Re: [Rdkit-discuss] Yet another build question - boost::thread_resource_error not found when building 2012_09_1.
On Fri, Nov 16, 2012 at 1:29 PM, Riccardo Vianello riccardo.viane...@gmail.com wrote: On Fri, Nov 16, 2012 at 11:54 AM, Jan Holst Jensen j...@biochemfusion.com wrote: [...] ../../lib/libSmilesParse.so.1.2012.09.1: undefined reference to `boost::thread_resource_error::~thread_resource_error()' collect2: ld returned 1 exit status make[2]: *** [Code/GraphMol/graphmolIterTest] Error 1 make[1]: *** [Code/GraphMol/CMakeFiles/graphmolIterTest.dir/all] Error 2 make: *** [all] Error 2 If I'm not wrong, a direct dependency from boost-thread is introduced in the GraphMol library by the QueryOps module, but I can't say why this results in a link error only in some cases. It's pretty clear that I screwed something up with the boost dependencies in the most recent release. I tried at the last minute to introduce compatibility with the newest versions of boost (1.49+), but in doing so I clearly broke things with older versions. I'll spend some time on trying to get this fixed this weekend and post whatever I find. -greg -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Yet another build question - boost::thread_resource_error not found when building 2012_09_1.
Hi Riccardo,
On 2012-11-16 13:29, Riccardo Vianello wrote:
Hi Jan,
On Fri, Nov 16, 2012 at 11:54 AM, Jan Holst Jensen
j...@biochemfusion.com wrote:
[...]
../../lib/libSmilesParse.so.1.2012.09.1: undefined reference to
`boost::thread_resource_error::~thread_resource_error()'
collect2: ld returned 1 exit status
make[2]: *** [Code/GraphMol/graphmolIterTest] Error 1
make[1]: *** [Code/GraphMol/CMakeFiles/graphmolIterTest.dir/all] Error 2
make: *** [all] Error 2
I encontered a similar link problem in building rdkit on an oldish
linux x86_64 machine with boost 1.39 (that, according to the cmake
build files, is the minimum required version), but I couldn't yet find
the time to investigate the details. For the time being I worked
around it with the addition of
find_package(Boost 1.39.0 COMPONENTS thread REQUIRED)
in $RDBASE/CMakeLists.txt (after the assignment of
Boost_ADDITIONAL_VERSIONS and before if(RDK_BUILD_PYTHON_WRAPPERS))
and with the addition of ${Boost_THREAD_LIBRARY} to the GraphMol's
LINK_LIBRARIES in $RDBASE/Code/GraphMol/CMakeLists.txt
Excellent! I added such a line to $RDBASE/CMakeLists.txt:
if(MSVC)
SET(Boost_ADDITIONAL_VERSIONS 1.481.48.0 1.45 1.45.0
1.44 1.44.0 1.43 1.43.0 1.42 1.42.0 1.41 1.41.0 1.40
1.40.0)
endif(MSVC)
+ find_package(Boost 1.40.0 COMPONENTS thread REQUIRED)
if(RDK_BUILD_PYTHON_WRAPPERS)
#---
and added ${Boost_THREAD_LIBRARY} after each occurrence of
LINK_LIBRARIES in $RDBASE/Code/GraphMol/CMakeLists.txt. I now have a
build of 2012_09_1 that passes all tests. Thanks :-) !!
Cheers
-- Jan
--
Monitor your physical, virtual and cloud infrastructure from a single
web console. Get in-depth insight into apps, servers, databases, vmware,
SAP, cloud infrastructure, etc. Download 30-day Free Trial.
Pricing starts from $795 for 25 servers or applications!
http://p.sf.net/sfu/zoho_dev2dev_nov
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Yet another build question - boost::thread_resource_error not found when building 2012_09_1.
Quick follow-up:
For the postgres cartridge I also needed to add this line to the Makefile:
SHLIB_LINK += -pthread
+ SHLIB_LINK += -lboost_thread
ifndef BOOSTHOME
BOOSTHOME=/usr/local/include
endif
Don't know if it is more appropriate to link boost_thread statically for
the cartridge, but this works OK for me - on that machine at least.
Cheers
-- Jan
__
Hi Riccardo,
On 2012-11-16 13:29, Riccardo Vianello wrote:
Hi Jan,
On Fri, Nov 16, 2012 at 11:54 AM, Jan Holst Jensen
j...@biochemfusion.com wrote:
[...]
../../lib/libSmilesParse.so.1.2012.09.1: undefined reference to
`boost::thread_resource_error::~thread_resource_error()'
collect2: ld returned 1 exit status
make[2]: *** [Code/GraphMol/graphmolIterTest] Error 1
make[1]: *** [Code/GraphMol/CMakeFiles/graphmolIterTest.dir/all] Error 2
make: *** [all] Error 2
I encontered a similar link problem in building rdkit on an oldish
linux x86_64 machine with boost 1.39 (that, according to the cmake
build files, is the minimum required version), but I couldn't yet find
the time to investigate the details. For the time being I worked
around it with the addition of
find_package(Boost 1.39.0 COMPONENTS thread REQUIRED)
in $RDBASE/CMakeLists.txt (after the assignment of
Boost_ADDITIONAL_VERSIONS and before if(RDK_BUILD_PYTHON_WRAPPERS))
and with the addition of ${Boost_THREAD_LIBRARY} to the GraphMol's
LINK_LIBRARIES in $RDBASE/Code/GraphMol/CMakeLists.txt
Excellent! I added such a line to $RDBASE/CMakeLists.txt:
if(MSVC)
SET(Boost_ADDITIONAL_VERSIONS 1.481.48.0 1.45 1.45.0
1.44 1.44.0 1.43 1.43.0 1.42 1.42.0 1.41 1.41.0 1.40
1.40.0)
endif(MSVC)
+ find_package(Boost 1.40.0 COMPONENTS thread REQUIRED)
if(RDK_BUILD_PYTHON_WRAPPERS)
#---
and added ${Boost_THREAD_LIBRARY} after each occurrence of
LINK_LIBRARIES in $RDBASE/Code/GraphMol/CMakeLists.txt. I now have a
build of 2012_09_1 that passes all tests. Thanks :-) !!
Cheers
-- Jan
--
Monitor your physical, virtual and cloud infrastructure from a single
web console. Get in-depth insight into apps, servers, databases, vmware,
SAP, cloud infrastructure, etc. Download 30-day Free Trial.
Pricing starts from $795 for 25 servers or applications!
http://p.sf.net/sfu/zoho_dev2dev_nov
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
