diff -Nru rdkit-201603.5/debian/changelog rdkit-201603.5+dfsg/debian/changelog --- rdkit-201603.5/debian/changelog 2016-11-07 12:16:00.000000000 +0000 +++ rdkit-201603.5+dfsg/debian/changelog 2018-02-01 16:13:01.000000000 +0000 @@ -1,3 +1,22 @@ +rdkit (201603.5+dfsg-1ubuntu1) bionic; urgency=medium + + * Fix build with glibc 2.26 + * Fix build with boost 1.65 + + -- Graham Inggs Thu, 01 Feb 2018 16:13:01 +0000 + +rdkit (201603.5+dfsg-1) unstable; urgency=medium + + * Team upload. + * Moved packaging from SVN to Git + * DEP5 + * Repack tarball to exclude *.chm file + * Build-Depends: latexmk + Closes: #872246 + * Standards-Version: 4.1.2 + + -- Andreas Tille Mon, 18 Dec 2017 12:09:00 +0100 + rdkit (201603.5-2) unstable; urgency=medium * Team upload. diff -Nru rdkit-201603.5/debian/control rdkit-201603.5+dfsg/debian/control --- rdkit-201603.5/debian/control 2016-11-07 11:50:00.000000000 +0000 +++ rdkit-201603.5+dfsg/debian/control 2018-02-01 16:13:01.000000000 +0000 @@ -1,7 +1,8 @@ Source: rdkit Section: science Priority: optional -Maintainer: Debichem Team +Maintainer: Ubuntu Developers +XSBC-Original-Maintainer: Debichem Team Uploaders: Michael Banck Build-Depends: bison, cmake, @@ -15,6 +16,7 @@ libboost-system-dev, libboost-thread-dev, libsqlite3-dev, + latexmk, pandoc, python-dev, python-epydoc, @@ -27,10 +29,10 @@ texlive-latex-base, texlive-latex-extra, texlive-latex-recommended -Standards-Version: 3.9.6 +Standards-Version: 4.1.2 +Vcs-Browser: https://anonscm.debian.org/cgit/debichem/packages/rdkit.git +Vcs-Git: https://anonscm.debian.org/git/debichem/packages/rdkit.git Homepage: http://www.rdkit.org -Vcs-Browser: http://anonscm.debian.org/viewvc/debichem/unstable/rdkit/ -Vcs-Svn: svn://anonscm.debian.org/debichem/unstable/rdkit/ Package: python-rdkit Section: python diff -Nru rdkit-201603.5/debian/copyright rdkit-201603.5+dfsg/debian/copyright --- rdkit-201603.5/debian/copyright 2016-08-30 14:38:00.000000000 +0000 +++ rdkit-201603.5+dfsg/debian/copyright 2017-12-18 11:09:00.000000000 +0000 @@ -1,32 +1,77 @@ -This work was packaged for Debian by: - - Michael Banck on Fri, 02 Sep 2011 23:19:25 +0200 - -It was downloaded from: - - http://sourceforge.net/projects/rdkit/files/rdkit/ - -The files under Docs/Book have been removed due to licensing issues (CC-BY-SA -2.5). - -Upstream Authors: - - Greg Landrum and Julie Penzotti - -Copyright: - -*: Copyright (c) 2006-2011 Rational Discovery LLC, Novartis Institutes for - BioMedical Research Inc, Greg Landrum, and Julie Penzotti -Code/cmake/Modules/FindInchi.cmake: Copyright (c) 2010 Marcus D. Hanwell -Code/cmake/Modules/FindBISON.cmake: Copyright (c) 2006 Tristan Carel -Code/cmake/Modules/FindFLEX.cmake: Copyright (c) 2006 Tristan Carel - -License: BSD +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: rdkit +Source: https://github.com/rdkit/rdkit/releases +Files-Excluded: */*.chm + +Files: * +Copyright: 2006-2016 Rational Discovery LLC, Novartis Institutes for + BioMedical Research Inc, Greg Landrum, and Julie Penzotti +License: BSD-3-clause + +Files: Code/cmake/Modules/FindInchi.cmake +Copyright: 2010 Marcus D. Hanwell +License: BSD-3-clause + +Files: Code/cmake/Modules/FindBISON.cmake + Code/cmake/Modules/FindFLEX.cmake: +Copyright: 2006 Tristan Carel +License: BSD-3-clause + +Files: debian/* +Copyright: 2011-2016 Michael Banck +License: BSD-3-clause + +Files: Code/RDGeneral/hash/* +Copyright: 2005-2009 Daniel James +License: Boost + +Files: Code/cmake/Modules/BoostUtils.cmake +Copyright: 2007 Troy Straszheim +License: Boost + +Files: Code/GraphMol/Substruct/ullmann.hpp +Copyright: 2003-2008 Vladimir J. Sykora + 2007-2008 NCU Studies Ltd +License: Boost + +Files: rdkit/sping/pid.py + rdkit/sping/PIL/pidPIL.py +Copyright: 1999 Joseph J. Strout +License: LGPL-2+ + +Files: rdkit/sping/Qt/pidQt.py + rdkit/sping/ReportLab/pidReportLab.py + rdkit/sping/SVG/pidSVG.py +Copyright: 2000-2005 Greg Landrum and Rational Discovery LLC +License: LGPL-2+ + +Files: rdkit/sping/WX/pidWX.py +Copyright: 2000 Paul & Kevin Jacobs +License: GPL-2+ + +Files: External/cmim-1.0/* +Copyright: 2004 EPFL +License: GPL-2 + +Files: Numerics/Alignment/AlignPoints.cpp +Copyright: 1990 Ohio Supercomputer Center, David J. Heisterberg +License: free + The program can be copied and distributed freely, provided that + this copyright in not removed. -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are -met: +Files: RDBoost/list_indexing_suite.hpp +Copyright: 2003 