ports/73250: update biology/hmmer to 2.3.2

Choe, Cheng-Dae whitekid at gmail.com
Thu Oct 28 18:20:27 UTC 2004 

>Number:         73250
>Category:       ports
>Synopsis:       update biology/hmmer to 2.3.2
>Confidential:   no
>Severity:       non-critical
>Priority:       medium
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Thu Oct 28 18:20:04 GMT 2004
>Closed-Date:
>Last-Modified:
>Originator:     "Choe, Cheng-Dae"
>Release:        FreeBSD 5.3-STABLE i386
>Organization:
>Environment:
System: FreeBSD comdongin.com 5.3-STABLE FreeBSD 5.3-STABLE #0: Thu Oct 21 09:48:27 KST 2004 root at comdongin.com:/usr/obj/data/src/sys/CDI i386
>Description:
      update biology/hmmer to 2.3.2
>How-To-Repeat:
      N/A
>Fix:
diff -ruN hmmer.orig/Makefile hmmer/Makefile
--- hmmer.orig/Makefile	Fri Oct 29 00:59:26 2004
+++ hmmer/Makefile	Fri Oct 29 01:52:53 2004
@@ -6,24 +6,22 @@
 #
 
 PORTNAME=	hmmer
-PORTVERSION=	2.2.g
-PORTREVISION=	1
+PORTVERSION=	2.3.2
+PORTREVISION=	0
 CATEGORIES=	biology
-MASTER_SITES=	ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/${VERSIONSTRING}/
-DISTNAME=	${PORTNAME}-${VERSIONSTRING}
+MASTER_SITES=	ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/${PORTVERSION}/
+DISTNAME=	${PORTNAME}-${PORTVERSION}
 
 MAINTAINER=	wjv at FreeBSD.org
 COMMENT=	Profile hidden Markov models for biological sequence analysis
 
 GNU_CONFIGURE=	yes
 USE_PERL5=	yes
-VERSIONSTRING=	${PORTVERSION:C|\.([^.]*)$|\1|}
 
 DOCFILES=	00README COPYRIGHT NOTES Userguide.pdf
-MAN1=		afetch.1 alistat.1 hmmalign.1 hmmbuild.1 hmmcalibrate.1 \
-		hmmconvert.1 hmmemit.1 hmmer.1 hmmfetch.1 hmmindex.1 \
-		hmmpfam.1 hmmsearch.1 seqstat.1 sfetch.1 shuffle.1 \
-		sreformat.1
+
+MAN1=		hmmalign.1 hmmcalibrate.1 hmmemit.1 hmmfetch.1 hmmpfam.1 \
+		hmmbuild.1 hmmconvert.1 hmmer.1 hmmindex.1 hmmsearch.1
 
 post-install:
 .if !defined(NOPORTDOCS)
diff -ruN hmmer.orig/distinfo hmmer/distinfo
--- hmmer.orig/distinfo	Fri Oct 29 00:59:26 2004
+++ hmmer/distinfo	Fri Oct 29 01:06:00 2004
@@ -1,2 +1,2 @@
-MD5 (hmmer-2.2g.tar.gz) = d7def2007a0aaf2eafb9a96a07986b8c
-SIZE (hmmer-2.2g.tar.gz) = 931569
+MD5 (hmmer-2.3.2.tar.gz) = 5f073340c0cf761288f961a73821228a
+SIZE (hmmer-2.3.2.tar.gz) = 1024933
diff -ruN hmmer.orig/files/patch-Makefile.in hmmer/files/patch-Makefile.in
--- hmmer.orig/files/patch-Makefile.in	Fri Oct 29 00:59:26 2004
+++ hmmer/files/patch-Makefile.in	Fri Oct 29 02:55:45 2004
@@ -1,27 +1,28 @@
---- Makefile.in.orig	Mon Aug  6 01:55:36 2001
-+++ Makefile.in	Wed Aug 22 14:52:30 2001
+
+$FreeBSD$
+
+--- Makefile.in.orig
++++ Makefile.in
 @@ -34,7 +34,7 @@
  # how to install the man pages; 
  # cp is generally fine, unless you preformat your pages.
  #
 -INSTMAN   = cp
-+INSTMAN   = $(BSD_INSTALL_MAN)
++INSTMAN   = ${INSTALL}
  MANSUFFIX = 1
  
