering -lvtkCommon -lvtkHybrid -lpng -lz \
-+        -lvtkftgl -lvtkfreetype -ljpeg -lvtkDICOMParser \
- 
- # for FreeBSD, need -lpng -ljpeg -lz instead of -lvtkpng -lvtkzlib -lvtkjpeg
- 
--- a/science/dtiquery/files/pkg-message.in
+++ b/science/dtiquery/files/pkg-message.in
@ -1,10 +0,0 @@
-=============================================================================
-DTI Query users will need %%PREFIX%%/bin in their PATH.
-
-For questions or comments regarding this port, please contact the
-port maintainer.
-
-For dtiquery usage, please visit the WEB site at
-
-http://graphics.stanford.edu/projects/dti/
-=============================================================================
--- a/science/dtiquery/pkg-descr
+++ b/science/dtiquery/pkg-descr
@ -1,3 +0,0 @@
-DTI visualization software from Stanford.
-
-WWW: http://graphics.stanford.edu/projects/dti/
--- a/science/elmer-hutiter/Makefile
+++ b/science/elmer-hutiter/Makefile
@ -1,54 +0,0 @@
-# Created by: Pedro Giffuni <giffunip@asme.org>
-# $FreeBSD$
-
-PORTNAME=	hutiter
-PORTVERSION=	5.4.0
-PORTREVISION=	6
-CATEGORIES=	science
-MASTER_SITES=	http://www.nic.funet.fi/index/files/index/elmer/src/old/ \
-		http://www.bezopasnik.org/unix/ports/distfiles/
-PKGNAMEPREFIX=	elmer-
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	HUTIter library for use in the ELMER FEM package
-
-LIB_DEPENDS=	libarpack.so:${PORTSDIR}/math/arpack
-
-USES=		fortran
-
-NO_STAGE=	yes
-.include <bsd.port.pre.mk>
-
-.if exists(${LOCALBASE}/lib/libatlas.so) && !defined(WITH_BLAS)
-WITH_ATLAS=	yes
-.endif
-.if defined(WITH_ATLAS)
-LIB_DEPENDS+=	libatlas.so:${PORTSDIR}/math/atlas
-BLAS=		-lf77blas
-LAPACK=		-lalapack -lcblas
-.else
-LIB_DEPENDS+=	liblapack.so:${PORTSDIR}/math/lapack
-LIB_DEPENDS+=	libblas.so:${PORTSDIR}/math/blas
-BLAS=		-lblas
-LAPACK=		-llapack
-.endif
-
-post-patch:
-	@${REINPLACE_CMD} -e 's|%%CC%%|${CC}|' -e 's|%%FC%%|${FC}|' ${WRKSRC}/configure.in
-
-GNU_CONFIGURE=	yes
-USE_AUTOTOOLS=	autoconf
-ALL_TARGET=
-
-PLIST_FILES=	include/huti_defs.h include/huti_fdefs.h lib/libhuti.a
-
-.if ${ARCH} == "amd64" || ${ARCH} == "ia64"
-CFLAGS+=	-fPIC
-FFLAGS+=	-fPIC
-
-post-configure:
-	@${REINPLACE_CMD} -e 's+-O +-O -fPIC +g;' ${WRKSRC}/src/Makefile
-
-.endif
-
-.include <bsd.port.post.mk>
--- a/science/elmer-hutiter/distinfo
+++ b/science/elmer-hutiter/distinfo
@ -1,2 +0,0 @@
-SHA256 (hutiter-5.4.0.tar.gz) = b5d7b01dc4a5b6da6147e6bf31d00048548c54609e77108cac0d359a0ee2379c
-SIZE (hutiter-5.4.0.tar.gz) = 172341
--- a/science/elmer-hutiter/pkg-descr
+++ b/science/elmer-hutiter/pkg-descr
@ -1,9 +0,0 @@
-HUTIter library for use in the Elmer FEM package.
-
-Elmer is an open-source computational tool for multi-physics problems.
-
-Elmer includes physical models of fluid dynamics, structural mechanics,
-electromagnetics and heat transfer. These are described by partial
-differential equations which Elmer solves by the Finite Element Method (FEM).
-
-WWW: http://www.csc.fi/elmer/
--- a/science/elmerpost/Makefile
+++ b/science/elmerpost/Makefile
@ -1,33 +0,0 @@
-# Created by: Pedro Giffuni <giffunip@asme.org>
-# $FreeBSD$
-
-PORTNAME=	elmerpost
-PORTVERSION=	5.4.0
-PORTREVISION=	7
-CATEGORIES=	science
-MASTER_SITES=	http://garr.dl.sourceforge.net/sourceforge/elmerfem/
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Visualization of Numerical Results in the ELMER FEM package
-
-BUILD_DEPENDS=	${LOCALBASE}/lib/libmatc.a:${PORTSDIR}/science/elmer-matc	\
-		wish8.4:${PORTSDIR}/x11-toolkits/tk84
-RUN_DEPENDS=	wish8.4:${PORTSDIR}/x11-toolkits/tk84
-
-# Elmer avoids the new C++ headers because they cause problems
-# on older systems (Irix)
-CXXFLAGS+=	-Wno-deprecated
-
-USE_GL=		yes
-USE_XORG=	x11 xt xi
-GNU_CONFIGURE=	yes
-USES=		gmake fortran
-
-NO_STAGE=	yes
-.include <bsd.port.pre.mk>
-
-.if ${ARCH} == "amd64"
-CFLAGS+=	-fPIC
-.endif
-
-.include <bsd.port.post.mk>
--- a/science/elmerpost/distinfo
+++ b/science/elmerpost/distinfo
@ -1,2 +0,0 @@
-SHA256 (elmerpost-5.4.0.tar.gz) = 196e8d9fb5ff9e9e30785b5c762eb45f41a664c3592595b23a0c1832ed4a9445
-SIZE (elmerpost-5.4.0.tar.gz) = 1424120
--- a/science/elmerpost/files/patch-src-Makefile.am
+++ b/science/elmerpost/files/patch-src-Makefile.am
@ -1,8 +0,0 @@
--- src/Makefile.am.orig	2009-07-05 17:46:44.000000000 -0300
-+++ src/Makefile.am	2009-07-05 17:47:17.000000000 -0300
-@@ -1,4 +1,4 @@
-SUBDIRS=tk glaux camera graphics modules sico2elmer objects visuals tcl elements 
-+SUBDIRS=tk glaux camera graphics modules objects visuals tcl elements 
- 
- if NOTWINDOWS
- 
--- a/science/elmerpost/files/patch-src-Makefile.in
+++ b/science/elmerpost/files/patch-src-Makefile.in
@ -1,11 +0,0 @@
--- src/Makefile.in.orig	2009-07-05 17:46:35.000000000 -0300
-+++ src/Makefile.in	2009-07-05 17:47:03.000000000 -0300
-@@ -235,7 +235,7 @@
- target_cpu = @target_cpu@
- target_os = @target_os@
- target_vendor = @target_vendor@
-SUBDIRS = tk glaux camera graphics modules sico2elmer objects visuals tcl elements 
-+SUBDIRS = tk glaux camera graphics modules objects visuals tcl elements 
- @NOTWINDOWS_FALSE@ElmerPost_SOURCES = \
- @NOTWINDOWS_FALSE@	ElmerPost.c \
- @NOTWINDOWS_FALSE@	elmerpost.h \
--- a/science/elmerpost/pkg-descr
+++ b/science/elmerpost/pkg-descr
@ -1,11 +0,0 @@
-ElmerPost - the Visualization of Numerical Results.
-
-The function of ElmerPost is to visualize the numerical results produced
-by ElmerSolver and other finite element programs. ElmerPost operates with
-the data specific to the unknown variables (temperature, velocity,
-pressure, displacement etc.) defined in the mathematical model. ElmerPost
-plots e.g. contours and vector fields, and can manipulate computed data
-into another form using the built-in MATC-language (for instance heat
-fluxes from temperature distributions).
-
-WWW:	http://www.csc.fi/elmer/elmerpost/
--- a/science/elmerpost/pkg-plist
+++ b/science/elmerpost/pkg-plist
@ -1,285 +0,0 @@
-bin/ElmerPost
-bin/QueryGLXExt
-%%DATADIR%%/help/dspl.html
-%%DATADIR%%/help/edit.html
-%%DATADIR%%/help/figs/a.log
-%%DATADIR%%/help/figs/background.gif
-%%DATADIR%%/help/figs/benzene_cut.gif
-%%DATADIR%%/help/figs/benzene_iso.gif
-%%DATADIR%%/help/figs/camera.gif
-%%DATADIR%%/help/figs/clip.gif
-%%DATADIR%%/help/figs/colormap.gif
-%%DATADIR%%/help/figs/cols.gif
-%%DATADIR%%/help/figs/cont.gif
-%%DATADIR%%/help/figs/crystal_flow.gif
-%%DATADIR%%/help/figs/crystal_stream.gif
-%%DATADIR%%/help/figs/crystal_temp.gif
-%%DATADIR%%/help/figs/diff.gif
-%%DATADIR%%/help/figs/elmer.gif
-%%DATADIR%%/help/figs/elmer_back.gif
-%%DATADIR%%/help/figs/elmer_general.gif
-%%DATADIR%%/help/figs/elmer_home.gif
-%%DATADIR%%/help/figs/elmer_who.gif
-%%DATADIR%%/help/figs/groups.gif
-%%DATADIR%%/help/figs/iso.gif
-%%DATADIR%%/help/figs/k1.gif
-%%DATADIR%%/help/figs/kide3d_cvec.gif
-%%DATADIR%%/help/figs/kide3d_part.gif
-%%DATADIR%%/help/figs/matc.gif
-%%DATADIR%%/help/figs/material.gif
-%%DATADIR%%/help/figs/mesh.gif
-%%DATADIR%%/help/figs/newshome.gif
-%%DATADIR%%/help/figs/particle.gif
-%%DATADIR%%/help/figs/putki3d.gif
-%%DATADIR%%/help/figs/putki3d_particles.gif
-%%DATADIR%%/help/figs/rb_temp.gif
-%%DATADIR%%/help/figs/rb_vect.gif
-%%DATADIR%%/help/figs/saab.gif
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-%%DATADIR%%/help/figs/sic_grid.jpg
-%%DATADIR%%/help/figs/sic_heating.jpg
-%%DATADIR%%/help/figs/sic_temperature.jpg
-%%DATADIR%%/help/figs/smelt_cut.gif
-%%DATADIR%%/help/figs/smelt_part.gif
-%%DATADIR%%/help/figs/spec1.gif
-%%DATADIR%%/help/figs/spec2.gif
-%%DATADIR%%/help/figs/sphere.gif
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-%%DATADIR%%/help/gallery.html
-%%DATADIR%%/help/help.tcl
-%%DATADIR%%/help/html_library-0.3/html_library.tcl
-%%DATADIR%%/help/html_library-0.3/license.terms
-%%DATADIR%%/help/http.tcl
-%%DATADIR%%/help/index.html
-%%DATADIR%%/help/main.html
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-%%DATADIR%%/help/matc/node5.html
-%%DATADIR%%/help/matc/node50.html
-%%DATADIR%%/help/matc/node51.html
-%%DATADIR%%/help/matc/node6.html
-%%DATADIR%%/help/matc/node7.html
-%%DATADIR%%/help/matc/node8.html
-%%DATADIR%%/help/matc/node9.html
-%%DATADIR%%/help/mouse.html
-%%DATADIR%%/lib/cameras/default
-%%DATADIR%%/lib/cameras/four_view.cam
-%%DATADIR%%/lib/cameras/koe.cam
-%%DATADIR%%/lib/cameras/single_ortho.cam
-%%DATADIR%%/lib/cameras/single_view.cam
-%%DATADIR%%/lib/cameras/three_view.cam
-%%DATADIR%%/lib/colormaps/Spectral_16.cm
-%%DATADIR%%/lib/colormaps/Spectral_256.cm
-%%DATADIR%%/lib/colormaps/Spectral_32.cm
-%%DATADIR%%/lib/colormaps/Spectral_512.cm
-%%DATADIR%%/lib/colormaps/black.cm
-%%DATADIR%%/lib/colormaps/default.cm
-%%DATADIR%%/lib/colormaps/gray_16.cm
-%%DATADIR%%/lib/colormaps/gray_256.cm
-%%DATADIR%%/lib/colormaps/gray_32.cm
-%%DATADIR%%/lib/colormaps/gray_4.cm
-%%DATADIR%%/lib/colormaps/gray_512.cm
-%%DATADIR%%/lib/colormaps/gray_8.cm
-%%DATADIR%%/lib/colormaps/white.cm
-%%DATADIR%%/lib/images/FILEOPEN.BMP
-%%DATADIR%%/lib/images/FILESAVE.BMP
-%%DATADIR%%/lib/images/WS_FTP.LOG
-%%DATADIR%%/lib/images/arrows.gif
-%%DATADIR%%/lib/images/cmesh.bmp
-%%DATADIR%%/lib/images/cmesh.gif
-%%DATADIR%%/lib/images/colscale.gif
-%%DATADIR%%/lib/images/cont.gif
-%%DATADIR%%/lib/images/down.gif
-%%DATADIR%%/lib/images/file.gif
-%%DATADIR%%/lib/images/fileopen.gif
-%%DATADIR%%/lib/images/isocont.gif
-%%DATADIR%%/lib/images/left.gif
-%%DATADIR%%/lib/images/lwait.cur
-%%DATADIR%%/lib/images/part.gif
-%%DATADIR%%/lib/images/play.gif
-%%DATADIR%%/lib/images/play.rgb
-%%DATADIR%%/lib/images/right.gif
-%%DATADIR%%/lib/images/rmx.gif
-%%DATADIR%%/lib/images/rmx_save.gif
-%%DATADIR%%/lib/images/rmy.gif
-%%DATADIR%%/lib/images/rpx.gif
-%%DATADIR%%/lib/images/rpy.gif
-%%DATADIR%%/lib/images/scaledown.gif
-%%DATADIR%%/lib/images/scaleup.gif
-%%DATADIR%%/lib/images/up.gif
-%%DATADIR%%/lib/images/vect.gif
-%%DATADIR%%/lib/mc.ini
-%%DATADIR%%/lib/rgb.txt
-%%DATADIR%%/modules/screensave.so
-%%DATADIR%%/tcl/COPYRIGHT.tcl
-%%DATADIR%%/tcl/LoadSicopolis.tcl
-%%DATADIR%%/tcl/Makefile
-%%DATADIR%%/tcl/Makefile.am
-%%DATADIR%%/tcl/Makefile.in
-%%DATADIR%%/tcl/args.tcl
-%%DATADIR%%/tcl/camera.tcl
-%%DATADIR%%/tcl/clip.tcl
-%%DATADIR%%/tcl/colormap.tcl
-%%DATADIR%%/tcl/colorscale.tcl
-%%DATADIR%%/tcl/contours.tcl
-%%DATADIR%%/tcl/dialog.tcl
-%%DATADIR%%/tcl/file.tcl
-%%DATADIR%%/tcl/group.tcl
-%%DATADIR%%/tcl/init.tcl
-%%DATADIR%%/tcl/init_interrupt.tcl
-%%DATADIR%%/tcl/isosurface.tcl
-%%DATADIR%%/tcl/loadsingle
-%%DATADIR%%/tcl/material.tcl
-%%DATADIR%%/tcl/math.tcl
-%%DATADIR%%/tcl/menu.tcl
-%%DATADIR%%/tcl/mesh.tcl
-%%DATADIR%%/tcl/message.tcl
-%%DATADIR%%/tcl/misc.tcl
-%%DATADIR%%/tcl/particle.tcl
-%%DATADIR%%/tcl/readfile.tcl
-%%DATADIR%%/tcl/saveimage.tcl
-%%DATADIR%%/tcl/sphere.tcl
-%%DATADIR%%/tcl/text.tcl
-%%DATADIR%%/tcl/timestep.tcl
-%%DATADIR%%/tcl/vectors.tcl
-@dirrm %%DATADIR%%/help/figs
-@dirrm %%DATADIR%%/help/html_library-0.3
-@dirrm %%DATADIR%%/help/matc/lh-figs
-@dirrm %%DATADIR%%/help/matc
-@dirrm %%DATADIR%%/help
-@dirrm %%DATADIR%%/lib/cameras
-@dirrm %%DATADIR%%/lib/colormaps
-@dirrm %%DATADIR%%/lib/images
-@dirrm %%DATADIR%%/lib
-@dirrm %%DATADIR%%/modules
-@dirrm %%DATADIR%%/tcl
-@dirrm %%DATADIR%%
--- a/science/g3data/Makefile
+++ b/science/g3data/Makefile
@ -1,34 +0,0 @@
-# Created by: trasz <trasz@pin.if.uz.zgora.pl>
-# $FreeBSD$
-
-PORTNAME=	g3data
-PORTVERSION=	1.5.3
-PORTREVISION=	5
-CATEGORIES=	science
-MASTER_SITES=	http://www.frantz.fi/software/
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Utility for extracting data from graphs
-
-BUILD_DEPENDS=	nsgmls:${PORTSDIR}/textproc/jade \
-		${LOCALBASE}/share/sgml/docbook/utils-0.6.14/helpers/docbook2man-spec.pl:${PORTSDIR}/textproc/docbook-utils \
-		${LOCALBASE}/share/sgml/docbook/4.1:${PORTSDIR}/textproc/docbook-sgml
-
-USES=		pkgconfig
-USE_GNOME=	gtk20
-ALL_TARGET=
-MAN1=		g3data.1
-MANCOMPRESSED=	yes
-PLIST_FILES=	bin/g3data %%EXAMPLESDIR%%/test1.png %%EXAMPLESDIR%%/test1.values \
-		%%EXAMPLESDIR%%/test2.png %%EXAMPLESDIR%%/test2.values
-PLIST_DIRS=	%%EXAMPLESDIR%%
-
-NO_STAGE=	yes
-post-install:
-		@${MKDIR} ${EXAMPLESDIR}
-		${INSTALL_DATA} ${WRKSRC}/test1.png ${EXAMPLESDIR}
-		${INSTALL_DATA} ${WRKSRC}/test1.values ${EXAMPLESDIR}
-		${INSTALL_DATA} ${WRKSRC}/test2.png ${EXAMPLESDIR}
-		${INSTALL_DATA} ${WRKSRC}/test2.values ${EXAMPLESDIR}
-
-.include <bsd.port.mk>
--- a/science/g3data/distinfo
+++ b/science/g3data/distinfo
@ -1,2 +0,0 @@
-SHA256 (g3data-1.5.3.tar.gz) = afedb9e4ad8968dbf8f0ffddab149f24c41f028fe984f4d0740009e8b2de1de0
-SIZE (g3data-1.5.3.tar.gz) = 52051
--- a/science/g3data/files/patch-Makefile
+++ b/science/g3data/files/patch-Makefile
@ -1,24 +0,0 @@
--- Makefile.orig	2008-12-14 09:20:17.000000000 +0100
-+++ Makefile	2009-01-11 15:19:56.000000000 +0100
-@@ -1,8 +1,7 @@
-CC=gcc
-CFLAGS=-Wall `pkg-config --cflags gtk+-2.0`
-+CFLAGS+=-Wall `pkg-config --cflags gtk+-2.0`
- LIBS=`pkg-config --libs gtk+-2.0`
-bindir ?= /usr/bin
-mandir ?= /usr/share/man
-+bindir= ${PREFIX}/bin
-+mandir= ${PREFIX}/man
- 
- .c.o:
- 	$(CC) -c $(CFLAGS) $(CPPFLAGS) $<
-@@ -21,7 +20,8 @@
- 
- g3data.1.gz: g3data.sgml
- 	rm -f *.1
-	onsgmls g3data.sgml | sgmlspl /usr/share/sgml/docbook/utils-0.6.14/helpers/docbook2man-spec.pl
-+	nsgmls g3data.sgml | sgmlspl /usr/local/share/sgml/docbook/utils-0.6.14/helpers/docbook2man-spec.pl
-+	mv *.1 g3data.1
- 	gzip g3data.1
- 
- clean:
--- a/science/g3data/pkg-descr
+++ b/science/g3data/pkg-descr
@ -1,5 +0,0 @@
-g3data is used for extracting data from graphs. In publications
-graphs often are included, but the actual data is missing. g3data
-makes the extracting process much easier.