Joel de Guzman +License: as_is + Permission to copy, use, modify, sell and distribute this software + is granted provided this copyright notice appears in all copies. This + software is provided "as is" without express or implied warranty, and + with no claim as to its suitability for any purpose. +License: BSD-3-clause + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are + met: + . * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above @@ -36,135 +81,79 @@ * Neither the name of Rational Discovery nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS -"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT -LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR -A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT -OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT -LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, -DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY -THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE -OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -Code/RDGeneral/hash/*: Copyright (c) 2005-2009 Daniel James -Code/cmake/Modules/BoostUtils.cmake: Copyright (c) 2007 Douglas Gregor -Code/cmake/Modules/BoostUtils.cmake: Copyright (c) 2007 Troy Straszheim -Code/GraphMol/Substruct/ullmann.hpp: Copyright (c) 2003-2008 Vladimir J. Sykora - Copyright (c) 2007-2008 NCU Studies Ltd - -License: Boost Software License, Version 1.0. - -Permission is hereby granted, free of charge, to any person or organization -obtaining a copy of the software and accompanying documentation covered by -this license (the "Software") to use, reproduce, display, distribute, -execute, and transmit the Software, and to prepare derivative works of the -Software, and to permit third-parties to whom the Software is furnished to -do so, all subject to the following: - -The copyright notices in the Software and this entire statement, including -the above license grant, this restriction and the following disclaimer, -must be included in all copies of the Software, in whole or in part, and -all derivative works of the Software, unless such copies or derivative -works are solely in the form of machine-executable object code generated by -a source language processor. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT -SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE -FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, -ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER -DEALINGS IN THE SOFTWARE. - -rdkit/sping/pid.py: Copyright (c) 1999 Joseph J. Strout -rdkit/sping/PIL/pidPIL.py: Copyright (c) 1999 Joseph J. Strout -rdkit/sping/Qt/pidQt.py: Copyright (c) 2002 Greg Landrum and Rational Discovery LLC -rdkit/sping/ReportLab/pidReportLab.py: Copyright (c) 2005 Greg Landrum and - Rational Discovery LLC -rdkit/sping/SVG/pidSVG.py: Copyright cC) 2000 Greg Landrum - -License: LGPLv2 or later - -This library is free software; you can redistribute it and/or -modify it under the terms of the GNU Lesser General Public -License as published by the Free Software Foundation; either -version 2 of the License, or (at your option) any later version. - -This library is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -Lesser General Public License for more details. - -You should have received a copy of the GNU Lesser General Public -License along with this library; if not, write to the Free Software -Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. - -On Debian GNU/Linux systems, the complete text of the GNU Lesser General -Public License v2 can be found in `/usr/share/common-licenses/LGPL-2'. - -rdkit/sping/WX/pidWX.py: Copyright (c) 2000 Paul & Kevin Jacobs - -License: GPLv2 or later - -This program is free software; you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation; either version 2, or (at your option) -any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program; if not, write to the Free Software -Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. - -On Debian GNU/Linux systems, the complete text of the latest GNU General -Public License v2 can be found in `/usr/share/common-licenses/GPL-2'. - -External/cmim-1.0/*: Copyright (c) 2004 EPFL - -License: GPLv2 - -This program is free software; you can redistribute it and/or -modify it under the terms of the GNU General Public License -version 2 as published by the Free Software Foundation. