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-rw-r--r--biology/crux/Makefile56
-rw-r--r--biology/crux/distinfo2
-rw-r--r--biology/crux/files/patch-lib_Crux_CxPpc.c18
-rw-r--r--biology/crux/files/pkg-install8
-rw-r--r--biology/crux/pkg-descr19
-rw-r--r--biology/crux/pkg-plist56
6 files changed, 0 insertions, 159 deletions
diff --git a/biology/crux/Makefile b/biology/crux/Makefile
deleted file mode 100644
index 339ee827f79c..000000000000
--- a/biology/crux/Makefile
+++ /dev/null
@@ -1,56 +0,0 @@
-# Created by: Jason Evans <jasone@FreeBSD.org>
-# $FreeBSD$
-
-PORTNAME= crux
-PORTVERSION= 1.2.0
-PORTREVISION= 9
-CATEGORIES= biology python
-MASTER_SITES= http://www.canonware.com/download/Crux/
-
-MAINTAINER= ports@FreeBSD.org
-COMMENT= Software toolkit for phylogenetic inference
-
-LICENSE= BSD2CLAUSE BSD3CLAUSE
-LICENSE_COMB= multi
-
-BROKEN= No public distfiles
-DEPRECATED= Broken for more than 6 months
-EXPIRATION_DATE= 2018-06-06
-BROKEN_aarch64= Fails to link: ImportError: /lib/libgcc_s.so.1: version GCC_4.5.0 required by /usr/local/lib/gcc5/libgfortran.so.3 not found
-BROKEN_armv6= Fails to link: ImportError: /usr/local/lib/gcc49/libgfortran.so.3: Undefined symbol "__aeabi_ldivmod"
-BROKEN_armv7= Fails to link: ImportError: /usr/local/lib/gcc49/libgfortran.so.3: Undefined symbol "__aeabi_ldivmod"
-
-USES= fortran gmake python tar:bzip2
-USE_CSTD= gnu99
-GNU_CONFIGURE= yes
-CONFIGURE_ARGS= --datadir=${PREFIX}/lib \
- --with-python=${PYTHON_CMD} \
- --disable-mpi
-
-CPPFLAGS+= -I${LOCALBASE}/include
-LDFLAGS+= -L${LOCALBASE}/lib
-
-MAKE_JOBS_UNSAFE= yes
-
-OPTIONS_DEFINE= SYS_LINALG
-
-SYS_LINALG_DESC= Enable system ATLAS/LAPACK
-SYS_LINALG_LIB_DEPENDS= libatlas.so:math/atlas
-SYS_LINALG_CONFIGURE_ENABLE= sys-linalg
-
-post-patch:
- @${REINPLACE_CMD} -e '/altivec/s|-f|-m|' ${WRKSRC}/configure
- @${REINPLACE_CMD} -e \
- 's|\([[:blank:]]\)\($$(BINDIR)\)|\1$$(DESTDIR)\2| ; \
- s|\([[:blank:]]\)\($$(DATADIR)\)|\1$$(DESTDIR)\2| ; \
- s|\(,\)\(@site_packages@\)|\1$$(DESTDIR)\2| ; \
- s|\([[:blank:]]\)\(@site_packages@\)|\1$$(DESTDIR)\2|' \
- ${WRKSRC}/Makefile.in
-
-post-install:
- @(${FIND} ${STAGEDIR}${PREFIX}/lib/Crux/lib -maxdepth 1 -type f \
- -name "*.so" | ${XARGS} ${STRIP_CMD})
- @(${FIND} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} -maxdepth 3 -type f \
- -name "*.so" | ${XARGS} ${STRIP_CMD})
-
-.include <bsd.port.mk>
diff --git a/biology/crux/distinfo b/biology/crux/distinfo
deleted file mode 100644
index 7a42e305350a..000000000000
--- a/biology/crux/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (crux-1.2.0.tar.bz2) = 11f677e8bf62db69e75271670ea50fb5a23c8a2c526fa9d16ccf2e736e5212c5
-SIZE (crux-1.2.0.tar.bz2) = 1187274
diff --git a/biology/crux/files/patch-lib_Crux_CxPpc.c b/biology/crux/files/patch-lib_Crux_CxPpc.c
deleted file mode 100644
index ea100b5c9928..000000000000
--- a/biology/crux/files/patch-lib_Crux_CxPpc.c
+++ /dev/null
@@ -1,18 +0,0 @@
---- lib/Crux/CxPpc.c.orig 2009-09-19 04:31:04 UTC
-+++ lib/Crux/CxPpc.c
-@@ -8,14 +8,11 @@ bool CxgPpcUseAltivec;
- void
- CxPpcCpuInit(void)
- {
-- int mib[2];
- int result, error;
- size_t len;
-
-- mib[0] = CTL_HW;
-- mib[1] = HW_VECTORUNIT;
- len = sizeof(result);
-- error = sysctl(mib, 2, &result, &len, NULL, 0);
-+ error = sysctlbyname("hw.altivec", &result, &len, NULL, 0);
- if (error != 0)
- {
- CxgPpcUseAltivec = false;
diff --git a/biology/crux/files/pkg-install b/biology/crux/files/pkg-install
deleted file mode 100644
index c2e494752edd..000000000000
--- a/biology/crux/files/pkg-install
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/sh
-
-case $2 in
-POST-INSTALL)
- ${PKG_PREFIX}/bin/crux -b -q /dev/null
- exit 0
- ;;
-esac
diff --git a/biology/crux/pkg-descr b/biology/crux/pkg-descr
deleted file mode 100644
index 5a27474d58b3..000000000000
--- a/biology/crux/pkg-descr
+++ /dev/null
@@ -1,19 +0,0 @@
-Crux is a software toolkit for molecular phylogenetic inference. It is
-structured as a set of Python modules, which makes it possible to quickly
-develop Python scripts that perform unique, non-canned analyses. Features
-include:
-* Tree log-likelihoods can be computed under a variety of models,
- including all specializations of GTR+I+G and mixture models. Tree
- likelihoods can be computed in parallel via pthreads.
