Date: Fri, 11 Jun 2021 09:58:08 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 89f32efeb5f4 - main - science/rdkit: Update 2020.09.5 -> 2021.03.3 Message-ID: <202106110958.15B9w82M078162@gitrepo.freebsd.org>
next in thread | raw e-mail | index | archive | help
The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=89f32efeb5f4a4fb5535594ee0c2a68e25ae5efb commit 89f32efeb5f4a4fb5535594ee0c2a68e25ae5efb Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2021-06-11 09:57:05 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2021-06-11 09:57:59 +0000 science/rdkit: Update 2020.09.5 -> 2021.03.3 Reported by: portscout --- science/rdkit/Makefile | 7 ++-- science/rdkit/distinfo | 12 ++++--- science/rdkit/files/patch-CMakeLists.txt | 15 ++------- science/rdkit/pkg-plist | 58 ++++++++++++++++++++++++++++++++ 4 files changed, 72 insertions(+), 20 deletions(-) diff --git a/science/rdkit/Makefile b/science/rdkit/Makefile index a98f8046a3d1..98db77376579 100644 --- a/science/rdkit/Makefile +++ b/science/rdkit/Makefile @@ -1,8 +1,10 @@ PORTNAME= rdkit DISTVERSIONPREFIX= Release_ -DISTVERSION= 2020_09_5 -PORTREVISION= 1 +DISTVERSION= 2021_03_3 CATEGORIES= science +MASTER_SITES= https://fonts.google.com/download?family=Comic%20Neue&dummy=/:font +DISTFILES= Comic_Neue.zip:font +DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Collection of cheminformatics and machine-learning software @@ -66,6 +68,7 @@ PLIST_SUB+= LITTLE_ENDIAN="@comment " post-extract: @${MKDIR} ${WRKSRC}/External/rapidjson-1.1.0 @cd ${WRKSRC}/External/rapidjson-1.1.0 && ${LN} -s ${LOCALBASE}/include/rapidjson include + @cd ${WRKSRC}/Data/Fonts && unzip ${DISTDIR}/${DIST_SUBDIR}/Comic_Neue.zip post-stage: # https://github.com/rdkit/rdkit/issues/2094 #@${MKDIR} ${STAGEDIR}${PREFIX}/lib/cmake diff --git a/science/rdkit/distinfo b/science/rdkit/distinfo index 6dbdf98eb071..9145c25037cf 100644 --- a/science/rdkit/distinfo +++ b/science/rdkit/distinfo @@ -1,5 +1,7 @@ -TIMESTAMP = 1614725230 -SHA256 (rdkit-rdkit-Release_2020_09_5_GH0.tar.gz) = 85cec9618e7ef6365b9b908ed674c073d898b6627521cc7fd8c2e05fea8a5def -SIZE (rdkit-rdkit-Release_2020_09_5_GH0.tar.gz) = 58609591 -SHA256 (rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715 -SIZE (rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931 +TIMESTAMP = 1623403789 +SHA256 (rdkit-2021.03.3/Comic_Neue.zip) = 9f254e5cd219c1aa9b1f18e73c2588d8cd8587ac16997eeff9adb0d556fa6461 +SIZE (rdkit-2021.03.3/Comic_Neue.zip) = 179735 +SHA256 (rdkit-2021.03.3/rdkit-rdkit-Release_2021_03_3_GH0.tar.gz) = e95f07adaee9280df077cb147210ee75e16957d81687ab0836d62ebf1f6f715f +SIZE (rdkit-2021.03.3/rdkit-rdkit-Release_2021_03_3_GH0.tar.gz) = 78186499 +SHA256 (rdkit-2021.03.3/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 944b5816712a48bbf88aa25d4300ce11871ddf6e971218eac08f90ed2192f715 +SIZE (rdkit-2021.03.3/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz) = 137931 diff --git a/science/rdkit/files/patch-CMakeLists.txt b/science/rdkit/files/patch-CMakeLists.txt index 5b5bb0dde652..a4594f30ae57 100644 --- a/science/rdkit/files/patch-CMakeLists.txt +++ b/science/rdkit/files/patch-CMakeLists.txt @@ -1,17 +1,6 @@ ---- CMakeLists.txt.orig 2021-03-01 16:43:06 UTC +--- CMakeLists.txt.orig 2020-06-10 03:59:48 UTC +++ CMakeLists.txt -@@ -68,8 +68,8 @@ if(NOT MSVC) - if(RDK_OPTIMIZE_POPCNT) - if(CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "aarch64") - message("RDK_OPTIMIZE_POPCNT is not available on aarch64") -- elseif(CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "ppc64le") -- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcntb") -+ elseif(CMAKE_HOST_SYSTEM_PROCESSOR MATCHES "^(ppc64|powerpc64)") -+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcntd") - else() - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mpopcnt") - endif() -@@ -459,12 +459,14 @@ if(NOT RDK_INSTALL_INTREE) +@@ -432,12 +432,14 @@ if(NOT RDK_INSTALL_INTREE) COMPONENT data PATTERN ".svn" EXCLUDE ) diff --git a/science/rdkit/pkg-plist b/science/rdkit/pkg-plist index bfab6a8f37f5..a1d51f03145b 100644 --- a/science/rdkit/pkg-plist +++ b/science/rdkit/pkg-plist @@ -1,4 +1,5 @@ include/rdkit/CIPLabeler/CIPLabeler.h +include/rdkit/CIPLabeler/TooManyNodesException.h include/rdkit/Catalogs/Catalog.h include/rdkit/Catalogs/CatalogEntry.h include/rdkit/Catalogs/CatalogParams.h @@ -185,6 +186,7 @@ include/rdkit/GraphMol/MolDraw2D/MolDraw2DJS.h include/rdkit/GraphMol/MolDraw2D/MolDraw2DSVG.h include/rdkit/GraphMol/MolDraw2D/MolDraw2DUtils.h include/rdkit/GraphMol/MolDraw2D/MolDraw2Dwx.h +include/rdkit/GraphMol/MolEnumerator/LinkNode.h include/rdkit/GraphMol/MolEnumerator/MolEnumerator.h include/rdkit/GraphMol/MolHash/MolHash.h include/rdkit/GraphMol/MolHash/nmmolhash.h @@ -293,6 +295,7 @@ include/rdkit/RDGeneral/Invariant.h include/rdkit/RDGeneral/LocaleSwitcher.h include/rdkit/RDGeneral/RDAny.h include/rdkit/RDGeneral/RDConfig.h +include/rdkit/RDGeneral/RDExportMacros.h include/rdkit/RDGeneral/RDLog.h include/rdkit/RDGeneral/RDProps.h include/rdkit/RDGeneral/RDThreads.h @@ -481,6 +484,9 @@ lib/libRDKitTautomerQuery.so.1.