-
-WWW:	http://www.frantz.fi/software/g3data.php
--- a/science/gamess/Makefile
+++ b/science/gamess/Makefile
@ -1,164 +0,0 @@
-# Created by: NAKATA Maho <maho@FreeBSD.org>
-# $FreeBSD$
-
-PORTNAME=	gamess
-PORTVERSION=	${SNAPDATE}
-PORTREVISION=	1
-CATEGORIES=	science
-MASTER_SITES=	#http://www.msg.ameslab.gov/GAMESS/License_Agreement.html
-DISTNAME=	gamess-current
-DIST_SUBDIR=	${PORTNAME}/${PORTVERSION}
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Freely obtainable ab-initio molecular orbital calculation program
-
-USES=		fortran gmake
-WRKSRC=		${WRKDIR}/gamess
-SNAPDATE=	20130501.1
-
-RESTRICTED=	No Redistribution
-
-.if !exists(${DISTDIR}/${DISTFILES})
-IGNORE=you must manually get the source distribution from master site. http://www.msg.ameslab.gov/GAMESS/download.html. Please select "Source code distribution", and check on "running on Intel compatible PC running Linux". You must have license, and freely obtainable
-.endif
-
-MANUAL_PACKAGE_BUILD=You must manually get the source distribution from master site. http://www.msg.ameslab.gov/GAMESS/download.html. Please select "Source code distribution", and check on "running on Intel compatible PC running Linux". You must have license, and freely obtainable.
-
-NO_STAGE=	yes
-.include <bsd.port.pre.mk>
-
-.if exists(${LOCALBASE}/lib/libgoto2.so)
-WITH_BLAS?=	gotoblas
-.elif exists(${LOCALBASE}/lib/libatlas.so)
-WITH_BLAS?=	atlas
-.else
-WITH_BLAS?=	reference
-.endif
-
-. if ${WITH_BLAS} == reference
-LIB_DEPENDS+=	libblas.so:${PORTSDIR}/math/blas
-LIB_DEPENDS+=	liblapack.so:${PORTSDIR}/math/lapack
-BLAS=		-lblas
-LAPACK=		-llapack
-.elif ${WITH_BLAS} == gotoblas
-LIB_DEPENDS+=	libgoto2.so:${PORTSDIR}/math/gotoblas
-BLAS=		-lgoto2p
-LAPACK=		-lgoto2p
-.elif ${WITH_BLAS} == atlas
-LIB_DEPENDS+=	libatlas.so:${PORTSDIR}/math/atlas
-BLAS=		-lptf77blas
-LAPACK=		-lalapack -lptcblas
-.endif
-
-.if defined(WITH_OPTIMIZED_FLAGS)
-.if ${ARCH} == "amd64"
-CFLAGS+=	-pipe -O3 -ffast-math -funroll-all-loops -fpeel-loops -ftracer -funswitch-loops -funit-at-a-time
-FFLAGS+=	-pipe -O3 -ffast-math -funroll-all-loops -fpeel-loops -ftracer -funswitch-loops -funit-at-a-time
-.elif ${ARCH} == "i386"
-CFLAGS+=	-pipe -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double -mcpu=i686 -march=i686 -mfancy-math-387
-FFLAGS+=	-pipe -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double -mcpu=i686 -march=i686 -mfancy-math-387
-.endif
-.endif
-
-#WITH_IFC=	yes #currently building with ifc is broken
-.if defined(WITH_IFC)
-FC=	${LOCALBASE}/intel_fc_80/bin/ifort
-F77=	${LOCALBASE}/intel_fc_80/bin/ifort
-CC=	${LOCALBASE}/intel_cc_80/bin/icc
-FFLAGS=	-axP -xW -ipo -O3 -Vaxlib
-CFLAGS=	-axP -xW -ipo -O3 -Vaxlib
-LIBSVM=	-lsvml
-LIBG2C=	-lg2c
-.else
-LIBG2C=
-LIBSVM=
-.endif
-
-.if defined(WITH_IFC)
-FORTRAN=	ifort
-.else
-FORTRAN=	gfortran
-.endif
-
-pre-build:
-	${CP} ${FILESDIR}/install.info ${WRKSRC}
-	${CP} ${FILESDIR}/Makefile.top ${WRKSRC}/Makefile
-	@${REINPLACE_CMD} -e 's+%%PREFIX%%+${PREFIX}+g' ${WRKSRC}/gms-files.csh
-.if ${ARCH} == "amd64"
-	@${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd64+g' ${WRKSRC}/comp
-	@${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd64+g' ${WRKSRC}/compall
-	@${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd64+g' ${WRKSRC}/ddi/compddi
-	@${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd64+g' ${WRKSRC}/lked
-	@${REINPLACE_CMD} -e 's+%%GMS_TARGET%%+freebsd64+g' ${WRKSRC}/install.info
-.elif ${ARCH} == "i386"
-	@${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd32+g' ${WRKSRC}/comp
-	@${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd32+g' ${WRKSRC}/compall
-	@${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd32+g' ${WRKSRC}/ddi/compddi
-	@${REINPLACE_CMD} -e 's+%%ARCH%%+freebsd32+g' ${WRKSRC}/lked
-	@${REINPLACE_CMD} -e 's+%%GMS_TARGET%%+freebsd32+g' ${WRKSRC}/install.info
-.endif
-	@${REINPLACE_CMD} -e 's+%%GMS_PATH%%+${WRKSRC}+g ; \
-			     s+%%GMS_BUILD_DIR%%+${WRKSRC}+g ; \
-				s+%%GMS_FORTRAN%%+${FORTRAN}+g ; \
-				s+%%FC%%+${FC}+g ; \
-				s+%%GMS_GFORTRAN_VERNO%%+${GCC_DEFAULT_VERSION}+g ; \
-				s+%%GMS_DDI_COMM%%+sockets+g ; \
-				s+%%GMS_MATHLIB%%+none+g ; \
-				s+%%GMS_MATHLIB_PATH%%+${LOCALBASE}/lib+g' ${WRKSRC}/install.info
-	${REINPLACE_CMD} -e 's+%%FC%%+${FC}+g ; \
-			      s+%%LDFLAGS%%+${LDFLAGS}+g ; \
-			      s+%%LOCALBASE%%+${LOCALBASE}+g ; \
-			      s+%%LIBSVM%%+${LIBSVM}+g ; \
-			      s+%%LIBG2C%%+${LIBG2C}+g ; \
-			      s+%%BLAS%%+${BLAS}+g ; \
-			      s+%%PTHREAD_LIBS%%+${PTHREAD_LIBS}+g' \
-			 ${WRKSRC}/lked
-	${REINPLACE_CMD} -e 's+%%FC%%+${FC}+g ; \
-			      s+%%FFLAGS%%+${FFLAGS}+g' \
-			 ${WRKSRC}/comp
-	${REINPLACE_CMD} -e 's+%%CC%%+${CC}+g' \
-			 ${WRKSRC}/compall
-	${REINPLACE_CMD} -e 's+%%PREFIX%%+${PREFIX}+g' \
-			 ${WRKSRC}/rungms
-	${REINPLACE_CMD} -e  's+%%FC%%+${FC}+g ; \
-		   	      s+%%GMS_FORTRAN%%+${FORTRAN}+g ; \
-			      s+%%PTHREAD_CFLAGS%%+${PTHREAD_CFLAGS}+g ; \
-			      s+%%PTHREAD_LIBS%%+${PTHREAD_LIBS}+g ; \
-			      s+%%UNDERSCORES%%+${UNDERSCORES}+g ; \
-			      s+%%CC%%+${CC}+g' \
-			 ${WRKSRC}/ddi/compddi
-
-	${CP} ${FILESDIR}/Makefile.tools ${WRKSRC}/tools/Makefile
-	${REINPLACE_CMD} -e 's+%%FC%%+${FC}+g ; \
-			      s+%%FFLAGS%%+${FFLAGS}+g' \
-		${WRKSRC}/tools/Makefile
-
-do-build:
-	(cd ${WRKSRC}; ${MAKE_CMD})
-
-do-install:
-	${MKDIR} ${PREFIX}/bin/gms
-	${MKDIR} ${PREFIX}/share/gamess
-	${MKDIR} ${PREFIX}/share/gamess/mcpdata
-	${MKDIR} ${PREFIX}/share/doc/gamess
-	${MKDIR} ${PREFIX}/share/examples/gamess
-	${INSTALL_SCRIPT}  ${WRKDIR}/gamess/rungms		${PREFIX}/bin/gamess
-	${CHMOD} 555 ${PREFIX}/bin/gamess
-	${INSTALL_SCRIPT} ${WRKDIR}/gamess/gms-files.csh          ${PREFIX}/bin/gms
-	${INSTALL_PROGRAM} ${WRKDIR}/gamess/gamess.00.x          ${PREFIX}/bin/gms
-	${INSTALL_PROGRAM} ${WRKDIR}/gamess/ddi/ddikick.x            ${PREFIX}/bin/gms
-	${INSTALL_DATA}    ${WRKDIR}/gamess/*.DOC                ${PREFIX}/share/doc/gamess/
-	${INSTALL_DATA}    ${WRKDIR}/gamess/tests/standard/*.inp          ${PREFIX}/share/examples/gamess/
-	${MKDIR} ${PREFIX}/share/gamess/auxdata
-	${MKDIR} ${PREFIX}/share/gamess/auxdata/BASES
-	${MKDIR} ${PREFIX}/share/gamess/auxdata/EFP
-	${MKDIR} ${PREFIX}/share/gamess/auxdata/MCP
-	${MKDIR} ${PREFIX}/share/gamess/auxdata/QUANPOL
-	${INSTALL_DATA}    ${WRKDIR}/gamess/auxdata/ericfmt.dat	${PREFIX}/share/gamess/auxdata/
-	${INSTALL_DATA}    ${WRKDIR}/gamess/auxdata/BASES/*	${PREFIX}/share/gamess/auxdata/BASES
-	${INSTALL_DATA}    ${WRKDIR}/gamess/auxdata/EFP/*	${PREFIX}/share/gamess/auxdata/EFP
-	${INSTALL_DATA}    ${WRKDIR}/gamess/auxdata/MCP/*	${PREFIX}/share/gamess/auxdata/MCP
-	${INSTALL_DATA}    ${WRKDIR}/gamess/auxdata/QUANPOL/*	${PREFIX}/share/gamess/auxdata/QUANPOL
-	${INSTALL_DATA}    ${WRKDIR}/gamess/ddi/readme.ddi       ${PREFIX}/share/doc/gamess/
-
-.include <bsd.port.post.mk>
--- a/science/gamess/distinfo
+++ b/science/gamess/distinfo
@ -1,2 +0,0 @@
-SHA256 (gamess/20130501.1/gamess-current.tar.gz) = 315e6fa8f1947d8419b6f1adccf3fc7dd47b581fce107d304b7b99ef0cb15498
-SIZE (gamess/20130501.1/gamess-current.tar.gz) = 29013211
--- a/science/gamess/files/Makefile.tools
+++ b/science/gamess/files/Makefile.tools
@ -1,11 +0,0 @@
-all: actvte.f actvte.x
-
-actvte.x: actvte.f
-	%%FC%% %%FFLAGS%% -o actvte.x actvte.f
-
-actvte.f: actvte.code 
-	sed 's/*UNX/    /g' < actvte.code > actvte.f
-
-clean: 
-	rm actvte.x actvte.f
-
--- a/science/gamess/files/Makefile.top
+++ b/science/gamess/files/Makefile.top
@ -1,11 +0,0 @@
-# Makefile for gamess
-all: gamess_exe
-
-gamess_exe: 
-	(cd tools ; ${MAKE} )
-	(cd ddi ; ./compddi )
-	./compall
-	csh lked
-
-clean:
-	rm -rf object/*.o  *.o *.f
--- a/science/gamess/files/install.info
+++ b/science/gamess/files/install.info
@ -1,15 +0,0 @@
-#!/bin/csh
-# $FreeBSD$
-#   compilation configuration for GAMESS
-setenv GMS_PATH            %%GMS_PATH%%
-setenv GMS_BUILD_DIR       %%GMS_BUILD_DIR%%
-#         machine type
-setenv GMS_TARGET          %%GMS_TARGET%%
-#         FORTRAN compiler setup
-setenv GMS_FORTRAN         %%GMS_FORTRAN%%
-setenv GMS_GFORTRAN_VERNO  %%GMS_GFORTRAN_VERNO%%
-#         mathematical library setup
-setenv GMS_MATHLIB         %%GMS_MATHLIB%%
-setenv GMS_MATHLIB_PATH    %%GMS_MATHLIB_PATH%%
-#         parallel message passing model setup
-setenv GMS_DDI_COMM        %%GMS_DDI_COMM%%
--- a/science/gamess/files/patch-comp
+++ b/science/gamess/files/patch-comp
@ -1,322 +0,0 @@
--- comp.orig	2012-12-05 05:49:41.000000000 +0900
-+++ comp	2013-02-27 15:56:56.000000000 +0900
-@@ -97,6 +97,8 @@
- if ($TARGET == ibm-bg)     set OK=true
- if ($TARGET == linux32)    set OK=true
- if ($TARGET == linux64)    set OK=true
-+if ($TARGET == freebsd32)    set OK=true
-+if ($TARGET == freebsd64)    set OK=true
- if ($TARGET == mac32)      set OK=true
- if ($TARGET == mac64)      set OK=true
- if ($TARGET == necsx)      set OK=true
-@@ -149,6 +151,8 @@
- if  ($TARGET == ibm-bg)       set BLAS3=true
- if (($TARGET == linux32) && ($GMS_MATHLIB != none)) set BLAS3=true
- if (($TARGET == linux64) && ($GMS_MATHLIB != none)) set BLAS3=true
-+if (($TARGET == freebsd32) && ($GMS_MATHLIB != none)) set BLAS3=true
-+if (($TARGET == freebsd64) && ($GMS_MATHLIB != none)) set BLAS3=true
- if  ($TARGET == mac32)        set BLAS3=true
- if  ($TARGET == mac64)        set BLAS3=true
- if  ($TARGET == sgi32)        set BLAS3=true
-@@ -579,6 +583,26 @@
-    endif
- endif
- #
-+if ($TARGET == freebsd32) then
-+                          setenv MACHIN '*I32'
-+   if ($MODULE == ddi)    setenv MACHIN '*SOC'
-+   if ($MODULE == iolib)  setenv MACHIN '*UNX'
-+   if ($MODULE == unport) setenv MACHIN '*L32'
-+endif
-+#
-+if ($TARGET == freebsd64) then
-+                          setenv MACHIN '*I64'
-+   if ($MODULE == ddi)    setenv MACHIN '*SOC'
-+   if ($MODULE == iolib)  setenv MACHIN '*UNX'
-+   if ($MODULE == unport) then
-+      if ($GMS_FORTRAN == ifort) then
-+         setenv MACHIN '*INT'
-+      else
-+         setenv MACHIN '*L64'
-+      endif
-+   endif
-+endif
-+
- if ($TARGET == mac32) then
-                           setenv MACHIN '*I32'
-    if ($MODULE == ddi)    setenv MACHIN '*SOC'
-@@ -1640,6 +1664,137 @@
-    endsw
- #                     ... end of Linux on 32 bit processors.