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program; if not, write to the Free Software -Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. - -On Debian GNU/Linux systems, the complete text of the GNU General -Public License v2 can be found in `/usr/share/common-licenses/GPL-2'. - -Numerics/Alignment/AlignPoints.cpp: Copyright (c) 1990 Ohio Supercomputer - Center, David J. Heisterberg - -License: - - The program can be copied and distributed freely, provided that - this copyright in not removed. - -RDBoost/list_indexing_suite.hpp: Copyright (c) 2003 Joel de Guzman - -License: - - Permission to copy, use, modify, sell and distribute this software - is granted provided this copyright notice appears in all copies. This - software is provided "as is" without express or implied warranty, and - with no claim as to its suitability for any purpose. - -The Debian packaging is: - - Copyright (C) 2011 Michael Banck - -and is licensed under the same BSD license as the main code above. + . + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +License: Boost + Permission is hereby granted, free of charge, to any person or organization + obtaining a copy of the software and accompanying documentation covered by + this license (the "Software") to use, reproduce, display, distribute, + execute, and transmit the Software, and to prepare derivative works of the + Software, and to permit third-parties to whom the Software is furnished to + do so, all subject to the following: + . + The copyright notices in the Software and this entire statement, including + the above license grant, this restriction and the following disclaimer, + must be included in all copies of the Software, in whole or in part, and + all derivative works of the Software, unless such copies or derivative + works are solely in the form of machine-executable object code generated by + a source language processor. + . + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR + IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, + FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT + SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE + FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, + ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + DEALINGS IN THE SOFTWARE. + +License: GPL-2 + This program is free software; you can redistribute it and/or + modify it under the terms of the GNU General Public License + version 2 as published by the Free Software Foundation. + . + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + . + On Debian GNU/Linux systems, the complete text of the GNU General + Public License v2 can be found in `/usr/share/common-licenses/GPL-2'. + +License: GPL-2+ + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2, or (at your option) + any later version. + . + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + . + On Debian GNU/Linux systems, the complete text of the latest GNU General + Public License v2 can be found in `/usr/share/common-licenses/GPL-2'. + +License: LGPL-2+ + This library is free software; you can redistribute it and/or + modify it under the terms of the GNU Lesser General Public + License as published by the Free Software Foundation; either + version 2 of the License, or (at your option) any later version. + . + This library is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + Lesser General Public License for more details. + . + On Debian GNU/Linux systems, the complete text of the GNU Lesser General + Public License v2 can be found in `/usr/share/common-licenses/LGPL-2'. diff -Nru rdkit-201603.5/debian/patches/boost1.65.patch rdkit-201603.5+dfsg/debian/patches/boost1.65.patch --- rdkit-201603.5/debian/patches/boost1.65.patch 1970-01-01 00:00:00.000000000 +0000 +++ rdkit-201603.5+dfsg/debian/patches/boost1.65.patch 2018-02-01 16:12:19.000000000 +0000 @@ -0,0 +1,124 @@ +Description: Use numpy not numeric for boost 1.65+ + boost python numeric no longer exists in boost 1.65, + so check boost version and conditionally use boost python numpy. +Origin: upstream, https://github.com/rdkit/rdkit/commit/9b90bc3d94f99e0aa913e92adbd339e077f5d6e3 +Author: Matt Swain +Last-Update: 2017-11-18 + +--- a/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp ++++ b/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp +@@ -10,7 +10,7 @@ + // + #define PY_ARRAY_UNIQUE_SYMBOL rdmetric_array_API + #include +-#include ++#include + + #include + #include +--- a/Code/DataStructs/Wrap/DataStructs.cpp ++++ b/Code/DataStructs/Wrap/DataStructs.cpp +@@ -15,7 +15,7 @@ + #include + #include + #include "DataStructs.h" +-#include ++#include + #include + #include + #include +--- a/Code/Demos/boost/numpy/linalg.cpp ++++ b/Code/Demos/boost/numpy/linalg.cpp +@@ -3,13 +3,13 @@ + // + + #include +-#include ++#include + #define PY_ARRAY_UNIQUE_SYMBOL RD_array_API + #include + + namespace python = boost::python; + +-double GetFirstElement(python::numeric::array &x) { ++double GetFirstElement(NumpyArrayType &x) { + PyArrayObject *ptr = (PyArrayObject *)x.ptr(); + void *data = PyArray_DATA(ptr); + double res = 0.0; +--- a/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp ++++ b/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp +@@ -13,7 +13,7 @@ + #define PY_ARRAY_UNIQUE_SYMBOL rdmolalign_array_API + #include + #include +-#include ++#include + #include "numpy/arrayobject.h" + #include + #include +--- a/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp ++++ b/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp +@@ -11,7 +11,7 @@ + + #define PY_ARRAY_UNIQUE_SYMBOL rdreducedgraphs_array_API + #include +-#include ++#include + + #include + #include +--- a/Code/Numerics/Alignment/Wrap/rdAlignment.cpp ++++ b/Code/Numerics/Alignment/Wrap/rdAlignment.cpp +@@ -10,7 +10,7 @@ + // + #define PY_ARRAY_UNIQUE_SYMBOL rdalignment_array_API + #include +-#include ++#include + #include + + #include +--- a/Code/RDBoost/CMakeLists.txt ++++ b/Code/RDBoost/CMakeLists.txt +@@ -4,6 +4,7 @@ + rdkit_headers(Wrap.h PySequenceHolder.h + list_indexing_suite.hpp + python.h ++ boost_numpy.h + python_streambuf.h + DEST RDBoost) + +--- /dev/null ++++ b/Code/RDBoost/boost_numpy.h +@@ -0,0 +1,9 @@ ++// Boost python numpy available in Boost 1.63+ ++// Boost python numeric removed in Boost 1.65+ ++#if BOOST_VERSION < 106500 ++#include ++typedef typename boost::python::numeric::array NumpyArrayType; ++#else ++#include ++typedef typename boost::python::numpy::ndarray NumpyArrayType; ++#endif +--- a/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp ++++ b/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp +@@ -12,7 +12,7 @@ + #define PY_ARRAY_UNIQUE_SYMBOL rdpicker_array_API + #include + +-#include ++#include + #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION + #include + #include +--- a/Code/SimDivPickers/Wrap/MaxMinPicker.cpp ++++ b/Code/SimDivPickers/Wrap/MaxMinPicker.cpp +@@ -12,7 +12,7 @@ + #define PY_ARRAY_UNIQUE_SYMBOL rdpicker_array_API + #include + #include +-#include ++#include + #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION + #include + #include diff -Nru rdkit-201603.5/debian/patches/glibc2.26.patch rdkit-201603.5+dfsg/debian/patches/glibc2.26.patch --- rdkit-201603.5/debian/patches/glibc2.26.patch 1970-01-01 00:00:00.000000000 +0000 +++ rdkit-201603.5+dfsg/debian/patches/glibc2.26.patch 2018-02-01 16:10:59.000000000 +0000 @@ -0,0 +1,19 @@ +Description: do not include xlocale.h, as it was removed in glibc 2.26 + According to + https://sourceware.org/glibc/wiki/Release/2.26#Removal_of_.27xlocale.h.27 + the defines were a subset of locale.h, that we include anyway +Origin: upstream, https://github.com/rdkit/rdkit/pull/1501/commits/04a796bd9d60c8f61c3f44ef25d48929abc57dfc +Author: Gianluca Sforna +Last-Update: 2017-07-11 + +--- a/Code/RDGeneral/LocaleSwitcher.cpp ++++ b/Code/RDGeneral/LocaleSwitcher.cpp +@@ -33,7 +33,7 @@ + // LocaleSwitcher Dependencies + #include + #ifndef _MSC_VER +-#include ++//#include + #include + #else + #include diff -Nru rdkit-201603.5/debian/patches/series rdkit-201603.5+dfsg/debian/patches/series --- rdkit-201603.5/debian/patches/series 2016-11-07 09:29:00.000000000 +0000 +++ rdkit-201603.5+dfsg/debian/patches/series 2018-02-01 16:09:25.000000000 +0000 @@ -0,0 +1,2 @@ +glibc2.26.patch +boost1.65.patch diff -Nru rdkit-201603.5/debian/watch rdkit-201603.5+dfsg/debian/watch --- rdkit-201603.5/debian/watch 2016-08-30 14:38:00.000000000 +0000 +++ rdkit-201603.5+dfsg/debian/watch 2017-12-18 11:09:00.000000000 +0000 @@ -1,6 +1,5 @@ # See uscan(1) for format -version=3 -opts=\ -uversionmangle=s#_##g \ -https://github.com/rdkit/rdkit/releases .*/archive/Release_([\d_]+)_(?:\d+)\.tar\.gz +version=4 +opts="uversionmangle=s#_##g,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \ + https://github.com/rdkit/rdkit/releases .*/archive/Release_([\d_]+)_(?:\d+)\.tar\.gz Binary files /tmp/tmp1Pkhy5/FNA8moWXbU/rdkit-201603.5/Docs/Programs/RDPharm3D/RDPharm3D.chm and /tmp/tmp1Pkhy5/1Yy33LuGeH/rdkit-201603.5+dfsg/Docs/Programs/RDPharm3D/RDPharm3D.chm differ