Date: Thu, 28 Oct 2004 18:15:52 GMT From: "Choe, Cheng-Dae" <whitekid@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/73250: update biology/hmmer to 2.3.2 Message-ID: <200410281815.i9SIFqee043372@www.freebsd.org> Resent-Message-ID: <200410281820.i9SIK51g096281@freefall.freebsd.org>
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>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@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@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:
>Unformatted:
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