- endif
-+if ($TARGET == freebsd32) then
-+#
-+#  there are three supported 32 bit compilers: g77, gfortran, ifort
-+#          g77,
-+#             the gnu FORTRAN being included in older Linux distributions
-+#             lacks support for unit numbers over 99, or REAL*16
-+#          gfortran,
-+#             the gnu FORTRAN being included in newer Linux distributions
-+#             this allows unit numbers over 99, but not REAL*16
-+#          Intel's commercial ifort,
-+#             supports unit numbers above 99 and REAL*16 (runs all of GAMESS)
-+
-+    switch ($GMS_FORTRAN)
-+#
-+#   The meaning of g77's flags are
-+#      -O0, -O1, -O2, -O3 are the optimization levels, -O means -O1
-+#      -Wno-globals -fno-globals together suppress argument type checking.
-+#      -fautomatic defeats use of static storage
-+#      -malign-double uses 64 bit data alignment
-+#   g77 does not support FORTRAN logical units above 99, or 128 bit math.
-+#
-+   case g77:
-+   set OPT = '-O2'
-+   if ($MODULE == ormas1) set OPT='-O2 -fno-move-all-movables' # RH9, g77 3.3
-+   if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
-+   if (($MODULE == qeigen) || ($MODULE == int2c)) then
-+      mv -f $MODULE_F $MODULE.junk
-+      sed -e "s/Q-/D-/g" \
-+          -e "s/Q+00/D+00/g" \
-+          -e "s/REAL\*16/DOUBLE PRECISION/" $MODULE.junk > $MODULE_F
-+      rm -f $MODULE.junk
-+   endif
-+   if (($MODULE == iolib) || ($MODULE == inputa) || \
-+       ($MODULE == gamess) || ($MODULE == mp2ims)) then
-+      mv -f $MODULE_F $MODULE.junk
-+      sed -e "s/MXUNIT=299/MXUNIT=99/g" $MODULE.junk > $MODULE_F
-+      rm -f $MODULE.junk
-+   endif
-+   set echo
-+   g77 -c $OPT -malign-double -fautomatic \
-+           -Wno-globals -fno-globals $MODULE_F
-+   unset echo
-+   breaksw
-+#
-+#   gfortran was included with Fedora Core distributions starting around FC4.
-+#   This is a 32 bit version, i.e. not using -fdefault-integer-8!
-+#   Unlike g77, gfortran allows for unit numbers above 100.
-+#   Like g77, gfortran does not support quadruple precision.
-+#      -Ox optimization level is from the gcc back end, x can be 0,1,2,3
-+#      -std=legacy  suppresses warnings about use of f77 constructs.
-+#
-+   case gfortran:
-+   set OPT='-O2'
-+   if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
-+   if ($MODULE == pcmcv2) set OPT='-O1'  # EFP+CPCM, ala Francois, v4.1.2
-+   if ($GMS_GFORTRAN_VERNO == 4.6) then
-+      if ($MODULE == cosmo)  set OPT='-O0'   # this issue seen in 4.6.x
-+      if ($MODULE == tddgrd) set OPT='-O0'   # this issue seen in 4.6.1
-+   endif
-+   if ($GMS_GFORTRAN_VERNO == 4.7) then
-+      if ($MODULE == cosmo)  set OPT='-O0'
-+      if ($MODULE == dcscf)  set OPT='-O0'
-+      if ($MODULE == rohfcc) set OPT='-O0'
-+      if ($MODULE == tddgrd) set OPT='-O0'
-+   endif
-+#        as of 4.6 tested in late 2011, gfortran can do q.p.!
-+   switch ($GMS_GFORTRAN_VERNO)
-+      case 4.0:
-+      case 4.1:
-+      case 4.2:
-+      case 4.3:
-+      case 4.4:
-+      case 4.5:
-+         set extraflags=''
-+         if (($MODULE == qeigen) || ($MODULE == int2c)) then
-+            mv -f $MODULE_F $MODULE.junk
-+            sed -e "s/Q-/D-/g" \
-+                -e "s/Q+00/D+00/g" \
-+                -e "s/REAL\*16/DOUBLE PRECISION/" $MODULE.junk > $MODULE_F
-+            rm -f $MODULE.junk
-+         endif
-+         breaksw
-+      case 4.6:
-+      case 4.7:
-+         set extraflags='-fno-whole-file'
-+         breaksw
-+      default:
-+         echo Unrecognized gfortran version
-+         exit 4
-+         breaksw
-+   endsw
-+#
-+   set echo
-+   %%FC%% -c $OPT -std=legacy $MODULE_F
-+   unset echo
-+   breaksw
-+#
-+#    3. Intel Fortran Compiler for Linux
-+#
-+#    Note that this is more agressive (-O3 compared to -O2) than the
-+#    64 bit compile below.  If an ifort version gives you problems,
-+#    drop the optimization back to -O2.
-+#    Dmitri likes to use "-O3 -xN -ssp -unroll8 -ip -pad -opt_report",
-+#    but that may cause certain ifort versions to fail on some files.
-+#    See http://staff.aist.go.jp/d.g.fedorov/compgms.html for aggressive
-+#    optimizations in 32 bit mode, as a function of the ifort version.
-+#
-+   case ifort:
-+   set OPT = '-O3'
-+   if ($MODULE == delocl) set OPT='-O0'  # from Cheol
-+   if ($MODULE == prpamm) set OPT='-O0'  # for exam13
-+   if ($MODULE == zheev)  set OPT='-O0'
-+   set EXTRAOPT=" "
-+   if ($GMS_IFORT_VERNO >=  8) set EXTRAOPT="$EXTRAOPT -assume byterecl"
-+   if ($GMS_IFORT_VERNO >= 10) set EXTRAOPT="$EXTRAOPT -vec-report0"
-+   if ($GMS_IFORT_VERNO  < 12) set EXTRAOPT="$EXTRAOPT -w95 -cm"
-+   if ($GMS_IFORT_VERNO >= 12) set EXTRAOPT="$EXTRAOPT -warn nousage -inline-level=0"
-+   set echo
-+   ifort -c -i4 $OPT -ftz -auto $EXTRAOPT $MODULE_F
-+   unset echo
-+   breaksw
-+#
-+   default:
-+      echo "Please spell your Linux 32 bit FORTRAN compiler name correctly."
-+      exit 4
-+      breaksw
-+   endsw
-+#                     ... end of FreeBSD on 32 bit processors.
-+endif
-+
-+
- #
- #   ------ Linux on 64 bit chips ------
- #   This should work on any 64 bit Linux release, for any type of
-@@ -1897,6 +2052,136 @@
-    endsw
- #                     ... end of Linux on 64 bit processors.
- endif
-+
-+if ($TARGET == freebsd64) then
-+#
-+#  there are two supported 64 bit compilers: gfortran, ifort
-+#
-+   switch ($GMS_FORTRAN)
-+
-+   case gfortran:
-+#           -finit-real=<zero|inf|-inf|nan>  could be interesting debug opt
-+#           -fno-automatic forces static storage of all local variables
-+#           -fno-whole-file suppresses argument's data type checking
-+      set OPT='-O2'
-+      if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS"
-+
-+      if ($GMS_GFORTRAN_VERNO == 4.6) then
-+         if ($MODULE == cosmo)  set OPT='-O0'   # this issue seen in 4.6.1
-+         if ($MODULE == tddgrd) set OPT='-O0'   # exam41, seen in 4.6.1
-+      endif
-+      if ($GMS_GFORTRAN_VERNO == 4.7) then
-+         if ($MODULE == cosmo)  set OPT='-O0'
-+         if ($MODULE == dcscf)  set OPT='-O0'   # exam44, seen in 4.7 only
-+         if ($MODULE == rohfcc) set OPT='-O0'   # exam47, seen in 4.7 only
-+         if ($MODULE == tddgrd) set OPT='-O0'
-+      endif
-+      if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
-+
-+      set EXTRAOPT=" "
-+
-+      if (($MODULE == cchem) || ($MODULE == ga)) then
-+         mv $MODULE.f $MODULE.F
-+         set MODULE_F=$MODULE.F
-+         if ($GMS_LIBCCHEM == true) then
-+            if ($MODULE == cchem) set EXTRAOPT="-DHAVE_CCHEM $extraflags"
-+            if ($MODULE == ga)    set EXTRAOPT="-I$GMS_PATH/libcchem/ga/include"
-+         endif
-+      endif
-+#
-+#        as of 4.6 tested in late 2011, gfortran can do q.p.!
-+      switch ($GMS_GFORTRAN_VERNO)
-+         case 4.0:
-+         case 4.1:
-+         case 4.2:
-+         case 4.3:
-+         case 4.4:
-+         case 4.5:
-+            if (($MODULE == qeigen) || ($MODULE == int2c)) then
-+               mv -f $MODULE_F $MODULE.junk
-+               sed -e "s/Q-/D-/g" \
-+                   -e "s/Q+00/D+00/g" \
-+                   -e "s/REAL\*16/DOUBLE PRECISION/" $MODULE.junk > $MODULE_F
-+               rm -f $MODULE.junk
-+            endif
-+            breaksw
-+         case 4.6:
-+         case 4.7:
-+            set EXTRAOPT="$EXTRAOPT -fno-whole-file"
-+            breaksw
-+         default:
-+            echo Unrecognized gfortran version
-+            exit 4
-+            breaksw
-+      endsw
-+
-+      set echo
-+      %%FC%% -c -fdefault-integer-8 $OPT -std=legacy $EXTRAOPT $MODULE_F
-+      unset echo
-+      breaksw
-+
-+   case ifort:
-+#     -i4/-i8 set default integer length
-+#     -On can have n=1,2,3.  Use of 3 caused problems with earlier
-+#          compilers, so it isn't being used here.  Try it if you like.
-+#     stack storage for locals is governed by -auto versus -save.
-+#     -assume byterecl was introduced at ifort 8.0 (older versions will
-+#        print a message saying this flag is ignored).  Newer versions
-+#        need this so that direct access file opens are measured in
-+#        bytes rather than the new default in v8.0, namely 4-byte units.
-+#     -vec-report0 suppresses loop vectorization messages (new in 10.0)
-+#     -w95 suppresses Hollerith initialization and other f90-like warnings
-+#     -cm  means suppress comments about programming practices,
-+#          these two options spelled '-warn nousage' at version 12.
-+#     -WB means warn but don't fail on out-of-bounds array references
-+#     -ftz flushes underflow results to zero
-+#
-+      set OPT = '-O2'
-+      if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS"
-+#       alas, I'm so tired of hearing about so many versions failing to
-+#       diagonalize, that this time critical code is run w/o optimization.
-+#       Very many (all?) ifort versions have problems with eigen.src.
-+      if ($MODULE == eigen)  set OPT='-O0' # read note just above.
-+      if ($MODULE == fmo)    set OPT='-O1' # 12.0.4, exam37
-+      if ($MODULE == guess)  set OPT='-O0' # 10.0, exam39
-+      if ($MODULE == locpol) set OPT='-O1' # 10.0, makefp/gmres
-+      if ($MODULE == morokm) set OPT='-O0' # Jan Fredin
-+      if ($MODULE == prpel)  set OPT='-O1' # 10.0, exam13
-+      if (($MODULE == rohfcc) && ($GMS_IFORT_VERNO == 12)) \
-+                             set OPT='-O0' # exam42+exam47 (op.sh.CC,IP-EOM)
-+      if ($MODULE == tdxitr) set OPT='-O1' # 10.0, exam39
-+      if ($MODULE == vscf)   set OPT='-O0' # intensities for combinations
-+      if ($MODULE == zheev)  set OPT='-O0' # defensive compiling
-+
-+      set EXTRAOPT=" "
-+
-+      if (($MODULE == cchem) || ($MODULE == ga)) then
-+         mv $MODULE.f $MODULE.F
-+         set MODULE_F=$MODULE.F
-+         if ($GMS_LIBCCHEM == true) then
-+            if ($MODULE == cchem) set EXTRAOPT="-DHAVE_CCHEM"
-+            if ($MODULE == ga)    set EXTRAOPT="-I$GMS_PATH/libcchem/ga/include"
-+         endif
-+      endif
-+
-+      if ($GMS_IFORT_VERNO >=  8) set EXTRAOPT="$EXTRAOPT -assume byterecl"
-+      if ($GMS_IFORT_VERNO >= 10) set EXTRAOPT="$EXTRAOPT -vec-report0"
-+      if ($GMS_IFORT_VERNO  < 12) set EXTRAOPT="$EXTRAOPT -w95 -cm"
-+      if ($GMS_IFORT_VERNO >= 12) set EXTRAOPT="$EXTRAOPT -warn nousage -inline-level=0"
-+      set echo
-+      ifort -c -i8 $OPT -ftz -auto $EXTRAOPT $MODULE_F
-+      unset echo
-+      breaksw
-+#
-+   default:
-+      echo "Please spell your FreeBSD 64 bit FORTRAN compiler name correctly."
-+      exit 4
-+      breaksw
-+   endsw
-+#                     ... end of FreeBSD on 64 bit processors.
-+endif
-+
-+
- #
- #   Apple Macintosh system using OS X
- #    jargon: 10.0=cheetah, 10.1=puma,     10.2=jaguar,   10.3=panther,
--- a/science/gamess/files/patch-compall
+++ b/science/gamess/files/patch-compall
@ -1,38 +0,0 @@
--- compall.orig	2012-09-07 22:32:57.000000000 +0900
-+++ compall	2013-02-27 15:59:37.000000000 +0900
-@@ -58,6 +58,8 @@
- if (($TARGET == ibm-bg) && ($GMS_BG_MODEL == P))  set CCOMP='bgxlc_r'
- if  ($TARGET == linux32)                          set CCOMP='gcc'
- if  ($TARGET == linux64)                          set CCOMP='gcc'
-+if  ($TARGET == freebsd32)                          set CCOMP='%%CC%%'
-+if  ($TARGET == freebsd64)                          set CCOMP='%%CC%%'
- if  ($TARGET == necsx)                            set CCOMP='c++'
- #
- unset extraflags
-@@ -96,6 +98,8 @@
-    if ($chip == x86_64) set extraflags='-DLINUX64 -m64'
-    if ($chip == ia64)   set extraflags='-DLINUX64'  # this always 64 bits
- endif
-+if ($TARGET == freebsd32) set extraflags='-DLINUX32'
-+if ($TARGET == freebsd64) set extraflags='-DLINUX64 -m64'
- if ($TARGET == mac32)        set extraflags='-DLINUX32'
- if ($TARGET == mac64)    set extraflags='-DLINUX64 -m64 -I/usr/include/malloc'
- if ($TARGET == necsx)        set extraflags='-DNECSX -size_t64'
-@@ -211,6 +215,8 @@
- if ($TARGET == ibm-bg)     ./comp blas
- if ($TARGET == linux32)    ./comp blas
- if ($TARGET == linux64)    ./comp blas
-+if ($TARGET == freebsd32)  ./comp blas
-+if ($TARGET == freebsd64)  ./comp blas
- if ($TARGET == mac64)      ./comp blas
- if ($TARGET == sun32)      ./comp blas
- if ($TARGET == sun64)      ./comp blas
-@@ -547,6 +553,8 @@
-                          set VB2000=false
- if ($TARGET == linux64)  set VB2000=true
- if ($TARGET == linux32)  set VB2000=true
-+if ($TARGET == freebsd64) set VB2000=true
-+if ($TARGET == freebsd32) set VB2000=true
- if ($TARGET == mac64)    set VB2000=true
- if ($VB2000 == true) then
-    ./comp vb2000
--- a/science/gamess/files/patch-compddi
+++ b/science/gamess/files/patch-compddi
@ -1,82 +0,0 @@
--- ddi/compddi.orig	2013-03-05 12:39:40.000000000 +0900
-+++ ddi/compddi	2013-03-05 12:40:52.000000000 +0900
-@@ -630,7 +630,79 @@
-      set FORT_FLAGS = '-O2 -qarch=440  -qflag=W:W -qhalt=W -qnosave '
-      set FORT_LIBS  = ''
-   endif
-+# --------------------------------------- #
-+# FreeBSD for x86 PCs                     #
-+# --------------------------------------- #
- 
-+  if($TARGET == freebsd32) then
-+
-+     set FORTRAN=%%GMS_FORTRAN%%      # choose from g77, gfortran, ifort, pgf77, f2c
-+
-+     set CC = %%CC%%
-+     set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./include"
-+
-+     switch ($FORTRAN)
-+        case g77:
-+        case pgf77:
-+        case f2c:
-+           set NumUS=2
-+           breaksw
-+        case gfortran:
-+           set CFLAGS = "$CFLAGS -Dgetarg_=_gfortran_getarg_i4"
-+           set CFLAGS = "$CFLAGS -Diargc_=_gfortran_iargc"
-+           set NumUS=1
-+           breaksw
-+        case ifort:
-+           set NumUS=1
-+           breaksw
-+        default:
-+           echo Please spell your ia32 compiler correctly.