  # your compiler and compiler flags
-@@ -144,12 +144,12 @@
+@@ -109,10 +109,12 @@
  #          installs man pages in MANDIR/man1/  (e.g. if MANSUFFIX is 1)
+ #          Creates these directories if they don't exist.
  install: 
- 	for file in $(PROGS) $(SQUIDPROGS) $(PVMPROGS); do\
--	   cp binaries/$$file $(BINDIR)/;\
-+	   $(BSD_INSTALL_PROGRAM) binaries/$$file $(BINDIR)/;\
++	(cd squid; make install)
++
+ 	mkdir -p ${BINDIR}
+ 	-mkdir -p ${MANDIR}/man${MANSUFFIX}
+ 	for file in $(PROGS) $(PVMPROGS); do\
+-	   cp src/$$file $(BINDIR)/;\
++	   ${INSTALL} src/$$file $(BINDIR)/;\
  	done
--	for file in hmmer $(PROGS) $(SQUIDPROGS); do\
-+	for file in hmmer $(PROGS); do\
+ 	-for file in hmmer $(PROGS); do\
  	   $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
- 	done
--	for file in $(SQUIDPROGS); do\
-+	for file in afetch alistat seqstat sfetch shuffle sreformat; do\
- 	   $(INSTMAN) squid/Man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
- 	done
- 
diff -ruN hmmer.orig/files/patch-configure hmmer/files/patch-configure
--- hmmer.orig/files/patch-configure	Fri Oct 29 00:59:26 2004
+++ hmmer/files/patch-configure	Thu Jan  1 09:00:00 1970
@@ -1,22 +0,0 @@
---- configure.orig	Mon Aug  6 01:55:52 2001
-+++ configure	Thu Jul 11 12:38:47 2002
-@@ -1094,6 +1094,9 @@
- 
-         acx_pthread_flags="-pthread -pthreads pthread -mt $acx_pthread_flags"
-         ;;
-+        *freebsd5*)
-+	acx_pthread_flags="-lc_r -kthread lthread -pthread"
-+        ;;
- esac
- 
- if test x"$acx_pthread_ok" = xno; then
-@@ -1418,6 +1421,9 @@
-         # we'll just look for -pthreads and -lpthread first:
- 
-         acx_pthread_flags="-pthread -pthreads pthread -mt $acx_pthread_flags"
-+        ;;
-+        *freebsd5*)
-+	acx_pthread_flags="-lc_r -kthread lthread -pthread"
-         ;;
- esac
- 
diff -ruN hmmer.orig/files/patch-squid_Makefile.in hmmer/files/patch-squid_Makefile.in
--- hmmer.orig/files/patch-squid_Makefile.in	Thu Jan  1 09:00:00 1970
+++ hmmer/files/patch-squid_Makefile.in	Fri Oct 29 02:55:47 2004
@@ -0,0 +1,30 @@
+
+$FreeBSD$
+
+--- squid/Makefile.in.orig
++++ squid/Makefile.in
+@@ -177,16 +177,17 @@
+ 	test -d $(SCRIPTDIR) || mkdir -p $(SCRIPTDIR)
+ 	test -d $(INCLUDEDIR)|| mkdir -p $(INCLUDEDIR)
+ 	test -d $(MANDIR)/man$(MANSUFFIX) || mkdir -p $(MANDIR)/man$(MANSUFFIX)
+-	cp libsquid.a $(LIBDIR)/
+-	cp $(HDRS)  $(INCLUDEDIR)/
+-	cp $(POSTCONFHDRS)  $(INCLUDEDIR)/
+-	cp $(PROGS) $(BINDIR)/
++	${INSTALL} libsquid.a $(LIBDIR)/
++	${INSTALL} $(HDRS)  $(INCLUDEDIR)/
++	${INSTALL} $(POSTCONFHDRS)  $(INCLUDEDIR)/
++	${INSTALL} $(PROGS) $(BINDIR)/
++# Hmmer packages has no script and manpages
+ #	for scriptfile in $(SCRIPTS); do\
+ #	  cp Scripts/$$scriptfile $(SCRIPTDIR)/;\
+ #	done
+-	@for manpage in $(MANS); do\
+-	  $(INSTMAN) Man/$$manpage.man $(MANDIR)/man$(MANSUFFIX)/$$manpage.$(MANSUFFIX);\
+-	done
++#	@for manpage in $(MANS); do\
++#	  $(INSTMAN) Man/$$manpage.man $(MANDIR)/man$(MANSUFFIX)/$$manpage.$(MANSUFFIX);\
++#	done
+ 
+ uninstall:
+ 	rm $(LIBDIR)/libsquid.a
diff -ruN hmmer.orig/pkg-plist hmmer/pkg-plist
--- hmmer.orig/pkg-plist	Fri Oct 29 00:59:26 2004
+++ hmmer/pkg-plist	Fri Oct 29 02:30:08 2004
@@ -1,5 +1,7 @@
 bin/afetch
 bin/alistat
+bin/compalign
+bin/compstruct
 bin/hmmalign
 bin/hmmbuild
 bin/hmmcalibrate
@@ -9,11 +11,27 @@
 bin/hmmindex
 bin/hmmpfam
 bin/hmmsearch
+bin/revcomp
+bin/seqsplit
 bin/seqstat
 bin/sfetch
 bin/shuffle
 bin/sindex
 bin/sreformat
+bin/translate
+bin/weight
+include/gki.h
+include/gsi.h
+include/msa.h
+include/rk.h
+include/sqfuncs.h
+include/squid.h
+include/squidconf.h
+include/sre_random.h
+include/ssi.h
+include/stopwatch.h
+include/vectorops.h
+lib/libsquid.a
 %%PORTDOCS%%%%DOCSDIR%%/00README
 %%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
 %%PORTDOCS%%%%DOCSDIR%%/NOTES

>Release-Note:
>Audit-Trail:
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