Date: Mon, 7 Jan 2013 17:36:05 GMT From: Robert Kruus <rob.kruus@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/175110: rpy2 and external lapack Message-ID: <201301071736.r07Ha51S009848@red.freebsd.org> Resent-Message-ID: <201301071740.r07HeeYH059839@freefall.freebsd.org>
next in thread | raw e-mail | index | archive | help
>Number: 175110 >Category: ports >Synopsis: rpy2 and external lapack >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: sw-bug >Submitter-Id: current-users >Arrival-Date: Mon Jan 07 17:40:00 UTC 2013 >Closed-Date: >Last-Modified: >Originator: Robert Kruus >Release: 8.1 >Organization: Government of Saskatchewan >Environment: FreeBSD wfm.gos.ca 8.1-RELEASE FreeBSD 8.1-RELEASE #0: Wed Aug 11 16:42:44 CST 2010 root@thunder.gos.ca:/usr/obj/usr/src/sys/GENERIC amd64 >Description: The latest version of rpy2 fails to build: /usr/bin/ld: cannot find -lalapack >How-To-Repeat: >Fix: Created a patch to add $LOCALBASE/lib to setup.cfg and patched the rpy2 Makefile accordingly. Patch attached with submission follows: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # ./ # ./pkg-descr # ./files # ./files/patch-setup.cfg # ./pkg-plist # ./distinfo # ./Makefile # echo c - ./ mkdir -p ./ > /dev/null 2>&1 echo x - ./pkg-descr sed 's/^X//' >./pkg-descr << '0e313719ff012ceaf97a028d51caa8f5' XRPy is a very simple, yet robust, Python interface to the R Programming XLanguage. It can manage all kinds of R objects and can execute arbitrary XR functions (including the graphic functions). All the errors from the XR language are converted to Python exceptions. Any module that later were Xinstalled on the R system, can easily be used from within Python, without Xintroducing any changes. X Xrpy2 is a redesign and rewrite of rpy. It is providing a low-level interface Xto R, a proposed high-level interface, including wrappers to graphical Xlibraries, as well as R-like structures and functions. X XWWW: http://rpy.sourceforge.net/rpy2.html 0e313719ff012ceaf97a028d51caa8f5 echo c - ./files mkdir -p ./files > /dev/null 2>&1 echo x - ./files/patch-setup.cfg sed 's/^X//' >./files/patch-setup.cfg << '6ce685d5b1fafecc657832ce933d7914' X--- setup.cfg.orig 2013-01-07 10:39:43.373742059 -0600 X+++ setup.cfg 2013-01-07 10:42:46.934896806 -0600 X@@ -1,4 +1,5 @@ X [egg_info] X tag_build = dev X tag_date = true X- X+[build_ext] X+library-dirs = %%LOCALBASE%%/lib 6ce685d5b1fafecc657832ce933d7914 echo x - ./pkg-plist sed 's/^X//' >./pkg-plist << 'ef3e7f63841ae908ba397c2bef1fbad6' X%%PYTHON_SITELIBDIR%%/rpy2/__init__.py X%%PYTHON_SITELIBDIR%%/rpy2/__init__.pyc X%%PYTHON_SITELIBDIR%%/rpy2/__init__.pyo X%%PYTHON_SITELIBDIR%%/rpy2/images/rpy2_logo.png X%%PYTHON_SITELIBDIR%%/rpy2/interactive/__init__.py X%%PYTHON_SITELIBDIR%%/rpy2/interactive/__init__.pyc X%%PYTHON_SITELIBDIR%%/rpy2/interactive/__init__.pyo X%%PYTHON_SITELIBDIR%%/rpy2/interactive/process_revents.py X%%PYTHON_SITELIBDIR%%/rpy2/interactive/process_revents.pyc X%%PYTHON_SITELIBDIR%%/rpy2/interactive/process_revents.pyo X%%PYTHON_SITELIBDIR%%/rpy2/interactive/tests/__init__.py X%%PYTHON_SITELIBDIR%%/rpy2/interactive/tests/__init__.pyc X%%PYTHON_SITELIBDIR%%/rpy2/interactive/tests/__init__.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/__init__.py X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/__init__.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/__init__.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/_rinterface.so X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/rpy_device.so X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/__init__.py X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/__init__.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/__init__.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_Device.py X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_Device.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_Device.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_EmbeddedR.py X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_EmbeddedR.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_EmbeddedR.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_Sexp.py X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_Sexp.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_Sexp.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpClosure.py X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpClosure.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpClosure.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpEnvironment.py X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpEnvironment.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpEnvironment.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpExtPtr.py X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpExtPtr.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpExtPtr.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpVector.py X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpVector.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpVector.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpVectorNumeric.py X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpVectorNumeric.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests/test_SexpVectorNumeric.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rlike/__init__.py X%%PYTHON_SITELIBDIR%%/rpy2/rlike/__init__.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rlike/__init__.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rlike/container.py X%%PYTHON_SITELIBDIR%%/rpy2/rlike/container.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rlike/container.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rlike/functional.py X%%PYTHON_SITELIBDIR%%/rpy2/rlike/functional.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rlike/functional.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rlike/indexing.py X%%PYTHON_SITELIBDIR%%/rpy2/rlike/indexing.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rlike/indexing.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/__init__.py X%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/__init__.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/__init__.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_container.py X%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_container.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_container.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_functional.py X%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_functional.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_functional.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_indexing.py X%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_indexing.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rlike/tests/test_indexing.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/__init__.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/__init__.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/__init__.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/constants.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/constants.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/constants.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/conversion.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/conversion.