-+           exit 4
-+     endsw
-+
-+     set CLIBS  = "%%PTHREAD_LIBS%%"
-+     set F77_OPTS = "-DINT_SIZE=int -D_UNDERSCORES=$NumUS"
-+     set FORT_FLAGS = '-O2'
-+     set AR_FLAGS     = 'cr'
-+     set RANLIB_FLAGS = ' '
-+     set FORT_LIBS = ' '
-+  endif
-+
-+# ------------- #
-+# FreeBSD amd64 #
-+# ------------- #
-+  if($TARGET == freebsd64) then
-+
-+     set CC = %%CC%%
-+     set CFLAGS = "-DLINUX -m64 -O3 -fstrict-aliasing -I./include"
-+
-+     set FORTRAN=%%GMS_FORTRAN%%
-+     switch ($FORTRAN)
-+        case g77:
-+        case pgf77:
-+        case f2c:
-+           set NumUS=2
-+           breaksw
-+        case gfortran:
-+           set CFLAGS = "$CFLAGS -Dgetarg_=_gfortran_getarg_i4"
-+           set CFLAGS = "$CFLAGS -Diargc_=_gfortran_iargc"
-+           set FORT_FLAGS = "-O2 $ARCH -fdefault-integer-8 -std=legacy"
-+           set NumUS=1
-+           breaksw
-+        case ifort:
-+           set NumUS=1
-+           breaksw
-+        default:
-+           echo Please spell your x86_64 compiler correctly.
-+           exit 4
-+     endsw
-+
-+     set CLIBS  = "%%PTHREAD_LIBS%%"
-+     set F77_OPTS = "-DINT_SIZE=long -D_UNDERSCORES=$NumUS"
-+     set AR_FLAGS     = 'cr'
-+     set RANLIB_FLAGS = ' '
-+     set FORT_LIBS = ' '
-+  endif
- 
- # ---------------------------------------- #
- # Linux for 32 bit systems (Red Hat, etc.) #
--- a/science/gamess/files/patch-gms-files.csh
+++ b/science/gamess/files/patch-gms-files.csh
@ -1,13 +0,0 @@
-$FreeBSD$
-
--- gms-files.csh	2013-03-05 18:04:02.000000000 +0900
-+++ gms-files.csh	2013-03-05 18:05:38.000000000 +0900
-@@ -28,7 +28,7 @@
- #     to see all the file definitions (one is just below).
- #
- #---quiet---set echo
-setenv AUXDATA $GMSPATH/auxdata
-+setenv AUXDATA %%PREFIX%%/share/gamess/auxdata
- setenv  EXTBAS /dev/null
- setenv  NUCBAS /dev/null
- setenv  POSBAS /dev/null
--- a/science/gamess/files/patch-lked
+++ b/science/gamess/files/patch-lked
@ -1,288 +0,0 @@
--- lked.orig	2012-10-27 01:12:07.000000000 +0900
-+++ lked	2013-02-27 16:06:32.000000000 +0900
-@@ -57,6 +57,8 @@
-                         set VB2000=false
- if ($TARGET == linux64) set VB2000=true
- if ($TARGET == linux32) set VB2000=true
-+if ($TARGET == freebsd64) set VB2000=true
-+if ($TARGET == freebsd32) set VB2000=true
- if ($TARGET == mac64)   set VB2000=true
- set XMVB=false
- #
-@@ -632,6 +634,243 @@
- endif
- #
- endif
-+
-+if ($TARGET == freebsd32) then
-+   set VECTOR=' '
-+   set QUICHE='zunix.o'
-+#
-+#  settings which depend on the compiler choice:
-+#
-+   switch ($GMS_FORTRAN)
-+     case g77:
-+        set LDR='g77'
-+        set LDOPTS=' '  # add '-Wl,-M' to see load map
-+        set FORTLIBS=' '
-+        breaksw
-+     case gfortran:
-+        set LDR=%%FC%%
-+        set LDOPTS=' '
-+        set FORTLIBS=' '
-+        breaksw
-+     case ifort:
-+        set LDR='ifort'
-+        set LDOPTS=' '  # add '-Wl,-M' to see load map
-+        set FORTLIBS='-Vaxlib'
-+        breaksw
-+     case f2c:
-+        set LDR='gcc'
-+        set LDOPTS=' '
-+        set FORTLIBS='-lf2c -lm'
-+        breaksw
-+     default:
-+        echo Please spell your freebsd32 compiler correctly.
-+        exit 4
-+   endsw
-+#
-+#  settings which depend on the math library: mkl, atlas, acml, none
-+#
-+   switch ($GMS_MATHLIB)
-+
-+#       for MKL, we lack experience.  The following is the 64-bit
-+#       stuff, with all 64's removed.  It might be right!
-+#       For the case of "11", this has actually been verified.
-+   case mkl:
-+      set mpath=$GMS_MATHLIB_PATH
-+      switch ($GMS_MKL_VERNO)
-+        case 8:
-+          set MATHLIBS="-L$mpath -lmkl_lapack   -lmkl -lguide -lpthread"
-+          breaksw
-+        case 9:
-+          set MATHLIBS="-L$mpath -lmkl_lapack   -lmkl -lguide -lpthread"
-+          breaksw
-+        case 10:
-+          #  next one forces single-threaded usage only...exactly what we want.
-+          set MATHLIBS="-L$mpath -lmkl_intel -lmkl_sequential -lmkl_core"
-+          breaksw
-+        case 11:
-+        case 12:
-+          # next attempts a static link, whereas 10 above is a dynamic link.
-+          # if this fails to work, try the version 10 lines shown just above.
-+          set MATHLIBS="$mpath/libmkl_intel.a"
-+          set MATHLIBS="$MATHLIBS $mpath/libmkl_sequential.a"
-+          set MATHLIBS="$MATHLIBS $mpath/libmkl_core.a"
-+          breaksw
-+        default:
-+          echo "unknown version number for MKL/linux32"
-+          echo "please edit 'lked' to select the right 32 bit MKL libraries."
-+          exit
-+          breaksw
-+      endsw
-+      set BLAS=' '
-+      breaksw
-+
-+   case atlas:
-+      #     If the ATLAS comes with static libraries, link to them,
-+      #     so that only the compile node has to have the libraries.
-+      #     Otherwise, attempt a link against shared object libs.
-+      #     See the 64 bit Atlas below for a way to fix the linker's
-+      #     not being able to locate -lf77blas, if that happens.
-+      if (-e $GMS_MATHLIB_PATH/libf77blas.a) then
-+         set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a"
-+         set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a"
-+      else
-+         set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas"
-+      endif
-+      set BLAS=' '
-+      breaksw
-+
-+   case acml:
-+      #     do a static link so that only compile node needs to install ACML
-+      set MATHLIBS="$GMS_MATHLIB_PATH/libacml.a"
-+      set BLAS=' '
-+      breaksw
-+
-+   case none:
-+   default:
-+      echo "Warning.  No math library was found, you should install one."
-+      echo "    MP2 calculations speed up about 2x with a math library."
-+      echo "CCSD(T) calculations speed up about 5x with a math library."
-+      set BLAS='%%BLAS%% %%LAPACK%%'
-+      set MATHLIBS=' '
-+      breaksw
-+   endsw
-+#
-+   set LIBRARIES="$FORTLIBS $MATHLIBS"
-+endif
-+#
-+#   ------ FreeBSD on 64 bit chips -----
-+#
-+if ($TARGET == freebsd64) then
-+   set VECTOR=' '
-+   set QUICHE='zunix.o'
-+#
-+#  settings which depend on the FORTRAN:
-+#
-+   switch ($GMS_FORTRAN)
-+      case gfortran:
-+         set LDR=%%FC%%
-+         set LDOPTS=' '
-+         set FORTLIBS=' '
-+         breaksw
-+      case ifort:
-+         set LDR='ifort'
-+         set LDOPTS='-i8'  # -Wl,-M generates a load map
-+#            this auxiliary library seems to have disappeared in ifort 10
-+         set FORTLIBS=' '
-+         if($GMS_IFORT_VERNO < 10) set FORTLIBS='-Vaxlib'
-+         breaksw
-+      default:
-+         echo "don't know how to use a freebsd64 compiler named $GMS_FORTRAN"
-+         exit 4
-+         breaksw
-+   endsw
-+#
-+#  settings which depend on the math library: mkl, atlas, acml, none
-+#
-+   switch ($GMS_MATHLIB)
-+
-+   case mkl:
-+      set mpath=$GMS_MATHLIB_PATH
-+      set mklver=$GMS_MKL_VERNO
-+      if ($CCHEM == true) set mklver=${mklver}-so
-+      switch ($mklver)
-+        case 8:
-+          set MATHLIBS="-L$mpath -lmkl_lapack64 -lmkl -lguide -lpthread"
-+          breaksw
-+        case 9:
-+          set MATHLIBS="-L$mpath -lmkl_lapack   -lmkl -lguide -lpthread"
-+          breaksw
-+          breaksw
-+        case 10:
-+        case 11:
-+        case 12:
-+          # next are a static link, in single-threaded mode (serial BLAS).
-+          # The choices preclude any need to
-+          #     a) install .so shared object libraries on every node,
-+          #     b) define LD_LIBRARY_PATH to find the .so libraries, or
-+          #     c) define MKL_NUM_THREADS=1
-+          # If desired, there is a single-threaded shared object link below.
-+          # Note, there's now a gfortran-specific compiler interface library.
-+          set iflib=intel
-+          if ($GMS_FORTRAN == gfortran) set iflib=gf
-+          set MATHLIBS="          $mpath/libmkl_${iflib}_ilp64.a"
-+          set MATHLIBS="$MATHLIBS $mpath/libmkl_sequential.a"
-+          set MATHLIBS="$MATHLIBS $mpath/libmkl_core.a"
-+          breaksw
-+        case 10-so:
-+        case 11-so:
-+        case 12-so:
-+          #  next one chooses dynamic linking (so= shared object libs)
-+          #  Just hand edit GMS_MKL_VERNO in your 'install.info' to use this.
-+          #  run-time libs (and LD_LIBRARY_PATH) needed on every compute node!
-+          #  note that it does force single-threaded usage.
-+          #  LIBCCHEM fails to link properly against static libraries.
-+          #  LIBCCHEM prefers to use threading
-+          set iflib=intel
-+          if ($GMS_FORTRAN == gfortran) set iflib=gf
-+          if ($CCHEM == false) then
-+             set MATHLIBS="-L$mpath -lmkl_${iflib}_ilp64 -lmkl_sequential -lmkl_core"
-+          else
-+             set MATHLIBS="-L$mpath -lmkl_${iflib}_ilp64 -lmkl_${iflib}_thread -lmkl_core -liomp5"
-+          endif
-+          breaksw
-+        default:
-+          echo "unknown version number for MKL/linux64"
-+          echo "please edit 'lked' to select the right 64 bit MKL libraries."
-+          exit
-+          breaksw
-+      endsw
-+      set BLAS=' '
-+      breaksw
-+
-+   case atlas:
-+      #     If the ATLAS comes with static libraries, link to them,
-+      #     so that only the compile node has to have the libraries.
-+      #     Otherwise, attempt a link against shared object libs.
-+      #
-+      #     Some versions of Atlas come without proper setup to use them.
-+      #     For example, you may need to give some specific version such
-+      #     as 3.0 some generic names, by doing the right soft links:
-+      #          chdir /usr/lib64/atlas   (just 'lib' for linux32)
-+      #          ln -s libatlas.so.3.0        libatlas.so
-+      #          ln -s libblas.so.3.0         libblas.so
-+      #          ln -s libcblas.so.3.0        libcblas.so
-+      #          ln -s libf77blas.so.3.0      libf77blas.so
-+      #          ln -s liblapack_atlas.so.3.0 liblapack.so
-+      #          ln -s liblapack.so.3.0       liblapack.so
-+      #     It is strange the RPM's don't do these soft links for us.
-+      if (-e $GMS_MATHLIB_PATH/libf77blas.a) then
-+         set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a"
-+         set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a"
-+      else
-+         set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas"
-+      endif
-+      set BLAS=' '
-+      breaksw
-+
-+   case acml:
-+      #     do a static link so that only compile node needs to install ACML
-+      set MATHLIBS="$GMS_MATHLIB_PATH/libacml.a"
-+      #     if you want to try a dynamic link, use this:
-+      #---set MATHLIBS="-L$GMS_MATHLIB_PATH -lacml -lacml_mv"
-+      set BLAS=' '
-+      breaksw
-+
-+   case none:
-+   default:
-+      echo "Warning.  No math library was found, you should install one."
-+      echo "    MP2 calculations speed up about 2x with a math library."
-+      echo "CCSD(T) calculations speed up about 5x with a math library."
-+      set BLAS='%%BLAS%% %%LAPACK%%'
-+      set MATHLIBS=' '
-+      breaksw
-+   endsw
-+#
-+   set LIBRARIES="$FORTLIBS $MATHLIBS"
-+endif
-+#
-+endif
-+
- #
- #      MacIntosh
- #
-@@ -675,6 +914,23 @@
-    set VECTOR=' '
-    set QUICHE='zunix.o'
- endif
-+#FreeBSD settings
-+if ($TARGET == freebsd32) then
-+   set LDR=%%FC%%
-+   set LDOPTS='%%LDFLAGS%%'
-+   set LIBRARIES=''
-+   set BLAS="-L%%LOCALBASE%%/lib %%BLAS%% %%LIBSVM%% %%LIBG2C%%"
-+   set VECTOR=' '
-+   set QUICHE='zunix.o'
-+endif
-+if ($TARGET == freebsd64) then
-+   set LDR=%%FC%%
-+   set LDOPTS='%%LDFLAGS%%'
-+   set LIBRARIES=''
-+   set BLAS="-L%%LOCALBASE%%/lib %%BLAS%%"
-+   set VECTOR=' '
-+   set QUICHE='zunix.o'
-+endif
- #
- if ($TARGET == necsx) then
-    set LDR='f90'
-@@ -1199,6 +1199,8 @@
-    case ibm64:
-    case linux32:
-    case linux64:
-+   case freebsd32:
-+   case freebsd64:
-    case mac32:
-    case mac64:
-    case sgi32:
--- a/science/gamess/files/patch-rungms
+++ b/science/gamess/files/patch-rungms
@ -1,21 +0,0 @@
--- rungms	2013-03-05 17:53:14.000000000 +0900
-+++ rungms	2013-03-05 17:53:45.000000000 +0900
-@@ -1,4 +1,4 @@
-#!/bin/csh
-+#!/bin/csh -f 
- #
- #  last update = 26 October 2012
- #
-@@ -60,9 +60,9 @@
- #       See also a very old LoadLeveler "ll-gms" for some IBM systems.
- #
- set TARGET=sockets
-set SCR=/scr/$USER
-set USERSCR=~$USER/scr
-set GMSPATH=/u1/mike/gamess
-+set SCR=.
-+set USERSCR=.
-+set GMSPATH=%%PREFIX%%/bin/gms/
- #
- set JOB=$1      # name of the input file xxx.inp, give only the xxx part
- set VERNO=$2    # revision number of the executable created by 'lked' step
--- a/science/gamess/files/patch-zunix.c
+++ b/science/gamess/files/patch-zunix.c
@ -1,10 +0,0 @@
--- source/zunix.c~	2008-10-31 23:05:41.000000000 +0900
-+++ source/zunix.c	2009-06-08 15:37:42.000000000 +0900
-@@ -440,7 +440,6 @@
- #ifdef LINUX64
- 
- #include <stdlib.h>
-#include <malloc.h>
- 
- #define FORTINT long
- 
--- a/science/gamess/pkg-descr
+++ b/science/gamess/pkg-descr
@ -1,16 +0,0 @@
-GAMESS is freely available ab-initio molecular orbital
-calculation program calculates energy, molecular structure,
-vibrational frequencies from the basic principle of quantum mechanics.
-
-A site license for GAMESS is available at no cost to both academic
-and industrial users. Please refer
-http://www.msg.ameslab.gov/gamess/download.html
-for details.
-
-We also included simple launcher called `gamess'
-for your convenience. You don't set any environment variable
-to run gamess. Just type 
-% gamess <somefile.inp>
-is enough.
-
-WWW: http://www.msg.ameslab.gov/gamess/gamess.html
--- a/science/gamess/pkg-message
+++ b/science/gamess/pkg-message
@ -1,13 +0,0 @@
-WARNING!!WARNING!!WARNING!!WARNING!!
-
-If you got the following error
-'Error ENOMEM: Not enough memory to allocate ** bytes of shared memory.',
-then add ipc memory by:
-sudo sysctl -w kern.ipc.shmmax=3064372224
-sudo sysctl -w kern.ipc.shmall=748137
-or if you want to enable at boot time
-add following lines to
-kern.ipc.shmmax=3064372224
-kern.ipc.shmall=748137
-/boot/loader.conf
-.
