--- Begin Message ---
Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: unblock
Please unblock package rdkit, it fixes big-endian architectures and
re-enables the test suite. See e.g.
https://buildd.debian.org/status/fetch.php?pkg=rdkit&arch=mips&ver=201203-1&stamp=1337431768
vs.
https://buildd.debian.org/status/fetch.php?pkg=rdkit&arch=mips&ver=201203-3&stamp=1343568733
(201203-2 had the test suite disabled, so it built successfully on e.g.
mips).
The corresponding patch has been developped by upstream on one of the
Debian porter boxes and consists of four subversion revisions, see
changelog. The debdiff is attached.
unblock rdkit/201203-3
Thanks in advance, regards
Michael
diff -Nru rdkit-201203/debian/changelog rdkit-201203/debian/changelog
--- rdkit-201203/debian/changelog 2012-06-12 13:45:12.000000000 +0200
+++ rdkit-201203/debian/changelog 2012-07-28 21:18:54.000000000 +0200
@@ -1,3 +1,12 @@
+rdkit (201203-3) unstable; urgency=low
+
+ * debian/patches/big-endian_support.patch: New patch, fixes big-endian
+ architectures, taken from upstream revisions 2071, 2079, 2080 and 2140.
+ * debian/rules (override_dh_auto_test): Activate testsuite again
+ (Closes: #678188).
+
+ -- Michael Banck <mbanck@debian.org> Sat, 28 Jul 2012 21:18:42 +0200
+
rdkit (201203-2) unstable; urgency=low
* debian/rules (override_dh_auto_test): Deactivated for now
diff -Nru rdkit-201203/debian/patches/big-endian_support.patch rdkit-201203/debian/patches/big-endian_support.patch
--- rdkit-201203/debian/patches/big-endian_support.patch 1970-01-01 01:00:00.000000000 +0100
+++ rdkit-201203/debian/patches/big-endian_support.patch 2012-07-28 19:38:13.000000000 +0200
@@ -0,0 +1,653 @@
+Description: Upstream changes to support big-endian architectures
+ This patch consists of upstream revisions 2071, 2079, 2080 and 2140.
+Author: Greg Landrum
+Origin: upstream
+Bug-Debian: http://bugs.debian.org/670054
+Last-Update: 2012-07-28
+
+--- rdkit-201203.orig/CMakeLists.txt
++++ rdkit-201203/CMakeLists.txt
+@@ -26,6 +26,9 @@ option(RDK_INSTALL_STATIC_LIBS "install
+ option(RDK_BUILD_SLN_SUPPORT "include support for the SLN format" ON )
+ option(RDK_TEST_MULTITHREADED "run some tests of multithreading" OFF )
+
++include(TestBigEndian)
++TEST_BIG_ENDIAN(RDK_BIG_ENDIAN)
++
+ # At build time put runtime binaries in the bin subdirectory
+ set(RDK_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/bin")
+ set(RDK_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/lib")
+--- rdkit-201203.orig/Code/CMakeLists.txt
++++ rdkit-201203/Code/CMakeLists.txt
+@@ -15,7 +15,11 @@ add_subdirectory(GraphMol)
+ add_subdirectory(Query)
+
+ add_subdirectory(DataManip)
+-add_subdirectory(SimDivPickers)
++if(RDK_BIG_ENDIAN)
++ message("Skipping build of SimDivPickers on big endian system")
++else(RDK_BIG_ENDIAN)
++ add_subdirectory(SimDivPickers)
++endif(RDK_BIG_ENDIAN)
+
+ add_subdirectory(ML)
+ add_subdirectory(ChemicalFeatures)
+--- rdkit-201203.orig/Code/DataStructs/BitVect.cpp
++++ rdkit-201203/Code/DataStructs/BitVect.cpp
+@@ -40,7 +40,7 @@ void BitVect::initFromText(const char *d
+
