From owner-svn-ports-head@freebsd.org Mon May 14 06:42:04 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 83538FDC2E5; Mon, 14 May 2018 06:42:04 +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 330D886030; Mon, 14 May 2018 06:42:04 +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 1188B18A2C; Mon, 14 May 2018 06:42:04 +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 w4E6g3Ou019540; Mon, 14 May 2018 06:42:03 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id w4E6g3U4019537; Mon, 14 May 2018 06:42:03 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201805140642.w4E6g3U4019537@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Mon, 14 May 2018 06:42:03 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r469854 - head/science/rdkit X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: head/science/rdkit X-SVN-Commit-Revision: 469854 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: 2.1.26 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: Mon, 14 May 2018 06:42:04 -0000 Author: yuri Date: Mon May 14 06:42:03 2018 New Revision: 469854 URL: https://svnweb.freebsd.org/changeset/ports/469854 Log: science/rdkit: Update 2017_09_3 -> 2018_03_1 Port changes: * Add GH_TUPLE for 2 new bundled dependencies * Add BUILD_DEPENDS and post-extract script for the new rapidjson dependency Reported by: portscout Modified: head/science/rdkit/Makefile head/science/rdkit/distinfo head/science/rdkit/pkg-plist Modified: head/science/rdkit/Makefile ============================================================================== --- head/science/rdkit/Makefile Mon May 14 06:04:13 2018 (r469853) +++ head/science/rdkit/Makefile Mon May 14 06:42:03 2018 (r469854) @@ -2,8 +2,7 @@ PORTNAME= rdkit DISTVERSIONPREFIX= Release_ -DISTVERSION= 2017_09_3 -PORTREVISION= 2 +DISTVERSION= 2018_03_1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org @@ -12,11 +11,14 @@ COMMENT= Collection of cheminformatics and machine-lea LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt -BUILD_DEPENDS= flex:textproc/flex +BUILD_DEPENDS= flex:textproc/flex \ + rapidjson>=0:devel/rapidjson LIB_DEPENDS= libboost_system.so:devel/boost-libs USES= bison:build cmake:outsource eigen:3 python USE_GITHUB= yes +GH_TUPLE= schrodinger:maeparser:8336829:maeparser/External/CoordGen/maeparser \ + schrodinger:coordgenlibs:ede3191:coordgenlibs/External/CoordGen/coordgenlibs USE_LDCONFIG= yes CMAKE_OFF= RDK_INSTALL_INTREE RDK_USE_FLEXBISON \ @@ -41,5 +43,9 @@ PYTHON_RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}reportlab>0:print/py-reportlab@${PY_FLAVOR} PORTDOCS= * + +post-extract: + @${MKDIR} ${WRKSRC}/External/rapidjson-1.1.0 + @cd ${WRKSRC}/External/rapidjson-1.1.0 && ${LN} -s ${LOCALBASE}/include/rapidjson include .include Modified: head/science/rdkit/distinfo ============================================================================== --- head/science/rdkit/distinfo Mon May 14 06:04:13 2018 (r469853) +++ head/science/rdkit/distinfo Mon May 14 06:42:03 2018 (r469854) @@ -1,3 +1,7 @@ -TIMESTAMP = 1521697971 -SHA256 (rdkit-rdkit-Release_2017_09_3_GH0.tar.gz) = 6a4d9e9eb0ca06cbcdc20505f0c6ea0b1167b4dcdf7d1185871ba16ce701a5f4 -SIZE (rdkit-rdkit-Release_2017_09_3_GH0.tar.gz) = 29567648 +TIMESTAMP = 1524726444 +SHA256 (rdkit-rdkit-Release_2018_03_1_GH0.tar.gz) = 9edac0f57c963947b59dfe6f5a84cf3bd2d93ca7111d4d3cf883c9c61756905d +SIZE (rdkit-rdkit-Release_2018_03_1_GH0.tar.gz) = 30290905 +SHA256 (schrodinger-maeparser-8336829_GH0.tar.gz) = b075902313b95e17057199591b90c801c922d63669e8900dea95bef74d41e600 +SIZE (schrodinger-maeparser-8336829_GH0.tar.gz) = 24974 +SHA256 (schrodinger-coordgenlibs-ede3191_GH0.tar.gz) = 85b1ab66647a523a87bee584533fa81315ea82fde42542aa59e1e08bdf734471 +SIZE (schrodinger-coordgenlibs-ede3191_GH0.tar.gz) = 3721485 Modified: head/science/rdkit/pkg-plist ============================================================================== --- head/science/rdkit/pkg-plist Mon May 14 06:04:13 2018 (r469853) +++ head/science/rdkit/pkg-plist Mon May 14 06:42:03 2018 (r469854) @@ -83,6 +83,7 @@ include/rdkit/GraphMol/ChemTransforms/ChemTransforms.h include/rdkit/GraphMol/ChemTransforms/MolFragmenter.h include/rdkit/GraphMol/Chirality.h include/rdkit/GraphMol/Conformer.h +include/rdkit/GraphMol/CoordGen.h include/rdkit/GraphMol/Depictor/DepictUtils.h include/rdkit/GraphMol/Depictor/EmbeddedFrag.h include/rdkit/GraphMol/Depictor/RDDepictor.h @@ -167,6 +168,8 @@ 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/MolTransforms/MolTransforms.h @@ -346,6 +349,9 @@ lib/libRDKitMolDraw2D.so.1.