Re: [Rdkit-discuss] compiling aggdraw on 64 bit systems for rdkit graphic output - Solution
Dear Hari,
Thanks for tracking down this problem and posting a solution.
-greg
On Tue, Jun 22, 2010 at 12:01 AM, hari jayaram wrote:
> I struggled a little bit with this today and thought I will post it
> to the group in case it helps someone.
>
> To build aggdraw for output from rdkit on 64 bit linux systems do the
> following:
> Based on a comment on the aggdraw blog page from osirius , you need to
> change a single line of code in the
> agg2/include/agg_array.h file as detailed on this post:
>
> http://www.pocketuniverse.ca/archive/2008/december/11/pil-and-aggdraw/
>
> Original solution by Subash chandra
> (http://timeless-scripts.blogspot.com/2007/08/patch-to-aggdraw-for-64-bit-machines.html)
>
>
>
>
> Index: agg2/include/agg_array.h
> ===
> --- agg2/include/agg_array.h (revision 521)
> +++ agg2/include/agg_array.h (working copy)
> @@ -520,7 +520,7 @@
> int8u* ptr = m_buf_ptr;
> if(alignment > 1)
> {
> - unsigned align = (alignment - unsigned(ptr) %
> alignment) % alignment;
> + unsigned align = (alignment - (unsigned
> long)(ptr) % alignment) % alignment;
> size += align;
> ptr += align;
> if(size <= m_rest)
>
>
> After that aggdraw builds fine with
>
> python setup.py build_ext -i
> sudo python setup.py install
>
>
>
> Hope this helps
>
> Hari
>
> --
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[Rdkit-discuss] compiling aggdraw on 64 bit systems for rdkit graphic output - Solution
I struggled a little bit with this today and thought I will post it
to the group in case it helps someone.
To build aggdraw for output from rdkit on 64 bit linux systems do the
following:
Based on a comment on the aggdraw blog page from osirius , you need to
change a single line of code in the
agg2/include/agg_array.h file as detailed on this post:
http://www.pocketuniverse.ca/archive/2008/december/11/pil-and-aggdraw/
Original solution by Subash chandra
(http://timeless-scripts.blogspot.com/2007/08/patch-to-aggdraw-for-64-bit-machines.html)
Index: agg2/include/agg_array.h
===
--- agg2/include/agg_array.h(revision 521)
+++ agg2/include/agg_array.h(working copy)
@@ -520,7 +520,7 @@
int8u* ptr = m_buf_ptr;
if(alignment > 1)
{
-unsigned align = (alignment - unsigned(ptr) %
alignment) % alignment;
+unsigned align = (alignment - (unsigned
long)(ptr) % alignment) % alignment;
size += align;
ptr += align;
if(size <= m_rest)
After that aggdraw builds fine with
python setup.py build_ext -i
sudo python setup.py install
Hope this helps
Hari
--
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Re: [Rdkit-discuss] python wrappers not installed by default? Ubuntu Lucid Lynx 10.04 64 bit - rdkit svn
Hey Greg, Thanks a lot for your help . As you said all the python modules were in /home/hari/rdkit/trunk So I had to add that to my PYTHONPATH . I also did put the *.so files to my LD_LIBRARY_PATH and set RDBASE appropriately. Once I did that I can indeed start using the module . I still have not managed to get the aggdraw module installed . I get a compilation error ( given below). I have emailed Fredrik Lundh about the error , but was wondering if you or anyone know how I can get it working. Thanks Hari # MY .bashrc contains # export PYTHONPATH="$PYTHONPATH:/usr/local/openbabel/lib/python2.6/site-packages:/home/hari/rdkit/trunk" export LD_LIBRARY_PATH="/usr/local/lib:$LD_LIBRARY_PATH:/usr/local/openbabel/lib:/home/hari/rdkit/trunk/bin" export RDBASE="/home/hari/rdkit/trunk" ### aggdraw compilation problem Ubuntu Lucid 10.04 gcc (Ubuntu 4.4.3-4ubuntu5) 4.4.3 ### h...