Update to 1.5

Submitted by:	distfile survey by kris, fenner

4 files changed, 229 insertions, 211 deletions

diff --git a/biology/garlic/Makefile b/biology/garlic/Makefile
index 6c24973fcf6e..cf78c720cec9 100644
--- a/biology/garlic/Makefile
+++ b/biology/garlic/Makefile
@@ -6,8 +6,7 @@
 #
 
 PORTNAME=	garlic
-PORTVERSION=	1.4
-PORTREVISION=	2
+PORTVERSION=	1.5
 CATEGORIES=	biology
 MASTER_SITES=	http://garlic.mefos.hr/sources/garlic-${PORTVERSION}/
 DISTFILES=	${DISTNAME}${EXTRACT_SUFX}
@@ -26,7 +25,7 @@ ALL_TARGET=	# empty
 
 .if defined(WITH_OPTIMIZED_FLAGS)
 CFLAGS+=	-O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double
-.if (${MACHINE_ARCH} == "i386")
+.if (${ARCH} == "i386")
 CFLAGS+=	-mfancy-math-387 -mpreferred-stack-boundary=3
 .endif # i386
 .endif
diff --git a/biology/garlic/distinfo b/biology/garlic/distinfo
index f3c4933e4394..472895f470b1 100644
--- a/biology/garlic/distinfo
+++ b/biology/garlic/distinfo
@@ -1,6 +1,6 @@
-MD5 (garlic-1.4.tar.gz) = 054b8fdb3575609229bac2f743c85cd9
-SHA256 (garlic-1.4.tar.gz) = 71588a28310fe528376b750756e5aeb754d52d19dfce075a8dbc42d35668682f
-SIZE (garlic-1.4.tar.gz) = 525932
-MD5 (garlic-1.4-doc.tar.gz) = f53f758ca785630c22d19d3744015122
-SHA256 (garlic-1.4-doc.tar.gz) = 684d743ea4fbbf15bdce20089d8424fd34fc43555c156b9a111558ec6699e7c3
-SIZE (garlic-1.4-doc.tar.gz) = 1144169
+MD5 (garlic-1.5.tar.gz) = a45b478ea1247fa9875b35cfa2001cb8
+SHA256 (garlic-1.5.tar.gz) = d0c1b97274dc1154490c1ee64201fc67fc7036442e18df41d72cb55b896bb334
+SIZE (garlic-1.5.tar.gz) = 561319
+MD5 (garlic-1.5-doc.tar.gz) = 6f407ecfc5bf9126b4a79b6c20e4edb8
+SHA256 (garlic-1.5-doc.tar.gz) = 927e9750500e1acb8c0299d273be19bafda0a9971badbc90d4866f696ef5bbe3
+SIZE (garlic-1.5-doc.tar.gz) = 1202222
diff --git a/biology/garlic/files/patch-Makefile b/biology/garlic/files/patch-Makefile
index 18a9d63d72af..63eb7c755204 100644
--- a/biology/garlic/files/patch-Makefile
+++ b/biology/garlic/files/patch-Makefile
@@ -1,15 +1,15 @@
---- Makefile.orig	Fri May 30 20:27:25 2003
-+++ Makefile	Mon Jul 28 12:01:48 2003
+--- Makefile.orig	Thu Mar  2 20:12:46 2006
++++ Makefile	Wed Mar 15 16:50:07 2006
 @@ -1,14 +1,14 @@
 -CC = gcc
 +CC = %%CC%%
  
  #CCOPT = -O
- #CCOPT = -O3
+-CCOPT = -O3
++CCOPT = %%CFLAGS%% -I%%LOCALBASE%%/include -I%%X11BASE%%/include
  #CCOPT = -O3 -g3
  #CCOPT = -ansi -pedantic -g3
--CCOPT = -ansi -pedantic -O -Wall -Wstrict-prototypes -g3
-+CCOPT = %%CFLAGS%% -I%%LOCALBASE%%/include -I%%X11BASE%%/include
+ #CCOPT = -ansi -pedantic -O -Wall -Wstrict-prototypes -g3
  
  HEADERS = defines.h typedefs.h
  