%%SHLIB_VER%% lib/libRDKitMolHash.so lib/libRDKitMolHash.so.1 lib/libRDKitMolHash.so.1.%%SHLIB_VER%% +lib/libRDKitMolInterchange.so +lib/libRDKitMolInterchange.so.1 +lib/libRDKitMolInterchange.so.1.%%SHLIB_VER%% lib/libRDKitMolTransforms.so lib/libRDKitMolTransforms.so.1 lib/libRDKitMolTransforms.so.1.%%SHLIB_VER%% @@ -397,9 +403,15 @@ lib/libRDKitSubstructMatch.so.1.%%SHLIB_VER%% lib/libRDKitTrajectory.so lib/libRDKitTrajectory.so.1 lib/libRDKitTrajectory.so.1.%%SHLIB_VER%% +lib/libRDKitcoordgenlib.so +lib/libRDKitcoordgenlib.so.1 +lib/libRDKitcoordgenlib.so.1.%%SHLIB_VER%% lib/libRDKithc.so lib/libRDKithc.so.1 lib/libRDKithc.so.1.%%SHLIB_VER%% +lib/libRDKitmaeparser.so +lib/libRDKitmaeparser.so.1 +lib/libRDKitmaeparser.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Avalon/__init__.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/AllChem.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/AtomPairs/Pairs.py @@ -438,6 +450,7 @@ lib/libRDKithc.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/EState/EState_VSA.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/EState/Fingerprinter.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/EState/__init__.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/EnumerateHeterocycles.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/EnumerateStereoisomers.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/FastSDMolSupplier.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/FeatFinderCLI.py @@ -521,6 +534,7 @@ lib/libRDKithc.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/inchi.py %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdChemReactions.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdChemicalFeatures.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdCoordGen.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdDepictor.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdDistGeom.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdFMCS.so @@ -531,6 +545,7 @@ lib/libRDKithc.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolChemicalFeatures.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolDescriptors.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolHash.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolInterchange.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdMolTransforms.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdPartialCharges.so %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/Chem/rdRGroupDecomposition.so @@ -847,8 +862,20 @@ lib/rdkit-targets.cmake %%DATADIR%%/Contrib/ConformerParser/Wrap/test_list.py %%DATADIR%%/Contrib/ConformerParser/test.cpp %%DATADIR%%/Contrib/ConformerParser/test_list.py +%%DATADIR%%/Contrib/Fastcluster/README.md +%%DATADIR%%/Contrib/Fastcluster/cdk2.smi +%%DATADIR%%/Contrib/Fastcluster/centroid.tsv +%%DATADIR%%/Contrib/Fastcluster/clustered.tsv +%%DATADIR%%/Contrib/Fastcluster/clustered_parse.tsv +%%DATADIR%%/Contrib/Fastcluster/fastcluster.py +%%DATADIR%%/Contrib/Fastcluster/fp.tsv +%%DATADIR%%/Contrib/Fastcluster/testdata/cdk2.sdf +%%DATADIR%%/Contrib/Fastcluster/testdata/converted.smi +%%DATADIR%%/Contrib/Fastcluster/testdata/sdf2smi.py %%DATADIR%%/Contrib/Glare/README.txt %%DATADIR%%/Contrib/Glare/glare.py +%%DATADIR%%/Contrib/IFG/README +%%DATADIR%%/Contrib/IFG/ifg.py %%DATADIR%%/Contrib/LEF/AddLabels.py %%DATADIR%%/Contrib/LEF/ClusterFps.py %%DATADIR%%/Contrib/LEF/CreateFps.py @@ -953,6 +980,7 @@ lib/rdkit-targets.cmake %%DATADIR%%/Data/struchk/checkfgs.chk %%DATADIR%%/Data/struchk/checkfgs.opt %%DATADIR%%/Data/struchk/checkfgs.trn +%%DATADIR%%/Data/templates.mae %%PYTHON%%%%DATADIR%%/Projects/DbCLI/CreateDb.py %%PYTHON%%%%DATADIR%%/Projects/DbCLI/SearchDb.py %%PYTHON%%%%DATADIR%%/Projects/DbCLI/TestDbCLI.py @@ -964,4 +992,7 @@ lib/rdkit-targets.cmake %%PYTHON%%%%DATADIR%%/Projects/DbCLI/testData/bzr_q1.mol %%PYTHON%%%%DATADIR%%/Projects/DbCLI/testData/pubchem.200.sdf %%DATADIR%%/README +%%PYTHON%%%%DATADIR%%/Scripts/FeatFinderCLI.py +%%PYTHON%%%%DATADIR%%/Scripts/PythonFormat.py +%%PYTHON%%%%DATADIR%%/Scripts/README.md %%DATADIR%%/license.txt