@hari:~/aggdraw$ python setup.py build running build running build_ext building 'aggdraw' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -DHAVE_FREETYPE2 -Iagg2/include -Iagg2/font_freetype -I./freetype-2.3.12/include -I./freetype-2.3.12/include/freetype2 -I/usr/include/python2.6 -c aggdraw.cxx -o build/temp.linux-x86_64-2.6/aggdraw.o cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++ In file included from agg2/include/agg_vertex_sequence.h:23, from agg2/include/agg_vcgen_contour.h:20, from agg2/include/agg_conv_contour.h:23, from aggdraw.cxx:62: agg2/include/agg_array.h: In member function ‘agg::int8u* agg::pod_allocator::allocate(unsigned int, unsigned int)’: agg2/include/agg_array.h:523: error: cast from ‘agg::int8u*’ to ‘unsigned int’ loses precision In file included from agg2/font_freetype/agg_font_freetype.h:28, from aggdraw.cxx:69: agg2/include/agg_scanline_storage_bin.h: In member function ‘unsigned int agg::scanline_storage_bin::byte_size() const’: agg2/include/agg_scanline_storage_bin.h:247: warning: unused variable ‘sp’ aggdraw.cxx: In function ‘void draw_setup(DrawObject*)’: aggdraw.cxx:457: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx:460: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx:463: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx:466: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx: In function ‘PyObject* draw_new(PyObject*, PyObject*)’: aggdraw.cxx:572: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx: In function ‘agg::rgba8 getcolor(PyObject*, int)’: aggdraw.cxx:778: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx: In function ‘PyObject* draw_flush(DrawObject*, PyObject*)’: aggdraw.cxx:1239: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx:1239: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx: In function ‘PyObject* pen_new(PyObject*, PyObject*, PyObject*)’: aggdraw.cxx:1331: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx:1331: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx:1331: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx: In function ‘PyObject* brush_new(PyObject*, PyObject*, PyObject*)’: aggdraw.cxx:1362: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx:1362: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx: In function ‘PyObject* font_new(PyObject*, PyObject*, PyObject*)’: aggdraw.cxx:1393: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx:1393: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx:1393: warning: deprecated conversion from string constant to ‘char*’ aggdraw.cxx:1393: warning: deprecated conversion from string constant to ‘char*’ In file included from agg2/font_freetype/agg_font_freetype.h:35, from aggdraw.cxx:69: agg2/include/agg_font_cache_manager.h: In member function ‘void agg::font_cache_manager::init_embedded_adaptors(const agg::glyph_cache*, double, double) [with FontEngine = agg::font_engine_freetype_int32]’: aggdraw.cxx:381: instantiated from ‘void draw_adaptor::drawtext(float*, PyObject*, FontObject*) [with PixFmt = agg::pixel_formats_rgba32]’ aggdraw.cxx:1940: instantiated from here agg2/include/agg_font_cache_manager.h:306: warning: enumeration value ‘glyph_data_invalid’ not handled in switch error: command 'gcc' failed with exit status 1 On Mon, Jun 21, 2010 at 11:48 AM, Greg Landrum wrote: > Dear Hari, > > > On Mon, Jun 21, 2010 at 5:44 PM, hari jayaram wrote: >> First off thanks for this toolkit . It seems very powerful in
Re: [Rdkit-discuss] A couple of questions regarding ReactionFromSmarts
Thanks Greg - this is great! I must confess, I was eager to try this out asap
- but have not built rdkit before. I did start having a go over the weekend on
my home PC (Windows MCE2005) but ran into a couple of unexpected issues with
the software installs that made me think I would wait and retry on my work PC.