diff --git a/biology/garlic/pkg-plist b/biology/garlic/pkg-plist
index f3bad703eb3e..5b3a1e3be93d 100644
--- a/biology/garlic/pkg-plist
+++ b/biology/garlic/pkg-plist
@@ -2,217 +2,245 @@ bin/garlic
 share/garlic/.garlicrc
 share/garlic/residues.pdb
 @dirrm share/garlic
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-%%PORTDOCS%%%%DOCSDIR%%/data/index.html
-%%PORTDOCS%%%%DOCSDIR%%/data/garlic.gif
-%%PORTDOCS%%%%DOCSDIR%%/favicon.ico
-%%PORTDOCS%%%%DOCSDIR%%/refcard/favicon.ico
-%%PORTDOCS%%%%DOCSDIR%%/refcard/index.html
-%%PORTDOCS%%%%DOCSDIR%%/refcard/garlic.gif
-%%PORTDOCS%%%%DOCSDIR%%/refcard/refcard.html
-%%PORTDOCS%%%%DOCSDIR%%/techinfo/favicon.ico
-%%PORTDOCS%%%%DOCSDIR%%/techinfo/index.html
-%%PORTDOCS%%%%DOCSDIR%%/techinfo/garlic.gif
-%%PORTDOCS%%%%DOCSDIR%%/mouse/favicon.ico
-%%PORTDOCS%%%%DOCSDIR%%/mouse/neighbor.gif
-%%PORTDOCS%%%%DOCSDIR%%/mouse/outplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/mouse/index.html
-%%PORTDOCS%%%%DOCSDIR%%/mouse/.xvpics/outplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/mouse/.xvpics/outstr.gif
-%%PORTDOCS%%%%DOCSDIR%%/mouse/.xvpics/outcomp.gif
-%%PORTDOCS%%%%DOCSDIR%%/mouse/.xvpics/outrama.gif
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-%%PORTDOCS%%%%DOCSDIR%%/mouse/outrama.gif
-%%PORTDOCS%%%%DOCSDIR%%/mouse/garlic.gif
 %%PORTDOCS%%%%DOCSDIR%%/README
-%%PORTDOCS%%%%DOCSDIR%%/download/favicon.ico
-%%PORTDOCS%%%%DOCSDIR%%/download/index.html
-%%PORTDOCS%%%%DOCSDIR%%/download/garlic.gif
-%%PORTDOCS%%%%DOCSDIR%%/scripts/favicon.ico
-%%PORTDOCS%%%%DOCSDIR%%/scripts/colors.script
-%%PORTDOCS%%%%DOCSDIR%%/scripts/atoms.script
-%%PORTDOCS%%%%DOCSDIR%%/scripts/probes.script
-%%PORTDOCS%%%%DOCSDIR%%/scripts/bonds.script
-%%PORTDOCS%%%%DOCSDIR%%/scripts/garlic.gif
-%%PORTDOCS%%%%DOCSDIR%%/license/favicon.ico
-%%PORTDOCS%%%%DOCSDIR%%/license/index.html
-%%PORTDOCS%%%%DOCSDIR%%/license/garlic.gif
-%%PORTDOCS%%%%DOCSDIR%%/docs.html
-%%PORTDOCS%%%%DOCSDIR%%/index.html
+%%PORTDOCS%%%%DOCSDIR%%/ascorbic_acid1.jpg
+%%PORTDOCS%%%%DOCSDIR%%/ascorbic_acid2.jpg
 %%PORTDOCS%%%%DOCSDIR%%/bold_statement.html
-%%PORTDOCS%%%%DOCSDIR%%/gallery/favicon.ico
-%%PORTDOCS%%%%DOCSDIR%%/gallery/index.html
-%%PORTDOCS%%%%DOCSDIR%%/gallery/small1.png
-%%PORTDOCS%%%%DOCSDIR%%/gallery/small2.png
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-%%PORTDOCS%%%%DOCSDIR%%/commands/rep.html
-%%PORTDOCS%%%%DOCSDIR%%/commands/favicon.ico
-%%PORTDOCS%%%%DOCSDIR%%/commands/sho.html
+%%PORTDOCS%%%%DOCSDIR%%/bugfixes/favicon.ico
+%%PORTDOCS%%%%DOCSDIR%%/bugfixes/garlic.gif
+%%PORTDOCS%%%%DOCSDIR%%/bugfixes/index.html
