Date: Wed, 19 Apr 2006 14:35:44 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/96063: [maintainer update] update biology/fasta3 Message-ID: <200604191735.k3JHZijt058323@omega.iib.unsam.edu.ar> Resent-Message-ID: <200604191740.k3JHeQ31075723@freefall.freebsd.org>
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>Number: 96063
>Category: ports
>Synopsis: [maintainer update] update biology/fasta3
>Confidential: no
>Severity: serious
>Priority: medium
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Wed Apr 19 17:40:24 GMT 2006
>Closed-Date:
>Last-Modified:
>Originator: Fernan Aguero
>Release: FreeBSD 6.0-RELEASE-p4 i386
>Organization:
IIB-UNSAM
>Environment:
System: FreeBSD omega.iib.unsam.edu.ar 6.0-RELEASE-p4 FreeBSD 6.0-RELEASE-p4 #0: Wed Jan 25 12:43:39 ART 2006 fernan@omega.iib.unsam.edu.ar:/usr/obj/usr/src/sys/OMEGA i386
>Description:
A new release of fasta3 is available, and apparently the
previous distfile has been removed from the MASTER_SITE,
making the port unfetchable.
The new release removed the top-level Makefile to force users to
use the corresponding Makefile for their OS.
I've generated a Makefile.freebsd for building fasta3. It is
included now in FILESDIR and has been sent to the author for
future inclusion in the fasta3 distribution. Whenever that
happens, it will be removed from FILESDIR.
The Makefile.freebsd can be used to build fasta3 standalone
(outside the ports system) or from ports (variable assignment is
done carefully to respect those already defined)
As a side note, I've been unable to get ${UNAME} to work and
have to use the absolute path to the executable insted.
>How-To-Repeat:
>Fix:
--- fasta3.diff begins here ---
diff -ruN /usr/ports/biology/fasta3/Makefile fasta3/Makefile
--- /usr/ports/biology/fasta3/Makefile Tue Mar 28 13:52:33 2006
+++ fasta3/Makefile Wed Apr 19 14:25:37 2006
@@ -7,7 +7,7 @@
#
PORTNAME= fasta3
-PORTVERSION= 34.t25.d5
+PORTVERSION= 34.t25.d6
CATEGORIES= biology
MASTER_SITES= ftp://ftp.virginia.edu/pub/fasta/
DISTNAME= fasta${PORTVERSION:S/.//g}
@@ -19,8 +19,13 @@
NO_CDROM= "May not be sold or incorporated into a commercial product"
WRKSRC= ${WRKDIR}/${PORTNAME}
SUB_FILES= pkg-message
+MAKEFILE= Makefile.freebsd
-MAKE_ENV+= THR_LIBS=${PTHREAD_LIBS}
+XDIR= ${PREFIX}/bin
+FASTA_HOST!= /usr/bin/uname -n
+
+MAKE_ENV+= THR_LIBS=${PTHREAD_LIBS} XDIR=${XDIR} \
+ FASTA_HOST='"${FASTA_HOST}"'
FASTA3_DOCS= README COPYRIGHT FASTA_LIST fasta3x.me fasta3x.doc \
fasta20.doc fasta_func.doc readme.* fasta.defaults
@@ -38,6 +43,9 @@
@ for file in ${EXTRACT_ONLY}; do \
cd ${WRKSRC} && (${GZCAT} ${DISTDIR}/$${file} | ${SH} >/dev/null); \
done
+
+post-extract:
+ @ cp ${FILESDIR}/Makefile.freebsd ${WRKSRC}
post-install:
${INSTALL_DATA} ${WRKSRC}/fastlibs ${PREFIX}/etc/fastlibs.sample
diff -ruN /usr/ports/biology/fasta3/distinfo fasta3/distinfo
--- /usr/ports/biology/fasta3/distinfo Tue Mar 28 13:52:33 2006
+++ fasta3/distinfo Sun Apr 16 21:19:34 2006
@@ -1,3 +1,3 @@
-MD5 (fasta34t25d5.shar.Z) = 500a449fe3eeebbeb3e7f53f652505c7
-SHA256 (fasta34t25d5.shar.Z) = bcb7c25b6e3d883cc4c61c35b94b4dc42c49a158859cfefbf6a3f9357c0e7482
-SIZE (fasta34t25d5.shar.Z) = 795675
+MD5 (fasta34t25d6.shar.Z) = 462419371d55afd787043d2104c461cc
+SHA256 (fasta34t25d6.shar.Z) = 409abdf657931cb07ea2ae38587d9387d418436662f1c1b889a3829302656449
+SIZE (fasta34t25d6.shar.Z) = 798483
diff -ruN /usr/ports/biology/fasta3/files/Makefile.freebsd fasta3/files/Makefile.freebsd
--- /usr/ports/biology/fasta3/files/Makefile.freebsd Wed Dec 31 21:00:00 1969
+++ fasta3/files/Makefile.freebsd Wed Apr 19 13:44:50 2006
@@ -0,0 +1,67 @@
+#
+# Makefile for building fasta3 on FreeBSD
+#
+# Fernan Aguero - <fernan@iib.unsam.edu.ar>
+
+# we take care of doing variable assignment using the '?=' and '+='
