diff -Nru rdkit-201603.5+dfsg/debian/changelog rdkit-201603.5+dfsg/debian/changelog --- rdkit-201603.5+dfsg/debian/changelog 2017-12-18 11:09:00.000000000 +0000 +++ rdkit-201603.5+dfsg/debian/changelog 2018-02-01 16:13:01.000000000 +0000 @@ -1,3 +1,10 @@ +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. diff -Nru rdkit-201603.5+dfsg/debian/control rdkit-201603.5+dfsg/debian/control --- rdkit-201603.5+dfsg/debian/control 2017-12-18 11:09:00.000000000 +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, diff -Nru rdkit-201603.5+dfsg/debian/patches/boost1.65.patch rdkit-201603.5+dfsg/debian/patches/boost1.65.patch --- rdkit-201603.5+dfsg/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+dfsg/debian/patches/glibc2.26.patch rdkit-201603.5+dfsg/debian/patches/glibc2.26.patch --- rdkit-201603.5+dfsg/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+dfsg/debian/patches/series rdkit-201603.5+dfsg/debian/patches/series --- rdkit-201603.5+dfsg/debian/patches/series 2017-12-18 11:09:00.000000000 +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