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/conversion.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/environments.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/environments.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/environments.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/functions.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/functions.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/functions.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/help.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/help.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/help.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/language.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/language.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/language.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/__init__.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/__init__.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/__init__.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/ggplot2.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/ggplot2.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/ggplot2.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/grid.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/grid.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/lib/grid.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/methods.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/methods.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/methods.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/numpy2ri.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/numpy2ri.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/numpy2ri.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/packages.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/packages.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/packages.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/robject.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/robject.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/robject.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/__init__.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/__init__.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/__init__.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testArray.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testArray.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testArray.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testDataFrame.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testDataFrame.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testDataFrame.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testEnvironment.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testEnvironment.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testEnvironment.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testFormula.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testFormula.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testFormula.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testFunction.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testFunction.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testFunction.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testHelp.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testHelp.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testHelp.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testLanguage.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testLanguage.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testLanguage.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testMethods.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testMethods.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testMethods.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testNumpyConversions.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testNumpyConversions.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testNumpyConversions.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testPackages.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testPackages.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testPackages.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testRObject.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testRObject.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testRObject.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testRobjects.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testRobjects.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testRobjects.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testVector.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testVector.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/tests/testVector.pyo X%%PYTHON_SITELIBDIR%%/rpy2/robjects/vectors.py X%%PYTHON_SITELIBDIR%%/rpy2/robjects/vectors.pyc X%%PYTHON_SITELIBDIR%%/rpy2/robjects/vectors.pyo X%%PYTHON_SITELIBDIR%%/rpy2/rpy_classic.py X%%PYTHON_SITELIBDIR%%/rpy2/rpy_classic.pyc X%%PYTHON_SITELIBDIR%%/rpy2/rpy_classic.pyo X%%PYTHON_SITELIBDIR%%/rpy2/tests.py X%%PYTHON_SITELIBDIR%%/rpy2/tests.pyc X%%PYTHON_SITELIBDIR%%/rpy2/tests.pyo X%%PYTHON_SITELIBDIR%%/rpy2/tests_rpy_classic.py X%%PYTHON_SITELIBDIR%%/rpy2/tests_rpy_classic.pyc X%%PYTHON_SITELIBDIR%%/rpy2/tests_rpy_classic.pyo X@dirrm %%PYTHON_SITELIBDIR%%/rpy2/images X@dirrm %%PYTHON_SITELIBDIR%%/rpy2/interactive/tests X@dirrm %%PYTHON_SITELIBDIR%%/rpy2/interactive X@dirrm %%PYTHON_SITELIBDIR%%/rpy2/rinterface/tests X@dirrm %%PYTHON_SITELIBDIR%%/rpy2/rinterface X@dirrm %%PYTHON_SITELIBDIR%%/rpy2/rlike/tests X@dirrm %%PYTHON_SITELIBDIR%%/rpy2/rlike X@dirrm %%PYTHON_SITELIBDIR%%/rpy2/robjects/lib X@dirrm %%PYTHON_SITELIBDIR%%/rpy2/robjects/tests X@dirrm %%PYTHON_SITELIBDIR%%/rpy2/robjects X@dirrm %%PYTHON_SITELIBDIR%%/rpy2 ef3e7f63841ae908ba397c2bef1fbad6 echo x - ./distinfo sed 's/^X//' >./distinfo << 'aec8793adfd5b7c3f00e62ae41a09ac2' XSHA256 (rpy2-2.2.6.tar.gz) = 7e6b3ac86edcc66e59a98d5821581e36d4bfe9552d7f2da95610b730e5f0ef28 XSIZE (rpy2-2.2.6.tar.gz) = 167112 aec8793adfd5b7c3f00e62ae41a09ac2 echo x - ./Makefile sed 's/^X//' >./Makefile << '464ef7c6571951809b23e262cbe26e19' X# Created by: ijliao X# $FreeBSD: ports/math/rpy2/Makefile,v 1.39 2013/01/04 18:45:35 svnexp Exp $ X XPORTNAME= rpy2 XPORTVERSION= 2.2.6 XPORTREVISION= 4 XCATEGORIES= math XMASTER_SITES= CHEESESHOP \ X SF X XMAINTAINER= wen@FreeBSD.org XCOMMENT= Python interface to the R Programming Language X XBUILD_DEPENDS= ${PYTHON_SITELIBDIR}/numpy:${PORTSDIR}/math/py-numpy \ X R:${PORTSDIR}/math/R XRUN_DEPENDS= ${PYTHON_SITELIBDIR}/numpy:${PORTSDIR}/math/py-numpy \ X R:${PORTSDIR}/math/R X XUSE_PYTHON= yes XUSE_PYDISTUTILS= yes X Xpost-patch: X @${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|g' ${WRKSRC}/setup.py X @${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|g' ${WRKSRC}/setup.cfg X Xpre-configure: X @(if [ ! -e ${LOCALBASE}/lib/R/lib/libR.so ] ; then \ X ${ECHO_MSG} "==> ${PKGNAME} requires math/R to be built WITH_LIBR" ; \ X exit 1; fi) X X.include <bsd.port.mk> 464ef7c6571951809b23e262cbe26e19 exit >Release-Note: >Audit-Trail: >Unformatted:
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201301071736.r07Ha51S009848>