-* Bayesian Markov chain Monte Carlo (MCMC) methods (with Metropolis
- coupling) can sample among non-nested models using reversible model
- jumps.
-* Crux is capable of simulating character data under any model its
- likelihood engine is capable of.
-* The neighbor joining (NJ) and relaxed neighbor joining (RNJ)
- implementations are among the fastest in existence.
-* Pairwise distances between sequences can be computed based on percent
- identity, or using methods that correct for multiple hits
- (Jukes-Cantor, Kimura, and logDet).
-
-WWW: http://www.canonware.com/Crux/
diff --git a/biology/crux/pkg-plist b/biology/crux/pkg-plist
deleted file mode 100644
index 643a68f48e4a..000000000000
--- a/biology/crux/pkg-plist
+++ /dev/null
@@ -1,56 +0,0 @@
-bin/crux
-bin/redpoint
-bin/MrRogers
-lib/Crux/lib/libCx.so
-lib/Crux/parsers/Fasta.log
-lib/Crux/parsers/Fasta.pickle
-%%PYTHON_SITELIBDIR%%/Crux/CTMatrix.so
-%%PYTHON_SITELIBDIR%%/Crux/Character.so
-%%PYTHON_SITELIBDIR%%/Crux/Config.py
-@rmtry %%PYTHON_SITELIBDIR%%/Crux/Config.pyo
-%%PYTHON_SITELIBDIR%%/Crux/Copying.py
-@rmtry %%PYTHON_SITELIBDIR%%/Crux/Copying.pyo
-%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/Nj.so
-%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.py
-%%PYTHON_SITELIBDIR%%/Crux/DistMatrix/__init__.so
-%%PYTHON_SITELIBDIR%%/Crux/Fasta.so
-%%PYTHON_SITELIBDIR%%/Crux/Mc3/Chain.so
-%%PYTHON_SITELIBDIR%%/Crux/Mc3/Post.so
-%%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.py
-%%PYTHON_SITELIBDIR%%/Crux/Mc3/__init__.so
-%%PYTHON_SITELIBDIR%%/Crux/Newick.so
-%%PYTHON_SITELIBDIR%%/Crux/Taxa.so
-%%PYTHON_SITELIBDIR%%/Crux/Tree/Bipart.so
-%%PYTHON_SITELIBDIR%%/Crux/Tree/Lik.so
-%%PYTHON_SITELIBDIR%%/Crux/Tree/Sumt.so
-%%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.py
-%%PYTHON_SITELIBDIR%%/Crux/Tree/__init__.so
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/CTMatrix.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Character.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxMath.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxMat.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxNewickLexer.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/CxRi.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Cx.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/DistMatrix/CxDistMatrixLexer.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Crux/Tree/CxLik.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/Nj.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/DistMatrix/__init__.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Fasta.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/Chain.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/Post.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Mc3/__init__.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Newick.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/SFMT/SFMT.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Taxa.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Bipart.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Lik.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/Sumt.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/Tree/__init__.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/__init__.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/libc.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Crux/libm.pxd
-%%PYTHON_SITELIBDIR%%/Crux/include/Parsing.pxd
-%%PYTHON_SITELIBDIR%%/Crux/__init__.py
-%%PYTHON_SITELIBDIR%%/Crux/__init__.so
-%%PYTHON_SITELIBDIR%%/Parsing.so
generated by cgit (git 2.34.1) at 2025-01-08 17:18:44 +0800