From owner-svn-ports-head@freebsd.org Thu Oct 25 07:00:53 2018 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id E0F37FFB4EA; Thu, 25 Oct 2018 07:00:52 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 943AB73F0B; Thu, 25 Oct 2018 07:00:52 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 75049659B; Thu, 25 Oct 2018 07:00:52 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id w9P70qio012114; Thu, 25 Oct 2018 07:00:52 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id w9P70psq012109; Thu, 25 Oct 2018 07:00:51 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201810250700.w9P70psq012109@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Thu, 25 Oct 2018 07:00:51 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r482955 - in head/science/rdkit: . files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/science/rdkit: . files X-SVN-Commit-Revision: 482955 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 25 Oct 2018 07:00:53 -0000 Author: yuri Date: Thu Oct 25 07:00:51 2018 New Revision: 482955 URL: https://svnweb.freebsd.org/changeset/ports/482955 Log: science/rdkit: Update 2018_03_4 -> 2018_09_1 Approved by: portscout Added: head/science/rdkit/files/patch-External_catch_CMakeLists.txt (contents, props changed) Modified: head/science/rdkit/Makefile head/science/rdkit/distinfo head/science/rdkit/files/patch-CMakeLists.txt head/science/rdkit/pkg-plist Modified: head/science/rdkit/Makefile ============================================================================== --- head/science/rdkit/Makefile Thu Oct 25 06:41:55 2018 (r482954) +++ head/science/rdkit/Makefile Thu Oct 25 07:00:51 2018 (r482955) @@ -2,7 +2,7 @@ PORTNAME= rdkit DISTVERSIONPREFIX= Release_ -DISTVERSION= 2018_03_4 +DISTVERSION= 2018_09_1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -11,7 +11,8 @@ COMMENT= Collection of cheminformatics and machine-lea LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt -BUILD_DEPENDS= flex:textproc/flex \ +BUILD_DEPENDS= catch>0:devel/catch \ + flex:textproc/flex \ rapidjson>=0:devel/rapidjson LIB_DEPENDS= libboost_system.so:devel/boost-libs @@ -23,7 +24,7 @@ USE_LDCONFIG= yes CMAKE_OFF= RDK_INSTALL_INTREE RDK_USE_FLEXBISON \ RDK_INSTALL_STATIC_LIBS RDK_SWIG_STATIC RDK_PGSQL_STATIC -CMAKE_ARGS= -DFREEBSD_DOCSDIR:PATH=${DOCSDIR} +CMAKE_ARGS= -DFREEBSD_DOCSDIR:PATH=${DOCSDIR} -DCATCH_DIR=${LOCALBASE} DATADIR= ${PREFIX}/share/RDKit DOCSDIR= ${PREFIX}/share/doc/RDKit @@ -47,5 +48,9 @@ PORTDOCS= * post-extract: @${MKDIR} ${WRKSRC}/External/rapidjson-1.1.0 @cd ${WRKSRC}/External/rapidjson-1.1.0 && ${LN} -s ${LOCALBASE}/include/rapidjson include + +post-stage: # https://github.com/rdkit/rdkit/issues/2094 + #@${MKDIR} ${STAGEDIR}${PREFIX}/lib/cmake + #@${MV} ${STAGEDIR}${PREFIX}/lib/*.cmake ${STAGEDIR}${PREFIX}/lib/cmake .include Modified: head/science/rdkit/distinfo ============================================================================== --- head/science/rdkit/distinfo Thu Oct 25 06:41:55 2018 (r482954) +++ head/science/rdkit/distinfo Thu Oct 25 07:00:51 2018 (r482955) @@ -1,6 +1,6 @@ -TIMESTAMP = 1534554734 -SHA256 (rdkit-rdkit-Release_2018_03_4_GH0.tar.gz) = 9e1a63f3b8c64b9754416073a20292ea79d33ac8aa1485259df1b8db2bfa0113 -SIZE (rdkit-rdkit-Release_2018_03_4_GH0.tar.gz) = 30304198 +TIMESTAMP = 1540446187 +SHA256 (rdkit-rdkit-Release_2018_09_1_GH0.tar.gz) = 61c14652a05a6f6b216ff099381c4dd32048861ba9d96f75a017084e81848baa +SIZE (rdkit-rdkit-Release_2018_09_1_GH0.tar.gz) = 54640418 SHA256 (schrodinger-maeparser-1.0.0_GH0.tar.gz) = f21e49d25fda5fb2ba4d698f104aa3fbfdd131d92f0807f3e617c15ebfc314aa SIZE (schrodinger-maeparser-1.0.0_GH0.tar.gz) = 26292 SHA256 (schrodinger-coordgenlibs-ede3191_GH0.tar.gz) = 85b1ab66647a523a87bee584533fa81315ea82fde42542aa59e1e08bdf734471 Modified: head/science/rdkit/files/patch-CMakeLists.txt ============================================================================== --- head/science/rdkit/files/patch-CMakeLists.txt Thu Oct 25 06:41:55 2018 (r482954) +++ head/science/rdkit/files/patch-CMakeLists.txt Thu Oct 25 07:00:51 2018 (r482955) @@ -1,6 +1,6 @@ ---- CMakeLists.txt.orig 2018-03-22 06:56:06 UTC +--- CMakeLists.txt.orig 2018-10-22 02:29:34 UTC +++ CMakeLists.txt -@@ -338,7 +338,7 @@ if(NOT RDK_INSTALL_INTREE) +@@ -410,7 +410,7 @@ if(NOT RDK_INSTALL_INTREE) PATTERN ".svn" EXCLUDE ) install(DIRECTORY Docs DESTINATION Added: head/science/rdkit/files/patch-External_catch_CMakeLists.txt ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/rdkit/files/patch-External_catch_CMakeLists.txt Thu Oct 25 07:00:51 2018 (r482955) @@ -0,0 +1,17 @@ +--- External/catch/CMakeLists.txt.orig 2018-10-22 02:29:34 UTC ++++ External/catch/CMakeLists.txt +@@ -3,7 +3,7 @@ add_custom_target(catch ALL) + if(NOT DEFINED CATCH_DIR) + set(CATCH_DIR "${CMAKE_CURRENT_SOURCE_DIR}/catch") + endif() +-if(NOT EXISTS "${CATCH_DIR}/single_include") ++if(NOT EXISTS "${CATCH_DIR}/include/catch2") + include(RDKitUtils) + set(RELEASE_NO "2.1.2") + downloadAndCheckMD5("https://github.com/catchorg/Catch2/archive/v${RELEASE_NO}.tar.gz" +@@ -17,4 +17,4 @@ else() + message("-- Found Catch2 source in ${CATCH_DIR}") + endif() + +-set(CATCH_INCLUDE_DIR "${CATCH_DIR}/single_include" PARENT_SCOPE) ++set(CATCH_INCLUDE_DIR "${CATCH_DIR}/include/catch2" PARENT_SCOPE) Modified: head/science/rdkit/pkg-plist ============================================================================== --- head/science/rdkit/pkg-plist Thu Oct 25 06:41:55 2018 (r482954) +++ head/science/rdkit/pkg-plist Thu Oct 25 07:00:51 2018 (r482955) @@ -92,6 +92,7 @@ include/rdkit/GraphMol/Descriptors/AUTOCORR3D.h include/rdkit/GraphMol/Descriptors/ConnectivityDescriptors.h include/rdkit/GraphMol/Descriptors/Crippen.h include/rdkit/GraphMol/Descriptors/Data3Ddescriptors.h +include/rdkit/GraphMol/Descriptors/EEM.h include/rdkit/GraphMol/Descriptors/GETAWAY.h include/rdkit/GraphMol/Descriptors/Lipinski.h include/rdkit/GraphMol/Descriptors/MORSE.h @@ -130,10 +131,16 @@ include/rdkit/GraphMol/FilterCatalog/FilterCatalogEntr include/rdkit/GraphMol/FilterCatalog/FilterMatcherBase.h include/rdkit/GraphMol/FilterCatalog/FilterMatchers.h include/rdkit/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h +include/rdkit/GraphMol/Fingerprints/AtomPairGenerator.h include/rdkit/GraphMol/Fingerprints/AtomPairs.h +include/rdkit/GraphMol/Fingerprints/FingerprintGenerator.h +include/rdkit/GraphMol/Fingerprints/FingerprintUtil.h include/rdkit/GraphMol/Fingerprints/Fingerprints.h include/rdkit/GraphMol/Fingerprints/MACCS.h include/rdkit/GraphMol/Fingerprints/MorganFingerprints.h +include/rdkit/GraphMol/Fingerprints/MorganGenerator.h +include/rdkit/GraphMol/Fingerprints/RDKitFPGenerator.h +include/rdkit/GraphMol/Fingerprints/TopologicalTorsionGenerator.h include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.h include/rdkit/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h include/rdkit/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h @@ -164,14 +171,30 @@ include/rdkit/GraphMol/MolDraw2D/MolDraw2DDetails.h include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h include/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.h include/rdkit/GraphMol/MolDraw2D/MolDraw2Dwx.h -include/rdkit/GraphMol/MolDrawing/DrawingToCairo.h -include/rdkit/GraphMol/MolDrawing/DrawingToSVG.h -include/rdkit/GraphMol/MolDrawing/MolDrawing.h include/rdkit/GraphMol/MolHash/MolHash.h include/rdkit/GraphMol/MolInterchange/MolInterchange.h include/rdkit/GraphMol/MolInterchange/details.h include/rdkit/GraphMol/MolOps.h include/rdkit/GraphMol/MolPickler.h +include/rdkit/GraphMol/MolStandardize/AcidBaseCatalogEntry.h +include/rdkit/GraphMol/MolStandardize/AcidBaseCatalogParams.h +include/rdkit/GraphMol/MolStandardize/AcidBaseCatalogUtils.h +include/rdkit/GraphMol/MolStandardize/Charge.h +include/rdkit/GraphMol/MolStandardize/Fragment.h +include/rdkit/GraphMol/MolStandardize/FragmentCatalogEntry.h +include/rdkit/GraphMol/MolStandardize/FragmentCatalogParams.h +include/rdkit/GraphMol/MolStandardize/FragmentCatalogUtils.h +include/rdkit/GraphMol/MolStandardize/Metal.h +include/rdkit/GraphMol/MolStandardize/MolStandardize.h +include/rdkit/GraphMol/MolStandardize/Normalize.h +include/rdkit/GraphMol/MolStandardize/Tautomer.h +include/rdkit/GraphMol/MolStandardize/TautomerCatalogEntry.h +include/rdkit/GraphMol/MolStandardize/TautomerCatalogParams.h +include/rdkit/GraphMol/MolStandardize/TautomerCatalogUtils.h +include/rdkit/GraphMol/MolStandardize/TransformCatalogEntry.h +include/rdkit/GraphMol/MolStandardize/TransformCatalogParams.h +include/rdkit/GraphMol/MolStandardize/TransformCatalogUtils.h +include/rdkit/GraphMol/MolStandardize/Validate.h include/rdkit/GraphMol/MolTransforms/MolTransforms.h include/rdkit/GraphMol/MonomerInfo.h include/rdkit/GraphMol/PartialCharges/GasteigerCharges.h @@ -200,6 +223,7 @@ include/rdkit/GraphMol/SmilesParse/SmilesParse.h include/rdkit/GraphMol/SmilesParse/SmilesParseOps.h include/rdkit/GraphMol/SmilesParse/SmilesWrite.h include/rdkit/GraphMol/SmilesParse/primes.h +include/rdkit/GraphMol/StereoGroup.h include/rdkit/GraphMol/StructChecker/Pattern.h include/rdkit/GraphMol/StructChecker/ReCharge.h include/rdkit/GraphMol/StructChecker/Stereo.h @@ -251,6 +275,7 @@ include/rdkit/RDGeneral/FileParseException.h include/rdkit/RDGeneral/Invariant.h include/rdkit/RDGeneral/LocaleSwitcher.h include/rdkit/RDGeneral/RDAny.h +include/rdkit/RDGeneral/RDConfig.h include/rdkit/RDGeneral/RDLog.h include/rdkit/RDGeneral/RDProps.h include/rdkit/RDGeneral/RDThreads.h @@ -259,18 +284,24 @@ include/rdkit/RDGeneral/RDValue-taggedunion.h include/rdkit/RDGeneral/RDValue.h include/rdkit/RDGeneral/Ranking.h include/rdkit/RDGeneral/StreamOps.h +include/rdkit/RDGeneral/export.h include/rdkit/RDGeneral/hanoiSort.h include/rdkit/RDGeneral/hash/hash/detail/float_functions.hpp include/rdkit/RDGeneral/hash/hash/detail/hash_float.hpp include/rdkit/RDGeneral/hash/hash/extensions.hpp include/rdkit/RDGeneral/hash/hash/hash.hpp include/rdkit/RDGeneral/hash/hash/hash_fwd.hpp +include/rdkit/RDGeneral/test.h include/rdkit/RDGeneral/types.h include/rdkit/RDGeneral/utils.h include/rdkit/RDGeneral/versions.h include/rdkit/SimDivPickers/DistPicker.h include/rdkit/SimDivPickers/HierarchicalClusterPicker.h include/rdkit/SimDivPickers/MaxMinPicker.h +lib/cmake/rdkit/rdkit-config-version.cmake +lib/cmake/rdkit/rdkit-config.cmake +lib/cmake/rdkit/rdkit-targets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/rdkit/rdkit-targets.cmake lib/libRDKitAlignment.so lib/libRDKitAlignment.so.1 lib/libRDKitAlignment.so.1.%%SHLIB_VER%% @@ -352,6 +383,9 @@ lib/libRDKitMolHash.so.1.%%SHLIB_VER%% lib/libRDKitMolInterchange.so lib/libRDKitMolInterchange.so.1 lib/libRDKitMolInterchange.so.1.%%SHLIB_VER%% +lib/libRDKitMolStandardize.so +lib/libRDKitMolStandardize.so.1 +lib/libRDKitMolStandardize.so.1.%%SHLIB_VER%% lib/libRDKitMolTransforms.so lib/libRDKitMolTransforms.so.1 lib/libRDKitMolTransforms.so.1.%%SHLIB_VER%% @@ -489,6 +523,19 @@ lib/libRDKitmaeparser.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolKey/InchiInfo.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolKey/MolKey.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolKey/__init__.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/__init__.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/charge.