Apply patches from Tyler Retzlaff in PR pkg/23083 to make this behave with

gcc3.  While here, update to version 2.12 (previous version was erraneously
named 2.1, when it should have been 2.10) which is the only distfile
available on the ftp site.
Changelog seems to say:
   - Fix bug on long-orfs.cc to avoid occasional array out-of-bounds
	error (detected on Mac OS X).

4 files changed, 38 insertions, 10 deletions

diff --git a/biology/glimmer/Makefile b/biology/glimmer/Makefile
index 5b9c3dbcf3f..4483ae0da18 100644
--- a/biology/glimmer/Makefile
+++ b/biology/glimmer/Makefile
@@ -1,9 +1,9 @@
-# $NetBSD: Makefile,v 1.1.1.1 2003/09/30 02:11:06 jschauma Exp $
+# $NetBSD: Makefile,v 1.2 2003/10/07 18:20:15 jschauma Exp $
 #
 
-DISTNAME=		glimmer21
-PKGNAME=		glimmer-2.1
-WRKSRC=                 ${WRKDIR}/glimmer2.10
+DISTNAME=		glimmer212
+PKGNAME=		glimmer-2.12
+WRKSRC=                 ${WRKDIR}/glimmer2.12
 CATEGORIES=		biology
 MASTER_SITES=		ftp://ftp.tigr.org/pub/software/Glimmer/
 
@@ -14,10 +14,12 @@ COMMENT=		System for finding genes in microbial DNA
 USE_BUILDLINK2=		yes
 
 do-install:
-.for PROGRAM in adjust anomaly build-icm check codon-usage compare-lists extract \
+.for PROGRAM in adjust anomaly build-icm check codon-usage compare-lists \
 	generate get-len get-putative glimmer2 long-orfs
 	${INSTALL_PROGRAM} ${WRKSRC}/${PROGRAM} ${PREFIX}/bin
 .endfor
+	# ``extract'' is also in the csound package, so rename to avoid conflict
+	${INSTALL_PROGRAM} ${WRKSRC}/extract ${PREFIX}/bin/glextract
 	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/glimmer
 	${CP} ${WRKSRC}/README ${WRKSRC}/run-glimmer2.readme
 .for DOC in run-glimmer2.readme build-icm.readme extract.readme glimmer2.readme long-orfs.readme
diff --git a/biology/glimmer/PLIST b/biology/glimmer/PLIST
index f4fde8226a4..98d3a6f5b7f 100644
--- a/biology/glimmer/PLIST
+++ b/biology/glimmer/PLIST
@@ -1,11 +1,11 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/30 02:11:06 jschauma Exp $
+@comment $NetBSD: PLIST,v 1.2 2003/10/07 18:20:15 jschauma Exp $
 bin/adjust
 bin/anomaly
 bin/build-icm
 bin/check
 bin/codon-usage
 bin/compare-lists
-bin/extract
+bin/glextract
 bin/generate
 bin/get-len
 bin/get-putative
diff --git a/biology/glimmer/distinfo b/biology/glimmer/distinfo
index 139ebb80861..cbb0bc6924c 100644
--- a/biology/glimmer/distinfo
+++ b/biology/glimmer/distinfo
@@ -1,5 +1,6 @@
-$NetBSD: distinfo,v 1.1.1.1 2003/09/30 02:11:06 jschauma Exp $
+$NetBSD: distinfo,v 1.2 2003/10/07 18:20:15 jschauma Exp $
 
-SHA1 (glimmer21.tar.gz) = 676bf2150389b4eb817ef2db7c646a332151eaf7
-Size (glimmer21.tar.gz) = 79091 bytes
+SHA1 (glimmer212.tar.gz) = f2291c3b9024c56b884d6dcab032cb36f54074f6
+Size (glimmer212.tar.gz) = 79431 bytes
 SHA1 (patch-aa) = ceb45f887c32e91bd96b9d2c8dae39c9cc6fc658
+SHA1 (patch-ab) = e2afaa9ff8e0d4a2647a77bbf7e1ba4012d53061
diff --git a/biology/glimmer/patches/patch-ab b/biology/glimmer/patches/patch-ab
new file mode 100644
index 00000000000..0ea7f46e901
--- /dev/null
+++ b/biology/glimmer/patches/patch-ab
@@ -0,0 +1,25 @@
+$NetBSD: patch-ab,v 1.1 2003/10/07 18:20:16 jschauma Exp $
+
+--- delcher.h.orig	2003-10-07 14:07:00.000000000 -0400
++++ delcher.h	2003-10-07 14:07:35.000000000 -0400
+@@ -18,9 +18,9 @@
+ 
+ #include  <stdio.h>
+ #include  <stdlib.h>
+-#include  <iostream.h>
+-#include  <iomanip.h>
+-#include  <fstream.h>
++#include  <iostream>
++#include  <iomanip>
++#include  <fstream>
+ #include  <math.h>
+ #include  <string.h>
+ #include  <ctype.h>
+@@ -31,6 +31,7 @@
+ #include  <errno.h>
+ #include  <unistd.h>
+ 
++using namespace std;
+ 
+ #define  TRUE  1
+ #define  FALSE  0