head 1.10; access; symbols pkgsrc-2023Q4:1.10.0.2 pkgsrc-2023Q4-base:1.10 pkgsrc-2023Q3:1.9.0.24 pkgsrc-2023Q3-base:1.9 pkgsrc-2023Q2:1.9.0.22 pkgsrc-2023Q2-base:1.9 pkgsrc-2023Q1:1.9.0.20 pkgsrc-2023Q1-base:1.9 pkgsrc-2022Q4:1.9.0.18 pkgsrc-2022Q4-base:1.9 pkgsrc-2022Q3:1.9.0.16 pkgsrc-2022Q3-base:1.9 pkgsrc-2022Q2:1.9.0.14 pkgsrc-2022Q2-base:1.9 pkgsrc-2022Q1:1.9.0.12 pkgsrc-2022Q1-base:1.9 pkgsrc-2021Q4:1.9.0.10 pkgsrc-2021Q4-base:1.9 pkgsrc-2021Q3:1.9.0.8 pkgsrc-2021Q3-base:1.9 pkgsrc-2021Q2:1.9.0.6 pkgsrc-2021Q2-base:1.9 pkgsrc-2021Q1:1.9.0.4 pkgsrc-2021Q1-base:1.9 pkgsrc-2020Q4:1.9.0.2 pkgsrc-2020Q4-base:1.9 pkgsrc-2020Q3:1.8.0.14 pkgsrc-2020Q3-base:1.8 pkgsrc-2020Q2:1.8.0.12 pkgsrc-2020Q2-base:1.8 pkgsrc-2020Q1:1.8.0.8 pkgsrc-2020Q1-base:1.8 pkgsrc-2019Q4:1.8.0.10 pkgsrc-2019Q4-base:1.8 pkgsrc-2019Q3:1.8.0.6 pkgsrc-2019Q3-base:1.8 pkgsrc-2019Q2:1.8.0.4 pkgsrc-2019Q2-base:1.8 pkgsrc-2019Q1:1.8.0.2 pkgsrc-2019Q1-base:1.8 pkgsrc-2018Q4:1.7.0.8 pkgsrc-2018Q4-base:1.7 pkgsrc-2018Q3:1.7.0.6 pkgsrc-2018Q3-base:1.7 pkgsrc-2018Q2:1.7.0.4 pkgsrc-2018Q2-base:1.7 pkgsrc-2018Q1:1.7.0.2 pkgsrc-2018Q1-base:1.7 pkgsrc-2017Q4:1.6.0.6 pkgsrc-2017Q4-base:1.6 pkgsrc-2017Q3:1.6.0.4 pkgsrc-2017Q3-base:1.6 pkgsrc-2017Q2:1.5.0.12 pkgsrc-2017Q2-base:1.5 pkgsrc-2017Q1:1.5.0.10 pkgsrc-2017Q1-base:1.5 pkgsrc-2016Q4:1.5.0.8 pkgsrc-2016Q4-base:1.5 pkgsrc-2016Q3:1.5.0.6 pkgsrc-2016Q3-base:1.5 pkgsrc-2016Q2:1.5.0.4 pkgsrc-2016Q2-base:1.5 pkgsrc-2016Q1:1.5.0.2 pkgsrc-2016Q1-base:1.5 pkgsrc-2015Q4:1.3.0.18 pkgsrc-2015Q4-base:1.3 pkgsrc-2015Q3:1.3.0.16 pkgsrc-2015Q3-base:1.3 pkgsrc-2015Q2:1.3.0.14 pkgsrc-2015Q2-base:1.3 pkgsrc-2015Q1:1.3.0.12 pkgsrc-2015Q1-base:1.3 pkgsrc-2014Q4:1.3.0.10 pkgsrc-2014Q4-base:1.3 pkgsrc-2014Q3:1.3.0.8 pkgsrc-2014Q3-base:1.3 pkgsrc-2014Q2:1.3.0.6 pkgsrc-2014Q2-base:1.3 pkgsrc-2014Q1:1.3.0.4 pkgsrc-2014Q1-base:1.3 pkgsrc-2013Q4:1.3.0.2 pkgsrc-2013Q4-base:1.3 pkgsrc-2013Q3:1.2.0.10 pkgsrc-2013Q3-base:1.2 pkgsrc-2013Q2:1.2.0.8 pkgsrc-2013Q2-base:1.2 pkgsrc-2013Q1:1.2.0.6 pkgsrc-2013Q1-base:1.2 pkgsrc-2012Q4:1.2.0.4 pkgsrc-2012Q4-base:1.2 pkgsrc-2012Q3:1.2.0.2 pkgsrc-2012Q3-base:1.2 pkgsrc-base:1.1.1.1 TNF:1.1.1; locks; strict; comment @# @; 1.10 date 2023.12.24.16.26.42; author bacon; state Exp; branches; next 1.9; commitid qCGgTyy48zu4KJRE; 1.9 date 2020.10.12.21.51.58; author bacon; state Exp; branches; next 1.8; commitid 568C66J21E1N0FrC; 1.8 date 2019.01.13.22.06.42; author bacon; state Exp; branches; next 1.7; commitid yICsZYhVfgx0GF7B; 1.7 date 2018.01.01.01.18.03; author