+ // earlier versions of the code did not have the version number encoded, so
+ // we'll use that to distinguish version 0
+- ss.read((char *)&size,sizeof(size));
++ RDKit::streamRead(ss,size);
+ if(size<0){
+ version = -1*size;
+ if (version == 16) {
+@@ -52,12 +52,12 @@ void BitVect::initFromText(const char *d
+ else {
+ throw ValueErrorException("bad version in BitVect pickle");
+ }
+-
+- ss.read((char *)&size,sizeof(size));
++ RDKit::streamRead(ss,size);
+ } else if( !allowOldFormat ) {
+ throw ValueErrorException("invalid BitVect pickle");
+ }
+- ss.read((char *)&nOn,sizeof(nOn));
++
++ RDKit::streamRead(ss,nOn);
+ _initForSize(static_cast<int>(size));
+
+ // if the either have older version or or version 16 with ints for on bits
+@@ -65,13 +65,13 @@ void BitVect::initFromText(const char *d
+ ( (format == 1) && (size >= std::numeric_limits<unsigned short>::max()) ) ) {
+ boost::uint32_t tmp;
+ for(unsigned int i=0; i<nOn; i++){
+- ss.read((char *)&tmp,sizeof(tmp));
++ RDKit::streamRead(ss,tmp);
+ setBit(tmp);
+ }
+ } else if (format == 1) { // version 16 and on bits stored as short ints
+ boost::uint16_t tmp;
+ for(unsigned int i=0; i<nOn; i++){
+- ss.read((char *)&tmp,sizeof(tmp));
++ RDKit::streamRead(ss,tmp);
+ setBit(tmp);
+ }
+ } else if (format == 2) { // run length encoded format
+--- rdkit-201203.orig/Code/DataStructs/BitOps.cpp
++++ rdkit-201203/Code/DataStructs/BitOps.cpp
+@@ -21,18 +21,20 @@
+
+ #include <boost/lexical_cast.hpp>
+
++using namespace RDKit;
++
+ int getBitId(const char *&text,int format,int size,int curr){
+ PRECONDITION(text,"no text");
+ int res=-1;
+ if( (format==0) ||
+ ( (format == 1) && (size >= std::numeric_limits<unsigned short>::max()) ) ) {
+ int tmp;
+- tmp = *(int *)text;
++ tmp = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(*(int *)text);
+ text += sizeof(tmp);
+ res=tmp;
+ } else if (format == 1) { // version 16 and on bits sotred as short ints
+ unsigned short tmp;
+- tmp = *(unsigned short *)text;
++ tmp = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(*(unsigned short *)text);
+ text += sizeof(tmp);
+ res=tmp;
+ } else if (format == 2) { // run length encoded format
+@@ -54,7 +56,7 @@ bool AllProbeBitsMatch(const char *probe
+ int refFormat=0;
+ int version=0;
+
+- int probeSize = *(int *)probe;
++ int probeSize = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(*(int *)probe);
+ probe+=sizeof(probeSize);
+ if(probeSize<0){
+ version = -1*probeSize;
+@@ -67,11 +69,11 @@ bool AllProbeBitsMatch(const char *probe
+ else {
+ throw("Unknown version type for the encode bit vect");
+ }
+- probeSize = *(int *)probe;
++ probeSize = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(*(int *)probe);
+ probe+=sizeof(probeSize);
+ }
+
+- int refSize = *(int *)ref;
++ int refSize = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(*(int *)ref);
+ ref+=sizeof(refSize);
+ if(refSize<0){
+ version = -1*refSize;
+@@ -84,14 +86,14 @@ bool AllProbeBitsMatch(const char *probe
+ else {
+ throw("Unknown version type for the encode bit vect");
+ }
+- refSize = *(int *)ref;