[not really relevant, but for interest - I think the problems may have been
related to the Visual Studio 2010 Express installation. The result was an
infuriating clicking in the audio when streaming live or recorded TV to an
extender!! Not an issue that I felt was easy to troubleshoot... I reinstalled
my system from a drive image backup and the problem was gone... That's when I
decided to leave well alone, as my family may not have seen the benefit of
up-to-the-minute builds at home at the expense of TV enjoyment : ) ]
I will get my PC at work setup to build from SVN snapshots - but I was very
pleased to see your post
(http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01097.html)
saying that Q2 binaries should be available next week - great news!
Kind regards
James
-Original Message-
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 18 June 2010 06:08
To: rdkit-discuss@lists.sourceforge.net
Cc: James Davidson
Subject: Re: [Rdkit-discuss] A couple of questions regarding ReactionFromSmarts
Dear all,
A followup/update on a request from a couple weeks ago:
On Fri, Jun 4, 2010 at 6:13 AM, Greg Landrum wrote:
> On Thu, Jun 3, 2010 at 7:51 PM, James Davidson
> wrote:
>>
>> (1) I see that the reaction objects can be created from MDL Reaction
>> Files/Blocks - is there a way to do the reverse, and save a reaction
>> object in MDL .rxn format? I tried using investigating the
>> rxn.ToBinary() attribute, but didn't get very far... The reason I
>> wanted to do this, is that I was trying to figure-out how to generate
>> a form of the reaction object (generated from reaction SMARTS) that
>> was suitable for converting into a 2D depiction of the transformation.
>
> At the moment the reactions are essentially input-only. There's really
> no way to get them out in any format that could be used elsewhere.
> This is a sadly missing feature: it would be really nice to be able to
> generate either .rxn files (or at least reaction smarts) from
> reactions. I will add a feature request for this, but it may take a
> while to happen.[1]
I've added a partial solution to this that at least provides some help with
visualizing reactions.
Here's my reaction:
[12]>>> rxn =
AllChem.ReactionFromSmarts('[C:1](=[O:2])-[O;-,H].[N;!$(N-C=[O,N,S]);!$(N=*):3]>>[C:1](=[O:2])-[N:3]')
You can now output reaction smarts:
[13]>>> AllChem.ReactionToSmarts(rxn)
Out[13]
'[C:1](=[O:2])-[O;-,H1].[N;!$(N-C=[O,N,S]);!$(N=*):3]>>[C:1](=[O:2])-[N:3]'
You can also generate coordinates for a reaction and the create an rxn file:
[14]>>> AllChem.Compute2DCoordsForReaction(rxn)
[15]>>> print AllChem.ReactionToRxnBlock(rxn)
--> print(AllChem.ReactionToRxnBlock(rxn))
$RXN
RDKit
2 1
$MOL
RDKit 2D
3 2 0 0 0 0 0 0 0 0999 V2000
-0.0.0. C 0 0 0 0 0 0 0 0 0 1 0 0
-0. -1.50000. O 0 0 0 0 0 0 0 0 0 2 0 0
-0.1.50000. * 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
1 3 1 0
V3 [O;-,H1]
M END
$MOL
RDKit 2D
1 0 0 0 0 0 0 0 0 0999 V2000
0.50000.0. * 0 0 0 0 0 0 0 0 0 3 0 0
V1 [N;!$(N-C=[O,N,S]);!$(N=*):3]
M END
$MOL
RDKit 2D
3 2 0 0 0 0 0 0 0 0999 V2000
1.50000.0. C 0 0 0 0 0 0 0 0 0 1 0 0
1.5000 -1.50000. O 0 0 0 0 0 0 0 0 0 2 0 0
1.50001.50000. N 0 0 0 0 0 0 0 0 0 3 0 0
1 2 2 0
1 3 1 0
M END
#
Notice that query features on atoms in the rxn blocks are not output as
property ctab query features. Instead I use the atom-value feature of ctabs and
output the SMARTS query for the atoms. This has the marked disadvantage that it
won't actually generate reactions that do sensible things in other tools, but
at least you can do some debugging of reactions. At some point in the future it
would be nice to have ctab queries handled correctly, but this is at least
something.
