[pkgsrc/trunk]: pkgsrc/biology/glimmer Apply patches from Tyler Retzlaff in P...

[jschauma <jschauma%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/1279a235cf3f
branches:  trunk
changeset: 462649:1279a235cf3f
user:      jschauma <jschauma%pkgsrc.org@localhost>
date:      Tue Oct 07 18:20:15 2003 +0000

description:
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).

diffstat:

 biology/glimmer/Makefile         |  12 +++++++-----
 biology/glimmer/PLIST            |   4 ++--
 biology/glimmer/distinfo         |   7 ++++---
 biology/glimmer/patches/patch-ab |  25 +++++++++++++++++++++++++
 4 files changed, 38 insertions(+), 10 deletions(-)

diffs (90 lines):

diff -r 7d30e4aedff1 -r 1279a235cf3f biology/glimmer/Makefile
--- a/biology/glimmer/Makefile  Tue Oct 07 17:50:37 2003 +0000
+++ b/biology/glimmer/Makefile  Tue Oct 07 18:20:15 2003 +0000
@@ -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 @@
 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 -r 7d30e4aedff1 -r 1279a235cf3f biology/glimmer/PLIST
--- a/biology/glimmer/PLIST     Tue Oct 07 17:50:37 2003 +0000
+++ b/biology/glimmer/PLIST     Tue Oct 07 18:20:15 2003 +0000
@@ -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 -r 7d30e4aedff1 -r 1279a235cf3f biology/glimmer/distinfo
--- a/biology/glimmer/distinfo  Tue Oct 07 17:50:37 2003 +0000
+++ b/biology/glimmer/distinfo  Tue Oct 07 18:20:15 2003 +0000
@@ -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 -r 7d30e4aedff1 -r 1279a235cf3f biology/glimmer/patches/patch-ab
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/glimmer/patches/patch-ab  Tue Oct 07 18:20:15 2003 +0000
@@ -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