++ refSize = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(*(int *)ref);
+ ref+=sizeof(refSize);
+ }
+
+
+- int nProbeOn = *(int *)probe;
++ int nProbeOn = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(*(int *)probe);
+ probe+=sizeof(nProbeOn);
+- int nRefOn = *(int *)ref;
++ int nRefOn = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(*(int *)ref);
+ ref+=sizeof(nRefOn);
+
+ int currProbeBit=0;
+@@ -121,7 +123,7 @@ bool AllProbeBitsMatch(const T1 &probe,c
+ const char *text=pkl.c_str();
+ int format=0;
+ int nOn=0,size,version=0;
+- size = *(int *)text;
++ size = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(*(int *)text);
+ text+=sizeof(size);
+ if(size<0){
+ version = -1*size;
+@@ -134,10 +136,10 @@ bool AllProbeBitsMatch(const T1 &probe,c
+ else {
+ throw("Unknown version type for the encode bit vect");
+ }
+- size = *(int *)text;
++ size = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(*(int *)text);
+ text+=sizeof(size);
+ }
+- nOn = *(int *)text;
++ nOn = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(*(int *)text);
+ text+=sizeof(nOn);
+
+ int currBit=0;
+--- rdkit-201203.orig/Code/DataStructs/DiscreteValueVect.cpp
++++ rdkit-201203/Code/DataStructs/DiscreteValueVect.cpp
+@@ -1,6 +1,6 @@
+ // $Id: DiscreteValueVect.cpp 1528 2010-09-26 17:04:37Z glandrum $
+ //
+-// Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
++// Copyright (C) 2004-2012 Greg Landrum and Rational Discovery LLC
+ //
+ // @@ All Rights Reserved @@
+ // This file is part of the RDKit.
+@@ -143,8 +143,15 @@ namespace RDKit {
+ streamWrite(ss,tInt);
+ tInt=d_numInts;
+ streamWrite(ss,tInt);
++
++#if defined(BOOST_BIG_ENDIAN)
++ boost::uint32_t *td = new boost::uint32_t[d_numInts];
++ for(unsigned int i=0;i<d_numInts;++i) td[i]=EndianSwapBytes<HOST_ENDIAN_ORDER,LITTLE_ENDIAN_ORDER>(d_data.get()[i]);
++ ss.write((const char *)td,d_numInts*sizeof(tInt));
++ delete [] td;
++#else
+ ss.write((const char *)d_data.get(),d_numInts*sizeof(tInt));
+-
++#endif
+ std::string res(ss.str());
+ return res;
+ };
+@@ -175,7 +182,15 @@ namespace RDKit {
+ d_numInts=tInt;
+ boost::uint32_t *data = new boost::uint32_t[d_numInts];
+ ss.read((char *)data,d_numInts*sizeof(boost::uint32_t));
++
++#if defined(BOOST_BIG_ENDIAN)
++ boost::uint32_t *td = new boost::uint32_t[d_numInts];
++ for(unsigned int i=0;i<d_numInts;++i) td[i]=EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(data[i]);
++ d_data.reset(td);
++ delete [] data;
++#else
+ d_data.reset(data);
++#endif
+
+ };
+
+--- rdkit-201203.orig/Code/DataStructs/testDatastructs.cpp
++++ rdkit-201203/Code/DataStructs/testDatastructs.cpp
+@@ -125,9 +125,13 @@ template<typename T> void Test(T arg){
+ delete t5;
+
+ std::string pkl=t1.toString();
++ BOOST_LOG(rdInfoLog) << " a" << std::endl;
+ const char *pkl64=Base64Encode(pkl.c_str(),pkl.size());
++ BOOST_LOG(rdInfoLog) << " b" << std::endl;
+ T t6(t1.getNumBits());
++ BOOST_LOG(rdInfoLog) << " c" << std::endl;
+ t6.initFromText(pkl64,strlen(pkl64),true);
++ BOOST_LOG(rdInfoLog) << " d" << std::endl;
+ delete [] pkl64;
+ TEST_ASSERT(t6==t1);
+ }