rillig; state Exp; branches; next 1.6; commitid 2susOFsS5zIfT6lA; 1.6 date 2017.09.03.08.36.50; author wiz; state Exp; branches; next 1.5; commitid WMTcdUJCUnzRaJ5A; 1.5 date 2016.02.25.11.21.11; author jperkin; state Exp; branches; next 1.4; commitid bK6wH0fALdElXhWy; 1.4 date 2015.12.29.04.54.37; author dholland; state Exp; branches; next 1.3; commitid u8BGzIq28fJjGNOy; 1.3 date 2013.12.10.14.20.49; author jperkin; state Exp; branches; next 1.2; commitid CuTcTYdTB805TAgx; 1.2 date 2012.09.14.17.56.15; author asau; state Exp; branches; next 1.1; 1.1 date 2012.09.14.17.46.23; author asau; state Exp; branches 1.1.1.1; next ; 1.1.1.1 date 2012.09.14.17.46.23; author asau; state Exp; branches; next ; desc @@ 1.10 log @biology/plink: Unbreak build on Darwin Remove -lcrypt from link: macOS does not have libcrypt, but has crypt() in libc @ text @# $NetBSD: Makefile,v 1.9 2020/10/12 21:51:58 bacon Exp $ DISTNAME= plink-1.07-src PKGNAME= ${DISTNAME:-src=} PKGREVISION= 1 CATEGORIES= biology #MASTER_SITES= http://pngu.mgh.harvard.edu/~purcell/plink/dist/ EXTRACT_SUFX= .zip MAINTAINER= bacon@@NetBSD.org #HOMEPAGE= http://pngu.mgh.harvard.edu/~purcell/plink/ COMMENT= Whole-genome association analysis toolset LICENSE= gnu-gpl-v2 USE_LANGUAGES= c c++ fortran77 USE_TOOLS+= gmake SUBST_CLASSES.Darwin+= crypt SUBST_STAGE.crypt= pre-build SUBST_SED.crypt= -e 's|-lcrypt||g' SUBST_FILES.crypt= Makefile CXXFLAGS+= -Dfopen64=fopen MAKE_FLAGS+= LIBDL=${DL_LIBS:Q} LIB_LAPACK= -L${LOCALBASE}/lib ${COMPILER_RPATH_FLAG}${LOCALBASE}/lib -llapack -lblas -lf2c MAKE_FLAGS+= WITH_LAPACK=1 LIB_LAPACK=${LIB_LAPACK:Q} MAKE_ENV.SunOS+= LIB="-lsocket -lnsl" INSTALLATION_DIRS= bin do-install: ${INSTALL_PROGRAM} ${WRKSRC}/plink ${DESTDIR}${PREFIX}/bin do-test: cd ${WRKSRC} && ./plink --file test cd ${WRKSRC} && ./plink --file test --freq cd ${WRKSRC} && ./plink --file test --assoc cd ${WRKSRC} && ./plink --file test --make-bed .include "../../devel/libf2c/buildlink3.mk" .include "../../devel/zlib/buildlink3.mk" .include "../../mk/blas.buildlink3.mk" .include "../../mk/dlopen.buildlink3.mk" .include "../../mk/bsd.pkg.mk" @ 1.9 log @math/blas, math/lapack: Install interchangeable BLAS system Install the new interchangeable BLAS system created by Thomas Orgis, currently supporting Netlib BLAS/LAPACK, OpenBLAS, cblas, lapacke, and Apple's Accelerate.framework. This system allows the user to select any BLAS implementation without modifying packages or using package options, by setting PKGSRC_BLAS_TYPES