These changes are checked into subversion and will be in the next release.
Best Regards,
-greg
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Re: [Rdkit-discuss] python wrappers not installed by default? Ubuntu Lucid Lynx 10.04 64 bit - rdkit svn
Dear Hari, On Mon, Jun 21, 2010 at 5:44 PM, hari jayaram wrote: > First off thanks for this toolkit . It seems very powerful indeed You're welcome; I hope it is useful to you. > I did run a make install . The output indicates that everything was > normal ( see below) Yep, looks good. > > On a probably unrelated note , I was able to call rdkit from cinfony > and calculate the molecular weight as indicated here ( > http://code.google.com/p/cinfony/wiki/InstallationOnLinuxV10) > But the rdk module does not seem to have gotten installed. Looks like things are installed in: /home/hari/rdkit/trunk/rdkit, which means you should make sure that /home/hari/rdkit/trunk is in your PYTHONPATH and RDBASE is /home/hari/rdkit/trunk. This ought to solve things. -greg -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] python wrappers not installed by default? Ubuntu Lucid Lynx 10.04 64 bit - rdkit svn
Hi Greg, First off thanks for this toolkit . It seems very powerful indeed. I did run a make install . The output indicates that everything was normal ( see below) On a probably unrelated note , I was able to call rdkit from cinfony and calculate the molecular weight as indicated here ( http://code.google.com/p/cinfony/wiki/InstallationOnLinuxV10) But the rdk module does not seem to have gotten installed. Hari h...@hari:~/rdkit/trunk/build$ make install [ 1%] Built target fastentropy [ 3%] Built target RDGeneral [ 3%] Built target testDict [ 3%] Built target RDBoost [ 3%] Built target rdBase [ 6%] Built target DataStructs [ 6%] Built target testDataStructs [ 8%] Built target cDataStructs [ 10%] Built target RDGeometryLib [ 10%] Built target testGrid [ 11%] Built target testTransforms [ 13%] Built target rdGeometry [ 13%] Built target testMatrices [ 13%] Built target Alignment [ 14%] Built target testAlignment [ 15%] Built target rdAlignment [ 15%] Built target EigenSolvers [ 16%] Built target Optimizer [ 16%] Built target testOptimizer [ 19%] Built target ForceField [ 19%] Built target testForceField [ 19%] Built target rdForceField [ 21%] Built target DistGeometry [ 22%] Built target testDistGeom [ 23%] Built target DistGeom [ 24%] Built target Catalogs [ 34%] Built target GraphMol [ 39%] Built target SmilesParse [ 40%] Built target graphmolIterTest [ 46%] Built target FileParsers [ 46%] Built target graphmolMolOpsTest [ 47%] Built target graphmolTest1 [ 47%] Built target graphmolcpTest [ 47%] Built target graphmolqueryTest [ 48%] Built target SubstructMatch [ 49%] Built target graphmoltestCanon [ 49%] Built target graphmoltestChirality [ 50%] Built target graphmoltestPickler [ 51%] Built target Depictor [ 51%] Built target testDepictor [ 52%] Built target rdDepictor [ 52%] Built target smaTest1 [ 52%] Built target smiTest1 [ 52%] Built target fileParsersTest1 [ 53%] Built target testMol2ToMol [ 54%] Built target testMolSupplier [ 55%] Built target testMolWriter [ 55%] Built target testTplParser [ 56%] Built target testSubstructMatch [ 58%] Built target ChemReactions [ 59%] Built target testReaction [ 60%] Built target rdChemReactions [ 61%] Built target ChemTransforms [ 61%] Built target testChemTransforms [ 62%] Built target Subgraphs [ 62%] Built target testSubgraphs1 [ 62%] Built target testSubgraphs2 [ 64%] Built target