+@@ -149,10 +153,14 @@ template<typename T> void TaniTest(T &ar
+ int idx=0;
+ for(int i=0;i<4;i++){
+ T v1(256);
++ BOOST_LOG(rdInfoLog) << " a "<<i << std::endl;
+ FromDaylightString(v1,fps[i]);
++ BOOST_LOG(rdInfoLog) << " b"<<i << std::endl;
+ for(int j=i;j<4;j++){
+ T v2(256);
++ BOOST_LOG(rdInfoLog) << " c " << j << std::endl;
+ FromDaylightString(v2,fps[j]);
++ BOOST_LOG(rdInfoLog) << " d " << j << std::endl;
+ double tani=TanimotoSimilarity(v1,v2);
+ TEST_ASSERT(feq(tani,dists[idx]));
+ tani = TverskySimilarity(v1,v2,1.,1.);
+@@ -1174,15 +1182,9 @@ int main(){
+
+ ss.write((const char *)&v1,sizeof(v1));
+ ss.write((const char *)&v2,sizeof(v2));
+-#if 0
+- ss.close();
+- fstream ss2("blah.bin",ios_base::binary|ios_base::in);
+- ss2.read((char *)&v3,sizeof(v3));
+- ss2.read((char *)&v4,sizeof(v4));
+-#endif
+ ss.seekp(0,ios_base::beg);
+- ss.read((char *)&v3,sizeof(v3));
+- ss.read((char *)&v4,sizeof(v4));
++ RDKit::streamRead(ss,v3);
++ RDKit::streamRead(ss,v4);
+
+ TXTMSG("v3",v3);
+ TXTMSG("v4",v4);
+@@ -1190,12 +1192,16 @@ int main(){
+ BOOST_LOG(rdInfoLog) << " SPARSE -----------------------------------" << std::endl;
+ SparseBitVect sparseFoo(10);
+ Test(sparseFoo);
++ BOOST_LOG(rdInfoLog) << " 1" << std::endl;
+ TaniTest(sparseFoo);
++ BOOST_LOG(rdInfoLog) << " 2" << std::endl;
+ ProbeTest(sparseFoo);
+ BOOST_LOG(rdInfoLog) << " Explicit ----------------------------------" << std::endl;
+ ExplicitBitVect explicitFoo(10);
+ Test(explicitFoo);
++ BOOST_LOG(rdInfoLog) << " 1" << std::endl;
+ TaniTest(explicitFoo);
++ BOOST_LOG(rdInfoLog) << " 2" << std::endl;
+ BOOST_LOG(rdInfoLog) << " Done" << std::endl;
+
+ BOOST_LOG(rdInfoLog) << " Test DiscreteValue Vectors 1 ----------------------------" << endl;
+--- rdkit-201203.orig/Code/DataStructs/SparseBitVect.cpp
++++ rdkit-201203/Code/DataStructs/SparseBitVect.cpp
+@@ -317,10 +317,15 @@ std::string SparseBitVect::toString() co
+
+ boost::int32_t tInt = ci_BITVECT_VERSION*-1;
+ RDKit::streamWrite(ss,tInt);
++std::cerr<<"version: "<<tInt<<std::endl;
+ tInt=d_size;
+ RDKit::streamWrite(ss,tInt);
++std::cerr<<"size: "<<tInt<<std::endl;
++
+ tInt=getNumOnBits();
+ RDKit::streamWrite(ss,tInt);
++std::cerr<<"nOn: "<<tInt<<std::endl;
++
+
+ int prev = -1;
+ unsigned int zeroes;
+--- rdkit-201203.orig/Code/RDGeneral/StreamOps.h
++++ rdkit-201203/Code/RDGeneral/StreamOps.h
+@@ -16,10 +16,72 @@
+ #include <sstream>
+ #include <iostream>
+ #include <boost/cstdint.hpp>
+-
++#include <boost/detail/endian.hpp>
+
+ namespace RDKit{
+-
++ // this code block for handling endian problems is from :
++ // http://stackoverflow.com/questions/105252/how-do-i-convert-between-big-endian-and-little-endian-values-in-c
++ enum EEndian
++ {
++ LITTLE_ENDIAN_ORDER,
++ BIG_ENDIAN_ORDER,
++#if defined(BOOST_LITTLE_ENDIAN)
++ HOST_ENDIAN_ORDER = LITTLE_ENDIAN_ORDER
++#elif defined(BOOST_BIG_ENDIAN)
++ HOST_ENDIAN_ORDER = BIG_ENDIAN_ORDER
++#else
++#error "Failed to determine the system endian value"
++#endif
++ };
++
++ // this function swap the bytes of values given it's size as a template
++ // parameter (could sizeof be used?).