--- a/science/gamess/pkg-plist
+++ b/science/gamess/pkg-plist
@ -1,154 +0,0 @@
-bin/gamess
-bin/gms/ddikick.x
-bin/gms/gamess.00.x
-bin/gms/gms-files.csh
-share/doc/gamess/INPUT.DOC
-share/doc/gamess/INTRO.DOC
-share/doc/gamess/IRON.DOC
-share/doc/gamess/PROG.DOC
-share/doc/gamess/REFS.DOC
-share/doc/gamess/TESTS.DOC
-share/doc/gamess/readme.ddi
-share/gamess/auxdata/ericfmt.dat
-share/gamess/auxdata/BASES/SPK-TZP
-share/gamess/auxdata/BASES/SPKRDZC
-share/gamess/auxdata/BASES/SPK-DZC
-share/gamess/auxdata/BASES/SPKRQZCD
-share/gamess/auxdata/BASES/SPK-QZP
-share/gamess/auxdata/BASES/SPKRTZP
-share/gamess/auxdata/BASES/SPKRAQZP
-share/gamess/auxdata/BASES/SPK-ADZP
-share/gamess/auxdata/BASES/SPKRTZC
-share/gamess/auxdata/BASES/SPK-ATZP
-share/gamess/auxdata/BASES/SPKRDZP
-share/gamess/auxdata/BASES/SPK-AQZP
-share/gamess/auxdata/BASES/SPKRQZP
-share/gamess/auxdata/BASES/SPKRQZC
-share/gamess/auxdata/BASES/SPKRATZP
-share/gamess/auxdata/BASES/SPK-QZC
-share/gamess/auxdata/BASES/SPKRADZP
-share/gamess/auxdata/BASES/SPKRDZCD
-share/gamess/auxdata/BASES/SPKRTZCD
-share/gamess/auxdata/BASES/SPK-DZP
-share/gamess/auxdata/BASES/SPK-QZCD
-share/gamess/auxdata/BASES/SPK-TZC
-share/gamess/auxdata/BASES/SPK-DZCD
-share/gamess/auxdata/BASES/SPK-TZCD
-share/gamess/auxdata/EFP/ADENI2.efp
-share/gamess/auxdata/EFP/THYMI2.efp
-share/gamess/auxdata/EFP/PYRAZI.efp
-share/gamess/auxdata/EFP/ADENIN.efp
-share/gamess/auxdata/EFP/PENTAN.efp
-share/gamess/auxdata/EFP/INDOLE.efp
-share/gamess/auxdata/EFP/PHENOL.efp
-share/gamess/auxdata/EFP/ACNH2B.efp
-share/gamess/auxdata/EFP/FORMID.efp
-share/gamess/auxdata/EFP/CYCPEN.efp
-share/gamess/auxdata/EFP/HCN.efp
-share/gamess/auxdata/EFP/URACIL.efp
-share/gamess/auxdata/EFP/BENZEN.efp
-share/gamess/auxdata/EFP/MENH2.efp
-share/gamess/auxdata/EFP/FORMIC.efp
-share/gamess/auxdata/EFP/PEPTID.efp
-share/gamess/auxdata/EFP/ACOHG.efp
-share/gamess/auxdata/EFP/METHAN.efp
-share/gamess/auxdata/EFP/MEOH.efp
-share/gamess/auxdata/EFP/THYMIN.efp
-share/gamess/auxdata/EFP/NEOPEN.efp
-share/gamess/auxdata/EFP/AMINOP.efp
-share/gamess/auxdata/EFP/PYRIDI.efp
-share/gamess/auxdata/EFP/AMONIA.efp
-share/gamess/auxdata/EFP/WATER.efp
-share/gamess/auxdata/EFP/PYRIDO.efp
-share/gamess/auxdata/EFP/ACNH2G.efp
-share/gamess/auxdata/EFP/ETHENE.efp
-share/gamess/auxdata/EFP/URACG.efp
-share/gamess/auxdata/EFP/ETHYNE.efp
-share/gamess/auxdata/EFP/ACOHB.efp
-share/gamess/auxdata/MCP/MCP-ATZP
-share/gamess/auxdata/MCP/MCPCDZP
-share/gamess/auxdata/MCP/ZFK5-DK3
-share/gamess/auxdata/MCP/MCPCTZP
-share/gamess/auxdata/MCP/MCPACQZP
-share/gamess/auxdata/MCP/ZFK4-DK3
-share/gamess/auxdata/MCP/IMCP-SR2
-share/gamess/auxdata/MCP/MCP-DZP
-share/gamess/auxdata/MCP/MCP-QZP
-share/gamess/auxdata/MCP/MCP-TZP
-share/gamess/auxdata/MCP/ZFK3-DK3
-share/gamess/auxdata/MCP/MCPACTZP
-share/gamess/auxdata/MCP/IMCP-NR1
-share/gamess/auxdata/MCP/ZFK5LDK3
-share/gamess/auxdata/MCP/MCPCQZP
-share/gamess/auxdata/MCP/ZFK3LDK3
-share/gamess/auxdata/MCP/MCPACDZP
-share/gamess/auxdata/MCP/ZFK4LDK3
-share/gamess/auxdata/MCP/IMCP-SR1
-share/gamess/auxdata/MCP/MCP-AQZP
-share/gamess/auxdata/MCP/IMCP-NR2
-share/gamess/auxdata/QUANPOL/RXNFLD3840.DAT
-share/gamess/auxdata/QUANPOL/CHARMM22.CMAP
-share/gamess/auxdata/QUANPOL/RXNFLD0060.DAT
-share/gamess/auxdata/QUANPOL/RXNFLD0240.DAT
-share/gamess/auxdata/QUANPOL/LOUT314159.TOP
-share/gamess/auxdata/QUANPOL/CHARMM22.LIB
-share/gamess/auxdata/QUANPOL/RXNFLD0960.DAT
-share/gamess/auxdata/QUANPOL/WATER4096.DAT
-share/gamess/auxdata/QUANPOL/LOUT314159.PAR
-share/examples/gamess/exam01.inp
-share/examples/gamess/exam02.inp
-share/examples/gamess/exam03.inp
-share/examples/gamess/exam04.inp
-share/examples/gamess/exam05.inp
-share/examples/gamess/exam06.inp
-share/examples/gamess/exam07.inp
-share/examples/gamess/exam08.inp
-share/examples/gamess/exam09.inp
-share/examples/gamess/exam10.inp
-share/examples/gamess/exam11.inp
-share/examples/gamess/exam12.inp
-share/examples/gamess/exam13.inp
-share/examples/gamess/exam14.inp
-share/examples/gamess/exam15.inp
-share/examples/gamess/exam16.inp
-share/examples/gamess/exam17.inp
-share/examples/gamess/exam18.inp
-share/examples/gamess/exam19.inp
-share/examples/gamess/exam20.inp
-share/examples/gamess/exam21.inp
-share/examples/gamess/exam22.inp
-share/examples/gamess/exam23.inp
-share/examples/gamess/exam24.inp
-share/examples/gamess/exam25.inp
-share/examples/gamess/exam26.inp
-share/examples/gamess/exam27.inp
-share/examples/gamess/exam28.inp
-share/examples/gamess/exam29.inp
-share/examples/gamess/exam30.inp
-share/examples/gamess/exam31.inp
-share/examples/gamess/exam32.inp
-share/examples/gamess/exam33.inp
-share/examples/gamess/exam34.inp
-share/examples/gamess/exam35.inp
-share/examples/gamess/exam36.inp
-share/examples/gamess/exam37.inp
-share/examples/gamess/exam38.inp
-share/examples/gamess/exam39.inp
-share/examples/gamess/exam40.inp
-share/examples/gamess/exam41.inp
-share/examples/gamess/exam42.inp
-share/examples/gamess/exam43.inp
-share/examples/gamess/exam44.inp
-share/examples/gamess/exam45.inp
-share/examples/gamess/exam46.inp
-share/examples/gamess/exam47.inp
-@dirrm bin/gms
-@dirrm share/doc/gamess
-@dirrm share/gamess/mcpdata
-@dirrm share/examples/gamess
-@dirrm share/gamess/auxdata/QUANPOL
-@dirrm share/gamess/auxdata/MCP
-@dirrm share/gamess/auxdata/EFP
-@dirrm share/gamess/auxdata/BASES
-@dirrm share/gamess/auxdata
-@dirrm share/gamess
--- a/science/mcstas/Makefile
+++ b/science/mcstas/Makefile
@ -1,44 +0,0 @@
-# Created by: Joerg Pulz <Joerg.Pulz@frm2.tum.de>
-# $FreeBSD$
-
-PORTNAME=	mcstas
-PORTVERSION=	1.12c
-PORTREVISION=	3
-CATEGORIES=	science
-MASTER_SITES=	http://www.mcstas.org/download/ \
-		http://www.c-s.li/ports/
-DISTNAME=	${PORTNAME}-${PORTVERSION}-src
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Neutron ray-trace simulation package
-
-LICENSE=	GPLv2
-
-BUILD_DEPENDS=	pgxwin_server:${PORTSDIR}/graphics/pgplot
-RUN_DEPENDS=	PDL>=0:${PORTSDIR}/math/PDL \
-		p5-Tk>=0:${PORTSDIR}/x11-toolkits/p5-Tk
-
-STRIP=
-USES=		perl5 gmake
-GNU_CONFIGURE=	yes
-NO_MTREE=	yes
-WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
-
-PERL_ARCHNAME!=	perl -V:archname 2>/dev/null || echo
-
-PLIST_SUB+=	PERL_PORT=perl5 PERL_ARCHNAME=${PERL_ARCHNAME:S/archname='//:S/';//}
-
-MAN1=		mcconvert.1 \
-		mcdisplay.1 \
-		mcdoc.1 \
-		mcformat.1 \
-		mcgui.1 \
-		mcplot.1 \
-		mcrun.1 \
-		mcstas.1 \
-
-NO_STAGE=	yes
-post-configure:
-		@cd ${WRKSRC}; make pgplot
-
-.include <bsd.port.mk>
--- a/science/mcstas/distinfo
+++ b/science/mcstas/distinfo
@ -1,2 +0,0 @@
-SHA256 (mcstas-1.12c-src.tar.gz) = 03c516bda33f140e4e92ba542235277165d6a79d29a63c1d4cd2366f0e5f6821
-SIZE (mcstas-1.12c-src.tar.gz) = 29424258
--- a/science/mcstas/files/patch-Makefile.in
+++ b/science/mcstas/files/patch-Makefile.in
@ -1,13 +0,0 @@
--- Makefile.in.orig	Thu Jun  9 09:13:42 2005
-+++ Makefile.in	Tue Feb 28 13:27:55 2006
-@@ -98,10 +98,6 @@
- 	for pgm in $(PERLBIN); do \
- 	  $(INSTALL_PROGRAM) $$pgm.fixpl $(bindir)/$$pgm; \
- 	done
-	if [ -d $(mc_libdir) ]; then \
-	  echo "Moving your old library dir $(mc_libdir) to $(mc_libdir).`date +%Y%m%d_%H.%M`"; \
-	  mv -f $(mc_libdir) $(mc_libdir).`date +%Y%m%d_%H.%M`;\
-        fi;
- 	$(srcdir)/mkinstalldirs $(mc_libdir)
- 	for file in `cd lib; ls`; do \
- 	  if [ -d lib/$$file ]; then \
--- a/science/mcstas/pkg-descr
+++ b/science/mcstas/pkg-descr
@ -1,21 +0,0 @@
-McStas - Monte Carlo simulation of neutron instruments
-
-McStas is an ongoing project to create a general tool for simulating neutron
-scattering instruments. The project is conducted at Risoe National Laboratory
-in cooperation with the ILL. The Risoe efforts have been funded through
-multiple EU programs. 
-
-McStas is based on a compiler that reads a high-level specification language
-defining the instrument to be simulated and produces C code that performs the
-Monte Carlo Simulation. The system is very fast in use, both when setting up
-the instrument definition and when doing calculations.
-Typical figures are 20000-50000 neutron histories per second on a fast PC. 
-
-McStas supports triple-axis,  time-of-flight instruments, and polarised
-neutrons. It comes with a comprehensive manual and a library of well-tested
-components that include most standard elements of neutron scattering
-instruments, including steady-state and pulsed sources,
-monochromators/analysers, guides, collimators, vanadium and powder samples,
-velocity selectors and choppers, and a variety of detectors. 
-
-WWW: http://www.mcstas.org/
--- a/science/mcstas/pkg-plist
+++ b/science/mcstas/pkg-plist
@ -1,865 +0,0 @@
-bin/gscan
-bin/mcconvert
-bin/mcdaemon
-bin/mcdisplay
-bin/mcdoc
-bin/mcformat
-bin/mcformatgui
-bin/mcgui
-bin/mcplot
-bin/mcresplot
-bin/mcrun
-bin/mcstas
-bin/mcstas2vitess
-lib/mcstas/LGPL
-lib/mcstas/LICENSE.LIB
-lib/mcstas/README
-lib/mcstas/contrib/Al_window.comp
-lib/mcstas/contrib/Al_window.html
-lib/mcstas/contrib/Collimator_ROC.comp
-lib/mcstas/contrib/Collimator_ROC.html
-lib/mcstas/contrib/Exact_radial_coll.comp
-lib/mcstas/contrib/Exact_radial_coll.html
-lib/mcstas/contrib/FermiChopper_ILL.comp
-lib/mcstas/contrib/FermiChopper_ILL.html
-lib/mcstas/contrib/Filter_graphite.comp
-lib/mcstas/contrib/Filter_graphite.html
-lib/mcstas/contrib/Gas_tables/BinBF3.table
-lib/mcstas/contrib/Gas_tables/BinCF4.table
-lib/mcstas/contrib/Gas_tables/He3inAr.table
-lib/mcstas/contrib/Gas_tables/He3inC3H8.table
-lib/mcstas/contrib/Gas_tables/He3inC4H10.table
-lib/mcstas/contrib/Gas_tables/He3inCF4.table
-lib/mcstas/contrib/Gas_tables/He3inCO2.table
-lib/mcstas/contrib/Gas_tables/He3inHe.table
-lib/mcstas/contrib/Gas_tables/He3inXeTMA2point5percent.table
-lib/mcstas/contrib/Gas_tables/He3inXeTMA5percent.table
-lib/mcstas/contrib/Gas_tables/NinCF4.table
-lib/mcstas/contrib/Gas_tables/NinN2.table
-lib/mcstas/contrib/Gas_tables/gas.table
-lib/mcstas/contrib/Guide_curved.comp
-lib/mcstas/contrib/Guide_curved.html
-lib/mcstas/contrib/Guide_four_side.comp
-lib/mcstas/contrib/Guide_four_side.html
-lib/mcstas/contrib/Guide_four_side_10_shells.comp
-lib/mcstas/contrib/Guide_four_side_10_shells.html
-lib/mcstas/contrib/Guide_four_side_2_shells.comp
-lib/mcstas/contrib/Guide_four_side_2_shells.html
-lib/mcstas/contrib/Guide_honeycomb.comp
-lib/mcstas/contrib/Guide_honeycomb.html
-lib/mcstas/contrib/He3_cell.comp
-lib/mcstas/contrib/He3_cell.html
-lib/mcstas/contrib/ISIS_moderator.comp
-lib/mcstas/contrib/ISIS_moderator.html
-lib/mcstas/contrib/ISIS_tables/h.broad
-lib/mcstas/contrib/ISIS_tables/h.ch4
-lib/mcstas/contrib/ISIS_tables/h.crisp
-lib/mcstas/contrib/ISIS_tables/h.groove
-lib/mcstas/contrib/ISIS_tables/h.h2
-lib/mcstas/contrib/ISIS_tables/h.hydrogen
-lib/mcstas/contrib/ISIS_tables/h.narrow
-lib/mcstas/contrib/ISIS_tables/h.water
-lib/mcstas/contrib/Lens.comp
-lib/mcstas/contrib/Lens.html
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-lib/mcstas/tools/scilab/plotlib/man/gcw.cat
-lib/mcstas/tools/scilab/plotlib/man/grid.cat
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-lib/mcstas/tools/scilab/plotlib/man/legend.cat
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-lib/mcstas/tools/scilab/plotlib/man/pcolor.cat
-lib/mcstas/tools/scilab/plotlib/man/plot.cat
-lib/mcstas/tools/scilab/plotlib/man/plot3.cat
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-lib/mcstas/tools/scilab/plotlib/man/semilogy.cat
-lib/mcstas/tools/scilab/plotlib/man/shading.cat
-lib/mcstas/tools/scilab/plotlib/man/shg.cat
-lib/mcstas/tools/scilab/plotlib/man/subplot.cat
-lib/mcstas/tools/scilab/plotlib/man/surf.cat
-lib/mcstas/tools/scilab/plotlib/man/surfl.cat
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-lib/mcstas/tools/scilab/plotlib/man/ylabel.cat
-lib/mcstas/tools/perl/modules/lib/%%PERL_PORT%%/%%PERL_VERSION%%/man/man3/Math::Amoeba.3
-lib/mcstas/tools/perl/modules/lib/%%PERL_PORT%%/%%PERL_VERSION%%/man/man3/Proc::Simple.3
-lib/mcstas/tools/perl/modules/lib/%%PERL_PORT%%/%%PERL_VERSION%%/man/man3/Tk::CodeText.3
-lib/mcstas/tools/perl/modules/lib/%%PERL_PORT%%/%%PERL_VERSION%%/man/man3/Tk::CodeText::McStas.3
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-lib/mcstas/tools/perl/modules/lib/%%PERL_PORT%%/%%PERL_VERSION%%/man/man3/Tk::CodeText::Xresources.3
-@dirrm lib/mcstas/tools/perl/modules/lib/%%PERL_PORT%%/%%PERL_VERSION%%/man/man3
-@dirrm lib/mcstas/tools/perl/modules/lib/%%PERL_PORT%%/%%PERL_VERSION%%/man
-@dirrm lib/mcstas/tools/perl/modules/lib/%%PERL_PORT%%/%%PERL_VERSION%%
-@dirrm lib/mcstas/tools/perl/modules/lib/%%PERL_PORT%%
-@dirrm lib/mcstas/tools/perl/modules/lib
-@dirrm lib/mcstas/tools/scilab/plotlib/man
-@dirrm lib/mcstas/tools/scilab/plotlib/macros
-@dirrm lib/mcstas/tools/scilab/plotlib
-@dirrm lib/mcstas/tools/scilab
-@dirrm lib/mcstas/tools/perl/modules/auto/Proc/Simple
-@dirrm lib/mcstas/tools/perl/modules/auto/Proc
-@dirrm lib/mcstas/tools/perl/modules/auto
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-@dirrm lib/mcstas/tools/perl/modules/%%PERL_ARCHNAME%%/auto/Proc
-@dirrm lib/mcstas/tools/perl/modules/%%PERL_ARCHNAME%%/auto/Math/Amoeba
-@dirrm lib/mcstas/tools/perl/modules/%%PERL_ARCHNAME%%/auto/Math
-@dirrm lib/mcstas/tools/perl/modules/%%PERL_ARCHNAME%%/auto
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-@dirrm lib/mcstas/tools/perl/modules/Math
-@dirrm lib/mcstas/tools/perl/modules
-@dirrm lib/mcstas/tools/perl
-@dirrm lib/mcstas/tools/matlab
-@dirrm lib/mcstas/tools
-@dirrm lib/mcstas/sources
-@dirrm lib/mcstas/share
-@dirrm lib/mcstas/samples
-@dirrm lib/mcstas/optics
-@dirrm lib/mcstas/obsolete
-@dirrm lib/mcstas/monitors
-@dirrm lib/mcstas/misc
-@dirrm lib/mcstas/examples
-@dirrm lib/mcstas/editors
-@dirrm lib/mcstas/doc/tutorial/pics
-@dirrm lib/mcstas/doc/tutorial/html
-@dirrm lib/mcstas/doc/tutorial
-@dirrm lib/mcstas/doc
-@dirrm lib/mcstas/data
-@dirrm lib/mcstas/contrib/doc
-@dirrm lib/mcstas/contrib/ISIS_tables
-@dirrm lib/mcstas/contrib/Gas_tables
-@dirrm lib/mcstas/contrib
-@dirrm lib/mcstas
--- a/science/minc/Makefile
+++ b/science/minc/Makefile
@ -1,79 +0,0 @@
-# Created by: jbacon
-# $FreeBSD$
-
-############################################################################
-# http://www.bic.mni.mcgill.ca/software/minc/
-# is the ultimate source for MINC, and will always contain the latest
-# source release.  If this port is not up to date enough for you,
-# you can download the latest sources and build manually.  On FreeBSD,
-# you must configure with the environment variable LDFLAGS set to
-# ${LOCALBASE}/lib so that the configure script will find libnetcdf.
