ports/97310: [maintainer-update] update biology/fasta3

[Fernan Aguero]

The following reply was made to PR ports/97310; it has been noted by GNATS.

From: Fernan Aguero <fernan at iib.unsam.edu.ar>
To: Sergey Matveychuk <sem at FreeBSD.org>
Cc: bug-followup at FreeBSD.org
Subject: Re: ports/97310: [maintainer-update] update biology/fasta3
Date: Tue, 16 May 2006 10:25:39 -0300

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 +----[ Sergey Matveychuk <sem at FreeBSD.org> (16.May.2006 04:04):
 |
 | fetch: ftp://ftp.virginia.edu/pub/fasta/fasta34t25d7.shar.Z: size
 | mismatch: expected 812709, actual 811798
 | 
 | -- 
 | Sem.
 |
 +----]
 
 Seems like they re-rolled the distfile yesterday ...
 attached is a new diff.
 
 Fernan
 
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 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 ${PREFIX}/etc/fastlibs.sample
 diff -ruN /usr/ports/biology/fasta3/distinfo fasta3/distinfo
 --- /usr/ports/biology/fasta3/distinfo	Wed May 10 14:31:51 2006
 +++ fasta3/distinfo	Tue May 16 10:13:39 2006
 @@ -1,3 +1,3 @@
 -MD5 (fasta34t25d6.shar.Z) = 462419371d55afd787043d2104c461cc
 -SHA256 (fasta34t25d6.shar.Z) = 409abdf657931cb07ea2ae38587d9387d418436662f1c1b889a3829302656449
 -SIZE (fasta34t25d6.shar.Z) = 798483
 +MD5 (fasta34t25d7.shar.Z) = e809d321f2577c02550a4e0364a92494
 +SHA256 (fasta34t25d7.shar.Z) = 94545124dfdb5f590bdb38da62d074db8b5696ab6e0ccbe5e0e821d1894c88fe
 +SIZE (fasta34t25d7.shar.Z) = 811798
 diff -ruN /usr/ports/biology/fasta3/files/Makefile.freebsd fasta3/files/Makefile.freebsd
 --- /usr/ports/biology/fasta3/files/Makefile.freebsd	Sun May  7 13:52:33 2006
 +++ fasta3/files/Makefile.freebsd	Wed Dec 31 21:00:00 1969
 @@ -1,67 +0,0 @@
 -#
 -# Makefile for building fasta3 on FreeBSD
 -#
 -# Fernan Aguero - <fernan at iib.unsam.edu.ar>
 -
 -# we take care of doing variable assignment using the '?=' and '+='
 -# operators to preserve the value of variables if they are already
 -# defined. In FreeBSD this happens when fasta3 is build from the port or
 -# when the user has set these variables -- most notably CC and/or CFLAGS
 -# -- in /etc/make.conf
 -
 -# Compiler executable, and optional flags
 -CC?=		gcc
 -CFLAGS?=	-g -O2
 -
 -# your FASTA host
 -FASTA_HOST?=	"your_fasta_host"
 -
 -# common CFLAGS. These are the set of CFLAGS that are always used
 -COMMON_CFLAGS=	-DSHOWSIM -DUNIX -DTIMES -DHZ=100 -c -DMAX_WORKERS=2 \
 -		-DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT \
 -		-D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO \
 -		-DHAS_INTTYPES -DSAMP_STATS
 -
 -# standard options, these will be added to the common CFLAGS if
 -# selected below
 -STANDARD_CFLAGS=	-DSFCHAR="':'" -DFASTA_HOST='${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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