+# operators to preserve the value of variables if they are already
+# defined. In FreeBSD this happens when fasta3 is build from the port or
+# when the user has set these variables -- most notably CC and/or CFLAGS
+# -- in /etc/make.conf
+
+# Compiler executable, and optional flags
+CC?= gcc
+CFLAGS?= -g -O2
+
+# your FASTA host
+FASTA_HOST?= "your_fasta_host"
+
+# common CFLAGS. These are the set of CFLAGS that are always used
+COMMON_CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -c -DMAX_WORKERS=2 \
+ -DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT \
+ -D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO \
+ -DHAS_INTTYPES -DSAMP_STATS
+
+# standard options, these will be added to the common CFLAGS if
+# selected below
+STANDARD_CFLAGS= -DSFCHAR="':'" -DFASTA_HOST='${FASTA_HOST}' \
+ -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DPGM_DOC
+
+# options for superfamily validations, these will be added to the common
+# CFLAGS if selected below
+SUPERFAMILY_CFLAGS= -DSFCHAR="'|'" -DSUPERFAMNUM -DBIG_LIB64
+
+# here we define CFLAGS to be the sum of common flags plus a subset of
+# optional flags that define our intended use.
+# The default standard flags are selected by default, although the user
+# can override this if s/he wants
+CFLAGS+= ${COMMON_CFLAGS} ${STANDARD_CFLAGS}
+
+XDIR?= /usr/local/bin
+
+LIB_M+= -lm
+
+HFLAGS+= -o
+NFLAGS+= -o
+
+
+
+# FreeBSD users BEWARE! Different threading models ahead!
+
+# The threading model has changed along the way from FreeBSD-4 to
+# FreeBSD-6. If you're building fasta3 on your own, you will need to
+# adjust this accordingly. The default works in FreeBSD-6x (currently
+# the recommended major version for use in production). Or better yet,
+# use the biology/fasta3 port from the ports collection, which will use
+# the correct threading library for your OSVERSION
+
+THR_SUBS?= pthr_subs2
+THR_LIBS?= -lpthread
+THR_CC?=
+
+DROPNFA_O = drop_nfa.o
+DROPGSW_O = dropgsw.o
+DROPRSS_O = dropnsw.o
+DROPTFA_O = drop_tfa.o
+
+include Makefile34m.common
diff -ruN /usr/ports/biology/fasta3/files/patch-Makefile fasta3/files/patch-Makefile
--- /usr/ports/biology/fasta3/files/patch-Makefile Wed Mar 1 20:11:41 2006
+++ fasta3/files/patch-Makefile Wed Dec 31 21:00:00 1969
@@ -1,33 +0,0 @@
---- Makefile.orig Thu Feb 9 12:03:37 2006
-+++ Makefile Thu Feb 9 12:07:21 2006
-@@ -7,7 +7,7 @@
- # in dropnfa.c (wrp 3/19/1998)
- #
-
--CC= gcc -g -O3
-+#CC= gcc -g -O3
- #CC=gcc -Wall -pedantic -ansi -g -O
- #CC = gcc -g -DDEBUG
- #CC= /opt/parasoft/bin.linux2/insure -g -pg -DDEBUG
-@@ -21,7 +21,7 @@
- #CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="'|'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DSUPERFAMNUM -DUSE_MMAP -D_REENTRANT -DBIG_LIB64 -D_LARGE_FILE_SOURCE -DUSE_FSEEKO -D_FILE_OFFSET_BITS=64 -DHAS_INTTYPES -DSAMP_STATS
-
- # standard options
--CFLAGS= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"wrpx00.bioch.virginia.edu/fasta/cgi"' -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
-+CFLAGS+= -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DSFCHAR="':'" -c -DMAX_WORKERS=2 -DTHR_EXIT=pthread_exit -DPROGRESS -DFASTA_HOST='"wrpx00.bioch.virginia.edu/fasta/cgi"' -DUSE_MMAP -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC
- # -I/usr/local/include/mysql -DMYSQL_DB
- #
- #(for mySQL databases) (also requires change to Makefile34.common)
-@@ -35,10 +35,10 @@
-
- # for Linux
- THR_SUBS = pthr_subs2
--THR_LIBS = -lpthread
-+#THR_LIBS = -lpthread
- THR_CC =
-
--XDIR = /seqprg/bin
-+XDIR = ${PREFIX}/bin
-
- DROPNFA_O = drop_nfa.o
- DROPGSW_O = dropgsw.o
--- fasta3.diff ends here ---
>Release-Note:
>Audit-Trail:
>Unformatted:
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