++ template <class T, unsigned int size>
++ inline T SwapBytes(T value)
++ {
++ union
++ {
++ T value;
++ char bytes[size];
++ } in, out;
++
++ in.value = value;
++
++ for (unsigned int i = 0; i < size / 2; ++i)
++ {
++ out.bytes[i] = in.bytes[size - 1 - i];
++ out.bytes[size - 1 - i] = in.bytes[i];
++ }
++
++ return out.value;
++ }
++
++ // Here is the function you will use. Again there is two compile-time assertion
++ // that use the boost librarie. You could probably comment them out, but if you
++ // do be cautious not to use this function for anything else than integers
++ // types. This function need to be calles like this :
++ //
++ // int x = someValue;
++ // int i = EndianSwapBytes<HOST_ENDIAN_ORDER, BIG_ENDIAN_ORDER>(x);
++ //
++ template<EEndian from, EEndian to, class T>
++ inline T EndianSwapBytes(T value)
++ {
++ // A : La donnée à swapper à une taille de 2, 4 ou 8 octets
++ BOOST_STATIC_ASSERT(sizeof(T)==1 || sizeof(T) == 2 || sizeof(T) == 4 || sizeof(T) == 8);
++ if(sizeof(T)==1) return value;
++
++ // A : La donnée à swapper est d'un type arithmetic
++ //BOOST_STATIC_ASSERT(boost::is_arithmetic<T>::value);
++
++ // Si from et to sont du même type on ne swap pas.
++ if (from == to)
++ return value;
++
++ return SwapBytes<T, sizeof(T)>(value);
++ }
++ // --------------------------------------
++
+ //! Packs an integer and outputs it to a stream
+ inline void appendPackedIntToStream(std::stringstream &ss, boost::uint32_t num) {
+ int nbytes, bix;
+@@ -27,7 +89,7 @@ namespace RDKit{
+ char tc;
+
+ CHECK_INVARIANT(num >= 0, "");
+- res = num;
++ res=num;
+ while (1) {
+ if (res < (1<<7)) {
+ val = (res<<1);
+@@ -53,9 +115,10 @@ namespace RDKit{
+ break;
+ }
+ else {
+- CHECK_INVARIANT(0, "ERROR: Integer to big to pack\n");
++ CHECK_INVARIANT(0, "ERROR: Integer too big to pack\n");
+ }
+ }
++ //val = EndianSwapBytes<HOST_ENDIAN_ORDER,LITTLE_ENDIAN_ORDER>(val);
+
+ for (bix = 0; bix < nbytes; bix++) {
+ tc = (char) (val & 255);
+@@ -100,6 +163,7 @@ namespace RDKit{
+ offset = (1<<7) + (1<<14) + (1<<21);
+ }
+ num = (val >> shift) + offset;
++ //num = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(num);
+ return num;
+ }
+
+@@ -147,18 +211,22 @@ namespace RDKit{
+ offset = (1<<7) + (1<<14) + (1<<21);
+ }
+ num = (val >> shift) + offset;
++ //num = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(num);
+ return num;
+ }
+
+ //! does a binary write of an object to a stream
+ template <typename T>
+ void streamWrite(std::ostream &ss,const T &val){
+- ss.write((const char *)&val,sizeof(T));
++ T tval=EndianSwapBytes<HOST_ENDIAN_ORDER,LITTLE_ENDIAN_ORDER>(val);
++ ss.write((const char *)&tval,sizeof(T));
+ }
+ //! does a binary read of an object from a stream
+ template <typename T>
+ void streamRead(std::istream &ss,T &loc){
+- ss.read((char *)&loc,sizeof(T));
++ T tloc;
++ ss.read((char *)&tloc,sizeof(T));
++ loc = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(tloc);
+ }
+
+ //! grabs the next line from an instream and returns it.
