Import of pkgsrc-2014Q1
This commit is contained in:
@@ -1,13 +1,16 @@
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# $NetBSD: Makefile,v 1.13 2012/09/11 20:32:12 asau Exp $
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# $NetBSD: Makefile,v 1.14 2013/07/21 15:58:51 wen Exp $
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#
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DISTNAME= hmmer-2.3.2
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DISTNAME= hmmer-3.0
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CATEGORIES= biology
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MASTER_SITES= ${MASTER_SITE_GENTOO:=distfiles/}
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MASTER_SITES= ${MASTER_SITE_GENTOO:=distfiles/} \
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http://selab.janelia.org/software/hmmer3/3.0/ \
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ftp://selab.janelia.org/pub/software/hmmer3/3.0/
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MAINTAINER= hdp@cs.nmsu.edu
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HOMEPAGE= http://hmmer.janelia.org/
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COMMENT= Implementation of profile HMM software for protein sequence analysis
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LICENSE= gnu-gpl-v3
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PKG_INSTALLATION_TYPES= overwrite pkgviews
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@@ -1,20 +1,13 @@
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@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/26 03:52:47 jschauma Exp $
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@comment $NetBSD: PLIST,v 1.2 2013/07/21 15:58:51 wen Exp $
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bin/hmmalign
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bin/hmmbuild
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bin/hmmcalibrate
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bin/hmmconvert
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bin/hmmemit
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bin/hmmfetch
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bin/hmmindex
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bin/hmmpfam
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bin/hmmpress
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bin/hmmscan
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bin/hmmsearch
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man/man1/hmmalign.1
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man/man1/hmmbuild.1
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man/man1/hmmcalibrate.1
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man/man1/hmmconvert.1
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man/man1/hmmemit.1
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man/man1/hmmer.1
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man/man1/hmmfetch.1
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man/man1/hmmindex.1
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man/man1/hmmpfam.1
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man/man1/hmmsearch.1
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bin/hmmsim
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bin/hmmstat
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bin/jackhmmer
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bin/phmmer
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@@ -1,6 +1,6 @@
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$NetBSD: distinfo,v 1.6 2009/07/16 14:53:19 joerg Exp $
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$NetBSD: distinfo,v 1.7 2013/07/21 15:58:51 wen Exp $
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SHA1 (hmmer-2.3.2.tar.gz) = aa34cb97cbc43ff3bd92dd111ba5677298fe2d40
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RMD160 (hmmer-2.3.2.tar.gz) = 4bf25fc71f332849c76b0a05bca24e88241cee67
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Size (hmmer-2.3.2.tar.gz) = 1024933 bytes
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SHA1 (patch-aa) = 1d5eae739096ec6398e7cd71b92019d76a677d50
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SHA1 (hmmer-3.0.tar.gz) = 77803c0bdb3ab07b7051a4c68c0564de31940c6d
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RMD160 (hmmer-3.0.tar.gz) = 681967fd0d2c0104ca9e080688d9652a187a8b45
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Size (hmmer-3.0.tar.gz) = 3952015 bytes
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SHA1 (patch-aa) = 8d0d3be4401590c20d102b7e0ebadcb1b6c03066
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@@ -1,63 +1,28 @@
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$NetBSD: patch-aa,v 1.4 2009/07/08 15:20:04 joerg Exp $
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--- Makefile.in.orig 2003-10-04 21:01:16.000000000 +0200
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$NetBSD: patch-aa,v 1.5 2013/07/21 15:58:51 wen Exp $
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replace "mkdir -p" with ${MKDIR}
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--- Makefile.in.orig 2013-07-21 23:25:33.000000000 +0000
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+++ Makefile.in
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@@ -30,11 +30,12 @@ prefix = @prefix@
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exec_prefix = @exec_prefix@
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BINDIR = @bindir@
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MANDIR = @mandir@
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+INSTBIN = ${BSD_INSTALL_PROGRAM}
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@@ -51,7 +51,7 @@ CPPFLAGS = @CPPFLAGS@
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# how to install the man pages;
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# cp is generally fine, unless you preformat your pages.
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# Other tools
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#
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-INSTMAN = cp
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+INSTMAN = ${BSD_INSTALL_MAN}
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MANSUFFIX = 1
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# your compiler and compiler flags
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@@ -109,13 +110,13 @@ src/libhmmer.a:
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# installs man pages in MANDIR/man1/ (e.g. if MANSUFFIX is 1)
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# Creates these directories if they don't exist.
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install:
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- mkdir -p ${BINDIR}
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- -mkdir -p ${MANDIR}/man${MANSUFFIX}
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+ ${MKDIR} ${DESTDIR}${BINDIR}
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+ -${MKDIR} ${DESTDIR}${MANDIR}/man${MANSUFFIX}
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for file in $(PROGS) $(PVMPROGS); do\
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- cp src/$$file $(BINDIR)/;\
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+ $(INSTBIN) src/$$file ${DESTDIR}$(BINDIR)/;\
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AR = @AR@ rcv
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LN = ln
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RANLIB = @RANLIB@
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@@ -176,11 +176,11 @@ testsuite: libraries
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# may be set on a make command line when building contrib RPMs).
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install: libraries programs
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cd ${PMARKDIR}; ${MAKE} profmark_progs
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- -mkdir -p ${DESTDIR}${bindir}
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+ -${MKDIR} ${DESTDIR}${bindir}
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for file in $(PROGS); do\
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- cp ${SRCDIR}/$$file ${DESTDIR}${bindir}/;\
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+ ${BSD_INSTALL_PROGRAM} ${SRCDIR}/$$file ${DESTDIR}${bindir}/;\
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done
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-for file in hmmer $(PROGS); do\
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- $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
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+ $(INSTMAN) documentation/man/$$file.man ${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
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done
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# uninstall: Reverses the steps of "make install".
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@@ -133,7 +134,7 @@ uninstall:
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# subdir, remove everything but binaries and Makefiles.
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#
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bindist:
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- mkdir binaries
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+ ${MKDIR} binaries
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for prog in $(PROGS); do\
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(cd binaries; ln -s ../src/$$prog .);\
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done
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@@ -205,7 +206,7 @@ dist:
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# in testsuite.
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#
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cp ssdk/sqc ${BASENAME}-${RELEASE}/testsuite/
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- mkdir ${BASENAME}-${RELEASE}/ssdk
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+ ${MKDIR} ${BASENAME}-${RELEASE}/ssdk
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cp ssdk/rmanprocess.pl ${BASENAME}-${RELEASE}/ssdk/
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#
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# Make the configure scripts from configure.ac
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@@ -288,7 +289,7 @@ dist:
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# directory.
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#
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ftpdist:
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- mkdir -p ${FTPDIR}
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+ ${MKDIR} ${FTPDIR}
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cp -f hmmer-$(RELEASE)/00README ${FTPDIR}
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cp -f hmmer-$(RELEASE)/COPYRIGHT ${FTPDIR}
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cp -f hmmer-$(RELEASE)/INSTALL ${FTPDIR}
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-# -mkdir -p ${DESTDIR}/${MANDIR}/man${MANSUFFIX}
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+# -${MKDIR} ${DESTDIR}/${MANDIR}/man${MANSUFFIX}
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# -for file in hmmer $(PROGS); do\
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# $(INSTMAN) documentation/man/$$file.man ${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
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# done
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