Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

2017-06-22 Thread JP
Just to give this closure on the list -- the problem was that I had static
libraries for boost (.a files).  Once I rebuilt boost as shared libraries
(.so) everything worked fine.

Thanks to Greg and Paolo for their help.

On 21 June 2017 at 11:02, Greg Landrum  wrote:

> Let's move this off the list for a bit until we get it resolved.
>
> Can you please do: "VERBOSE=1 make testReaction" and send the output just
> to me?
>
> Thanks,
> -greg
>
>
> On Wed, Jun 21, 2017 at 10:24 AM, JP  wrote:
>
>> Looks like it is finding the correct version of boost (and it is finding
>> boost serialize).
>>
>> /opt/rdkit/rdkit-Release_2017_03_2/build$ cmake -D
>> RDK_BUILD_INCHI_SUPPORT=ON -D BOOST_ROOT=/opt/boost_1_61_0/ -D
>> Boost_NO_SYSTEM_PATHS=ON ..
>> -- Could NOT find InChI in system locations (missing:  INCHI_LIBRARY
>> INCHI_INCLUDE_DIR)
>> CUSTOM_INCHI_PATH = /opt/rdkit/rdkit-Release_2017_03_2/External/INCHI-API
>> -- Found InChI software locally
>> -- Boost version: 1.61.0
>> -- Found the following Boost libraries:
>> --   python
>> -- Boost version: 1.61.0
>> -- Found the following Boost libraries:
>> --   thread
>> --   system
>> --   chrono
>> --   date_time
>> --   atomic
>> -- Boost version: 1.61.0
>> -- Found the following Boost libraries:
>> --   serialization
>> == Using strict rotor definition
>> == Updating Filters.cpp from pains file
>> == Done updating pains files
>> -- Boost version: 1.61.0
>> -- Found the following Boost libraries:
>> --   regex
>> -- Configuring done
>> -- Generating done
>> -- Build files have been written to: /opt/rdkit/rdkit-Release_2017_
>> 03_2/build
>>
>> But the error prevails.
>>
>> If I set up rdkit to use just the system wide boost (1.58), not my
>> specific install (1.61), rdkit builds successfully.  I do this by clearing
>> BOOST_ROOT, LD_LIBRARY_PATH, and removing the boost-related cmake flags.
>> So this is certainly an issue with wrong libraries being picked up.
>>
>>
>>
>>
>> On 21 June 2017 at 07:29, Greg Landrum  wrote:
>>
>>> did you build boost serialize?
>>>
>>> On Mon, Jun 19, 2017 at 12:03 PM, JP 
>>> wrote:
>>>
 Hi Greg !

 Unfortunately that didn't help (I delete everything in my build
 directory, then):

 cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/
 -DBoost_NO_SYSTEM_PATHS=ON ..

 and make as usual.

 [ 62%] Linking CXX executable testReaction
 ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference
 to `boost::archive::text_iarchive_impl>>> chive>::load_override(boost::archive::class_name_type&)'
 ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference
 to 
 `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception
 const&)'
 collect2: error: ld returned 1 exit status
 Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
 recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed
 make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
 CMakeFiles/Makefile2:4157: recipe for target
 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed
 make[1]: *** [Code/GraphMol/ChemReactions/C
 MakeFiles/testReaction.dir/all] Error 2
 Makefile:160: recipe for target 'all' failed
 make: *** [all] Error 2

 Perhaps this isn't related to the system vs user-install, boost after
 all?


 On 19 June 2017 at 10:38, Greg Landrum  wrote:

> If you have a system boost install that you do not want to use, you
> should be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake 
> arguments.
> This will (well, should) disable any usage of the system boost.
>
> -greg
>
>
> On Mon, Jun 19, 2017 at 9:39 AM, JP 
> wrote:
>
>> HI Paul,
>>
>> Funny you should mention that.  I have boost 1.61 (installed manually
>> in /opt) and system boost I installed via sudo apt-get install
>>
>> /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev |
>> grep 'Version'
>> Version: 1.58.0.1ubuntu1
>>
>> However I pass the BOOST path to cmake via:
>>
>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/
>>  ..
>>
>> (I also have the $BOOST_ROOT env variable set, so I think that is
>> redundant.  Whatever).  cmake output clearly shows it is finding/using
>> boost 1.61
>>
>> Using make VERBOSE=1 I get:
>>
>> [ 62%] Linking CXX executable testReaction
>> cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions
>> && /usr/bin/cmake -E cmake_link_script 
>> CMakeFiles/testReaction.dir/link.txt
>> --verbose=1
>> /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function
>> -fno-strict-aliasing 

Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

2017-06-21 Thread Greg Landrum
Let's move this off the list for a bit until we get it resolved.