FragCatalog [ 64%] Built target testFragCatalog [ 66%] Built target rdfragcatalog [ 67%] Built target Descriptors [ 68%] Built target testDescriptors [ 69%] Built target Fingerprints [ 69%] Built target rdMolDescriptors [ 70%] Built target testFingerprints [ 71%] Built target PartialCharges [ 72%] Built target rdPartialCharges [ 72%] Built target MolTransforms [ 72%] Built target testMolTransforms [ 72%] Built target rdMolTransforms [ 72%] Built target MolAlign [ 72%] Built target ForceFieldHelpers [ 72%] Built target DistGeomHelpers [ 73%] Built target testForceFieldHelpers [ 73%] Built target rdForceFieldHelpers [ 73%] Built target testDistGeomHelpers [ 73%] Built target rdDistGeom [ 73%] Built target testMolAlign [ 74%] Built target rdMolAlign [ 76%] Built target MolChemicalFeatures [ 76%] Built target testFeatures [ 78%] Built target rdMolChemicalFeatures [ 79%] Built target ShapeHelpers [ 80%] Built target testShapeHelpers [ 81%] Built target rdShapeHelpers [ 82%] Built target MolCatalog [ 82%] Built target testMolCatalog [ 82%] Built target rdMolCatalog [ 84%] Built target SLNParse [ 84%] Built target testSLNParse [ 84%] Built target rdSLNParse [ 87%] Built target rdchem [ 90%] Built target rdmolfiles [ 91%] Built target rdmolops [ 91%] Built target testQuery [ 92%] Built target testMatCalc [ 92%] Built target rdMetricMatrixCalc [ 92%] Built target hc [ 93%] Built target SimDivPickers [ 94%] Built target rdSimDivPickers [ 95%] Built target Clustering [ 96%] Built target rdFeatSelect [ 97%] Built target InfoTheory [ 98%] Built target cEntropy [ 99%] Built target rdInfoTheory [ 99%] Built target cQuantize [ 99%] Built target ChemicalFeatures [100%] Built target testChemicalFeatures [100%] Built target rdChemicalFeatures Install the project... -- Install configuration: "Release" -- Up-to-date: /home/hari/rdkit/trunk/bin/libRDGeneral.so -- Up-to-date: /home/hari/rdkit/trunk/bin/libRDBoost.so -- Up-to-date: /home/hari/rdkit/trunk/rdkit/rdBase.so -- Up-to-date: /home/hari/rdkit/trunk/bin/libDataStructs.so -- Up-to-date: /home/hari/rdkit/trunk/rdkit/DataStructs/cDataStructs.so -- Up-to-date: /home/hari/rdkit/trunk/bin/libRDGeometryLib.so -- Up-to-date: /home/hari/rdkit/trunk/rdkit/Geometry/rdGeometry.so -- Up-to-date: /home/hari/rdkit/trunk/bin/libAlignment.so -- Up-to-date: /home/hari/rdkit/trunk/rdkit/Numerics/rdAlignment.so -- Up-to-date: /home/hari/rdkit/trunk/bin/libEigenSolvers.so -- Up-to-date: /home/hari/rdkit/trunk/bin/libOptimizer.so -- Up-to-date: /home/hari/rdkit/trunk/bin/libForceField.so -- Up-to-date: /home/hari/rdkit/trunk/rdkit/ForceField/rdForceField.so
Re: [Rdkit-discuss] python wrappers not installed by default? Ubuntu Lucid Lynx 10.04 64 bit - rdkit svn
dumb question: did you run "make install" after running cmake? -greg On Mon, Jun 21, 2010 at 5:02 PM, hari jayaram wrote: > Hi I am trying to install the python wrappers with subversion trunk > build of rdkit on a 64 bit Ubuntu 10.04 Lucid-Lynx. I did see on the > wiki that Greg Landrum has gotten rdkit to build on this system. > > For cmake I used the command below And got the rdkit build to complete to > 100%. > > cmake -DBOOST_ROOT=/usr/local/lib -D RDK_BUILD_PYTHON_WRAPPERS=on -D > PYTHON_EXECUTABLE=/usr/bin/python .. > > The cmake script seems to find all components . But still I dont see > any python wrappers installed anywhere. I am sorry I am a newbie , can > someone tell me how to get rdkit to build the python wrappers. > > > Thanks > Hari > > > h...