-# Of course, the netcdf port must be installed first.
-
-PORTNAME=	minc
-PORTVERSION=	1.5.1
-PORTREVISION=	1
-CATEGORIES=	science biology
-MASTER_SITES=	http://www.nitrc.org/frs/downloadlink.php/400/
-
-MAINTAINER=	jwbacon@tds.net
-COMMENT=	Medical Imaging NetCDF
-
-BROKEN=		Fails to build
-
-LIB_DEPENDS=	libnetcdf.so:${PORTSDIR}/science/netcdf
-
-USE_AUTOTOOLS=	libtool
-USE_LDCONFIG=	yes
-GNU_CONFIGURE=	yes
-CPPFLAGS+=	-I${LOCALBASE}/include
-LDFLAGS+=	-L${LOCALBASE}/lib
-CONFIGURE_ARGS=	--enable-static=yes --enable-shared=yes
-
-CONFLICTS=	minc-2* zh-tk-[0-9]*
-
-WRKSRC=		${WRKDIR}/${PORTNAME}-1.5
-
-MAN1=	dcm2mnc.1 \
-	ecattominc.1 \
-	invert_raw_image.1 \
-	minc_modify_header.1 \
-	mincaverage.1 \
-	minccalc.1 \
-	mincconcat.1 \
-	minccopy.1 \
-	mincdiff.1 \
-	mincedit.1 \
-	mincexpand.1 \
-	mincextract.1 \
-	mincheader.1 \
-	minchistory.1 \
-	mincinfo.1 \
-	minclookup.1 \
-	mincmakescalar.1 \
-	mincmakevector.1 \
-	mincmath.1 \
-	mincpik.1 \
-	mincresample.1 \
-	mincreshape.1 \
-	mincstats.1 \
-	minctoecat.1 \
-	minctoraw.1 \
-	mincview.1 \
-	mincwindow.1 \
-	mnc2nii.1 \
-	nii2mnc.1 \
-	rawtominc.1 \
-	transformtags.1 \
-	upet2mnc.1 \
-	voxeltoworld.1 \
-	xfmconcat.1 \
-	xfminvert.1
-
-MAN3=	ParseArgv.3
-
-NO_STAGE=	yes
-post-install:
-	@${CAT} ${PKGMESSAGE}
-
-.include <bsd.port.mk>
--- a/science/minc/distinfo
+++ b/science/minc/distinfo
@ -1,2 +0,0 @@
-SHA256 (minc-1.5.1.tar.gz) = 3ca7045c6eaa32daea184af3f78e30969bb0a0dddce2a1b292ba1624d23a61c9
-SIZE (minc-1.5.1.tar.gz) = 1356462
--- a/science/minc/files/patch-conversionminctoecatmachine_indep.c
+++ b/science/minc/files/patch-conversionminctoecatmachine_indep.c
@ -1,11 +0,0 @@
--- conversion/minctoecat/machine_indep.c.orig	2012-07-20 17:16:13.000000000 +0200
-+++ conversion/minctoecat/machine_indep.c	2012-07-20 17:17:48.000000000 +0200
-@@ -84,7 +84,7 @@
- 	bufr[1] =  ret >>16;
- }
- #else  /* BIG ENDIAN : sun hp sgi*/
-ftovaxf(orig,number)
-+void ftovaxf(orig,number)
-   unsigned short number[2];
-   float orig;
- {
--- a/science/minc/pkg-descr
+++ b/science/minc/pkg-descr
@ -1,10 +0,0 @@
-MINC (Medical Imaging NetCDF) is a medical imaging data format and an 
-associated set of tools and libraries. MINC was created in 1993 by Peter 
-Neelin at the McConnell Brain Imaging Centre of the Montreal Neurological 
-Institute. Many others have contributed to the design and implementation 
-MINC over the years.
-
-WWW: http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC
-
-Port maintainer: Jason W. Bacon
-		 jwbacon@tds.net
--- a/science/minc/pkg-message
+++ b/science/minc/pkg-message
@ -1,8 +0,0 @@
-=============================================================================
-For questions or comments regarding this port, please contact the
-port maintainer: jwbacon@tds.net
-
-For MINC usage, please visit the MINC WEB site at
-
-http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC
-=============================================================================
--- a/science/minc/pkg-plist
+++ b/science/minc/pkg-plist
@ -1,68 +0,0 @@
-bin/dcm2mnc
-bin/ecattominc
-bin/invert_raw_image
-bin/minc_modify_header
-bin/mincaverage
-bin/minccalc
-bin/mincconcat
-bin/minccopy
-bin/mincdiff
-bin/mincedit
-bin/mincexpand
-bin/mincextract
-bin/mincheader
-bin/minchistory
-bin/mincinfo
-bin/minclookup
-bin/mincmakescalar
-bin/mincmakevector
-bin/mincmath
-bin/mincpik
-bin/mincresample
-bin/mincreshape
-bin/mincstats
-bin/minctoecat
-bin/minctoraw
-bin/mincview
-bin/mincwindow
-bin/mnc2nii
-bin/nii2mnc
-bin/rawtominc
-bin/transformtags
-bin/upet2mnc
-bin/voxeltoworld
-bin/worldtovoxel
-bin/xfmconcat
-bin/xfminvert
-include/ParseArgv.h
-include/minc.h
-include/minc_simple.h
-include/nd_loop.h
-include/time_stamp.h
-include/volume_io.h
-include/volume_io/alloc.h
-include/volume_io/arrays.h
-include/volume_io/basic.h
-include/volume_io/def_math.h
-include/volume_io/files.h
-include/volume_io/geom_structs.h
-include/volume_io/geometry.h
-include/volume_io/internal_volume_io.h
-include/volume_io/multidim.h
-include/volume_io/progress.h
-include/volume_io/string_funcs.h
-include/volume_io/system_dependent.h
-include/volume_io/transforms.h
-include/volume_io/vol_io_prototypes.h
-include/volume_io/volume.h
-include/volume_io/volume_cache.h
-include/voxel_loop.h
-lib/libminc.a
-lib/libminc.la
-lib/libminc.so
-lib/libminc.so.1
-lib/libvolume_io.a
-lib/libvolume_io.la
-lib/libvolume_io.so
-lib/libvolume_io.so.0
-@dirrm include/volume_io
--- a/science/psi3/Makefile
+++ b/science/psi3/Makefile
@ -1,110 +0,0 @@
-# Created by: NAKATA Maho <maho@FreeBSD.org>
-# $FreeBSD$
-
-PORTNAME=	psi3
-PORTVERSION=	3.4.0
-PORTREVISION=	4
-CATEGORIES=	science
-MASTER_SITES=	SF/psicode/psi/${PORTVERSION} \
-		http://www.psicode.org/doc/:doc \
-		${MASTER_SITE_LOCAL:S|%SUBDIR%|maho/psi3|}:doc
-
-DISTNAME=	psi-${PORTVERSION}
-.if !defined(NOPORTDOCS)
-DISTFILES+=	${DISTNAME}${EXTRACT_SUFX} installation.pdf:doc userman.pdf:doc progman.pdf:doc
-.endif
-DIST_SUBDIR=	psi3
-EXTRACT_ONLY=	${DISTNAME}${EXTRACT_SUFX}
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Electronic structure programs for high-accuracy computations
-
-BROKEN=		Fails to build
-
-.if exists(${LOCALBASE}/lib/libgoto2.so)
-WITH_BLAS?=     gotoblas
-.elif exists(${LOCALBASE}/lib/libatlas.so)
-WITH_BLAS?=     atlas
-.else
-WITH_BLAS?=	reference
-.endif
-
-. if ${WITH_BLAS} == reference
-LIB_DEPENDS+=	libblas.so:${PORTSDIR}/math/blas
-LIB_DEPENDS+=	liblapack.so:${PORTSDIR}/math/lapack
-BLAS=		-lblas
-LAPACK=		-llapack
-.elif ${WITH_BLAS} == gotoblas
-LIB_DEPENDS+=	libgoto2.so:${PORTSDIR}/math/gotoblas
-LIB_DEPENDS+=	liblapack.so:${PORTSDIR}/math/lapack
-BLAS=		-lgoto2p
-LAPACK=		-lgoto2p
-.elif ${WITH_BLAS} == atlas
-LIB_DEPENDS+=	libatlas.so:${PORTSDIR}/math/atlas
-BLAS=		-lptf77blas
-LAPACK=		-lalapack -lptcblas
-.endif
-
-GNU_CONFIGURE=	yes
-USES=		fortran gmake tar:bzip2
-CONFIGURE_ARGS=	--with-cc=${CC} \
-		--with-cxx=${CXX} \
-		--with-fc=${FC} \
-		--with-opt="${CFLAGS}" \
-		--with-lapack="${LAPACK}" \
-		--with-blas="${BLAS}" \
-		--datadir=${PREFIX}/share/psi3 \
-		--docdir=${WRKSRC}/tmpdoc/ \
-		--with-libdirs="-L${LOCALBASE}/lib" \
-		--with-libs="-lcompat"
-CFLAGS+=	-Wno-error=return-type
-
-NO_STAGE=	yes
-.include <bsd.port.pre.mk>
-
-.if defined(WITH_OPTIMIZED_FLAGS)
-FFLAGS+=	-O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double
-CFLAGS+=	-O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double
-CXXFLAGS+=	-O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double  -Wno-multichar
-.if (${ARCH} == "i386")
-FFLAGS+=	-mfancy-math-387
-CFLAGS+=	-mfancy-math-387
-CXXFLAGS+=	-mfancy-math-387
-.endif # i386
-.endif
-
-WRKSRC=	${WRKDIR}/${PORTNAME}
-MAN1=	ccenergy.1 cceom.1 cints.1 clag.1 cscf.1 dboc.1 detcas.1 \
-	detcasman.1 detci.1 geom.1 input.1 intder.1 mocube.1 mp2.1 mp2r12.1 \
-	nonbonded.1 oeprop.1 optking.1 psi3.1 psiclean.1 stable.1 tocprint.1 \
-	transqt.1
-
-pre-configure:
-	@${ECHO} "You can optimize by setting WITH_OPTIMIZED_FLAGS=yes."