+--- rdkit-201203.orig/Code/ML/CMakeLists.txt
++++ rdkit-201203/Code/ML/CMakeLists.txt
+@@ -1,4 +1,8 @@
+-add_subdirectory(Cluster)
+-add_subdirectory(FeatureSelect)
++if(RDK_BIG_ENDIAN)
++ message("Skipping build of clustering and cmim libraries on big endian system")
++else(RDK_BIG_ENDIAN)
++ add_subdirectory(Cluster)
++ add_subdirectory(FeatureSelect)
++endif(RDK_BIG_ENDIAN)
+ add_subdirectory(InfoTheory)
+ add_subdirectory(Data)
+--- rdkit-201203.orig/Code/ML/FeatureSelect/Wrap/testCMIM.py
++++ rdkit-201203/Code/ML/FeatureSelect/Wrap/testCMIM.py
+@@ -31,13 +31,13 @@ class TestCase(unittest.TestCase):
+ examples.append([0,bv,1])
+
+ r = FS.selectCMIM(examples,2)
+- self.failUnless(r==(2,4))
++ self.failUnlessEqual(r,(2,4))
+
+ r = FS.selectCMIM(examples,1)
+- self.failUnless(r==(2,))
++ self.failUnlessEqual(r,(2,))
+
+ r = FS.selectCMIM(examples,3)
+- self.failUnless(r==(2,4,-1))
++ self.failUnlessEqual(r,(2,4,-1))
+
+ def test1FromList(self) :
+ examples = []
+@@ -63,13 +63,13 @@ class TestCase(unittest.TestCase):
+ examples.append([0,bv,1])
+
+ r = FS.selectCMIM(examples,2)
+- self.failUnless(r==(2,4))
++ self.failUnlessEqual(r,(2,4))
+
+ r = FS.selectCMIM(examples,1)
+- self.failUnless(r==(2,))
++ self.failUnlessEqual(r,(2,))
+
+ r = FS.selectCMIM(examples,3)
+- self.failUnless(r==(2,4,-1))
++ self.failUnlessEqual(r,(2,4,-1))
+
+
+ if __name__ == '__main__':
+--- rdkit-201203.orig/rdkit/DataStructs/VectCollection.py
++++ rdkit-201203/rdkit/DataStructs/VectCollection.py
+@@ -230,12 +230,13 @@ class VectCollection(object):
+ # set up our support for pickling:
+ #
+ def __getstate__(self):
+- pkl = struct.pack('I',len(self.__vects))
++ pkl = struct.pack('<I',len(self.__vects))
+ for k,v in self.__vects.iteritems():
+- pkl += struct.pack('I',k)
++ pkl += struct.pack('<I',k)
+ p = v.ToBinary()
+ l = len(p)
+- pkl += struct.pack('I%ds'%(l),l,p)
++ pkl += struct.pack('<I',l)
++ pkl += struct.pack('%ds'%(l),p)
+ return pkl
+
+ def __setstate__(self,pkl):
+@@ -245,12 +246,12 @@ class VectCollection(object):
+ self.__needReset=True
+ szI = struct.calcsize('I')
+ offset = 0
+- nToRead = struct.unpack('I',pkl[offset:offset+szI])[0]
++ nToRead = struct.unpack('<I',pkl[offset:offset+szI])[0]
+ offset += szI
+ for i in range(nToRead):
+- k = struct.unpack('I',pkl[offset:offset+szI])[0]
++ k = struct.unpack('<I',pkl[offset:offset+szI])[0]
+ offset += szI
+- l = struct.unpack('I',pkl[offset:offset+szI])[0]
++ l = struct.unpack('<I',pkl[offset:offset+szI])[0]
+ offset += szI
+ sz = struct.calcsize('%ds'%l)
+ bv = DataStructs.ExplicitBitVect(struct.unpack('%ds'%l,pkl[offset:offset+sz])[0])
+--- rdkit-201203.orig/rdkit/SimDivFilters/__init__.py
++++ rdkit-201203/rdkit/SimDivFilters/__init__.py
