Attachment 65716 Details for Bug 97310 – fasta3.diff

[patch] fasta3.diff

fasta3.diff (text/plain), 3.59 KB, created by Fernan Aguero on 2006-05-15 18:10:15 UTC

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Creator: Fernan Aguero

Created: 2006-05-15 18:10:15 UTC

Size: 3.59 KB

patch

obsolete

>diff -ruN /usr/ports/biology/fasta3/Makefile fasta3/Makefile
>--- /usr/ports/biology/fasta3/Makefile	Wed May 10 14:31:51 2006
>+++ fasta3/Makefile	Mon May 15 13:17:30 2006
>@@ -7,7 +7,7 @@
> #
> 
> PORTNAME=	fasta3
>-PORTVERSION=	34.t25.d6
>+PORTVERSION=	34.t25.d7
> CATEGORIES=	biology
> MASTER_SITES=	ftp://ftp.virginia.edu/pub/fasta/
> DISTNAME=	fasta${PORTVERSION:S/.//g}
>@@ -43,9 +43,6 @@
> 	@ 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 ${PREFIX}/etc/fastlibs.sample
>diff -ruN /usr/ports/biology/fasta3/distinfo fasta3/distinfo
>--- /usr/ports/biology/fasta3/distinfo	Wed May 10 14:31:51 2006
>+++ fasta3/distinfo	Mon May 15 13:12:07 2006
>@@ -1,3 +1,3 @@
>-MD5 (fasta34t25d6.shar.Z) = 462419371d55afd787043d2104c461cc
>-SHA256 (fasta34t25d6.shar.Z) = 409abdf657931cb07ea2ae38587d9387d418436662f1c1b889a3829302656449
>-SIZE (fasta34t25d6.shar.Z) = 798483
>+MD5 (fasta34t25d7.shar.Z) = 9361050336f7b20cace9b65f14eb8f68
>+SHA256 (fasta34t25d7.shar.Z) = c5d813760bc9cad91388a3bebf4fd12ced23caf39fd600cb14dedf3a1edd09ae
>+SIZE (fasta34t25d7.shar.Z) = 812709
>diff -ruN /usr/ports/biology/fasta3/files/Makefile.freebsd fasta3/files/Makefile.freebsd
>--- /usr/ports/biology/fasta3/files/Makefile.freebsd	Sun May  7 13:52:33 2006
>+++ fasta3/files/Makefile.freebsd	Wed Dec 31 21:00:00 1969
>@@ -1,67 +0,0 @@
>-#
>-# Makefile for building fasta3 on FreeBSD
>-#
>-# Fernan Aguero - <fernan@iib.unsam.edu.ar>
>-
>-# we take care of doing variable assignment using the '?=' and '+='
>-# operators to preserve the value of variables if they are already
>-# defined. In FreeBSD this happens when fasta3 is build from the port or
>-# when the user has set these variables -- most notably CC and/or CFLAGS
>-# -- in /etc/make.conf
>-
>-# Compiler executable, and optional flags
>-CC?=		gcc
>-CFLAGS?=	-g -O2
>-
>-# your FASTA host
>-FASTA_HOST?=	"your_fasta_host"
>-
>-# common CFLAGS. These are the set of CFLAGS that are always used
>-COMMON_CFLAGS=	-DSHOWSIM -DUNIX -DTIMES -DHZ=100 -c -DMAX_WORKERS=2 \
>-		-DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT \
>-		-D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO \
>-		-DHAS_INTTYPES -DSAMP_STATS
>-
>-# standard options, these will be added to the common CFLAGS if
>-# selected below
>-STANDARD_CFLAGS=	-DSFCHAR="':'" -DFASTA_HOST='${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

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