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authorjschauma <jschauma@pkgsrc.org>2003-10-07 18:20:15 +0000
committerjschauma <jschauma@pkgsrc.org>2003-10-07 18:20:15 +0000
commit7e5f7ad7b81c3c5cb0a1c1ccff9e2b7b351e87f1 (patch)
tree53596c562f40eb9496118c11bb7954db97fafe46 /biology
parentfe1458e85e62ec356b3f14da9de26741822782a2 (diff)
downloadpkgsrc-7e5f7ad7b81c3c5cb0a1c1ccff9e2b7b351e87f1.tar.gz
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 (limited to 'biology')
-rw-r--r--biology/glimmer/Makefile12
-rw-r--r--biology/glimmer/PLIST4
-rw-r--r--biology/glimmer/distinfo7
-rw-r--r--biology/glimmer/patches/patch-ab25
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