From nobody Wed Mar 27 11:51:55 2024 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4V4Q4q4Tzgz5FKjM; Wed, 27 Mar 2024 11:51:55 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4V4Q4q40HHz4jWS; Wed, 27 Mar 2024 11:51:55 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1711540315; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=+UtL/4p10vUTh12DRlTmBjk1Bmz7tLmEpqVWFqdAgvs=; b=RsrkBZ7SIL/28XiRGfy9K69Lr+5qHV5b9esIqLHYxwN485kLlXU2Q46Kt+4qQ6LQotgFX7 T5cG14aLyaFHUvcAPE9TcAluT4d1YN1C1/BFKLlwEKFpK05NDoPLOza277kqPDlFjMoQlg 1RKuCedZDZiXlwv41kzwhWZmjWnq58t1GOZ6rN+zfcbAt2VJaBoXxq3Q5ICXhkTUfTqUXU tPfCqvhhdHnZ8iTZrDjV3vdrXfMsT+E8AAePmwL+Gjigomqo+k+sfjEh47PKhiHwTHBGon 2jbHBcPClSXfG82+WCVc70IXTClk2Nrk+Ii4RU59X0XrMkWoOZpcLIXOqCgCVg== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1711540315; a=rsa-sha256; cv=none; b=yvvZZ6nSbuSExPVcnin50+OEJzcWvWQNPttikXExPOpAhT5uQueqik8NL3CP1rIaxj1DqX 52peUZzLgkNNj+gUlBchDBPMsmR4IZcpZW1YPp/QKwIPhmUlTh20+uID/jfPnBtf0lNpMx Gx4C6OzWRWKbTpY7b0ESAi7FmKc8KxG83mZgHhC9RFWWHzujqmrDDO/VAdjGkzRMnpLlgE aTVwdf36JnfTXPFQqY+NjQWE1pbW8SUHREdygVRdKKUI4GXq9Gy64KRaNOFmLadDftvIwd tVzWW3vKYTillXzUi7sSebhGspjEagjgG5AYlNuPHabW3+4zDH0wwICRjwWWGQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1711540315; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=+UtL/4p10vUTh12DRlTmBjk1Bmz7tLmEpqVWFqdAgvs=; b=HFy7v6ucPpN9QunQcWpi6U9RvCj8M8zj2+HC8RjoI6Ry/SFh/XozDfexHtyAtPuJrI808G 24J454EJazOF1xKvoo6X4k2dQczg/e3ItJp9RLzfz1SKdTxn3EtMzNtr48p5hcqkY5APmP xhwKKlQ8Vfc4KC5UZ5xSTg/zc2tvL8FNHBvkY3NvZxA5If5nxFS+r5ncgZ02zZQAsrqOpT xgVfe0mxaqzpaj3fIlTD4g1sQbE2/X33nx+GU6Y5IfObtmsJgFmLQuEmcVI+/TsRl+lmDd 1hNC7KonEhmfL6TvtAsAQgVfKyj0I7BL7b+mAX6a98m6k267C17RcyKW+ceskQ== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4V4Q4q3cgszhsg; Wed, 27 Mar 2024 11:51:55 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 42RBptsL053152; Wed, 27 Mar 2024 11:51:55 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 42RBpt8S053149; Wed, 27 Mar 2024 11:51:55 GMT (envelope-from git) Date: Wed, 27 Mar 2024 11:51:55 GMT Message-Id: <202403271151.42RBpt8S053149@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Nuno Teixeira Subject: git: c492a5b3d4b1 - main - biology/migrate: Update to 5.0.5 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: eduardo X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: c492a5b3d4b19112ddfe49fb196b54ccfbc29996 Auto-Submitted: auto-generated The branch main has been updated by eduardo: URL: https://cgit.FreeBSD.org/ports/commit/?id=c492a5b3d4b19112ddfe49fb196b54ccfbc29996 commit c492a5b3d4b19112ddfe49fb196b54ccfbc29996 Author: Nuno Teixeira AuthorDate: 2024-03-27 11:48:46 +0000 Commit: Nuno Teixeira CommitDate: 2024-03-27 11:51:44 +0000 biology/migrate: Update to 5.0.5 - Switch to DISTVERSION - Add license - Pet portlint, portclippy and portfmt - Take maintainership ChangeLog: https://peterbeerli.com/programs/migrate/distribution_4.x/HISTORY --- biology/migrate/Makefile | 30 ++++++++++++++++-------------- biology/migrate/distinfo | 5 +++-- biology/migrate/files/patch-Makefile.in | 23 ++++++++--------------- 3 files changed, 27 insertions(+), 31 deletions(-) diff --git a/biology/migrate/Makefile b/biology/migrate/Makefile index 6d17d8438450..1f04a5ee0923 100644 --- a/biology/migrate/Makefile +++ b/biology/migrate/Makefile @@ -1,30 +1,32 @@ PORTNAME= migrate -PORTVERSION= 3.6.11 -PORTREVISION= 1 +DISTVERSION= 5.0.5 CATEGORIES= biology -MASTER_SITES= http://popgen.sc.fsu.edu/currentversions/ +MASTER_SITES= https://peterbeerli.com/migrate-html5/download_version4/ DISTNAME= ${PORTNAME}-${PORTVERSION}.src -MAINTAINER= ports@FreeBSD.org +MAINTAINER= eduardo@FreeBSD.org COMMENT= Program to estimate population sizes and migration rates WWW= https://popgen.sc.fsu.edu/Migrate/Migrate-n.html -BROKEN_armv6= fails to build: make[2]: cannot open makefile -BROKEN_armv7= fails to build: make[2]: cannot open makefile -BROKEN_mips= fails to build: make[2]: cannot open makefile -BROKEN_riscv64= fails to build: make[2]: cannot open makefile +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/../README -WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/src -EXTRACT_AFTER_ARGS=--exclude zlib +# Waiting on build reports, 2024-03-27 +#BROKEN_armv6= fails to build: make[2]: cannot open makefile +#BROKEN_armv7= fails to build: make[2]: cannot open makefile +#BROKEN_mips= fails to build: make[2]: cannot open makefile +#BROKEN_riscv64= fails to build: make[2]: cannot open makefile GNU_CONFIGURE= yes CONFIGURE_ENV= ac_cv_prog_GMAKE="${MAKE}" -MAKE_ARGS= PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu \ - -DPRETTY -lstdc++" +MAKE_ARGS= PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++" CONFLICTS_INSTALL= py*-sqlalchemy-migrate # bin/migrate -PORTDOCS= HISTORY README README_PARALLEL_GENERAL ${PORTNAME}.html +EXTRACT_AFTER_ARGS= --exclude zlib +WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/src + +PORTDOCS= ${PORTNAME}.html HISTORY README README_PARALLEL_GENERAL PORTEXAMPLES= * OPTIONS_DEFINE= DOCS EXAMPLES THREAD @@ -33,7 +35,7 @@ THREAD_ALL_TARGET= thread post-patch: @${REINPLACE_CMD} -e 's|="-O "|="$$CFLAGS"|g' ${WRKSRC}/configure - @${REINPLACE_CMD} -e '/PRETTY$$/d' ${WRKSRC}/definitions.h + @${REINPLACE_CMD} -e '/PRETTY$$/d' ${WRKSRC}/src/definitions.h @${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/haru/makefile.gcc do-install: diff --git a/biology/migrate/distinfo b/biology/migrate/distinfo index 6d0ec05f83bb..498a5f72dd3d 100644 --- a/biology/migrate/distinfo +++ b/biology/migrate/distinfo @@ -1,2 +1,3 @@ -SHA256 (migrate-3.6.11.src.tar.gz) = a9ba06a4e995a45b8d04037f5f2da23e1fe64a2f3565189bdd50c62c6fe01fb8 -SIZE (migrate-3.6.11.src.tar.gz) = 27809896 +TIMESTAMP = 1711535851 +SHA256 (migrate-5.0.5.src.tar.gz) = 43d456f2432c0ec77ad33877f184d3b4b36f61e416f8fffa51077768df91ea51 +SIZE (migrate-5.0.5.src.tar.gz) = 4746835 diff --git a/biology/migrate/files/patch-Makefile.in b/biology/migrate/files/patch-Makefile.in index 814875b4b1a8..0119cb51c758 100644 --- a/biology/migrate/files/patch-Makefile.in +++ b/biology/migrate/files/patch-Makefile.in @@ -1,18 +1,11 @@ ---- Makefile.in.orig 2015-06-24 02:57:05 UTC +--- Makefile.in.orig 2024-03-27 11:13:06 UTC +++ Makefile.in -@@ -89,7 +89,7 @@ PAPERFORMAT = @PAPERFORMAT@ - # -DINTEGRATEDLIKE may be used to get a marginal likelihood different to the current thermodynamic integr and harmonic mean [does not work] - # -UEP calculates unique event polymorphism [not checked in a long time -- most likely does not work] - NEWSTUFF = -DNEXUSTREE --COMMONFLAGS = $(ARCH) $(MACOSVERSION) $(NEWSTUFF) $(HAVE_ZNZ) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS) -+COMMONFLAGS = $(MACOSVERSION) $(NEWSTUFF) $(HAVE_ZNZ) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS) +@@ -94,7 +94,7 @@ NEWSTUFF = + # -DTHERMOCHECK prints heated likelihood into mixfile (needs to be added the parmfile) + #NEWSTUFF = -DNEWVERSION + NEWSTUFF = +-COMMONFLAGS = $(ARCH) $(MACOSVERSION) $(NEWSTUFF) $(HAVE_ZNZ) -DNEXUSTREE -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS) ++COMMONFLAGS = $(MACOSVERSION) $(NEWSTUFF) $(HAVE_ZNZ) -DNEXUSTREE -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS) + VALGRINDCOMMONFLAGS = $(ARCH) $(MACOSVERSION) $(NEWSTUFF) $(HAVE_ZNZ) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) # # combine the common flags with the version number and subversion number - COMMONVFLAGS = $(COMMONFLAGS) -DMIGRATESUBVERSION=\"\\\"$(MIGRATESUBVERSION)\\\"\" -@@ -544,4 +544,4 @@ parallel_short_test:: - #---------------------------------------------------------------- - # BEAGLE - beagle: -- $(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS) $(BEAGLEFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS =$(LDFLAGS) $(EXCEPTIONS) `pkg-config /Users/beerli/src/beagle-lib/hmsbeagle-1.0.pc --cflags --libs` -framework OpenCL" -\ No newline at end of file -+ $(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS) $(BEAGLEFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)" "LDFLAGS =$(LDFLAGS) $(EXCEPTIONS) `pkg-config /Users/beerli/src/beagle-lib/hmsbeagle-1.0.pc --cflags --libs` -framework OpenCL"