-	@${REINPLACE_CMD} -e 's|%%PTHREAD_CFLAGS%%|${PTREAD_CFLAGS}|g ; \
-			      s|%%PTHREAD_LIBS%%|${PTHREAD_LIBS}|g'  ${WRKSRC}/src/bin/cints/Makefile.in
-	@${REINPLACE_CMD} -e 's|%%PTHREAD_CFLAGS%%|${PTREAD_CFLAGS}|g ; \
-			      s|%%PTHREAD_LIBS%%|${PTHREAD_LIBS}|g'  ${WRKSRC}/src/bin/detci/Makefile.in
-
-MAKE_ENV+=	SCRATCH=${WRKSRC}/tmp
-
-do-build:
-	@(cd ${WRKSRC} ; ${SETENV} ${MAKE_ENV} ${MAKE_CMD})
-
-do-install:
-	@(cd ${WRKSRC} ; ${SETENV} ${MAKE_ENV} ${MAKE_CMD} install)
-	@${TAR} cf - -C ${WRKSRC}/tmpdoc/man .  | ${TAR} xf - -C ${PREFIX}/man
-.if !defined(NOPORTDOCS)
-	@${MKDIR} ${PREFIX}/share/doc/psi3
-	@${TAR} cf - -C ${WRKSRC}/tmpdoc/html . | ${TAR} xf - -C ${PREFIX}/share/doc/psi3
-	@${TAR} cf - -C ${WRKSRC}/tmpdoc/txt  . | ${TAR} xf - -C ${PREFIX}/share/doc/psi3
-	@${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/installation.pdf ${DOCSDIR}
-	@${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/userman.pdf ${DOCSDIR}
-	@${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/progman.pdf ${DOCSDIR}
-.endif
-.if !defined(NOPORTEXAMPLES)
-	@${MKDIR} ${PREFIX}/share/examples/psi3
-	@${TAR} cf - -C ${WRKSRC}/tests .       | ${TAR} xf - -C ${PREFIX}/share/examples/psi3
-.endif
-
-.include <bsd.port.post.mk>
--- a/science/psi3/distinfo
+++ b/science/psi3/distinfo
@ -1,8 +0,0 @@
-SHA256 (psi3/psi-3.4.0.tar.bz2) = 8776cc5ed8358ff2eba74ae02b5d3d6a80d61cd7c68d4cf76febfea3992d52b5
-SIZE (psi3/psi-3.4.0.tar.bz2) = 5806391
-SHA256 (psi3/installation.pdf) = 7f0a58f074d35d0f8e6c2a1d6e18232b9fafb28a161a2af82e6d0e56e90d4488
-SIZE (psi3/installation.pdf) = 76622
-SHA256 (psi3/userman.pdf) = 6b2fb4c42b248eda4f6f421f1369dfe2e0fd7f69744c710f7d39e1099fcdb4d6
-SIZE (psi3/userman.pdf) = 331573
-SHA256 (psi3/progman.pdf) = ea406c1df4902e6a42cc26ede515ebde4f96eb5b81fc6de82382f3a00b361358
-SIZE (psi3/progman.pdf) = 1693839
--- a/science/psi3/files/patch-cstdio
+++ b/science/psi3/files/patch-cstdio
@ -1,72 +0,0 @@
--- src/lib/libpsio/psio.hpp~	2008-11-25 02:50:44.000000000 +0900
-+++ src/lib/libpsio/psio.hpp	2009-08-03 19:03:57.000000000 +0900
-@@ -3,7 +3,7 @@
- 
- #include <string>
- #include <map>
-
-+#include <cstdio>
- #include <libpsio/config.h>
- 
- namespace psi {
--- src/lib/libutil/libutil.h~	2008-12-09 05:23:16.000000000 +0900
-+++ src/lib/libutil/libutil.h	2009-08-03 19:07:37.000000000 +0900
-@@ -4,6 +4,7 @@
- #include <vector>
- #include <iostream>
- #include <sstream>
-+#include <cstdio>
- #include <sys/time.h>
- 
- extern FILE *outfile;
--- src/bin/mcscf/block_matrix.h~	2008-12-09 05:23:16.000000000 +0900
-+++ src/bin/mcscf/block_matrix.h	2009-08-03 19:37:15.000000000 +0900
-@@ -4,7 +4,7 @@
- #include "block_vector.h"
- #include "matrix_base.h"
- #include <string>
-
-+#include <cstdio>
- extern FILE* outfile;
- 
- namespace psi{ namespace mcscf{
--- src/bin/mcscf/sblock_vector.cc~	2008-12-09 05:23:16.000000000 +0900
-+++ src/bin/mcscf/sblock_vector.cc	2009-08-03 20:00:47.000000000 +0900
-@@ -2,6 +2,7 @@
- #include <psifiles.h>
- 
- #include "sblock_vector.h"
-+#include <cstdio>
- 
- extern FILE* outfile;
- 
--- src/bin/mcscf/block_vector.cc~	2008-12-09 05:23:16.000000000 +0900
-+++ src/bin/mcscf/block_vector.cc	2009-08-03 20:27:14.000000000 +0900
-@@ -1,6 +1,7 @@
- #include "block_vector.h"
- #include "vector_base.h"
- #include "memory_manager.h"
-+#include <cstdio>
- 
- extern FILE* outfile;
- 
--- src/bin/mcscf/memory_manager.h~	2008-12-09 05:23:16.000000000 +0900
-+++ src/bin/mcscf/memory_manager.h	2009-08-03 21:09:02.000000000 +0900
-@@ -3,6 +3,7 @@
- 
- #include <map>
- #include <vector>
-+#include <cstdio>
- #include <string>
- 
- namespace psi{ namespace mcscf{
--- src/bin/psimrcc/memory_manager.h~	2008-08-14 07:25:41.000000000 +0900
-+++ src/bin/psimrcc/memory_manager.h	2009-08-03 21:10:00.000000000 +0900
-@@ -10,6 +10,7 @@
- #include <map>
- #include <vector>
- #include <string>
-+#include <cstdio>
- 
- namespace psi{ namespace psimrcc{
- 
--- a/science/psi3/files/patch-src+bin+cints+Makefile.in
+++ b/science/psi3/files/patch-src+bin+cints+Makefile.in
@ -1,21 +0,0 @@
--- src/bin/cints/Makefile.in~	2008-12-19 06:51:42.000000000 +0900
-+++ src/bin/cints/Makefile.in	2009-04-13 16:42:30.000000000 +0900
-@@ -92,15 +92,15 @@
- 
- include ../MakeVars
- 
-CFLAGS = $(CDBG) $(COPT) $(CDEF) $(COTH) $(CINC)
-+CFLAGS = $(CDBG) $(COPT) $(CDEF) $(COTH) $(CINC) %%PTHREAD_CFLAGS%%
- CINC += -I$(srcdir) $(DIRS:%=-I$(srcdir)/%)
- CDEF += $(OPTIONS)
- 
-CXXFLAGS = $(CXXDBG) $(CXXOPT) $(CXXDEF) $(CXXOTH) $(CXXINC)
-+CXXFLAGS = $(CXXDBG) $(CXXOPT) $(CXXDEF) $(CXXOTH) $(CXXINC) %%PTHREAD_CFLAGS%%
- CXXINC += -I$(srcdir) $(DIRS:%=-I$(srcdir)/%)
- CXXDEF += $(OPTIONS)
- 
-LDLIBS += $(BLAS) -lpthread
-+LDLIBS += $(BLAS) -lpthread %%PTHREAD_LIBS%%
- PSILIBS = -lPSI_qt -lPSI_chkpt $(INTLIBS) -lPSI_iwl \
-           -lPSI_psio -lPSI_ciomr -lPSI_ipv1
- ifeq ($(findstring CC,$(SUBDIRS)),CC)
--- a/science/psi3/files/patch-src+util+tocprint+Makefile.in
+++ b/science/psi3/files/patch-src+util+tocprint+Makefile.in
@ -1,11 +0,0 @@
--- src/util/tocprint/Makefile.in.org	Fri Mar 19 17:32:31 2004
-+++ src/util/tocprint/Makefile.in	Fri Mar 19 17:33:46 2004
-@@ -18,4 +18,4 @@
- 
- install_man:: tocprint.1
- 	$(MKDIRS) $(mandir)/man1
-	$(INSTALL_PROGRAM) $(srcdir)/tocprint.1 $(mandir)/man1
-+	$(INSTALL_INCLUDE) $^ $(mandir)/man1
-
-
-        
--- a/science/psi3/files/patch-src-bin-clag-clag.cc
+++ b/science/psi3/files/patch-src-bin-clag-clag.cc
@ -1,10 +0,0 @@
--- src/bin/clag/clag.cc.orig
-+++ src/bin/clag/clag.cc
-@@ -46,6 +46,7 @@
- /***************************************************************************/
- using namespace psi::clag;
- 
-+int
- main(int argc, char **argv) 
- {
- 
--- a/science/psi3/files/patch-src-bin-geom-geom.cc
+++ b/science/psi3/files/patch-src-bin-geom-geom.cc
@ -1,10 +0,0 @@
--- src/bin/geom/geom.cc.orig
-+++ src/bin/geom/geom.cc
-@@ -115,6 +115,7 @@
- void fill_sym_matrix(double **A, int size);
- }} // namespace psi::geom
- 
-+int
- main(int argc, char* argv[])
- {
-   using namespace psi::geom;
--- a/science/psi3/files/patch-src-bin-nonbonded-nonbonded.cc
+++ b/science/psi3/files/patch-src-bin-nonbonded-nonbonded.cc
@ -1,10 +0,0 @@
--- src/bin/nonbonded/nonbonded.cc.orig
-+++ src/bin/nonbonded/nonbonded.cc
-@@ -32,7 +32,6 @@
- #include <physconst.h>
- #include <psifiles.h>
- #include <masses.h>
-#include <string>
- 
- #include "globals.h"
- #include "nonbonded.h"
--- a/science/psi3/files/patch-src-bin-transqt2-transqt.cc
+++ b/science/psi3/files/patch-src-bin-transqt2-transqt.cc
@ -1,10 +0,0 @@
--- src/bin/transqt2/transqt.cc.orig
-+++ src/bin/transqt2/transqt.cc
-@@ -65,6 +65,7 @@
- 
- using namespace psi::transqt2;
- 
-+int
- main(int argc, char *argv[])
- {
-   int nso, nmo, ntri_so, ntri_mo, nirreps;
--- a/science/psi3/files/patch-src-lib-libbasis-combinate.cc
+++ b/science/psi3/files/patch-src-lib-libbasis-combinate.cc
@ -1,12 +0,0 @@
--- src/lib/libbasis/combinate.cc.orig
-+++ src/lib/libbasis/combinate.cc
-@@ -3,9 +3,7 @@
-     \brief Enter brief description of file here 
- */
- 
-extern "C" {
- #include <libciomr/libciomr.h>
-}
- 
- #include <stdexcept>
- #include "combinate.h"
--- a/science/psi3/files/patch-src-lib-libipv1-ip_read.cc
+++ b/science/psi3/files/patch-src-lib-libipv1-ip_read.cc
@ -1,20 +0,0 @@
--- src/lib/libipv1/ip_read.cc.orig
-+++ src/lib/libipv1/ip_read.cc
-@@ -12,7 +12,9 @@
- #include "ip_types.h"
- #define _IP_ALLOCATE_GLOBAL_
- #include "ip_global.h"
-+extern "C" {
- #include "y.tab.h"
-+}
- 
- #include "ip_read.gbl"
- #include "ip_read.lcl"
-@@ -27,7 +29,6 @@
- 
- /* The input for yacc. */
- extern FILE *yyin;
-extern void yyparse(void);
- 
- /* Set up static variables. */
- /*static ip_keyword_tree_t *sub_tree = NULL;*/
--- a/science/psi3/files/patch-src-lib-libpsio-psio.hpp
+++ b/science/psi3/files/patch-src-lib-libpsio-psio.hpp
@ -1,17 +0,0 @@
--- src/lib/libpsio/psio.hpp.orig
-+++ src/lib/libpsio/psio.hpp
-@@ -157,10 +157,11 @@
- 
-   };
-   
-extern "C" {
-  extern int psiopp_ipv1_config(PSIO *psio_obj);
-}
-   extern PSIO* _default_psio_lib_;
- }
- 
-+extern "C" {
-+  int psiopp_ipv1_config(psi::PSIO *psio_obj);
-+}
-+
- #endif /* header guard */
--- a/science/psi3/pkg-descr
+++ b/science/psi3/pkg-descr
@ -1,21 +0,0 @@
-The PSI3 suite of quantum chemical programs is designed for efficient,
-high-accuracy calculations of properties of small to medium-sized molecules.
-The package's current capabilities include a variety of Hartree-Fock,
-coupled cluster, complete-active-space self-consistent-field, and
-multi-reference configuration interaction models. Molecular point-group
-symmetry is utilized throughout to maximize efficiency.
-
-    * Arbitrarily high angular momentum levels in integrals
-       and derivative integrals. (Up to k-type functions have been tested.)
-    * Coupled cluster methods including CCSD and CCSD(T) with 
-      RHF, ROHF, UHF, and Brueckner orbitals.
-    * Determinant-based CI including CASSCF, RAS-CI, and Full CI.
-    * Multithreaded integral-direct SCF, MP2, and MP2-R12.
-    * Excited state methods: CIS, CIS(D), RPA, and EOM-CCSD.
-    * Analytic energy gradients for CCSD with RHF, ROHF, and UHF orbitals.
-    * Coupled cluster linear response methods for static and
-       dynamic polarizabilities and optical rotation.
-    * Diagonal Born-Oppenheimer correction (DBOC) for 
-       RHF, ROHF, UHF, and CI wave functions. 
-
-WWW: http://www.psicode.org/
--- a/science/psi3/pkg-message
+++ b/science/psi3/pkg-message
@ -1,6 +0,0 @@
-The following citation should be used in any publication
-utilizing the PSI3 program package:
-
-"T. Daniel Crawford, C. David Sherrill, Edward F. Valeev, Justin T. Fermann,
-Rollin A. King, Matthew L. Leininger, Shawn T. Brown, Curtis L. Janssen,
-Edward T. Seidl, Joseph P. Kenny, and Wesley D. Allen, PSI 3.2, 2003."
--- a/science/psi3/pkg-plist
+++ b/science/psi3/pkg-plist
@ -1,939 +0,0 @@
-bin/ccdensity
-bin/ccenergy
-bin/cceom
-bin/cchbar
-bin/cclambda
-bin/ccresponse
-bin/ccsort
-bin/cctriples
-bin/cints
-bin/cis
-bin/clag
-bin/cphf
-bin/cscf
-bin/dboc
-bin/detcas
-bin/detcasman
-bin/detci
-bin/extrema
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-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt6/file11.ref
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt6/input.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt6/output.ref
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt7/Makefile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt7/Makefile.in
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt7/file11.ref
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt7/input.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt7/output.ref
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt9/Makefile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt9/Makefile.in
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt9/file11.ref
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt9/input.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt9/output.ref
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-polar/Makefile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-polar/Makefile.in
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-polar/input.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-polar/output.ref
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-symm-fc-numer/Makefile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-symm-fc-numer/Makefile.in
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-symm-fc-numer/file11.ref
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-symm-fc-numer/input.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-symm-fc-numer/output.ref
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-lindep1/Makefile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-lindep1/Makefile.in
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-lindep1/input.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-lindep1/output.ref
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-stab-follow/Makefile.in
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-stab-follow/input.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-stab-follow/output.ref
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-stab-follow/uhf-stab-follow.pl.in
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-stab/Makefile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-stab/Makefile.in
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-stab/input.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-stab/output.ref
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-stab/uhf-stab.pl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-stab/uhf-stab.pl.in
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/zaptn-nh2/Makefile
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/zaptn-nh2/Makefile.in
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/zaptn-nh2/input.dat
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/zaptn-nh2/output.ref
-share/psi3/psi/pbasis.dat
-share/psi3/psi/psi.dat
-share/psi3/psi/ruby/ccdensity.rb
-share/psi3/psi/ruby/ccenergy.rb
-share/psi3/psi/ruby/cceom.rb
-share/psi3/psi/ruby/cchbar.rb
-share/psi3/psi/ruby/cclambda.rb
-share/psi3/psi/ruby/ccsort.rb
-share/psi3/psi/ruby/cctriples.rb
-share/psi3/psi/ruby/chkpt.rb
-share/psi3/psi/ruby/cints.rb
-share/psi3/psi/ruby/clean.rb
-share/psi3/psi/ruby/color.rb
-share/psi3/psi/ruby/cphf.rb
-share/psi3/psi/ruby/deriv.rb
-share/psi3/psi/ruby/deriv2.rb
-share/psi3/psi/ruby/detci.rb
-share/psi3/psi/ruby/frequencies.rb
-share/psi3/psi/ruby/input.rb
-share/psi3/psi/ruby/mp2.rb
-share/psi3/psi/ruby/oeprop.rb
-share/psi3/psi/ruby/optking.rb
-share/psi3/psi/ruby/pes.rb
-share/psi3/psi/ruby/propint.rb
-share/psi3/psi/ruby/psi3.rb
-share/psi3/psi/ruby/scf.rb
-share/psi3/psi/ruby/symbols.rb
-share/psi3/psi/ruby/testcases.rb
-share/psi3/psi/ruby/transqt.rb
-@dirrm share/psi3/psi/ruby
-@dirrm share/psi3/psi
-@dirrm share/psi3
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/zaptn-nh2
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-stab-follow
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-stab
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/uhf-lindep1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-symm-fc-numer
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-polar
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt9
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt7
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt6
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt5
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt4
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt3
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt2-numer
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt2
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt12
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt11
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt10
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt-numer
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt-fragments
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-opt
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-mvd-opt-puream
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-mvd-opt-numer-puream
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-mvd-opt-numer
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-mvd-opt
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-freq-none-5
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-freq-none-3
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-freq-first-5a
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-freq-first-5
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-freq-first-3a
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-freq-first-3
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-freq
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf-fc-numer
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf+d-opt1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/scf+d-freq
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/rohf-stab
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/rohf-lindep1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/rhf-stab
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/rhf-oeprop
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/rhf-lindep1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/rb-scf-opt-numer
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/rb-fci-h2o
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/rb-ccsd_t-sp
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/rb-ccsd-opt-grad
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/rasscf-sp
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/psimrcc-sp1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/psi_start
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mp2r12-sp1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mp2-sp
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mp2-scs
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mp2-opt-numer
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mp2-opt-fragments
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mp2-opt
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mp2-oeprop
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mp2-direct-sp
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mcscf-twocon1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mcscf-rohf1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mcscf-rhf1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fci-trans
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fci-h2o-fzcv
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fci-h2o-clpse
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fci-h2o-2
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fci-h2o
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fci-dipole
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/extrema-zmat
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/extrema-deloc
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dboc-uhf1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dboc-rohf1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dboc-rocisd1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dboc-rhf1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dboc-rcisd1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cisd-sp-2
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cisd-sp
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cisd-opt-numer
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cisd-h2o+-2
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cisd-h2o+-1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cisd-h2o+-0
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cis-sp
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cints-d1eri
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ci-tdm
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc9a
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc9
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc8a
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc8
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc7
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc6
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc50
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc5
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc49
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc48
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc47
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc46
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc45
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc44
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc43
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc42
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc41
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc40
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc4
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc39
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc38
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc37
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc36
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc35
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc34
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc33
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc32
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc31
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc30
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc3
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc29
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc28
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc27
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc26
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc25
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc24
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc23
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc22
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc21
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc2
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc19
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc18
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc17
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc16
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc15
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc14
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc13a
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc13
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc12
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc11
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc10
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cc1
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/casscf-sp-reorder
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/casscf-sp
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/casscf-sa-sp
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/casscf-opt-numer
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/casscf-opt
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/casscf-fzc-sp
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Basis_Tests
-@dirrm %%PORTEXAMPLES%%%%EXAMPLESDIR%%
-@dirrm share/doc/psi3
-@dirrm include/libutil
-@dirrm include/libr12
-@dirrm include/libqt
-@dirrm include/libpsio
-@dirrm include/liboptions
-@dirrm include/libmoinfo
-@dirrm include/libmints
-@dirrm include/libiwl
-@dirrm include/libipv1
-@dirrm include/libint
-@dirrm include/libdpd
-@dirrm include/libderiv
-@dirrm include/libciomr
-@dirrm include/libchkpt
-@dirrm include/libbasis
--- a/science/x11iraf/Makefile
+++ b/science/x11iraf/Makefile
@ -1,43 +0,0 @@
-# Created by: David Syphers <dsyphers@u.washington.edu>
-# $FreeBSD$
-
-PORTNAME=	x11iraf
-PORTVERSION=	1.3.1
-PORTREVISION=	3
-CATEGORIES=	science astro
-MASTER_SITES=	ftp://iraf.noao.edu/iraf/x11iraf/
-DISTNAME=	x11iraf-v${PORTVERSION}-bin.freebsd
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Provides graphical tools to work with IRAF
-
-CONFLICTS=	xterm-[0-9]*
-
-LIB_DEPENDS=	libc.so.4:${PORTSDIR}/misc/compat4x
-
-NO_BUILD=	yes
-
-# this may work on other archs, but I'm making no bets
-ONLY_FOR_ARCHS=	i386
-
-BINS=		ism_wcspix.e obmsh resize vximtool xgterm ximtool xtapemon
-
-MAN1=		obmsh.1		\
-		resize.1	\
-		vximtool.1	\
-		xgterm.1	\
-		ximtool.1	\
-		xtapemon.1
-
-NO_STAGE=	yes
-do-install:
-	@${ECHO_MSG} "===>  Installing binaries"
-	@${INSTALL_PROGRAM} ${BINS:S|^|${WRKDIR}/bin.freebsd/|} ${PREFIX}/bin/
-	@${INSTALL_SCRIPT} ${WRKDIR}/bin.freebsd/ximtool-alt ${PREFIX}/bin/
-	@${ECHO_MSG} "===>  Installing manpages"
-	@${INSTALL_MAN} ${WRKDIR}/man/* ${PREFIX}/man/man1/
-	@${ECHO_MSG} "===>  Installing CDL library"
-	@${INSTALL_DATA} ${WRKDIR}/include/* ${PREFIX}/include/
-	@${INSTALL_DATA} ${WRKDIR}/lib.freebsd/libcdl.a ${PREFIX}/lib/
-
-.include <bsd.port.mk>
--- a/science/x11iraf/distinfo
+++ b/science/x11iraf/distinfo
@ -1,2 +0,0 @@
-SHA256 (x11iraf-v1.3.1-bin.freebsd.tar.gz) = 04b1a5e1f337459f5389fb901566314eacf2ae3a6ba79bd7623314c5d5a4747d
-SIZE (x11iraf-v1.3.1-bin.freebsd.tar.gz) = 2238249
--- a/science/x11iraf/pkg-descr
+++ b/science/x11iraf/pkg-descr
@ -1,9 +0,0 @@
-x11iraf provides graphical tools to work with IRAF, notably xgterm and XImtool.