@hari:~/rdkit/trunk/build$ cmake -DBOOST_ROOT=/usr/local/lib -D > RDK_BUILD_PYTHON_WRAPPERS=on -D PYTHON_EXECUTABLE=/usr/bin/python .. > -- The C compiler identification is GNU > -- The CXX compiler identification is GNU > -- Check for working C compiler: /usr/bin/gcc > -- Check for working C compiler: /usr/bin/gcc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Check for working CXX compiler: /usr/bin/c++ > -- Check for working CXX compiler: /usr/bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Found PythonLibs: /usr/lib/libpython2.6.so > -- Found PythonInterp: /usr/bin/python > -- Boost version: 1.43.0 > -- Found the following Boost libraries: > -- python > -- Found BISON: /usr/bin/bison > -- Found FLEX: /usr/bin/flex > -- Boost version: 1.43.0 > -- Found the following Boost libraries: > -- regex > -- Configuring done > -- Generating done > -- Build files have been written to: /home/hari/rdkit/trunk/build > > -- > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] python wrappers not installed by default? Ubuntu Lucid Lynx 10.04 64 bit - rdkit svn
Hi I am trying to install the python wrappers with subversion trunk build of rdkit on a 64 bit Ubuntu 10.04 Lucid-Lynx. I did see on the wiki that Greg Landrum has gotten rdkit to build on this system. For cmake I used the command below And got the rdkit build to complete to 100%. cmake -DBOOST_ROOT=/usr/local/lib -D RDK_BUILD_PYTHON_WRAPPERS=on -D PYTHON_EXECUTABLE=/usr/bin/python .. The cmake script seems to find all components . But still I dont see any python wrappers installed anywhere. I am sorry I am a newbie , can someone tell me how to get rdkit to build the python wrappers. Thanks Hari h...@hari:~/rdkit/trunk/build$ cmake -DBOOST_ROOT=/usr/local/lib -D RDK_BUILD_PYTHON_WRAPPERS=on -D PYTHON_EXECUTABLE=/usr/bin/python .. -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Found PythonLibs: /usr/lib/libpython2.6.so -- Found PythonInterp: /usr/bin/python -- Boost version: 1.43.0 -- Found the following Boost libraries: -- python -- Found BISON: /usr/bin/bison -- Found FLEX: /usr/bin/flex -- Boost version: 1.43.0 -- Found the following Boost libraries: -- regex -- Configuring done -- Generating done -- Build files have been written to: /home/hari/rdkit/trunk/build -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] svn compilation problem on Ubuntu Lucid-Lynx: libboost_regex-mt.a: could not read symbols: Bad value
Hi, Thanks to the excellent instructions at http://code.google.com/p/rdkit/wiki/BuildingWithCmake which I failed to read before I sent my previous post out I have successfully build rdkit on ubuntu Lucid. Thanks everyone for such great documentation. Hari Here is what I did: -1) Installed boost 1.43.0 as instructed in wiki article :http://code.google.com/p/rdkit/wiki/BuildingWithCmake 0) removed the libboost-all-dev and libbbost-dev version 1.40.0 which I had previoudly installed 1) Start from scratch by cleaning out my build directory 2) set my LD_LIBRARY_PATH to include /usr/local/lib where libboost_python.so, libboost_regex.so were installed and also setup RDBASE to point to the root directory of my build (/home/hari/rdkit/trunk) 3) cmake -DBOOST_ROOT=/usr/local/lib .. 