Can you please do: "VERBOSE=1 make testReaction" and send the output just
to me?

Thanks,
-greg


On Wed, Jun 21, 2017 at 10:24 AM, JP  wrote:

> Looks like it is finding the correct version of boost (and it is finding
> boost serialize).
>
> /opt/rdkit/rdkit-Release_2017_03_2/build$ cmake -D
> RDK_BUILD_INCHI_SUPPORT=ON -D BOOST_ROOT=/opt/boost_1_61_0/ -D
> Boost_NO_SYSTEM_PATHS=ON ..
> -- Could NOT find InChI in system locations (missing:  INCHI_LIBRARY
> INCHI_INCLUDE_DIR)
> CUSTOM_INCHI_PATH = /opt/rdkit/rdkit-Release_2017_03_2/External/INCHI-API
> -- Found InChI software locally
> -- Boost version: 1.61.0
> -- Found the following Boost libraries:
> --   python
> -- Boost version: 1.61.0
> -- Found the following Boost libraries:
> --   thread
> --   system
> --   chrono
> --   date_time
> --   atomic
> -- Boost version: 1.61.0
> -- Found the following Boost libraries:
> --   serialization
> == Using strict rotor definition
> == Updating Filters.cpp from pains file
> == Done updating pains files
> -- Boost version: 1.61.0
> -- Found the following Boost libraries:
> --   regex
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /opt/rdkit/rdkit-Release_2017_
> 03_2/build
>
> But the error prevails.
>
> If I set up rdkit to use just the system wide boost (1.58), not my
> specific install (1.61), rdkit builds successfully.  I do this by clearing
> BOOST_ROOT, LD_LIBRARY_PATH, and removing the boost-related cmake flags.
> So this is certainly an issue with wrong libraries being picked up.
>
>
>
>
> On 21 June 2017 at 07:29, Greg Landrum  wrote:
>
>> did you build boost serialize?
>>
>> On Mon, Jun 19, 2017 at 12:03 PM, JP  wrote:
>>
>>> Hi Greg !
>>>
>>> Unfortunately that didn't help (I delete everything in my build
>>> directory, then):
>>>
>>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/
>>> -DBoost_NO_SYSTEM_PATHS=ON ..
>>>
>>> and make as usual.
>>>
>>> [ 62%] Linking CXX executable testReaction
>>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference
>>> to `boost::archive::text_iarchive_impl>> chive>::load_override(boost::archive::class_name_type&)'
>>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference
>>> to 
>>> `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception
>>> const&)'
>>> collect2: error: ld returned 1 exit status
>>> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
>>> recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed
>>> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
>>> CMakeFiles/Makefile2:4157: recipe for target
>>> 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed
>>> make[1]: *** [Code/GraphMol/ChemReactions/C
>>> MakeFiles/testReaction.dir/all] Error 2
>>> Makefile:160: recipe for target 'all' failed
>>> make: *** [all] Error 2
>>>
>>> Perhaps this isn't related to the system vs user-install, boost after
>>> all?
>>>
>>>
>>> On 19 June 2017 at 10:38, Greg Landrum  wrote:
>>>
 If you have a system boost install that you do not want to use, you
 should be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake arguments.
 This will (well, should) disable any usage of the system boost.

 -greg


 On Mon, Jun 19, 2017 at 9:39 AM, JP 
 wrote:

> HI Paul,
>
> Funny you should mention that.  I have boost 1.61 (installed manually
> in /opt) and system boost I installed via sudo apt-get install
>
> /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | grep
> 'Version'
> Version: 1.58.0.1ubuntu1
>
> However I pass the BOOST path to cmake via:
>
> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/  ..
>
> (I also have the $BOOST_ROOT env variable set, so I think that is
> redundant.  Whatever).  cmake output clearly shows it is finding/using
> boost 1.61
>
> Using make VERBOSE=1 I get:
>
> [ 62%] Linking CXX executable testReaction
> cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions
> && /usr/bin/cmake -E cmake_link_script 
> CMakeFiles/testReaction.dir/link.txt
> --verbose=1
> /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function
> -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG
> CMakeFiles/testReaction.dir/testReaction.cpp.o  -o testReaction
> -rdynamic ../../../lib/libRDKitChemReactions.so.1.2017.03.2
> ../../../lib/libRDKitChemTransforms.so.1.2017.03.2
> ../../../lib/libRDKitDescriptors.so.1.2017.03.2
> ../../../lib/libRDKitFingerprints.so.1.2017.03.2
> ../../../lib/libRDKitDepictor.so.1.2017.03.2
> ../../../lib/libRDKitFileParsers.so.1.2017.03.2 

Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

2017-06-21 Thread JP
Looks like it is finding the correct version of boost (and it is finding
boost serialize).

/opt/rdkit/rdkit-Release_2017_03_2/build$ cmake -D
RDK_BUILD_INCHI_SUPPORT=ON -D BOOST_ROOT=/opt/boost_1_61_0/ -D
Boost_NO_SYSTEM_PATHS=ON ..
-- Could NOT find InChI in system locations (missing:  INCHI_LIBRARY
INCHI_INCLUDE_DIR)
CUSTOM_INCHI_PATH = /opt/rdkit/rdkit-Release_2017_03_2/External/INCHI-API
-- Found InChI software locally
-- Boost version: 1.61.0
-- Found the following Boost libraries:
--   python
-- Boost version: 1.61.0
-- Found the following Boost libraries:
--   thread
--   system
--   chrono
--   date_time
--   atomic
-- Boost version: 1.61.0
-- Found the following Boost libraries:
--   serialization
== Using strict rotor definition
== Updating Filters.cpp from pains file
== Done updating pains files
-- Boost version: 1.61.0
-- Found the following Boost libraries:
--   regex
-- Configuring done
-- Generating done
-- Build files have been written to: /opt/rdkit/rdkit-Release_2017_
03_2/build

But the error prevails.

If I set up rdkit to use just the system wide boost (1.58), not my specific
install (1.61), rdkit builds successfully.  I do this by clearing
BOOST_ROOT, LD_LIBRARY_PATH, and removing the boost-related cmake flags.
So this is certainly an issue with wrong libraries being picked up.




On 21 June 2017 at 07:29, Greg Landrum  wrote:

> did you build boost serialize?
>
> On Mon, Jun 19, 2017 at 12:03 PM, JP  wrote:
>
>> Hi Greg !
>>
>> Unfortunately that didn't help (I delete everything in my build
>> directory, then):
>>
>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/
>> -DBoost_NO_SYSTEM_PATHS=ON ..
>>
>> and make as usual.
>>
>> [ 62%] Linking CXX executable testReaction
>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference
>> to `boost::archive::text_iarchive_impl> iarchive>::load_override(boost::archive::class_name_type&)'
>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference
>> to 
>> `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception
>> const&)'
>> collect2: error: ld returned 1 exit status
>> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
>> recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed
>> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
>> CMakeFiles/Makefile2:4157: recipe for target
>> 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed
>> make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all]
>> Error 2
>> Makefile:160: recipe for target 'all' failed
>> make: *** [all] Error 2
>>
>> Perhaps this isn't related to the system vs user-install, boost after all?
>>
>>
>> On 19 June 2017 at 10:38, Greg Landrum  wrote:
>>
>>> If you have a system boost install that you do not want to use, you
>>> should be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake arguments.
>>> This will (well, should) disable any usage of the system boost.
>>>
>>> -greg
>>>
>>>
>>> On Mon, Jun 19, 2017 at 9:39 AM, JP  wrote:
>>>
 HI Paul,

 Funny you should mention that.  I have boost 1.61 (installed manually
 in /opt) and system boost I installed via sudo apt-get install

 /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | grep
 'Version'
 Version: 1.58.0.1ubuntu1

 However I pass the BOOST path to cmake via:

 cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/  ..