-
-Note: IRAF = Image Reduction and Analysis Facility, a general purpose software
-system for the reduction and analysis of astronomical data.
-
-WWW: http://iraf.noao.edu
-
-David Syphers
-dsyphers@u.washington.edu
--- a/science/x11iraf/pkg-plist
+++ b/science/x11iraf/pkg-plist
@ -1,12 +0,0 @@
-bin/ism_wcspix.e
-bin/obmsh
-bin/resize
-bin/vximtool
-bin/xgterm
-bin/ximtool
-bin/ximtool-alt
-bin/xtapemon
-include/cdl.h
-include/cdlftn.inc
-include/cdlspp.h
-lib/libcdl.a
--- a/science/xmds/Makefile
+++ b/science/xmds/Makefile
@ -1,31 +0,0 @@
-# Created by: EelVex
-# $FreeBSD$
-
-PORTNAME=	xmds
-PORTVERSION=	1.6
-CATEGORIES=	science
-MASTER_SITES=	SF/${PORTNAME}/${PORTNAME}/${PORTNAME}-${PORTVERSION}.5
-DISTNAME=	xmds-1.6.5
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	XMDS is a code generator that integrates equations;
-
-MAN1=	loadxsil.1 xmds.1 xsil2graphics.1
-
-OPTIONS_DEFINE=	FFTW3
-FFTW3_DESC=	Use fftw3 instead of fftw2
-
-GNU_CONFIGURE=	yes
-
-NO_STAGE=	yes
-.include <bsd.port.options.mk>
-
-.if ${PORT_OPTIONS:MFFTW3}
-BUILD_DEPENDS=	${LOCALBASE}/include/fftw3.h:${PORTSDIR}/math/fftw3
-CONFIGURE_ARGS=	--enable-fftw3 --with-fftw3-path=${LOCALBASE}
-.else
-BUILD_DEPENDS=	${LOCALBASE}/include/fftw.h:${PORTSDIR}/math/fftw
-CONFIGURE_ARGS=	--with-fftw-path=${LOCALBASE}
-.endif
-
-.include <bsd.port.mk>
--- a/science/xmds/distinfo
+++ b/science/xmds/distinfo
@ -1,2 +0,0 @@
-SHA256 (xmds-1.6.5.tar.gz) = f7128c7c847bafd3a5ed582415cbddd1f31234278d62231faaeb9bec04d6b5ff
-SIZE (xmds-1.6.5.tar.gz) = 528593
--- a/science/xmds/files/patch-Makefile.in
+++ b/science/xmds/files/patch-Makefile.in
@ -1,82 +0,0 @@
--- Makefile.in.orig	2008-02-25 21:32:56.000000000 -0600
-+++ Makefile.in	2010-09-22 14:22:17.000000000 -0500
-@@ -150,4 +150,5 @@
- EXTRA_DIST = $(example_files) $(m4files) $(manfiles) MANIFEST README.Windows source/loadxsil.m
-dist_doc_data = AUTHORS NEWS COPYING README README.Windows source/loadxsil.m
-doc_examplesdir = ${docdir}/examples
-+xmdsdocdir = ${datadir}/doc/xmds-${VERSION}
-+dist_xmdsdoc_DATA = AUTHORS NEWS COPYING README README.Windows source/loadxsil.m
-+doc_examplesdir = ${xmdsdocdir}/examples
- dist_doc_examples_DATA = $(example_files)
-@@ -162,3 +163,3 @@
- MANS = $(man1_MANS)
-DATA = $(dist_doc_examples_DATA)
-+DATA = $(dist_doc_examples_DATA) $(dist_xmdsdoc_DATA)
- 
-@@ -169,5 +170,5 @@
- 	uninstall-recursive check-recursive installcheck-recursive
-DIST_COMMON = README $(dist_doc_examples_DATA) AUTHORS COPYING \
-	ChangeLog INSTALL Makefile.am Makefile.in NEWS TODO \
-	acinclude.m4 aclocal.m4 config.guess config.sub configure \
-+DIST_COMMON = README $(dist_doc_examples_DATA) $(dist_xmdsdoc_DATA) \
-+	AUTHORS COPYING ChangeLog INSTALL Makefile.am Makefile.in NEWS \
-+	TODO acinclude.m4 aclocal.m4 config.guess config.sub configure \
- 	configure.in depcomp install-sh ltmain.sh missing mkinstalldirs
-@@ -255,2 +256,20 @@
- 	done
-+dist_xmdsdocDATA_INSTALL = $(INSTALL_DATA)
-+install-dist_xmdsdocDATA: $(dist_xmdsdoc_DATA)
-+	@$(NORMAL_INSTALL)
-+	$(mkinstalldirs) $(DESTDIR)$(xmdsdocdir)
-+	@list='$(dist_xmdsdoc_DATA)'; for p in $$list; do \
-+	  if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
-+	  f="`echo $$p | sed -e 's|^.*/||'`"; \
-+	  echo " $(dist_xmdsdocDATA_INSTALL) $$d$$p $(DESTDIR)$(xmdsdocdir)/$$f"; \
-+	  $(dist_xmdsdocDATA_INSTALL) $$d$$p $(DESTDIR)$(xmdsdocdir)/$$f; \
-+	done
-+
-+uninstall-dist_xmdsdocDATA:
-+	@$(NORMAL_UNINSTALL)
-+	@list='$(dist_xmdsdoc_DATA)'; for p in $$list; do \
-+	  f="`echo $$p | sed -e 's|^.*/||'`"; \
-+	  echo " rm -f $(DESTDIR)$(xmdsdocdir)/$$f"; \
-+	  rm -f $(DESTDIR)$(xmdsdocdir)/$$f; \
-+	done
- 
-@@ -458,3 +477,3 @@
- installdirs-am:
-	$(mkinstalldirs) $(DESTDIR)$(man1dir) $(DESTDIR)$(doc_examplesdir)
-+	$(mkinstalldirs) $(DESTDIR)$(man1dir) $(DESTDIR)$(doc_examplesdir) $(DESTDIR)$(xmdsdocdir)
- 
-@@ -500,3 +519,4 @@
- 
-install-data-am: install-dist_doc_examplesDATA install-man
-+install-data-am: install-dist_doc_examplesDATA install-dist_xmdsdocDATA \
-+	install-man
- 
-@@ -519,4 +539,4 @@
- 
-uninstall-am: uninstall-dist_doc_examplesDATA uninstall-info-am \
-	uninstall-man
-+uninstall-am: uninstall-dist_doc_examplesDATA uninstall-dist_xmdsdocDATA \
-+	uninstall-info-am uninstall-man
- 
-@@ -532,10 +552,12 @@
- 	install-data-recursive install-dist_doc_examplesDATA \
-	install-exec install-exec-am install-exec-recursive \
-	install-info install-info-am install-info-recursive install-man \
-	install-man1 install-recursive install-strip installcheck \
-	installcheck-am installdirs installdirs-am \
-	installdirs-recursive maintainer-clean maintainer-clean-generic \
-+	install-dist_xmdsdocDATA install-exec install-exec-am \
-+	install-exec-recursive install-info install-info-am \
-+	install-info-recursive install-man install-man1 \
-+	install-recursive install-strip installcheck installcheck-am \
-+	installdirs installdirs-am installdirs-recursive \
-+	maintainer-clean maintainer-clean-generic \
- 	maintainer-clean-recursive mostlyclean mostlyclean-generic \
- 	mostlyclean-recursive tags tags-recursive uninstall \
-	uninstall-am uninstall-dist_doc_examplesDATA uninstall-info-am \
-+	uninstall-am uninstall-dist_doc_examplesDATA \
-+	uninstall-dist_xmdsdocDATA uninstall-info-am \
- 	uninstall-info-recursive uninstall-man uninstall-man1 \
--- a/science/xmds/pkg-descr
+++ b/science/xmds/pkg-descr
@ -1,25 +0,0 @@
-eXtensible multi-dimensional Simulator
-    * An open-source XML based simulation package
-    * From Ordinary Differential Equations (ODEs) up to stochastic Partial
-      Differential Equations (PDEs)
-    * Many applications:
-          o physics
-          o mathematics
-          o engineering
-          o finance
-          o economics
-          o chemistry
-          o theoretical biology
-    * Generates fast, C++ compiled code
-    * Documentation and source are free!
-    * Runs on Linux, Unix, MacOS X and Cygwin (Windows)
-XMDS is a code generator that integrates equations. You write them down in
-human readable form in an XML file, and it goes away and writes and compiles a
-C++ program that integrates those equations as fast as it can possibly be done
-in your architecture. 
-
-Author:	Paul Cochrane (principal developer) 	cochrane@physics.uq.edu.au
-	Joseph Hope (second author) 		Joseph.Hope@anu.edu.au
-	Peter Drummond (xmds project leader)	drummond@physics.uq.edu.au
-
-WWW:	http://www.xmds.org/
--- a/science/xmds/pkg-plist
+++ b/science/xmds/pkg-plist
@ -1,52 +0,0 @@
-bin/xmds
-bin/xsil2graphics
-include/getopt_xmds.h
-include/xmds_complex.h
-include/xmds_config.h
-lib/libxmds.a
-share/doc/xmds-1.6.5/AUTHORS
-share/doc/xmds-1.6.5/COPYING
-share/doc/xmds-1.6.5/NEWS
-share/doc/xmds-1.6.5/README
-share/doc/xmds-1.6.5/README.Windows
-share/doc/xmds-1.6.5/examples/HighdimPlotExample.nb
-share/doc/xmds-1.6.5/examples/atomlaser.xmds
-share/doc/xmds-1.6.5/examples/branch.xmds
-share/doc/xmds-1.6.5/examples/brusselator.xmds
-share/doc/xmds-1.6.5/examples/catcycle.xmds
-share/doc/xmds-1.6.5/examples/chain.xmds
-share/doc/xmds-1.6.5/examples/chemkin.xmds
-share/doc/xmds-1.6.5/examples/diffusion.xmds
-share/doc/xmds-1.6.5/examples/duffing.xmds
-share/doc/xmds-1.6.5/examples/fibre.xmds
-share/doc/xmds-1.6.5/examples/fisher_reaction_diffusion.xmds
-share/doc/xmds-1.6.5/examples/fullpos3D.xmds
-share/doc/xmds-1.6.5/examples/gaugeatomlaser.xmds
-share/doc/xmds-1.6.5/examples/groundstate.xmds
-share/doc/xmds-1.6.5/examples/highdim.xmds
-share/doc/xmds-1.6.5/examples/highdim_vector_version.xmds
-share/doc/xmds-1.6.5/examples/hires.xmds
-share/doc/xmds-1.6.5/examples/krebs.xmds
-share/doc/xmds-1.6.5/examples/kubo.xmds
-share/doc/xmds-1.6.5/examples/lane_emden.xmds
-share/doc/xmds-1.6.5/examples/lorenz.xmds
-share/doc/xmds-1.6.5/examples/lorenzInput.dat
-share/doc/xmds-1.6.5/examples/lotka_volterra.xmds
-share/doc/xmds-1.6.5/examples/nan.xmds
-share/doc/xmds-1.6.5/examples/ndparamp.xmds
-share/doc/xmds-1.6.5/examples/nlse.xmds
-share/doc/xmds-1.6.5/examples/oregonator.xmds
-share/doc/xmds-1.6.5/examples/paraxial_wave.xmds
-share/doc/xmds-1.6.5/examples/pendulum.xmds
-share/doc/xmds-1.6.5/examples/ring_modulator.xmds
-share/doc/xmds-1.6.5/examples/sech_soliton.xmds
-share/doc/xmds-1.6.5/examples/sech_soliton_tdepk.xmds
-share/doc/xmds-1.6.5/examples/sine.xmds
-share/doc/xmds-1.6.5/examples/soliton.xmds
-share/doc/xmds-1.6.5/examples/thermkin.xmds
-share/doc/xmds-1.6.5/examples/tla.xmds
-share/doc/xmds-1.6.5/examples/van_der_pol.xmds
-share/doc/xmds-1.6.5/examples/vibstring.xmds
-share/doc/xmds-1.6.5/loadxsil.m
-@dirrm share/doc/xmds-1.6.5/examples
-@dirrm share/doc/xmds-1.6.5
--- a/security/Makefile
+++ b/security/Makefile
@ -35,7 +35,6 @@
    SUBDIR += belier
    SUBDIR += bfbtester
    SUBDIR += binwalk
-    SUBDIR += bioapi
    SUBDIR += blindelephant
    SUBDIR += botan110
    SUBDIR += bro
@ -44,7 +43,6 @@
    SUBDIR += bruteforceblocker
    SUBDIR += bsdsfv
    SUBDIR += bsmtrace
-    SUBDIR += bsp_upektfmess
    SUBDIR += bugs
    SUBDIR += burpsuite
    SUBDIR += ca_root_nss
@ -101,7 +99,6 @@
    SUBDIR += dirbuster
    SUBDIR += dirmngr
    SUBDIR += distcache
-    SUBDIR += distcache-devel
    SUBDIR += dmitry
    SUBDIR += doorman
    SUBDIR += doscan
@ -327,7 +324,6 @@
    SUBDIR += mhash
    SUBDIR += mindterm-binary
    SUBDIR += monkeysphere
-    SUBDIR += mosref
    SUBDIR += munge
    SUBDIR += mussh
    SUBDIR += nacl
@ -377,7 +373,6 @@
    SUBDIR += openvpn-admin
    SUBDIR += openvpn-auth-ldap
    SUBDIR += openvpn-auth-radius
-    SUBDIR += openvpn-beta
    SUBDIR += openvpn-devel
    SUBDIR += ophcrack
    SUBDIR += orthrus
@ -619,7 +614,6 @@
    SUBDIR += pad
    SUBDIR += pam-mysql
    SUBDIR += pam-pgsql
-    SUBDIR += pam_bsdbioapi
    SUBDIR += pam_fprint
    SUBDIR += pam_google_authenticator
    SUBDIR += pam_helper
@ -688,9 +682,6 @@
    SUBDIR += pgpdump
    SUBDIR += pgpgpg
    SUBDIR += pgpin
-    SUBDIR += php-Auth_OpenID
-    SUBDIR += php-Auth_OpenID2
-    SUBDIR += php-openid-ldap
    SUBDIR += php-suhosin
    SUBDIR += php5-filter
    SUBDIR += php5-hash
@ -895,15 +886,11 @@
    SUBDIR += rubygem-twitter_oauth
    SUBDIR += safesh
    SUBDIR += samba-virusfilter
-    SUBDIR += samhain
-    SUBDIR += samhain-client
-    SUBDIR += samhain-server
    SUBDIR += sancp
    SUBDIR += sasp
    SUBDIR += scamp
    SUBDIR += scanhill
    SUBDIR += scanlogd
-    SUBDIR += scannedonly
    SUBDIR += scanssh
    SUBDIR += scrypt
    SUBDIR += seahorse
@ -983,7 +970,6 @@
    SUBDIR += tclsasl
    SUBDIR += tinc
    SUBDIR += tinyca
-    SUBDIR += tinysu
    SUBDIR += tlswrap
    SUBDIR += tor
    SUBDIR += tor-devel
--- a/security/bioapi/Makefile
+++ b/security/bioapi/Makefile
@ -1,24 +0,0 @@
-# Created by: Fredrik Lindberg <fli@shapeshifter.se>
-# $FreeBSD$
-
-PORTNAME=	bioapi
-PORTVERSION=	1.2.2
-PORTREVISION=	5
-CATEGORIES=	security
-MASTER_SITES=	http://www.qrivy.net/~michael/blua/bioapi/ \
-		http://shapeshifter.se/pub/bioapi/
-
-MAINTAINER= ports@FreeBSD.org
-COMMENT=	BioAPI library implementation
-
-USE_AUTOTOOLS=	libtool
-USES=	tar:bzip2
-GNU_CONFIGURE=	yes
-# Problems reported with higher optimization levels
-CFLAGS+=	-O
-CONFIGURE_ARGS=	--localstatedir=/var/db/ --with-Qt-dir=no
-
-USE_LDCONFIG=	yes
-
-NO_STAGE=	yes
-.include <bsd.port.mk>
--- a/Show More
+++ b/Show More