4) Then ran make On Mon, Jun 21, 2010 at 9:06 AM, hari jayaram wrote: > Hello, > Newbie Alert. I am trying to compile the rdkit svn version 1433 on 64 > bit ununtu Lucid. > I am using the ubuntu supplied boost library , 1.40.0.1. > > The rdkit build completes to 84% and stops with the following error ( > see below). > > I am confused as to how to get the correct version of boost which I am > imagining will fix the problem. I downloaded Release 1.43.0 , but dont > know how to point the rdkit build to this boost library since I am > new to bjam and cmake. > > Any help will be greatly appreciated. > Thanks > Hari > > > [ 82%] Built target rdMolCatalog > Linking CXX shared library libSLNParse.so > /usr/bin/ld: > /usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib/libboost_regex-mt.a(instances.o): > relocation R_X86_64_32 against > `boost::object_cache, > boost::re_detail::cpp_regex_traits_implementation >>::do_get(boost::re_detail::cpp_regex_traits_base const&, > unsigned long)::s_data' can not be used when making a shared object; > recompile with -fPIC > /usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib/libboost_regex-mt.a: > could not read symbols: Bad value > collect2: ld returned 1 exit status > make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Error 1 > make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error 2 > make: *** [all] Error 2 > > > ~/rdkit/trunk/build$ dpkg --list | grep "boost" > ii libboost-all-dev 1.40.0.1 > Boost C++ Libraries development files (ALL, > ii libboost-date-time1.40-dev 1.40.0-4ubuntu4 > set of date-time libraries based on generic > ii libboost-date-time1.40.0 1.40.0-4ubuntu4 > set of date-time libraries based on generic > ii libboost-dev 1.40.0.1 > Boost C++ Libraries development files (defau > ii libboost-filesystem1.40-dev 1.40.0-4ubuntu4 > filesystem operations (portable paths, itera > ii libboost-filesystem1.40.0 1.40.0-4ubuntu4 > filesystem operations (portable paths, itera > ii libboost-graph1.40-dev 1.40.0-4ubuntu4 > generic graph components and algorithms in C > ii libboost-graph1.40.0 1.40.0-4ubuntu4 > generic graph components and algorithms in C > ii libboost-iostreams1.40-dev 1.40.0-4ubuntu4 > Boost.Iostreams Library development files > ii libboost-iostreams1.40.0 1.40.0-4ubuntu4 > Boost.Iostreams Library > ii libboost-math1.40-dev 1.40.0-4ubuntu4 > Boost.Math Library development files > ii libboost-math1.40.0 1.40.0-4ubuntu4 > Boost.Math Library > ii libboost-program-options1.40-dev 1.40.0-4ubuntu4 > program options library for C++ > ii libboost-program-options1.40.0 1.40.0-4ubuntu4 > program options library for C++ > ii libboost-python1.40-dev 1.40.0-4ubuntu4 > Boost.Python Library development files > ii libboost-python1.40.0 1.40.0-4ubuntu4 > Boost.Python Library > ii libboost-regex-dev 1.40.0.1 > regular expression library for C++ (default > ii libboost-regex1.40-dev 1.40.0-4ubuntu4 > regular expression library for C++ > ii libboost-regex1.40.0 1.40.0-4ubuntu4 > regular expression library for C++ > ii libboost-serialization1.40-dev 1.40.0-4ubuntu4 > serialization library for C++ > ii libboost-serialization1.40.0 1.40.0-4ubuntu4 > serialization library for C++ > ii libboost-signals1.40-dev 1.40.0-4ubuntu4 > managed signals and slots library for C++ > ii libboost-signals1.40.0 1.40.0-4ubuntu4 > managed signals and slots library for C++ > ii libboost-system1.40-dev 1.40.0-4ubuntu4 > Operating system (e.g. diagnostics support) > ii libboost
[Rdkit-discuss] svn compilation problem on Ubuntu Lucid-Lynx: libboost_regex-mt.a: could not read symbols: Bad value