+%%PORTDOCS%%%%DOCSDIR%%/changes/favicon.ico
+%%PORTDOCS%%%%DOCSDIR%%/changes/garlic.gif
+%%PORTDOCS%%%%DOCSDIR%%/changes/index.html
 %%PORTDOCS%%%%DOCSDIR%%/commands/aacodes.gif
-%%PORTDOCS%%%%DOCSDIR%%/commands/pro_hint.gif
-%%PORTDOCS%%%%DOCSDIR%%/commands/res.html
+%%PORTDOCS%%%%DOCSDIR%%/commands/add.html
+%%PORTDOCS%%%%DOCSDIR%%/commands/ang.html
+%%PORTDOCS%%%%DOCSDIR%%/commands/ato.html
+%%PORTDOCS%%%%DOCSDIR%%/commands/atoms.gif
+%%PORTDOCS%%%%DOCSDIR%%/commands/bac.html
+%%PORTDOCS%%%%DOCSDIR%%/commands/bal.html
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-%%PORTDOCS%%%%DOCSDIR%%/commands/plot2.gif
-%%PORTDOCS%%%%DOCSDIR%%/commands/plot3.gif
-%%PORTDOCS%%%%DOCSDIR%%/commands/wheel.gif
+%%PORTDOCS%%%%DOCSDIR%%/commands/bg.html
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+%%PORTDOCS%%%%DOCSDIR%%/commands/bon.html
+%%PORTDOCS%%%%DOCSDIR%%/commands/bonds.gif
+%%PORTDOCS%%%%DOCSDIR%%/commands/cat.html
+%%PORTDOCS%%%%DOCSDIR%%/commands/cen.html
+%%PORTDOCS%%%%DOCSDIR%%/commands/chi_angles.gif
+%%PORTDOCS%%%%DOCSDIR%%/commands/col.html
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+%%PORTDOCS%%%%DOCSDIR%%/commands/hid.html
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+%%PORTDOCS%%%%DOCSDIR%%/index.html
+%%PORTDOCS%%%%DOCSDIR%%/install/favicon.ico
+%%PORTDOCS%%%%DOCSDIR%%/install/garlic.gif
+%%PORTDOCS%%%%DOCSDIR%%/install/index.html
+%%PORTDOCS%%%%DOCSDIR%%/install/macosx.html
+%%PORTDOCS%%%%DOCSDIR%%/install/mol_path.html
+%%PORTDOCS%%%%DOCSDIR%%/install/octane.html
+%%PORTDOCS%%%%DOCSDIR%%/install/rs6000.html
+%%PORTDOCS%%%%DOCSDIR%%/license/favicon.ico
+%%PORTDOCS%%%%DOCSDIR%%/license/garlic.gif
+%%PORTDOCS%%%%DOCSDIR%%/license/index.html
+%%PORTDOCS%%%%DOCSDIR%%/monster.gif
+%%PORTDOCS%%%%DOCSDIR%%/mouse/.xvpics/outcomp.gif
+%%PORTDOCS%%%%DOCSDIR%%/mouse/.xvpics/outplot.gif
+%%PORTDOCS%%%%DOCSDIR%%/mouse/.xvpics/outrama.gif
+%%PORTDOCS%%%%DOCSDIR%%/mouse/.xvpics/outstr.gif
+%%PORTDOCS%%%%DOCSDIR%%/mouse/favicon.ico
+%%PORTDOCS%%%%DOCSDIR%%/mouse/garlic.gif
+%%PORTDOCS%%%%DOCSDIR%%/mouse/index.html
+%%PORTDOCS%%%%DOCSDIR%%/mouse/neighbor.gif
+%%PORTDOCS%%%%DOCSDIR%%/mouse/outcomp.gif
+%%PORTDOCS%%%%DOCSDIR%%/mouse/outplot.gif
+%%PORTDOCS%%%%DOCSDIR%%/mouse/outrama.gif
+%%PORTDOCS%%%%DOCSDIR%%/mouse/outstr.gif
+%%PORTDOCS%%%%DOCSDIR%%/options/favicon.ico
+%%PORTDOCS%%%%DOCSDIR%%/options/garlic.gif
+%%PORTDOCS%%%%DOCSDIR%%/options/index.html
+%%PORTDOCS%%%%DOCSDIR%%/precompiled_packages/garlic.gif
+%%PORTDOCS%%%%DOCSDIR%%/precompiled_packages/index.html
+%%PORTDOCS%%%%DOCSDIR%%/refcard/favicon.ico
