Date: Wed, 27 Mar 2024 11:51:55 GMT From: Nuno Teixeira <eduardo@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: c492a5b3d4b1 - main - biology/migrate: Update to 5.0.5 Message-ID: <202403271151.42RBpt8S053149@gitrepo.freebsd.org>
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The branch main has been updated by eduardo: URL: https://cgit.FreeBSD.org/ports/commit/?id=c492a5b3d4b19112ddfe49fb196b54ccfbc29996 commit c492a5b3d4b19112ddfe49fb196b54ccfbc29996 Author: Nuno Teixeira <eduardo@FreeBSD.org> AuthorDate: 2024-03-27 11:48:46 +0000 Commit: Nuno Teixeira <eduardo@FreeBSD.org> 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"
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