 (I also have the $BOOST_ROOT env variable set, so I think that is
 redundant.  Whatever).  cmake output clearly shows it is finding/using
 boost 1.61

 Using make VERBOSE=1 I get:

 [ 62%] Linking CXX executable testReaction
 cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions
 && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt
 --verbose=1
 /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function
 -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG
 CMakeFiles/testReaction.dir/testReaction.cpp.o  -o testReaction
 -rdynamic ../../../lib/libRDKitChemReactions.so.1.2017.03.2
 ../../../lib/libRDKitChemTransforms.so.1.2017.03.2
 ../../../lib/libRDKitDescriptors.so.1.2017.03.2
 ../../../lib/libRDKitFingerprints.so.1.2017.03.2
 ../../../lib/libRDKitDepictor.so.1.2017.03.2
 ../../../lib/libRDKitFileParsers.so.1.2017.03.2 -lboost_serialization
 ../../../lib/libRDKitPartialCharges.so.1.2017.03.2
 ../../../lib/libRDKitMolTransforms.so.1.2017.03.2
 ../../../lib/libRDKitEigenSolvers.so.1.2017.03.2
 ../../../lib/libRDKitFilterCatalog.so.1.2017.03.2
 ../../../lib/libRDKitSubgraphs.so.1.2017.03.2
 ../../../lib/libRDKitSmilesParse.so.1.2017.03.2
 ../../../lib/libRDKitSubstructMatch.so.1.2017.03.2
 

Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

2017-06-20 Thread Greg Landrum
did you build boost serialize?

On Mon, Jun 19, 2017 at 12:03 PM, JP  wrote:

> Hi Greg !
>
> Unfortunately that didn't help (I delete everything in my build directory,
> then):
>
> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/
> -DBoost_NO_SYSTEM_PATHS=ON ..
>
> and make as usual.
>
> [ 62%] Linking CXX executable testReaction
> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to
> `boost::archive::text_iarchive_impl text_iarchive>::load_override(boost::archive::class_name_type&)'
> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to
> `boost::archive::archive_exception::archive_exception(
> boost::archive::archive_exception const&)'
> collect2: error: ld returned 1 exit status
> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
> recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed
> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
> CMakeFiles/Makefile2:4157: recipe for target 'Code/GraphMol/ChemReactions/
> CMakeFiles/testReaction.dir/all' failed
> make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all]
> Error 2
> Makefile:160: recipe for target 'all' failed
> make: *** [all] Error 2
>
> Perhaps this isn't related to the system vs user-install, boost after all?
>
>
> On 19 June 2017 at 10:38, Greg Landrum  wrote:
>
>> If you have a system boost install that you do not want to use, you
>> should be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake arguments.
>> This will (well, should) disable any usage of the system boost.
>>
>> -greg
>>
>>
>> On Mon, Jun 19, 2017 at 9:39 AM, JP  wrote:
>>
>>> HI Paul,
>>>
>>> Funny you should mention that.  I have boost 1.61 (installed manually in
>>> /opt) and system boost I installed via sudo apt-get install
>>>
>>> /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | grep
>>> 'Version'
>>> Version: 1.58.0.1ubuntu1
>>>
>>> However I pass the BOOST path to cmake via:
>>>
>>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/  ..
>>>
>>> (I also have the $BOOST_ROOT env variable set, so I think that is
>>> redundant.  Whatever).  cmake output clearly shows it is finding/using
>>> boost 1.61
>>>
>>> Using make VERBOSE=1 I get:
>>>
>>> [ 62%] Linking CXX executable testReaction
>>> cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions
>>> && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt
>>> --verbose=1
>>> /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function
>>> -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG
>>> CMakeFiles/testReaction.dir/testReaction.cpp.o  -o testReaction
>>> -rdynamic ../../../lib/libRDKitChemReactions.so.1.2017.03.2
>>> ../../../lib/libRDKitChemTransforms.so.1.2017.03.2
>>> ../../../lib/libRDKitDescriptors.so.1.2017.03.2
>>> ../../../lib/libRDKitFingerprints.so.1.2017.03.2
>>> ../../../lib/libRDKitDepictor.so.1.2017.03.2
>>> ../../../lib/libRDKitFileParsers.so.1.2017.03.2 -lboost_serialization
>>> ../../../lib/libRDKitPartialCharges.so.1.2017.03.2
>>> ../../../lib/libRDKitMolTransforms.so.1.2017.03.2
>>> ../../../lib/libRDKitEigenSolvers.so.1.2017.03.2
>>> ../../../lib/libRDKitFilterCatalog.so.1.2017.03.2
>>> ../../../lib/libRDKitSubgraphs.so.1.2017.03.2
>>> ../../../lib/libRDKitSmilesParse.so.1.2017.03.2
>>> ../../../lib/libRDKitSubstructMatch.so.1.2017.03.2
>>> ../../../lib/libRDKitGraphMol.so.1.2017.03.2
>>> ../../../lib/libRDKitRDGeometryLib.so.1.2017.03.2
>>> ../../../lib/libRDKitDataStructs.so.1.2017.03.2 -lboost_serialization
>>> ../../../lib/libRDKitCatalogs.so.1.2017.03.2
>>> ../../../lib/libRDKitRDGeneral.so.1.2017.03.2 -lboost_thread
>>> -lboost_system -lpthread -Wl,-rpath,/opt/rdkit/rdkit-Re
>>> lease_2017_03_2/build/lib
>>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference
>>> to `boost::archive::text_iarchive_impl>> chive>::load_override(boost::archive::class_name_type&)'
>>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference
>>> to 
>>> `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception
>>> const&)'
>>> collect2: error: ld returned 1 exit status
>>> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
>>> recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed
>>> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
>>> make[2]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build'
>>> CMakeFiles/Makefile2:4157: recipe for target
>>> 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed
>>> make[1]: *** [Code/GraphMol/ChemReactions/C
>>> MakeFiles/testReaction.dir/all] Error 2
>>> make[1]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build'
>>> Makefile:160: recipe for target 'all' failed
>>> make: *** [all] Error 2
>>>
>>> /opt/boost_1_61_0/lib is also the first path in 

Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

2017-06-19 Thread JP
Hi Greg !

Unfortunately that didn't help (I delete everything in my build directory,
then):

cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/
-DBoost_NO_SYSTEM_PATHS=ON ..

and make as usual.

[ 62%] Linking CXX executable testReaction
../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to
`boost::archive::text_iarchive_impl::load_override(boost::archive::class_name_type&)'
../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to
`boost::archive::archive_exception::archive_exception(boost::archive::archive_exception
const&)'
collect2: error: ld returned 1 exit status
Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed
make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
CMakeFiles/Makefile2:4157: recipe for target
'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed
make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all]
Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2

Perhaps this isn't related to the system vs user-install, boost after all?


On 19 June 2017 at 10:38, Greg Landrum  wrote:

> If you have a system boost install that you do not want to use, you should
> be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake arguments. This
> will (well, should) disable any usage of the system boost.
>
> -greg
>
>
> On Mon, Jun 19, 2017 at 9:39 AM, JP  wrote:
>
>> HI Paul,
>>
>> Funny you should mention that.  I have boost 1.61 (installed manually in
>> /opt) and system boost I installed via sudo apt-get install
>>
>> /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | grep
>> 'Version'
>> Version: 1.58.0.1ubuntu1
>>
>> However I pass the BOOST path to cmake via:
>>
>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/  ..
>>
>> (I also have the $BOOST_ROOT env variable set, so I think that is
>> redundant.  Whatever).  cmake output clearly shows it is finding/using
>> boost 1.61
>>
>> Using make VERBOSE=1 I get:
>>
>> [ 62%] Linking CXX executable testReaction
>> cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions
>> && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt
>> --verbose=1
>> /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function
>> -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG
>> CMakeFiles/testReaction.dir/testReaction.cpp.o  -o testReaction
>> -rdynamic ../../../lib/libRDKitChemReactions.so.1.2017.03.2
>> ../../../lib/libRDKitChemTransforms.so.1.2017.03.2
>> ../../../lib/libRDKitDescriptors.so.1.2017.03.2
>> ../../../lib/libRDKitFingerprints.so.1.2017.03.2
>> ../../../lib/libRDKitDepictor.so.1.2017.03.2
>> ../../../lib/libRDKitFileParsers.so.1.2017.03.2 -lboost_serialization
>> ../../../lib/libRDKitPartialCharges.so.1.2017.03.2
>> ../../../lib/libRDKitMolTransforms.so.1.2017.03.2
>> ../../../lib/libRDKitEigenSolvers.so.1.2017.03.2
>> ../../../lib/libRDKitFilterCatalog.so.1.2017.03.2
>> ../../../lib/libRDKitSubgraphs.so.1.2017.03.2
>> ../../../lib/libRDKitSmilesParse.so.1.2017.03.2
>> ../../../lib/libRDKitSubstructMatch.so.1.2017.03.2
>> ../../../lib/libRDKitGraphMol.so.1.2017.03.2
>> ../../../lib/libRDKitRDGeometryLib.so.1.2017.03.2
>> ../../../lib/libRDKitDataStructs.so.1.2017.03.2 -lboost_serialization
>> ../../../lib/libRDKitCatalogs.so.1.2017.03.2
>> ../../../lib/libRDKitRDGeneral.so.1.2017.03.2 -lboost_thread
>> -lboost_system -lpthread -Wl,-rpath,/opt/rdkit/rdkit-Re
>> lease_2017_03_2/build/lib
>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference
>> to `boost::archive::text_iarchive_impl> iarchive>::load_override(boost::archive::class_name_type&)'
>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference
>> to 
>> `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception
>> const&)'
>> collect2: error: ld returned 1 exit status
>> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
>> recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed
>> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
>> make[2]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build'
>> CMakeFiles/Makefile2:4157: recipe for target
>> 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed
>> make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all]
>> Error 2
>> make[1]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build'
>> Makefile:160: recipe for target 'all' failed
>> make: *** [all] Error 2
>>
>> /opt/boost_1_61_0/lib is also the first path in LD_LIBRARY_PATH.
>>
>> Thanks for your help and time.  I really appreciate it.
>>
>> Cheers
>>
>> On 16 June 2017 at 14:12, Paul Emsley  wrote:
>>
>>> On 16/06/2017 12:08, JP wrote:
>>>
 Hi Folks,