Hello, Newbie Alert. I am trying to compile the rdkit svn version 1433 on 64 bit ununtu Lucid. I am using the ubuntu supplied boost library , 1.40.0.1. The rdkit build completes to 84% and stops with the following error ( see below). I am confused as to how to get the correct version of boost which I am imagining will fix the problem. I downloaded Release 1.43.0 , but dont know how to point the rdkit build to this boost library since I am new to bjam and cmake. Any help will be greatly appreciated. Thanks Hari [ 82%] Built target rdMolCatalog Linking CXX shared library libSLNParse.so /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib/libboost_regex-mt.a(instances.o): relocation R_X86_64_32 against `boost::object_cache, boost::re_detail::cpp_regex_traits_implementation >::do_get(boost::re_detail::cpp_regex_traits_base const&, unsigned long)::s_data' can not be used when making a shared object; recompile with -fPIC /usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib/libboost_regex-mt.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Error 1 make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error 2 make: *** [all] Error 2 ~/rdkit/trunk/build$ dpkg --list | grep "boost" ii libboost-all-dev 1.40.0.1 Boost C++ Libraries development files (ALL, ii libboost-date-time1.40-dev 1.40.0-4ubuntu4 set of date-time libraries based on generic ii libboost-date-time1.40.0 1.40.0-4ubuntu4 set of date-time libraries based on generic ii libboost-dev 1.40.0.1 Boost C++ Libraries development files (defau ii libboost-filesystem1.40-dev 1.40.0-4ubuntu4 filesystem operations (portable paths, itera ii libboost-filesystem1.40.01.40.0-4ubuntu4 filesystem operations (portable paths, itera ii libboost-graph1.40-dev 1.40.0-4ubuntu4 generic graph components and algorithms in C ii libboost-graph1.40.0 1.40.0-4ubuntu4 generic graph components and algorithms in C ii libboost-iostreams1.40-dev 1.40.0-4ubuntu4 Boost.Iostreams Library development files ii libboost-iostreams1.40.0 1.40.0-4ubuntu4 Boost.Iostreams Library ii libboost-math1.40-dev1.40.0-4ubuntu4 Boost.Math Library development files ii libboost-math1.40.0 1.40.0-4ubuntu4 Boost.Math Library ii libboost-program-options1.40-dev 1.40.0-4ubuntu4 program options library for C++ ii libboost-program-options1.40.0 1.40.0-4ubuntu4 program options library for C++ ii libboost-python1.40-dev 1.40.0-4ubuntu4 Boost.Python Library development files ii libboost-python1.40.01.40.0-4ubuntu4 Boost.Python Library ii libboost-regex-dev 1.40.0.1 regular expression library for C++ (default ii libboost-regex1.40-dev 1.40.0-4ubuntu4 regular expression library for C++ ii libboost-regex1.40.0 1.40.0-4ubuntu4 regular expression library for C++ ii libboost-serialization1.40-dev 1.40.0-4ubuntu4 serialization library for C++ ii libboost-serialization1.40.0 1.40.0-4ubuntu4 serialization library for C++ ii libboost-signals1.40-dev 1.40.0-4ubuntu4 managed signals and slots library for C++ ii libboost-signals1.40.0 1.40.0-4ubuntu4 managed signals and slots library for C++ ii libboost-system1.40-dev 1.40.0-4ubuntu4 Operating system (e.g. diagnostics support) ii libboost-system1.40.01.40.0-4ubuntu4 Operating system (e.g. diagnostics support) ii libboost-test1.40-dev1.40.0-4ubuntu4 components for writing and executing test su ii libboost-test1.40.0 1.40.0-4ubuntu4 components for writing and executing test su ii libboost-thread1.40-dev 1.40.0-4ubuntu4 portable C++ multi-threading ii libboost-thread1.40.01.40.0-4ubuntu4 portable C++ multi-threading ii libboost-wave1.40-dev1.40.0-4ubuntu4 C99/C++ preprocessor library ii libboost-wave1.40.0 1.40.0-4ubuntu4 C99/C++ preprocessor library ii libboost1.40-all-dev 1.40.0-4ubuntu4 Boost C++ Libraries development files (ALL) ii libboost1.40-dev 1.40.0-4ubuntu4 Boost C++ Libraries development files ---