+%%PORTDOCS%%%%DOCSDIR%%/refcard/garlic.gif
+%%PORTDOCS%%%%DOCSDIR%%/refcard/index.html
+%%PORTDOCS%%%%DOCSDIR%%/refcard/refcard.html
+%%PORTDOCS%%%%DOCSDIR%%/scripts/atoms.script
+%%PORTDOCS%%%%DOCSDIR%%/scripts/bonds.script
+%%PORTDOCS%%%%DOCSDIR%%/scripts/colors.script
+%%PORTDOCS%%%%DOCSDIR%%/scripts/favicon.ico
+%%PORTDOCS%%%%DOCSDIR%%/scripts/garlic.gif
+%%PORTDOCS%%%%DOCSDIR%%/scripts/probes.script
+%%PORTDOCS%%%%DOCSDIR%%/support/favicon.ico
+%%PORTDOCS%%%%DOCSDIR%%/support/garlic.gif
+%%PORTDOCS%%%%DOCSDIR%%/support/index.html
+%%PORTDOCS%%%%DOCSDIR%%/techinfo/favicon.ico
+%%PORTDOCS%%%%DOCSDIR%%/techinfo/garlic.gif
+%%PORTDOCS%%%%DOCSDIR%%/techinfo/index.html
+%%PORTDOCS%%%%DOCSDIR%%/tolower.script
 %%PORTDOCS%%%%DOCSDIR%%/tutorial/favicon.ico
+%%PORTDOCS%%%%DOCSDIR%%/tutorial/garlic.gif
+%%PORTDOCS%%%%DOCSDIR%%/tutorial/index.html
+%%PORTDOCS%%%%DOCSDIR%%/tutorial/lesson1.html
 %%PORTDOCS%%%%DOCSDIR%%/tutorial/lesson10.html
 %%PORTDOCS%%%%DOCSDIR%%/tutorial/lesson11.html
 %%PORTDOCS%%%%DOCSDIR%%/tutorial/lesson12.html
-%%PORTDOCS%%%%DOCSDIR%%/tutorial/index.html
-%%PORTDOCS%%%%DOCSDIR%%/tutorial/lesson1.html
 %%PORTDOCS%%%%DOCSDIR%%/tutorial/lesson2.html
 %%PORTDOCS%%%%DOCSDIR%%/tutorial/lesson3.html
 %%PORTDOCS%%%%DOCSDIR%%/tutorial/lesson4.html
@@ -225,34 +253,18 @@ share/garlic/residues.pdb
 %%PORTDOCS%%%%DOCSDIR%%/tutorial/script2.html
 %%PORTDOCS%%%%DOCSDIR%%/tutorial/script3.html
 %%PORTDOCS%%%%DOCSDIR%%/tutorial/script4.html
-%%PORTDOCS%%%%DOCSDIR%%/tutorial/garlic.gif
 %%PORTDOCS%%%%DOCSDIR%%/tutorial/window.gif
+%%PORTDOCS%%%%DOCSDIR%%/versions.html
 %%PORTDOCS%%%%DOCSDIR%%/whatis/favicon.ico
-%%PORTDOCS%%%%DOCSDIR%%/whatis/index.html
 %%PORTDOCS%%%%DOCSDIR%%/whatis/garlic.gif
-%%PORTDOCS%%%%DOCSDIR%%/competition/index.html
-%%PORTDOCS%%%%DOCSDIR%%/competition/garlic.gif
-%%PORTDOCS%%%%DOCSDIR%%/versions.html
-%%PORTDOCS%%%%DOCSDIR%%/options/favicon.ico
-%%PORTDOCS%%%%DOCSDIR%%/options/index.html
-%%PORTDOCS%%%%DOCSDIR%%/options/garlic.gif
-%%PORTDOCS%%%%DOCSDIR%%/garlic.gif
-%%PORTDOCS%%%%DOCSDIR%%/install/favicon.ico
-%%PORTDOCS%%%%DOCSDIR%%/install/macosx.html
-%%PORTDOCS%%%%DOCSDIR%%/install/index.html
-%%PORTDOCS%%%%DOCSDIR%%/install/octane.html
-%%PORTDOCS%%%%DOCSDIR%%/install/mol_path.html
-%%PORTDOCS%%%%DOCSDIR%%/install/garlic.gif
-%%PORTDOCS%%%%DOCSDIR%%/install/rs6000.html
-%%PORTDOCS%%%%DOCSDIR%%/changes/favicon.ico
-%%PORTDOCS%%%%DOCSDIR%%/changes/index.html
-%%PORTDOCS%%%%DOCSDIR%%/changes/garlic.gif
+%%PORTDOCS%%%%DOCSDIR%%/whatis/index.html
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/whatis