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/errors.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/fragment.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/metal.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/normalize.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/rdMolStandardize.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/resonance.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/standardize.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/tautomer.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/utils.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/validate.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolStandardize/validations.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/MolSurf.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/PandasTools.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/PeriodicTable.py @@ -538,6 +585,7 @@ lib/libRDKitmaeparser.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdDepictor.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdDistGeom.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdFMCS.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdFingerprintGenerator.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdForceFieldHelpers.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMMPA.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolAlign.so @@ -696,7 +744,6 @@ lib/libRDKitmaeparser.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/VLib/__init__.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/__init__.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/_py2_pickle.py -%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/epydoc.config %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/rdBase.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/six.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/sping/PDF/__init__.py @@ -847,12 +894,10 @@ lib/libRDKitmaeparser.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/test1.gif %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/test2.gif %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/test3.gif -lib/rdkit-config-version.cmake -lib/rdkit-config.cmake -lib/rdkit-targets-%%CMAKE_BUILD_TYPE%%.cmake -lib/rdkit-targets.cmake %%DATADIR%%/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py %%DATADIR%%/Contrib/CMakeLists.txt +%%DATADIR%%/Contrib/ChiralPairs/ChiralDescriptors.py +%%DATADIR%%/Contrib/ChiralPairs/README.txt %%DATADIR%%/Contrib/ConformerParser/CMakeLists.txt %%DATADIR%%/Contrib/ConformerParser/ConformerParser.cpp %%DATADIR%%/Contrib/ConformerParser/ConformerParser.h @@ -885,6 +930,7 @@ lib/rdkit-targets.cmake %%DATADIR%%/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef %%DATADIR%%/Contrib/M_Kossner/Frames.py %%DATADIR%%/Contrib/M_Kossner/README +%%DATADIR%%/Contrib/MolVS/molvs_cli.py %%DATADIR%%/Contrib/NP_Score/README %%DATADIR%%/Contrib/NP_Score/npscorer.py %%DATADIR%%/Contrib/NP_Score/publicnp.model.gz @@ -959,6 +1005,11 @@ lib/rdkit-targets.cmake %%DATADIR%%/Data/FragmentDescriptors.csv %%DATADIR%%/Data/FunctionalGroups.txt %%DATADIR%%/Data/Functional_Group_Hierarchy.txt +%%DATADIR%%/Data/MolStandardize/acid_base_pairs.txt +%%DATADIR%%/Data/MolStandardize/acid_base_pairs2.txt +%%DATADIR%%/Data/MolStandardize/fragmentPatterns.txt +%%DATADIR%%/Data/MolStandardize/normalizations.txt +%%DATADIR%%/Data/MolStandardize/tautomerTransforms.in %%DATADIR%%/Data/NCI/first_200.props.sdf %%DATADIR%%/Data/NCI/first_200.tpsa.csv %%DATADIR%%/Data/NCI/first_5K.smi @@ -995,4 +1046,5 @@ lib/rdkit-targets.cmake %%PYTHON%%%%DATADIR%%/Scripts/FeatFinderCLI.py %%PYTHON%%%%DATADIR%%/Scripts/PythonFormat.py %%PYTHON%%%%DATADIR%%/Scripts/README.md +%%PYTHON%%%%DATADIR%%/Scripts/create_deb_packages.sh %%DATADIR%%/license.txt