%%SHLIB_VER%% lib/libRDKitTrajectory.so lib/libRDKitTrajectory.so.1 lib/libRDKitTrajectory.so.1.%%SHLIB_VER%% +lib/libRDKitga.so +lib/libRDKitga.so.1 +lib/libRDKitga.so.1.%%SHLIB_VER%% %%LITTLE_ENDIAN%%lib/libRDKithc.so %%LITTLE_ENDIAN%%lib/libRDKithc.so.1 %%LITTLE_ENDIAN%%lib/libRDKithc.so.1.%%SHLIB_VER%% @@ -940,6 +946,44 @@ lib/libRDKitTrajectory.so.1.%%SHLIB_VER%% %%PYTHON%%%%PYTHON_SITELIBDIR%%/rdkit/utils/test3.gif %%DATADIR%%/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py %%DATADIR%%/Contrib/CMakeLists.txt +%%DATADIR%%/Contrib/CalcLigRMSD/CalcLigRMSD.py +%%DATADIR%%/Contrib/CalcLigRMSD/Examples_CalcLigRMSD.ipynb +%%DATADIR%%/Contrib/CalcLigRMSD/README.md +%%DATADIR%%/Contrib/CalcLigRMSD/data/1C9_renamed.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/3m11_AKI.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/3w2c_N15.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/4i23_1C9.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/4i24_1C9.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/5dpv.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/5dt0.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/6c83.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_1.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/ACP_renamed.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/AKI_renamed.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/BEG_test.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/JVE_renamed.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/N15_renamed.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/SKE_renamed.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/crystal_aligned.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/data/lig_crystal_aligned.pdb +%%DATADIR%%/Contrib/CalcLigRMSD/figures/1C9.png +%%DATADIR%%/Contrib/CalcLigRMSD/figures/5dpv_complex.png +%%DATADIR%%/Contrib/CalcLigRMSD/figures/6c83_complex.png +%%DATADIR%%/Contrib/CalcLigRMSD/figures/AKI.png +%%DATADIR%%/Contrib/CalcLigRMSD/figures/BEG.png +%%DATADIR%%/Contrib/CalcLigRMSD/figures/JVE.png +%%DATADIR%%/Contrib/CalcLigRMSD/figures/N15.png %%DATADIR%%/Contrib/ChiralPairs/ChiralDescriptors.py %%DATADIR%%/Contrib/ChiralPairs/README.txt %%DATADIR%%/Contrib/ConformerParser/CMakeLists.txt @@ -975,6 +1019,13 @@ lib/libRDKitTrajectory.so.1.%%SHLIB_VER%% %%DATADIR%%/Contrib/M_Kossner/Frames.py %%DATADIR%%/Contrib/M_Kossner/README %%DATADIR%%/Contrib/MolVS/molvs_cli.py +%%DATADIR%%/Contrib/NIBRSubstructureFilters/FilterSet_NIBR2019_wPubChemExamples.html +%%DATADIR%%/Contrib/NIBRSubstructureFilters/README.md +%%DATADIR%%/Contrib/NIBRSubstructureFilters/SubstructureFilter_HitTriaging_wPubChemExamples.csv +%%DATADIR%%/Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py +%%DATADIR%%/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100.csv +%%DATADIR%%/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100_out.csv +%%DATADIR%%/Contrib/NIBRSubstructureFilters/filterExamples.png %%DATADIR%%/Contrib/NP_Score/README %%DATADIR%%/Contrib/NP_Score/npscorer.py %%DATADIR%%/Contrib/NP_Score/publicnp.model.gz @@ -1047,6 +1098,13 @@ lib/libRDKitTrajectory.so.1.%%SHLIB_VER%% %%DATADIR%%/Data/DTDs/RD_Model.dtd %%DATADIR%%/Data/DTDs/validate.py %%DATADIR%%/Data/Fonts/Amadeus.ttf +%%DATADIR%%/Data/Fonts/ComicNeue-Bold.ttf +%%DATADIR%%/Data/Fonts/ComicNeue-BoldItalic.ttf +%%DATADIR%%/Data/Fonts/ComicNeue-Italic.ttf +%%DATADIR%%/Data/Fonts/ComicNeue-Light.ttf +%%DATADIR%%/Data/Fonts/ComicNeue-LightItalic.ttf +%%DATADIR%%/Data/Fonts/ComicNeue-Regular.ttf +%%DATADIR%%/Data/Fonts/OFL.txt %%DATADIR%%/Data/Fonts/Telex-Regular.ttf %%DATADIR%%/Data/Fonts/amadeus_font_license.txt %%DATADIR%%/Data/Fonts/telex_font_license.txt
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?202106110958.15B9w82M078162>