ports/154267: [maintainer-update] upgrade biology/fasta3 to v36, fix fetch issue
Fernan Aguero
fernan.aguero at gmail.com
Mon Jan 24 15:30:14 UTC 2011
>Number: 154267
>Category: ports
>Synopsis: [maintainer-update] upgrade biology/fasta3 to v36, fix fetch issue
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Mon Jan 24 15:30:13 UTC 2011
>Closed-Date:
>Last-Modified:
>Originator: Fernan Aguero
>Release: FreeBSD 6.3-RELEASE-p1 i386
>Organization:
IIB-UNSAM
>Environment:
FreeBSD gama.iib.unsam.edu.ar 6.3-RELEASE-p1 FreeBSD 6.3-RELEASE-p1 #0:
Wed Apr 2 18:37:14 ART 2008
fernan at gama.iib.unsam.edu.ar:/usr/obj/freebsd/freebsd-6.3/src/sys/GAMA
i386
<machine, os, target, libraries (multiple lines)>
>Description:
<precise description of the problem (multiple lines)>
FASTA is reportedly broken, as the old distfiles have been
removed from upstream sources.
http://pointyhat-west.isc.freebsd.org/errorlogs/amd64-errorlogs/a.7.4-release.20110113192327.pointyhat-west/fasta3-35.4.9.log
Upgrade FASTA to latest v.36, and fix the fetch issue
>How-To-Repeat:
<code/input/activities to reproduce the problem (multiple lines)>
>Fix:
<how to correct or work around the problem, if known (multiple lines)>
--- fasta3.diff begins here ---
diff --exclude CVS -u /usr/ports/biology/fasta3/Makefile fasta3/Makefile
--- /usr/ports/biology/fasta3/Makefile 2009-08-23 12:47:37.000000000 -0300
+++ fasta3/Makefile 2011-01-21 18:15:44.000000000 -0300
@@ -7,9 +7,9 @@
#
PORTNAME= fasta3
-PORTVERSION= 35.4.9
+PORTVERSION= 36.3.2
CATEGORIES= biology
-MASTER_SITES= http://faculty.virginia.edu/wrpearson/fasta/fasta3/
+MASTER_SITES= http://faculty.virginia.edu/wrpearson/fasta/fasta36/
DISTNAME= fasta-${PORTVERSION}
MAINTAINER= fernan at iib.unsam.edu.ar
@@ -34,12 +34,12 @@
DATA= data/*.mat
EXAMPLES= seq/*.aa seq/*.lc seq/*.seq seq/*.lib
-MAN1= fasta35.1 map_db.1 ps_lav.1 pvcomp.1
-MLINKS= fasta35.1 tfasta35.1 fasta35.1 fastx35.1 fasta35.1 tfastx35.1 \
- fasta35.1 fasty35.1 fasta35.1 tfasty35.1 fasta35.1 ssearch35.1 \
- fasta35.1 fastf35.1 fasta35.1 fasts35.1 fasta35.1 tfasts35.1 \
- fasta35.1 fastm35.1 fasta35.1 tfastf35.1 fasta35.1 ggsearch35.1 \
- fasta35.1 lalign35.1 fasta35.1 prss35.1 fasta35.1 prfx35.1
+MAN1= fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1
+MLINKS= fasta36.1 tfasta35.1 fasta36.1 fastx35.1 fasta36.1 tfastx35.1 \
+ fasta36.1 fasty35.1 fasta36.1 tfasty35.1 fasta36.1 ssearch35.1 \
+ fasta36.1 fastf35.1 fasta36.1 fasts35.1 fasta36.1 tfasts35.1 \
+ fasta36.1 fastm35.1 fasta36.1 tfastf35.1 fasta36.1 ggsearch35.1 \
+ fasta36.1 lalign35.1 fasta36.1 prss35.1 fasta36.1 prfx35.1
PLIST_SUB= VER=${PORTVERSION:R:R}
post-patch:
diff --exclude CVS -u /usr/ports/biology/fasta3/distinfo fasta3/distinfo
--- /usr/ports/biology/fasta3/distinfo 2009-08-23 12:47:37.000000000 -0300
+++ fasta3/distinfo 2011-01-21 18:03:08.000000000 -0300
@@ -1,3 +1,2 @@
-MD5 (fasta-35.4.9.tar.gz) = 6bf19b771f2c64287b7713864b9f0a69
-SHA256 (fasta-35.4.9.tar.gz) =
4beaed42557572a1c8e5480e93641af175fa43c545f75c4bf06db62dced6bd39
-SIZE (fasta-35.4.9.tar.gz) = 630748
+SHA256 (fasta-36.3.2.tar.gz) =
1eddb7dac3a52311d43bac854b2153c13aa23cbb163952c9e385a75aa2b9e446
+SIZE (fasta-36.3.2.tar.gz) = 711876
Common subdirectories: /usr/ports/biology/fasta3/files and fasta3/files
diff --exclude CVS -u /usr/ports/biology/fasta3/pkg-plist fasta3/pkg-plist
--- /usr/ports/biology/fasta3/pkg-plist 2009-06-09 04:53:37.000000000 -0300
+++ fasta3/pkg-plist 2011-01-21 18:26:39.000000000 -0300
@@ -17,7 +17,6 @@
bin/lalign%%VER%%
bin/lav2ps
bin/lav2svg
-bin/list_db
bin/map_db
bin/ssearch%%VER%%
bin/ssearch%%VER%%_t
@@ -39,10 +38,6 @@
%%PORTDOCS%%%%DOCSDIR%%/fasta3x.doc
%%PORTDOCS%%%%DOCSDIR%%/fasta20.doc
%%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc
-%%PORTDOCS%%%%DOCSDIR%%/readme.mpi_3.3
-%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.2
-%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.3
-%%PORTDOCS%%%%DOCSDIR%%/readme.pvm_3.4
%%PORTDOCS%%%%DOCSDIR%%/readme.v30
%%PORTDOCS%%%%DOCSDIR%%/readme.v30t6
%%PORTDOCS%%%%DOCSDIR%%/readme.v30t7
@@ -52,12 +47,14 @@
%%PORTDOCS%%%%DOCSDIR%%/readme.v33t0
%%PORTDOCS%%%%DOCSDIR%%/readme.v34t0
%%PORTDOCS%%%%DOCSDIR%%/readme.v35
+%%PORTDOCS%%%%DOCSDIR%%/readme.v36
%%PORTDOCS%%%%DOCSDIR%%/readme.w32
%%PORTDOCS%%%%DOCSDIR%%/fasta.defaults
%%PORTDOCS%%%%DOCSDIR%%/fasta.options
%%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html
%%PORTDOCS%%%%DOCSDIR%%/changes_v34.html
%%PORTDOCS%%%%DOCSDIR%%/changes_v35.html
+%%PORTDOCS%%%%DOCSDIR%%/changes_v36.html
%%EXAMPLESDIR%%/egmsmg.aa
%%EXAMPLESDIR%%/gstt1_drome.aa
%%EXAMPLESDIR%%/gtm1_human.aa
@@ -95,6 +92,7 @@
%%EXAMPLESDIR%%/hsgstm1b.seq
%%EXAMPLESDIR%%/humgstd.seq
%%EXAMPLESDIR%%/mgstm1.seq
+%%EXAMPLESDIR%%/mgstm1_genclone.seq
%%EXAMPLESDIR%%/mgtt2_x.seq
%%EXAMPLESDIR%%/titin_hum.seq
%%EXAMPLESDIR%%/mu.lib
--- fasta3.diff ends here ---
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>Release-Note:
>Audit-Trail:
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