 Must have been eons 

Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

2017-06-19 Thread Greg Landrum
If you have a system boost install that you do not want to use, you should
be sure to add "-D Boost_NO_SYSTEM_PATHS=ON" to the cmake arguments. This
will (well, should) disable any usage of the system boost.

-greg


On Mon, Jun 19, 2017 at 9:39 AM, JP  wrote:

> HI Paul,
>
> Funny you should mention that.  I have boost 1.61 (installed manually in
> /opt) and system boost I installed via sudo apt-get install
>
> /opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | grep
> 'Version'
> Version: 1.58.0.1ubuntu1
>
> However I pass the BOOST path to cmake via:
>
> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/  ..
>
> (I also have the $BOOST_ROOT env variable set, so I think that is
> redundant.  Whatever).  cmake output clearly shows it is finding/using
> boost 1.61
>
> Using make VERBOSE=1 I get:
>
> [ 62%] Linking CXX executable testReaction
> cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions
> && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt
> --verbose=1
> /usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function
> -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG
> CMakeFiles/testReaction.dir/testReaction.cpp.o  -o testReaction -rdynamic
> ../../../lib/libRDKitChemReactions.so.1.2017.03.2 ../../../lib/
> libRDKitChemTransforms.so.1.2017.03.2 ../../../lib/
> libRDKitDescriptors.so.1.2017.03.2 
> ../../../lib/libRDKitFingerprints.so.1.2017.03.2
> ../../../lib/libRDKitDepictor.so.1.2017.03.2 ../../../lib/
> libRDKitFileParsers.so.1.2017.03.2 -lboost_serialization ../../../lib/
> libRDKitPartialCharges.so.1.2017.03.2 ../../../lib/
> libRDKitMolTransforms.so.1.2017.03.2 ../../../lib/
> libRDKitEigenSolvers.so.1.2017.03.2 ../../../lib/
> libRDKitFilterCatalog.so.1.2017.03.2 ../../../lib/
> libRDKitSubgraphs.so.1.2017.03.2 ../../../lib/
> libRDKitSmilesParse.so.1.2017.03.2 ../../../lib/
> libRDKitSubstructMatch.so.1.2017.03.2 
> ../../../lib/libRDKitGraphMol.so.1.2017.03.2
> ../../../lib/libRDKitRDGeometryLib.so.1.2017.03.2 ../../../lib/
> libRDKitDataStructs.so.1.2017.03.2 -lboost_serialization
> ../../../lib/libRDKitCatalogs.so.1.2017.03.2 ../../../lib/
> libRDKitRDGeneral.so.1.2017.03.2 -lboost_thread -lboost_system -lpthread
> -Wl,-rpath,/opt/rdkit/rdkit-Release_2017_03_2/build/lib
> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to
> `boost::archive::text_iarchive_impl text_iarchive>::load_override(boost::archive::class_name_type&)'
> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to
> `boost::archive::archive_exception::archive_exception(
> boost::archive::archive_exception const&)'
> collect2: error: ld returned 1 exit status
> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
> recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed
> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
> make[2]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build'
> CMakeFiles/Makefile2:4157: recipe for target 'Code/GraphMol/ChemReactions/
> CMakeFiles/testReaction.dir/all' failed
> make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all]
> Error 2
> make[1]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build'
> Makefile:160: recipe for target 'all' failed
> make: *** [all] Error 2
>
> /opt/boost_1_61_0/lib is also the first path in LD_LIBRARY_PATH.
>
> Thanks for your help and time.  I really appreciate it.
>
> Cheers
>
> On 16 June 2017 at 14:12, Paul Emsley  wrote:
>
>> On 16/06/2017 12:08, JP wrote:
>>
>>> Hi Folks,
>>>
>>> Must have been eons ago last time I posted to this mailing list.  The
>>> italians have a saying "chi non muore si rivede".
>>>
>>> I am trying to install the RDKit (release 2017_03_2) from source,
>>> without conda, and I thought this will be a breeze.  But I am getting an
>>> error.  I am pretty sure this is because of the boost version I am using
>>> (1.61).
>>>
>>> The error is:
>>>
>>> [ 62%] Linking CXX executable testReaction
>>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined
>>> reference to
>>> `boost::archive::text_iarchive_impl>> chive>::load_override(boost::archive::class_name_type&)'
>>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined
>>> reference to
>>> `boost::archive::archive_exception::archive_exception(boost:
>>> :archive::archive_exception
>>> const&)'
>>> collect2: error: ld returned 1 exit status
>>> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
>>> recipe for
>>> target 'Code/GraphMol/ChemReactions/testReaction' failed
>>> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
>>> CMakeFiles/Makefile2:4157: recipe for target
>>> 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed
>>> make[1]: *** [Code/GraphMol/ChemReactions/C
>>> MakeFiles/testReaction.dir/all] Error 2
>>>

Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

2017-06-19 Thread JP
HI Paul,

Funny you should mention that.  I have boost 1.61 (installed manually in
/opt) and system boost I installed via sudo apt-get install

/opt/rdkit/rdkit-Release_2017_03_2/build$ dpkg -s libboost-dev | grep
'Version'
Version: 1.58.0.1ubuntu1

However I pass the BOOST path to cmake via:

cmake -DRDK_BUILD_INCHI_SUPPORT=ON -DBOOST_ROOT=/opt/boost_1_61_0/  ..

(I also have the $BOOST_ROOT env variable set, so I think that is
redundant.  Whatever).  cmake output clearly shows it is finding/using
boost 1.61

Using make VERBOSE=1 I get:

[ 62%] Linking CXX executable testReaction
cd /opt/rdkit/rdkit-Release_2017_03_2/build/Code/GraphMol/ChemReactions &&
/usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt
--verbose=1
/usr/bin/c++-mpopcnt -Wno-deprecated -Wno-unused-function
-fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG
CMakeFiles/testReaction.dir/testReaction.cpp.o  -o testReaction -rdynamic
../../../lib/libRDKitChemReactions.so.1.2017.03.2
../../../lib/libRDKitChemTransforms.so.1.2017.03.2
../../../lib/libRDKitDescriptors.so.1.2017.03.2
../../../lib/libRDKitFingerprints.so.1.2017.03.2
../../../lib/libRDKitDepictor.so.1.2017.03.2
../../../lib/libRDKitFileParsers.so.1.2017.03.2 -lboost_serialization
../../../lib/libRDKitPartialCharges.so.1.2017.03.2
../../../lib/libRDKitMolTransforms.so.1.2017.03.2
../../../lib/libRDKitEigenSolvers.so.1.2017.03.2
../../../lib/libRDKitFilterCatalog.so.1.2017.03.2
../../../lib/libRDKitSubgraphs.so.1.2017.03.2
../../../lib/libRDKitSmilesParse.so.1.2017.03.2
../../../lib/libRDKitSubstructMatch.so.1.2017.03.2
../../../lib/libRDKitGraphMol.so.1.2017.03.2
../../../lib/libRDKitRDGeometryLib.so.1.2017.03.2
../../../lib/libRDKitDataStructs.so.1.2017.03.2 -lboost_serialization
../../../lib/libRDKitCatalogs.so.1.2017.03.2
../../../lib/libRDKitRDGeneral.so.1.2017.03.2 -lboost_thread -lboost_system
-lpthread -Wl,-rpath,/opt/rdkit/rdkit-Release_2017_03_2/build/lib
../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to
`boost::archive::text_iarchive_impl::load_override(boost::archive::class_name_type&)'
../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to
`boost::archive::archive_exception::archive_exception(boost::archive::archive_exception
const&)'
collect2: error: ld returned 1 exit status
Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
recipe for target 'Code/GraphMol/ChemReactions/testReaction' failed
make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
make[2]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build'
CMakeFiles/Makefile2:4157: recipe for target
'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed
make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all]
Error 2
make[1]: Leaving directory '/opt/rdkit/rdkit-Release_2017_03_2/build'
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2