+@@ -3,4 +3,8 @@
+ # All Rights Reserved
+ #
+ from rdkit import rdBase
+-from rdSimDivPickers import *
++try:
++ import rdSimDivPickers
++ from rdSimDivPickers import *
++except ImportError:
++ rdSimDivPickers=None
+--- rdkit-201203.orig/rdkit/ML/test_list.py
++++ rdkit-201203/rdkit/ML/test_list.py
+@@ -5,7 +5,7 @@ tests=[
+ ("python","UnitTestAnalyzeComposite.py",{}),
+ ]
+
+-for dir in ['Cluster','Composite','Data','DecTree','Descriptors','FeatureSelect','InfoTheory','KNN','ModelPackage','NaiveBayes','Neural','SLT']:
++for dir in ['Cluster','Composite','Data','DecTree','Descriptors','InfoTheory','KNN','ModelPackage','NaiveBayes','Neural','SLT']:
+ tests.append(('python','test_list.py',{'dir':dir}))
+
+ longTests=[
+--- rdkit-201203.orig/rdkit/ML/InfoTheory/BitClusterer.py
++++ rdkit-201203/rdkit/ML/InfoTheory/BitClusterer.py
+@@ -3,6 +3,8 @@
+ #
+
+ from rdkit.SimDivFilters import rdSimDivPickers as rdsimdiv
++if rdsimdiv is None:
++ raise ImportError,'rdSimDivPickers not built'
+ from rdkit import DataStructs
+ import numpy
+
+--- rdkit-201203.orig/rdkit/ML/InfoTheory/testCorrMatGen.py
++++ rdkit-201203/rdkit/ML/InfoTheory/testCorrMatGen.py
+@@ -2,7 +2,11 @@
+
+ from rdkit import RDConfig
+ import unittest
+-from rdkit.ML.InfoTheory import rdInfoTheory, BitClusterer
++from rdkit.ML.InfoTheory import rdInfoTheory
++try:
++ from rdkit.ML.InfoTheory import BitClusterer
++except ImportError:
++ BitClusterer=None
+ from rdkit.ML.Data import DataUtils
+ from rdkit import DataStructs
+ import random
+@@ -64,6 +68,8 @@ class TestCase(unittest.TestCase):
+ assert 2*navr/self.nbits == 158.3,2*navr/self.nbits
+
+ def test1Cluster(self) :
++ if BitClusterer is None:
++ return
+ cmg = rdInfoTheory.BitCorrMatGenerator()
+ cmg.SetBitList(self.blist)
+ for fp in self.fps:
+--- rdkit-201203.orig/rdkit/ML/Cluster/UnitTestCluster.py
++++ rdkit-201203/rdkit/ML/Cluster/UnitTestCluster.py
+@@ -14,7 +14,11 @@
+ from rdkit import RDConfig
+ import unittest
+ from rdkit.ML.Cluster import Standardize,ClusterUtils
+-from rdkit.ML.Cluster import Clusters,Murtagh
++from rdkit.ML.Cluster import Clusters
++try:
++ from rdkit.ML.Cluster import Murtagh
++except ImportError:
++ Murtagh=None
+ import numpy
+ import cPickle
+
+@@ -57,6 +61,7 @@ class TestCase(unittest.TestCase):
+ assert indices==[8,7,5,6],'bad index order'
+
+ def testMurtaghUPGMA(self):
++ if Murtagh is None: return
+ nPts = 5
+ sz = 5
+ dataP = numpy.random.random((nPts,sz))
+--- rdkit-201203.orig/rdkit/ML/FeatureSelect/UnitTestCMIM.py
++++ rdkit-201203/rdkit/ML/FeatureSelect/UnitTestCMIM.py
+@@ -1,4 +1,7 @@
+-from rdkit.ML.FeatureSelect import CMIM
++try:
++ from rdkit.ML.FeatureSelect import CMIM
++except ImportError:
