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| author | tijl <tijl@FreeBSD.org> | 2014-02-17 01:15:31 +0800 |
|---|---|---|
| committer | tijl <tijl@FreeBSD.org> | 2014-02-17 01:15:31 +0800 |
| commit | f86cbfadd2dbfab1dc1ea72e5084a23c10b1dc6c (patch) | |
| tree | 49e521faa408bc4bd163bfb0febf91e262772c1c /biology | |
| parent | e04e533cf1bc01e44ad69d14d5c6c205e25bfe3a (diff) | |
| download | freebsd-ports-gnome-f86cbfadd2dbfab1dc1ea72e5084a23c10b1dc6c.tar.gz freebsd-ports-gnome-f86cbfadd2dbfab1dc1ea72e5084a23c10b1dc6c.tar.zst freebsd-ports-gnome-f86cbfadd2dbfab1dc1ea72e5084a23c10b1dc6c.zip | |
Convert all USE_FORTRAN=yes to "USES=fortran, USE_GCC=yes". In most cases
USE_GCC=yes has been omitted though.
Remove USE_FORTRAN handling from bsd.port.mk and bsd.gcc.mk.
Minor cleanups in some ports like USE_GMAKE, NOPORTDOCS,...
Exp-run: bdrewery
Approved by: portmgr (bdrewery)
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/crux/Makefile | 6 | ||||
| -rw-r--r-- | biology/plink/Makefile | 13 | ||||
| -rw-r--r-- | biology/plink/files/patch-Makefile | 9 |
3 files changed, 13 insertions, 15 deletions
diff --git a/biology/crux/Makefile b/biology/crux/Makefile index b303a7f992bb..b6e7dce08b3e 100644 --- a/biology/crux/Makefile +++ b/biology/crux/Makefile @@ -10,22 +10,20 @@ MASTER_SITES= http://www.canonware.com/download/Crux/ MAINTAINER= jasone@FreeBSD.org COMMENT= Software toolkit for phylogenetic inference +USES= fortran gmake USE_BZIP2= yes GNU_CONFIGURE= yes CONFIGURE_ARGS= --with-python=${PYTHON_CMD} --disable-mpi USE_CSTD= gnu99 -USE_GMAKE= yes USE_PYTHON= yes OPTIONS_DEFINE= SYS_LINALG SYS_LINALG_DESC= Enable system ATLAS/LAPACK NO_STAGE= yes -.include <bsd.port.pre.mk> CPPFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib -USE_FORTRAN= yes .include <bsd.port.options.mk> @@ -43,4 +41,4 @@ BROKEN= Does not build on powerpc-9: error in pthreads post-install: @${PREFIX}/bin/crux -b -q /dev/null -.include <bsd.port.post.mk> +.include <bsd.port.mk> diff --git a/biology/plink/Makefile b/biology/plink/Makefile index bfd37ec1e825..a9711e69d1b5 100644 --- a/biology/plink/Makefile +++ b/biology/plink/Makefile @@ -3,10 +3,11 @@ PORTNAME= plink PORTVERSION= 1.07 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology science MASTER_SITES= http://pngu.mgh.harvard.edu/~purcell/plink/dist/ DISTNAME= ${PORTNAME}-${PORTVERSION}-src +EXTRACT_SUFX= .zip MAINTAINER= jwbacon@tds.net COMMENT= Whole genome association analysis toolset @@ -15,15 +16,13 @@ LICENSE= GPLv2 LIB_DEPENDS= liblapack.so:${PORTSDIR}/math/lapack -USES= gmake -USE_ZIP= yes -USE_FORTRAN= yes # Make it use the same compiler as lapack +# We need Fortran LDFLAGS to link with Lapack. +USES= fortran gmake PLIST_FILES= bin/plink -NO_STAGE= yes do-install: - ${MKDIR} ${PREFIX}/bin - ${INSTALL_PROGRAM} ${WRKSRC}/plink ${PREFIX}/bin + ${MKDIR} ${STAGEDIR}${PREFIX}/bin + ${INSTALL_PROGRAM} ${WRKSRC}/plink ${STAGEDIR}${PREFIX}/bin .include <bsd.port.mk> diff --git a/biology/plink/files/patch-Makefile b/biology/plink/files/patch-Makefile index cb1e7f5fc537..e98b69aa6559 100644 --- a/biology/plink/files/patch-Makefile +++ b/biology/plink/files/patch-Makefile @@ -1,15 +1,16 @@ --- Makefile.orig 2009-10-10 11:00:20.000000000 -0500 +++ Makefile 2012-09-07 08:24:26.000000000 -0500 -@@ -26,7 +26,7 @@ +@@ -26,25 +26,25 @@ WITH_WEBCHECK = 1 FORCE_32BIT = WITH_ZLIB = 1 -WITH_LAPACK = +-FORCE_DYNAMIC = +WITH_LAPACK = 1 - FORCE_DYNAMIC = ++FORCE_DYNAMIC = 1 # Put C++ compiler here; Windows has it's own specific version -@@ -34,17 +34,17 @@ + CXX_UNIX = g++ CXX_WIN = c:\bin\mingw\bin\mingw32-g++.exe # Any other compiler flags here ( -Wall, -g, etc) @@ -18,7 +19,7 @@ # Misc -LIB_LAPACK = /usr/lib/liblapack.so.3 -+LIB_LAPACK = -L${LOCALBASE}/lib -llapack -lblas -lgfortran ++LIB_LAPACK = ${LDFLAGS} -L${LOCALBASE}/lib -llapack -lblas # -------------------------------------------------------------------- |