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biology/migrate: Update to 5.0.5

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- Switch to DISTVERSION
- Add license
- Pet portlint, portclippy and portfmt
- Take maintainership

ChangeLog: https://peterbeerli.com/programs/migrate/distribution_4.x/HISTORY
This commit is contained in:
Nuno Teixeira
2024-03-27 11:48:46 +00:00
parent 36d8056d81
commit c492a5b3d4
3 changed files with 27 additions and 31 deletions
Download Patch File Download Diff File Expand all files Collapse all files
biology/migrate/Makefile
+16 -14
View File
@@ -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:
biology/migrate/distinfo
+3 -2
View File
@@ -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
biology/migrate/files/patch-Makefile.in
+8 -15
View File
@@ -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"