++ CMIM = None
+ from rdkit import DataStructs as DS
+ from rdkit import RDConfig
+ import unittest
+@@ -8,6 +11,8 @@ class TestCase(unittest.TestCase):
+ pass
+
+ def test0FromList(self) :
++ if CMIM is None:
++ return
+ examples = []
+
+ bv = DS.ExplicitBitVect(5)
+--- rdkit-201203.orig/rdkit/ML/DecTree/BuildSigTree.py
++++ rdkit-201203/rdkit/ML/DecTree/BuildSigTree.py
+@@ -12,7 +12,10 @@
+ import numpy
+ from rdkit.ML.DecTree import SigTree
+ from rdkit.ML import InfoTheory
+-from rdkit.ML.FeatureSelect import CMIM
++try:
++ from rdkit.ML.FeatureSelect import CMIM
++except ImportError:
++ CMIM=None
+ from rdkit.DataStructs.VectCollection import VectCollection
+ import copy
+ import random
+@@ -136,7 +139,7 @@ def BuildSigTree(examples,nPossibleRes,e
+ nBits = fp.GetNumBits()
+ ranker = InfoTheory.InfoBitRanker(nBits,nPossibleRes,metric)
+ if biasList: ranker.SetBiasList(biasList)
+- if useCMIM > 0 and not ensemble:
++ if CMIM is not None and useCMIM > 0 and not ensemble:
+ ensemble = CMIM.SelectFeatures(examples,useCMIM,bvCol=1)
+ if random:
+ if ensemble:
+--- rdkit-201203.orig/rdkit/ML/NaiveBayes/CrossValidate.py
++++ rdkit-201203/rdkit/ML/NaiveBayes/CrossValidate.py
+@@ -9,14 +9,17 @@ and evaluation of individual models
+ """
+ from rdkit.ML.NaiveBayes.ClassificationModel import NaiveBayesClassifier
+ from rdkit.ML.Data import SplitData
+-from rdkit.ML.FeatureSelect import CMIM
++try:
++ from rdkit.ML.FeatureSelect import CMIM
++except ImportError:
++ CMIM=None
+
+ def makeNBClassificationModel(trainExamples, attrs, nPossibleValues, nQuantBounds,
+ mEstimateVal=-1.0,
+ useSigs=False,
+ ensemble=None,useCMIM=0,
+ **kwargs) :
+- if useCMIM > 0 and useSigs and not ensemble:
++ if CMIM is not None and useCMIM > 0 and useSigs and not ensemble:
+ ensemble = CMIM.SelectFeatures(trainExamples,useCMIM,bvCol=1)
+ if ensemble:
+ attrs = ensemble
diff -Nru rdkit-201203/debian/patches/series rdkit-201203/debian/patches/series
--- rdkit-201203/debian/patches/series 1970-01-01 01:00:00.000000000 +0100
+++ rdkit-201203/debian/patches/series 2012-07-28 19:38:34.000000000 +0200
@@ -0,0 +1 @@
+big-endian_support.patch
diff -Nru rdkit-201203/debian/rules rdkit-201203/debian/rules
--- rdkit-201203/debian/rules 2012-06-12 13:44:36.000000000 +0200
+++ rdkit-201203/debian/rules 2012-07-28 19:54:12.000000000 +0200
@@ -21,5 +21,5 @@
dh_auto_configure -- -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF
override_dh_auto_test:
-# cp -r rdkit obj-*/
-# RDBASE=$(CURDIR) PYTHONPATH=$(wildcard $(CURDIR)/obj-*/) dh_auto_test -O--buildsystem=cmake
+ cp -r rdkit obj-*/
+ RDBASE=$(CURDIR) PYTHONPATH=$(wildcard $(CURDIR)/obj-*/) dh_auto_test -O--buildsystem=cmake
--- End Message ---