diff options
| author | jschauma <jschauma@pkgsrc.org> | 2003-10-07 18:20:15 +0000 |
|---|---|---|
| committer | jschauma <jschauma@pkgsrc.org> | 2003-10-07 18:20:15 +0000 |
| commit | 7e5f7ad7b81c3c5cb0a1c1ccff9e2b7b351e87f1 (patch) | |
| tree | 53596c562f40eb9496118c11bb7954db97fafe46 /biology/glimmer | |
| parent | fe1458e85e62ec356b3f14da9de26741822782a2 (diff) | |
| download | pkgsrc-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/glimmer')
| -rw-r--r-- | biology/glimmer/Makefile | 12 | ||||
| -rw-r--r-- | biology/glimmer/PLIST | 4 | ||||
| -rw-r--r-- | biology/glimmer/distinfo | 7 | ||||
| -rw-r--r-- | biology/glimmer/patches/patch-ab | 25 |
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 |