in mk.conf. See mk/blas.buildlink3.mk for details. This commit should not alter behavior of existing packages as the system defaults to Netlib BLAS/LAPACK, which until now has been the only supported implementation. Details: Add new mk/blas.buildlink3.mk for inclusion in dependent packages Install compatible Netlib math/blas and math/lapack packages Update math/blas and math/lapack MAINTAINER approved by adam@@ OpenBLAS, cblas, and lapacke will follow in separate commits Update direct dependents to use mk/blas.buildlink3.mk Perform recursive revbump @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.8 2019/01/13 22:06:42 bacon Exp $ d18 5 @ 1.8 log @Multiple packages: Replace obsolete maintainer email jwbacon@@tds.net ==> bacon@@NetBSD.org @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.7 2018/01/01 01:18:03 rillig Exp $ d5 1 d40 1 a40 2 .include "../../math/lapack/buildlink3.mk" .include "../../math/blas/buildlink3.mk" @ 1.7 log @Cleanup: replace curly braces with parentheses. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.6 2017/09/03 08:36:50 wiz Exp $ d9 1 a9 1 MAINTAINER= jwbacon@@tds.net @ 1.6 log @Comment out dead MASTER_SITES/HOMEPAGEs. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.5 2016/02/25 11:21:11 jperkin Exp $ d4 1 a4 1 PKGNAME= $(DISTNAME:-src=) d32 4 a35 4 cd $(WRKSRC) && ./plink --file test cd $(WRKSRC) && ./plink --file test --freq cd $(WRKSRC) && ./plink --file test --assoc cd $(WRKSRC) && ./plink --file test --make-bed @ 1.5 log @Use OPSYSVARS. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.4 2015/12/29 04:54:37 dholland Exp $ d6 1 a6 1 MASTER_SITES= http://pngu.mgh.harvard.edu/~purcell/plink/dist/ d10 1 a10 1 HOMEPAGE= http://pngu.mgh.harvard.edu/~purcell/plink/ @ 1.4 log @Whitespace. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.3 2013/12/10 14:20:49 jperkin Exp $ d24 1 a24 4 .include "../../mk/bsd.prefs.mk" .if ${OPSYS} == "SunOS" MAKE_ENV+= LIB="-lsocket -lnsl" .endif @ 1.3 log @Add socket libraries on SunOS. Patch from Sebastian Wiedenroth. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.2 2012/09/14 17:56:15 asau Exp $ d26 1 a26 1 MAKE_ENV+= LIB="-lsocket -lnsl" @ 1.2 log @Fix PKGNAME. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.1.1.1 2012/09/14 17:46:23 asau Exp $ d24 5 @ 1.1 log @Initial revision @ text @d1 1 a1 1 # $NetBSD$ d4 1 @ 1.1.1.1 log @Import PLINK 1.07 as biology/plink From Jason Bacon via pkgsrc-wip. PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results. @ text @@