From owner-freebsd-ports-bugs@FreeBSD.ORG Sun Sep 2 17:10:05 2007 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 5B2DD16A46C for ; Sun, 2 Sep 2007 17:10:05 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id 5635413C46C for ; Sun, 2 Sep 2007 17:10:05 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.14.1/8.14.1) with ESMTP id l82HA5Dt008985 for ; Sun, 2 Sep 2007 17:10:05 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.1/8.14.1/Submit) id l82HA5Zx008984; Sun, 2 Sep 2007 17:10:05 GMT (envelope-from gnats) Resent-Date: Sun, 2 Sep 2007 17:10:05 GMT Resent-Message-Id: <200709021710.l82HA5Zx008984@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, KATO Tsuguru Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 3F90C16A420 for ; Sun, 2 Sep 2007 17:01:22 +0000 (UTC) (envelope-from tkato432@yahoo.com) Received: from msa01.dion.ne.jp (msa01.dion.ne.jp [222.3.140.164]) by mx1.freebsd.org (Postfix) with ESMTP id EA53813C46A for ; Sun, 2 Sep 2007 17:01:21 +0000 (UTC) (envelope-from tkato432@yahoo.com) Received: from localhost.localdomain (ZT067179.ppp.dion.ne.jp [59.128.67.179]) by msa101.dion.ne.jp (DION MAIL) with ESMTP id 4312C8A8041 for ; Mon, 3 Sep 2007 02:00:50 +0900 (JST) Message-Id: <20070903020016.3942b8bf.tkato432@yahoo.com> Date: Mon, 3 Sep 2007 02:00:16 +0900 From: KATO Tsuguru To: FreeBSD-gnats-submit@FreeBSD.org Cc: Subject: ports/116017: Update port: biology/lamarc to 2.1 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 02 Sep 2007 17:10:05 -0000 >Number: 116017 >Category: ports >Synopsis: Update port: biology/lamarc to 2.1 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Sun Sep 02 17:10:04 GMT 2007 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 6.2-RELEASE-p7 i386 >Organization: >Environment: >Description: - Update to version 2.1 New file: distinfo files/patch-Makefile.in files/patch-configure files/patch-src__control__defaults.h >How-To-Repeat: >Fix: diff -urN /usr/ports/biology/lamarc/Makefile biology/lamarc/Makefile --- /usr/ports/biology/lamarc/Makefile Thu Jan 25 20:10:43 2007 +++ biology/lamarc/Makefile Fri Aug 31 02:58:06 2007 @@ -6,22 +6,29 @@ # PORTNAME= lamarc -PORTVERSION= 2001.08.06 -PORTREVISION= 1 +PORTVERSION= 2.1 +PORTEPOCH= 1 CATEGORIES= biology -MASTER_SITES= # empty -DISTFILES= # none -EXTRACT_ONLY= # empty +MASTER_SITES= http://evolution.gs.washington.edu/lamarc/download/ +EXTRACT_SUFX= .src.tar.gz MAINTAINER= ports@FreeBSD.org COMMENT= A package of programs for computing population parameters -RUN_DEPENDS= fluctuate:${PORTSDIR}/biology/fluctuate \ - migrate:${PORTSDIR}/biology/migrate \ - recombine:${PORTSDIR}/biology/recombine +USE_GNOME= gnometarget +GNU_CONFIGURE= yes -NO_BUILD= yes +.if defined(WITH_WXGTK2) +USE_WX= 2.8 +CONFIGURE_ARGS+= --with-wx-config=${WX_CONFIG} +PLIST_SUB+= WXGTK2="" +.else +CONFIGURE_ARGS+= --disable-converter +PLIST_SUB+= WXGTK2="@comment " +.endif -do-install: # empty +.if defined(NOPORTDOCS) +INSTALL_TARGET= install-exec-am +.endif .include diff -urN /usr/ports/biology/lamarc/distinfo biology/lamarc/distinfo --- /usr/ports/biology/lamarc/distinfo Thu Jan 1 09:00:00 1970 +++ biology/lamarc/distinfo Thu Aug 30 13:26:41 2007 @@ -0,0 +1,3 @@ +MD5 (lamarc-2.1.src.tar.gz) = ed98383ed97acb99330d080a3b457ab0 +SHA256 (lamarc-2.1.src.tar.gz) = 3a17b6dec3c313193b48b94d0b4f8b3bbd01badb7f0c6f179aabbf3dfba625e2 +SIZE (lamarc-2.1.src.tar.gz) = 23427309 diff -urN /usr/ports/biology/lamarc/files/patch-Makefile.in biology/lamarc/files/patch-Makefile.in --- /usr/ports/biology/lamarc/files/patch-Makefile.in Thu Jan 1 09:00:00 1970 +++ biology/lamarc/files/patch-Makefile.in Fri Aug 31 01:11:13 2007 @@ -0,0 +1,65 @@ +--- Makefile.in.orig Mon May 7 06:58:52 2007 ++++ Makefile.in Fri Aug 31 01:11:04 2007 +@@ -51,7 +51,7 @@ + @OSX_APP_FALSE@am__append_8 = -ggdb + @NODATA_TRUE@am__append_9 = -DSTATIONARIES -DNOPROGRESSBAR + @DEBUG_TRUE@am__append_10 = $(debugflags) +-@DEBUG_FALSE@am__append_11 = -O3 -funroll-loops -DNDEBUG ++@DEBUG_FALSE@am__append_11 = -DNDEBUG + @DMALLOC_TRUE@am__append_12 = -ldmallocxx + @DMALLOC_TRUE@am__append_13 = -DDMALLOC_FUNC_CHECK + @EFENCE_TRUE@am__append_14 = -lefence +@@ -1155,7 +1155,7 @@ + CPPFLAGS = @CPPFLAGS@ + CXX = @CXX@ + CXXDEPMODE = @CXXDEPMODE@ +-CXXFLAGS = ++CXXFLAGS = @CXXFLAGS@ + CYGPATH_W = @CYGPATH_W@ + DEBUG_FALSE = @DEBUG_FALSE@ + DEBUG_TRUE = @DEBUG_TRUE@ +@@ -1994,7 +1994,7 @@ + EXTRA_batch_lam_conv_SOURCES = $(tinyxml_suite) + lam_conv_app_SOURCES = + lamarc_app_SOURCES = +-htmldir = $(prefix)/html/lamarc ++htmldir = $(prefix)/share/doc/lamarc + html_DATA = \ + doc/html/bayes.html \ + doc/html/bayes_howto.html \ +@@ -2037,7 +2037,7 @@ + doc/html/viral_data.html \ + doc/html/xmlinput.html + +-htmlimgdir = $(prefix)/html/lamarc/images ++htmlimgdir = $(prefix)/share/doc/lamarc/images + htmlimg_DATA = \ + doc/html/images/browser-gtk.gif \ + doc/html/images/correlated1.gif \ +@@ -2054,7 +2054,7 @@ + doc/html/images/uncorrelated.gif \ + doc/html/images/variably_correlated.gif + +-htmlbconvdir = $(prefix)/html/lamarc/batch_converter ++htmlbconvdir = $(prefix)/share/doc/lamarc/batch_converter + htmlbconv_DATA = \ + doc/html/batch_converter/README.txt \ + doc/html/batch_converter/chrom1_lamarc.xml \ +@@ -2068,7 +2068,7 @@ + doc/html/batch_converter/exported-lamarc-input.xml \ + doc/html/batch_converter/sample-conv-cmd.xml + +-htmlbconvimgdir = $(prefix)/html/lamarc/batch_converter/images ++htmlbconvimgdir = $(prefix)/share/doc/lamarc/batch_converter/images + htmlbconvimg_DATA = \ + doc/html/batch_converter/images/lam_conv_chrom1_export_file_selection.png \ + doc/html/batch_converter/images/lam_conv_chrom1_export_warn_1.png \ +@@ -2082,7 +2082,7 @@ + doc/html/batch_converter/images/lam_conv_chrom3_region_table.png \ + doc/html/batch_converter/images/lam_conv_chrom3_segment_snp.png + +-htmltraitdir = $(prefix)/html/lamarc/trait_mapping ++htmltraitdir = $(prefix)/share/doc/lamarc/trait_mapping + htmltrait_DATA = \ + doc/html/trait_mapping/README.txt \ + doc/html/trait_mapping/lamarc-trait-input.xml \ diff -urN /usr/ports/biology/lamarc/files/patch-configure biology/lamarc/files/patch-configure --- /usr/ports/biology/lamarc/files/patch-configure Thu Jan 1 09:00:00 1970 +++ biology/lamarc/files/patch-configure Thu Aug 30 18:26:53 2007 @@ -0,0 +1,11 @@ +--- configure.orig Wed May 2 05:59:05 2007 ++++ configure Thu Aug 30 18:26:42 2007 +@@ -1494,7 +1494,7 @@ + OSTYPE=MACOSX + GUI_PKG=mac + ;; +- linux*) ++ freebsd*|linux*) + OSTYPE=LINUX + GUI_PKG=gtk2 + ;; diff -urN /usr/ports/biology/lamarc/files/patch-src__control__defaults.h biology/lamarc/files/patch-src__control__defaults.h --- /usr/ports/biology/lamarc/files/patch-src__control__defaults.h Thu Jan 1 09:00:00 1970 +++ biology/lamarc/files/patch-src__control__defaults.h Thu Aug 30 18:27:59 2007 @@ -0,0 +1,11 @@ +--- src/control/defaults.h.orig Sat Apr 28 04:56:55 2007 ++++ src/control/defaults.h Thu Aug 30 17:31:51 2007 +@@ -243,7 +243,7 @@ + static const verbosity_type verbosity; + static const verbosity_type progress; + +- static const long programstarttime; ++ static const time_t programstarttime; + static const long randomseed; + + static const bool plotpost; diff -urN /usr/ports/biology/lamarc/pkg-descr biology/lamarc/pkg-descr --- /usr/ports/biology/lamarc/pkg-descr Tue Aug 7 17:17:58 2001 +++ biology/lamarc/pkg-descr Thu Aug 30 01:14:15 2007 @@ -4,10 +4,4 @@ this by using likelihoods for samples of data (sequences, microsatellites, and electrophoretic polymorphisms) from populations. -This port does not contain anything by itself; it is a "meta-port" which -installs the four packages that make up LAMARC: Coalesce, Fluctuate, Migrate -and Recombine. - -WWW: http://evolution.genetics.washington.edu/lamarc.html - --- Johann Visagie +WWW: http://evolution.genetics.washington.edu/lamarc/ diff -urN /usr/ports/biology/lamarc/pkg-plist biology/lamarc/pkg-plist --- /usr/ports/biology/lamarc/pkg-plist Tue Aug 7 17:17:58 2001 +++ biology/lamarc/pkg-plist Fri Aug 31 02:57:31 2007 @@ -1 +1,88 @@ -@comment this plist intentionally left empty +bin/lamarc +%%WXGTK2%%bin/lam_conv +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/README.txt +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom1.mig +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom1_lamarc.xml +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom2.mig +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom2_lamarc.xml +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom3_lamarc.xml +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom3_phase_cmd.xml +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom3microsat.mig +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/chrom3snp.mig +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/exported-lamarc-input.xml +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom1_export_file_selection.png +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom1_export_warn_1.png +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom1_input.png +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom1_segment_panel.png +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom2_segment1.png +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom3_error_map_position.png +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom3_error_phase_file_needed.png +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom3_input.png +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom3_region_panel.png +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom3_region_table.png +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/images/lam_conv_chrom3_segment_snp.png +%%PORTDOCS%%%%DOCSDIR%%/batch_converter/sample-conv-cmd.xml +%%PORTDOCS%%%%DOCSDIR%%/bayes.html +%%PORTDOCS%%%%DOCSDIR%%/bayes_howto.html +%%PORTDOCS%%%%DOCSDIR%%/changes.html +%%PORTDOCS%%%%DOCSDIR%%/comparing_curvefiles.sxc +%%PORTDOCS%%%%DOCSDIR%%/comparing_curvefiles.xls +%%PORTDOCS%%%%DOCSDIR%%/compiling.html +%%PORTDOCS%%%%DOCSDIR%%/converter.html +%%PORTDOCS%%%%DOCSDIR%%/converter_cmd.html +%%PORTDOCS%%%%DOCSDIR%%/curve-smoothing.html +%%PORTDOCS%%%%DOCSDIR%%/data_models.html +%%PORTDOCS%%%%DOCSDIR%%/data_required.html +%%PORTDOCS%%%%DOCSDIR%%/forces.html +%%PORTDOCS%%%%DOCSDIR%%/gamma.html +%%PORTDOCS%%%%DOCSDIR%%/genetic_map.html +%%PORTDOCS%%%%DOCSDIR%%/genotype.html +%%PORTDOCS%%%%DOCSDIR%%/glossary.html +%%PORTDOCS%%%%DOCSDIR%%/growthmenu.html +%%PORTDOCS%%%%DOCSDIR%%/images/browser-gtk.gif +%%PORTDOCS%%%%DOCSDIR%%/images/correlated1.gif +%%PORTDOCS%%%%DOCSDIR%%/images/correlated2.gif +%%PORTDOCS%%%%DOCSDIR%%/images/gui_lam_conv.gif +%%PORTDOCS%%%%DOCSDIR%%/images/lam_conv.gif +%%PORTDOCS%%%%DOCSDIR%%/images/lamarc.gif +%%PORTDOCS%%%%DOCSDIR%%/images/loci-gtk.png +%%PORTDOCS%%%%DOCSDIR%%/images/loci2-gtk.png +%%PORTDOCS%%%%DOCSDIR%%/images/partitions-gtk.png +%%PORTDOCS%%%%DOCSDIR%%/images/partitions2-gtk.png +%%PORTDOCS%%%%DOCSDIR%%/images/populations-gtk.png +%%PORTDOCS%%%%DOCSDIR%%/images/startup-gtk.png +%%PORTDOCS%%%%DOCSDIR%%/images/uncorrelated.gif +%%PORTDOCS%%%%DOCSDIR%%/images/variably_correlated.gif +%%PORTDOCS%%%%DOCSDIR%%/index.html +%%PORTDOCS%%%%DOCSDIR%%/insumfile.2reg3rep.xml +%%PORTDOCS%%%%DOCSDIR%%/insumfile.3rep.xml +%%PORTDOCS%%%%DOCSDIR%%/limitations.html +%%PORTDOCS%%%%DOCSDIR%%/mapping.html +%%PORTDOCS%%%%DOCSDIR%%/menu.html +%%PORTDOCS%%%%DOCSDIR%%/messages.html +%%PORTDOCS%%%%DOCSDIR%%/output.html +%%PORTDOCS%%%%DOCSDIR%%/outsumfile.2reg3rep.xml +%%PORTDOCS%%%%DOCSDIR%%/outsumfile.3rep.xml +%%PORTDOCS%%%%DOCSDIR%%/overview.html +%%PORTDOCS%%%%DOCSDIR%%/parallel.html +%%PORTDOCS%%%%DOCSDIR%%/parameters.html +%%PORTDOCS%%%%DOCSDIR%%/regions.html +%%PORTDOCS%%%%DOCSDIR%%/search.html +%%PORTDOCS%%%%DOCSDIR%%/tracer.html +%%PORTDOCS%%%%DOCSDIR%%/trait_mapping/README.txt +%%PORTDOCS%%%%DOCSDIR%%/trait_mapping/lamarc-trait-input.xml +%%PORTDOCS%%%%DOCSDIR%%/trait_mapping/outfile.txt +%%PORTDOCS%%%%DOCSDIR%%/trait_mapping/traitCmd.xml +%%PORTDOCS%%%%DOCSDIR%%/trait_mapping/traitCmd.xml.txt +%%PORTDOCS%%%%DOCSDIR%%/trait_mapping/traitData.mig +%%PORTDOCS%%%%DOCSDIR%%/troubleshooting.html +%%PORTDOCS%%%%DOCSDIR%%/tutorial.html +%%PORTDOCS%%%%DOCSDIR%%/tutorial2.html +%%PORTDOCS%%%%DOCSDIR%%/upcoming.html +%%PORTDOCS%%%%DOCSDIR%%/viral_data.html +%%PORTDOCS%%%%DOCSDIR%%/xmlinput.html +%%PORTDOCS%%@dirrm %%DOCSDIR%%/trait_mapping +%%PORTDOCS%%@dirrm %%DOCSDIR%%/images +%%PORTDOCS%%@dirrm %%DOCSDIR%%/batch_converter/images +%%PORTDOCS%%@dirrm %%DOCSDIR%%/batch_converter +%%PORTDOCS%%@dirrm %%DOCSDIR%% >Release-Note: >Audit-Trail: >Unformatted: