- Update to 34.t25.d6

PR:		ports/96063
Submitted by:	maintainer

4 files changed, 80 insertions, 38 deletions

diff --git a/biology/fasta3/Makefile b/biology/fasta3/Makefile
index 9b1eeef3ae98..f15f6141aaac 100644
--- a/biology/fasta3/Makefile
+++ b/biology/fasta3/Makefile
@@ -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 @@ COMMENT=	A collection of programs for searching DNA and protein databases
 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
@@ -39,6 +44,9 @@ do-extract:
 	  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
 	@ ${MKDIR} ${DATADIR}
diff --git a/biology/fasta3/distinfo b/biology/fasta3/distinfo
index c277112983b1..59552fe2f1bd 100644
--- a/biology/fasta3/distinfo
+++ b/biology/fasta3/distinfo
@@ -1,3 +1,3 @@
-MD5 (fasta34t25d5.shar.Z) = 500a449fe3eeebbeb3e7f53f652505c7
-SHA256 (fasta34t25d5.shar.Z) = bcb7c25b6e3d883cc4c61c35b94b4dc42c49a158859cfefbf6a3f9357c0e7482
-SIZE (fasta34t25d5.shar.Z) = 795675
+MD5 (fasta34t25d6.shar.Z) = 462419371d55afd787043d2104c461cc
+SHA256 (fasta34t25d6.shar.Z) = 409abdf657931cb07ea2ae38587d9387d418436662f1c1b889a3829302656449
+SIZE (fasta34t25d6.shar.Z) = 798483
diff --git a/biology/fasta3/files/Makefile.freebsd b/biology/fasta3/files/Makefile.freebsd
new file mode 100644
index 000000000000..5bd489001187
--- /dev/null
+++ b/biology/fasta3/files/Makefile.freebsd
@@ -0,0 +1,67 @@
+#
+# Makefile for building fasta3 on FreeBSD
+#
+# Fernan Aguero - <fernan@iib.unsam.edu.ar>
+
+# we take care of doing variable assignment using the '?=' and '+='
+# operators to preserve the value of variables if they are already
+# defined. In FreeBSD this happens when fasta3 is build from the port or
+# when the user has set these variables -- most notably CC and/or CFLAGS
+# -- in /etc/make.conf
+
+# Compiler executable, and optional flags
+CC?=		gcc
+CFLAGS?=	-g -O2
+
+# your FASTA host
+FASTA_HOST?=	"your_fasta_host"
+
+# common CFLAGS. These are the set of CFLAGS that are always used
+COMMON_CFLAGS=	-DSHOWSIM -DUNIX -DTIMES -DHZ=100 -c -DMAX_WORKERS=2 \
+		-DTHR_EXIT=pthread_exit -DPROGRESS -DUSE_MMAP -D_REENTRANT \
+		-D_LARGE_FILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO \
+		-DHAS_INTTYPES -DSAMP_STATS
+
+# standard options, these will be added to the common CFLAGS if
+# selected below
+STANDARD_CFLAGS=	-DSFCHAR="':'" -DFASTA_HOST='${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 --git a/biology/fasta3/files/patch-Makefile b/biology/fasta3/files/patch-Makefile
deleted file mode 100644
index 60b18c9b84a0..000000000000
--- a/biology/fasta3/files/patch-Makefile
+++ /dev/null
@@ -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