/opt/boost_1_61_0/lib is also the first path in LD_LIBRARY_PATH.

Thanks for your help and time.  I really appreciate it.

Cheers

On 16 June 2017 at 14:12, Paul Emsley  wrote:

> On 16/06/2017 12:08, JP wrote:
>
>> Hi Folks,
>>
>> Must have been eons ago last time I posted to this mailing list.  The
>> italians have a saying "chi non muore si rivede".
>>
>> I am trying to install the RDKit (release 2017_03_2) from source, without
>> conda, and I thought this will be a breeze.  But I am getting an error.  I
>> am pretty sure this is because of the boost version I am using (1.61).
>>
>> The error is:
>>
>> [ 62%] Linking CXX executable testReaction
>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined
>> reference to
>> `boost::archive::text_iarchive_impl> iarchive>::load_override(boost::archive::class_name_type&)'
>> ../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined
>> reference to
>> `boost::archive::archive_exception::archive_exception(boost:
>> :archive::archive_exception
>> const&)'
>> collect2: error: ld returned 1 exit status
>> Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116:
>> recipe for
>> target 'Code/GraphMol/ChemReactions/testReaction' failed
>> make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
>> CMakeFiles/Makefile2:4157: recipe for target
>> 'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed
>> make[1]: *** [Code/GraphMol/ChemReactions/C
>> MakeFiles/testReaction.dir/all] Error 2
>> Makefile:160: recipe for target 'all' failed
>> make: *** [all] Error 2
>>
>
> If you are using an outdated version of boost, this is not the most
> elegant way for RDKit to tell you so.
>
> But I don't think that that's the case. I think that you are not linking
> with the correct boost libraries. Hard to say at the moment.
>
> $ make  VERBOSE=1
>
>>
>> As I side note, but this is just a deprecation warning, I do get a ton of
>> these,
>> 

Re: [Rdkit-discuss] Installation woes: Ubuntu 16.04, Boost 1.61, and RDKit not living so peacefully together after all ...

2017-06-16 Thread Paul Emsley

On 16/06/2017 12:08, JP wrote:

Hi Folks,

Must have been eons ago last time I posted to this mailing list.  The italians have a saying 
"chi non muore si rivede".


I am trying to install the RDKit (release 2017_03_2) from source, without conda, and I 
thought this will be a breeze.  But I am getting an error.  I am pretty sure this is because 
of the boost version I am using (1.61).


The error is:

[ 62%] Linking CXX executable testReaction
../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to

`boost::archive::text_iarchive_impl::load_override(boost::archive::class_name_type&)'
../../../lib/libRDKitChemReactions.so.1.2017.03.2: undefined reference to

`boost::archive::archive_exception::archive_exception(boost::archive::archive_exception
const&)'
collect2: error: ld returned 1 exit status
Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make:116: 
recipe for
target 'Code/GraphMol/ChemReactions/testReaction' failed
make[2]: *** [Code/GraphMol/ChemReactions/testReaction] Error 1
CMakeFiles/Makefile2:4157: recipe for target
'Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all' failed
make[1]: *** [Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/all] 
Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2


If you are using an outdated version of boost, this is not the most elegant way for RDKit to 
tell you so.


But I don't think that that's the case. I think that you are not linking with the correct 
boost libraries. Hard to say at the moment.


$ make  VERBOSE=1


As I side note, but this is just a deprecation warning, I do get a ton of these,
/opt/boost_1_61_0/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: 
#pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated

  # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is 
deprecated")


I see such things also - I comment out the pragmas in the header.


Paul.

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