Date: Tue, 27 May 2014 21:30:32 +0600 (BDT) From: Muhammad Moinur Rahman <5u623l20@gmail.com> To: FreeBSD-gnats-submit@FreeBSD.org Cc: wen@FreeBSD.org Subject: ports/190314: [PATCH] science/py-mlpy: update to 3.5.0, Added STAGE support Message-ID: <201405271530.s4RFUW5k067801@bofh.1asiacom.net> Resent-Message-ID: <201405271540.s4RFe0mC014870@freefall.freebsd.org>
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>Number: 190314 >Category: ports >Synopsis: [PATCH] science/py-mlpy: update to 3.5.0, Added STAGE support >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Tue May 27 15:40:00 UTC 2014 >Closed-Date: >Last-Modified: >Originator: Muhammad Moinur Rahman >Release: FreeBSD 11.0-CURRENT amd64 >Organization: >Environment: System: FreeBSD bofh.1asiacom.net 11.0-CURRENT FreeBSD 11.0-CURRENT #2 r265972: Wed May 14 02:05:04 BDT >Description: - Added STAGE support - Update to 3.5.0 For Committer's reference: http://pdr.s.ubze.ro/bulk/latest-per-pkg/py27-mlpy/3.5.0/ Port maintainer (wen@FreeBSD.org) is cc'd. Generated with FreeBSD Port Tools 1.02 (mode: update, diff: ports) >How-To-Repeat: >Fix: --- py-mlpy-3.5.0.patch begins here --- diff -ruN /usr/ports//science/py-mlpy/Makefile ./Makefile --- /usr/ports//science/py-mlpy/Makefile 2014-03-11 02:55:20.000000000 +0600 +++ ./Makefile 2014-05-27 21:07:19.626722742 +0600 @@ -2,26 +2,26 @@ # $FreeBSD: head/science/py-mlpy/Makefile 347809 2014-03-10 20:55:20Z gerald $ PORTNAME= mlpy -PORTVERSION= 2.2.2 -PORTREVISION= 4 +PORTVERSION= 3.5.0 CATEGORIES= science python -MASTER_SITES= https://mlpy.fbk.eu/download/src/ +MASTER_SITES= SF/${PORTNAME}/${PORTNAME}%20${PORTVERSION} PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} -DISTNAME= MLPY-${PORTVERSION} MAINTAINER= wen@FreeBSD.org COMMENT= High performance Python package for predictive modeling +LICENSE= GPLv3 + BUILD_DEPENDS= ${PYTHON_SITELIBDIR}/numpy:${PORTSDIR}/math/py-numpy \ cython>0:${PORTSDIR}/lang/cython RUN_DEPENDS:= ${BUILD_DEPENDS} -LIB_DEPENDS= gsl:${PORTSDIR}/math/gsl +LIB_DEPENDS= libgsl.so:${PORTSDIR}/math/gsl +USE_LDCONFIG= yes CFLAGS+= -I${LOCALBASE}/include -I${PYTHON_SITELIBDIR}/numpy/core LDFLAGS+= -L${LOCALBASE}/lib USE_PYTHON= yes USE_PYDISTUTILS= yes -PYDISTUTILS_PKGNAME= MLPY +PYDISTUTILS_AUTOPLIST= yes -NO_STAGE= yes .include <bsd.port.mk> diff -ruN /usr/ports//science/py-mlpy/distinfo ./distinfo --- /usr/ports//science/py-mlpy/distinfo 2014-01-22 21:30:13.000000000 +0600 +++ ./distinfo 2014-05-27 20:33:43.741863451 +0600 @@ -1,2 +1,2 @@ -SHA256 (MLPY-2.2.2.tar.gz) = 2c2864834ced9caddea83bc05ffc7526325cf5bffcfd6c3c4cf13097312b0057 -SIZE (MLPY-2.2.2.tar.gz) = 235665 +SHA256 (mlpy-3.5.0.tar.gz) = 344fa75fbf9f76af72f6a346d5309613defc4d244bac13c218e509a51d68bf6a +SIZE (mlpy-3.5.0.tar.gz) = 1961206 diff -ruN /usr/ports//science/py-mlpy/files/patch-mlpy-cwt-cwb.c ./files/patch-mlpy-cwt-cwb.c --- /usr/ports//science/py-mlpy/files/patch-mlpy-cwt-cwb.c 2014-01-22 23:40:44.000000000 +0600 +++ ./files/patch-mlpy-cwt-cwb.c 1970-01-01 06:00:00.000000000 +0600 @@ -1,17 +0,0 @@ ---- mlpy/cwt/cwb.c.orig 2010-12-21 09:10:04.000000000 +0800 -+++ mlpy/cwt/cwb.c 2010-12-21 09:12:05.000000000 +0800 -@@ -142,9 +142,12 @@ - complex double p = 0.0 + 0.0I; - double sw, norm = 1.0; - -- -+#ifndef __STD_IEC_559_COMPLEX__ /* FreeBSD lacks C99 cpow() */ -+ p = - gsl_complex_pow(0.0 + 1.0I, order) / sqrt(gsl_sf_gamma(order + 0.5)); -+#else - p = - cpow(0.0 + 1.0I, order) / sqrt(gsl_sf_gamma(order + 0.5)); -- -+#endif /* __STD_IEC_559_COMPLEX__ */ -+ - for (i=0; i<n; i++) - { - if (nm == 1) diff -ruN /usr/ports//science/py-mlpy/files/patch-setup.py ./files/patch-setup.py --- /usr/ports//science/py-mlpy/files/patch-setup.py 2014-01-22 23:40:44.000000000 +0600 +++ ./files/patch-setup.py 1970-01-01 06:00:00.000000000 +0600 @@ -1,17 +0,0 @@ ---- setup.py.orig 2010-10-18 20:08:13.000000000 +0800 -+++ setup.py 2010-12-23 15:19:09.000000000 +0800 -@@ -158,11 +158,13 @@ - "mlpy/liblinear/liblinear/blas/daxpy.c", - "mlpy/liblinear/liblinear/blas/ddot.c", - "mlpy/liblinear/liblinear/blas/dnrm2.c", -- "mlpy/liblinear/liblinear/blas/dscal.c"], -+ "mlpy/liblinear/liblinear/blas/dscal.c"], -+ include_dirs=base_include, - extra_compile_args=extra_compile_args), - Extension("mlpy.libsvm", - ["mlpy/libsvm/libsvm/svm.cpp", - "mlpy/libsvm/libsvm.pyx"], -+ include_dirs=base_include, - extra_compile_args=extra_compile_args) - ], - scripts=["mlpy/tools/mlpy-test"], diff -ruN /usr/ports//science/py-mlpy/pkg-descr ./pkg-descr --- /usr/ports//science/py-mlpy/pkg-descr 2014-01-22 21:44:51.000000000 +0600 +++ ./pkg-descr 2014-05-27 20:22:04.699909932 +0600 @@ -8,4 +8,4 @@ resampling, error evaluation and experiment landscaping.The package includes tools to measure stability in sets of ranked feature lists. -WWW: http://mlpy.fbk.eu/ +WWW: http://mlpy.sourceforge.net/ diff -ruN /usr/ports//science/py-mlpy/pkg-plist ./pkg-plist --- /usr/ports//science/py-mlpy/pkg-plist 2014-01-22 21:16:56.000000000 +0600 +++ ./pkg-plist 1970-01-01 06:00:00.000000000 +0600 @@ 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-%%PYTHON_SITELIBDIR%%/mlpy/_irelief.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_iuwt.py -%%PYTHON_SITELIBDIR%%/mlpy/_iuwt.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_iuwt.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_kernel.py -%%PYTHON_SITELIBDIR%%/mlpy/_kernel.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_kernel.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_kmeans.py -%%PYTHON_SITELIBDIR%%/mlpy/_kmeans.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_kmeans.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_kmedoids.py -%%PYTHON_SITELIBDIR%%/mlpy/_kmedoids.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_kmedoids.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_knn.py -%%PYTHON_SITELIBDIR%%/mlpy/_knn.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_lars.py -%%PYTHON_SITELIBDIR%%/mlpy/_lars.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_lars.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_knn.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_metrics.py -%%PYTHON_SITELIBDIR%%/mlpy/_metrics.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_metrics.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_minkowski.py -%%PYTHON_SITELIBDIR%%/mlpy/_minkowski.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_minkowski.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_pda.py -%%PYTHON_SITELIBDIR%%/mlpy/_pda.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_pda.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_ranking.py -%%PYTHON_SITELIBDIR%%/mlpy/_ranking.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_ranking.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_resampling.py -%%PYTHON_SITELIBDIR%%/mlpy/_resampling.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_resampling.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_ridgeregression.py -%%PYTHON_SITELIBDIR%%/mlpy/_ridgeregression.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_ridgeregression.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_spectralreg.py -%%PYTHON_SITELIBDIR%%/mlpy/_spectralreg.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_spectralreg.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_srda.py -%%PYTHON_SITELIBDIR%%/mlpy/_srda.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_srda.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_svm.py -%%PYTHON_SITELIBDIR%%/mlpy/_svm.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_svm.pyo -%%PYTHON_SITELIBDIR%%/mlpy/_uwt.py -%%PYTHON_SITELIBDIR%%/mlpy/_uwt.pyc -%%PYTHON_SITELIBDIR%%/mlpy/_uwt.pyo -%%PYTHON_SITELIBDIR%%/mlpy/canberra.so -%%PYTHON_SITELIBDIR%%/mlpy/cwb.so -%%PYTHON_SITELIBDIR%%/mlpy/dtw.so -%%PYTHON_SITELIBDIR%%/mlpy/dwt.so -%%PYTHON_SITELIBDIR%%/mlpy/elasticnet.so -%%PYTHON_SITELIBDIR%%/mlpy/fssun.so -%%PYTHON_SITELIBDIR%%/mlpy/hc.so -%%PYTHON_SITELIBDIR%%/mlpy/irregularuwt.so -%%PYTHON_SITELIBDIR%%/mlpy/gslpy.so -%%PYTHON_SITELIBDIR%%/mlpy/kmeans.so -%%PYTHON_SITELIBDIR%%/mlpy/kernel.so -%%PYTHON_SITELIBDIR%%/mlpy/knn.so -%%PYTHON_SITELIBDIR%%/mlpy/liblinear.so -%%PYTHON_SITELIBDIR%%/mlpy/libsvm.so -%%PYTHON_SITELIBDIR%%/mlpy/misc.so -%%PYTHON_SITELIBDIR%%/mlpy/peaksd.so -%%PYTHON_SITELIBDIR%%/mlpy/spectralreg.so -%%PYTHON_SITELIBDIR%%/mlpy/svm.so -%%PYTHON_SITELIBDIR%%/mlpy/uwt.so -%%PYTHON_SITELIBDIR%%/mlpy/version.py -%%PYTHON_SITELIBDIR%%/mlpy/version.pyc -%%PYTHON_SITELIBDIR%%/mlpy/version.pyo -@dirrm %%PYTHON_SITELIBDIR%%/mlpy --- py-mlpy-3.5.0.patch ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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