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorial
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/techinfo
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/support
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/scripts
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/refcard
+%%PORTDOCS%%@dirrm %%DOCSDIR%%/precompiled_packages
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/options
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/mouse/.xvpics
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/mouse
@@ -270,16 +282,23 @@ share/garlic/residues.pdb
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/changes
 %%PORTDOCS%%@dirrm %%DOCSDIR%%/bugfixes
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
+%%PORTDOCS%%%%EXAMPLESDIR%%/18-porins.script
+%%PORTDOCS%%%%EXAMPLESDIR%%/18porins.script
+%%PORTDOCS%%%%EXAMPLESDIR%%/18porins2.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/1mal.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/2fcp.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/2omf.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/2por.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/adrenalin.pdb
 %%PORTDOCS%%%%EXAMPLESDIR%%/arrow.pdb
+%%PORTDOCS%%%%EXAMPLESDIR%%/ascorbic-acid.pdb
 %%PORTDOCS%%%%EXAMPLESDIR%%/atoms.script
+%%PORTDOCS%%%%EXAMPLESDIR%%/b.script
+%%PORTDOCS%%%%EXAMPLESDIR%%/barrel.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/bonds.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/borneol.pdb
 %%PORTDOCS%%%%EXAMPLESDIR%%/box.pdb
+%%PORTDOCS%%%%EXAMPLESDIR%%/ccacaa.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/colors.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/dance.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/gallery.script
@@ -290,7 +309,6 @@ share/garlic/residues.pdb
 %%PORTDOCS%%%%EXAMPLESDIR%%/patterns2.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/patterns3.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/phe.pdb
-%%PORTDOCS%%%%EXAMPLESDIR%%/porin.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/porins.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/porins2.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/porins3.script
@@ -303,5 +321,6 @@ share/garlic/residues.pdb
 %%PORTDOCS%%%%EXAMPLESDIR%%/singlebond.pdb
 %%PORTDOCS%%%%EXAMPLESDIR%%/test.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/trp.pdb
+%%PORTDOCS%%%%EXAMPLESDIR%%/two-positive.script
 %%PORTDOCS%%%%EXAMPLESDIR%%/water.pdb
 %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%