Problem compiling IMP trunk on a Mac with Lion
Hi all,
I have a problem trying to compile the latest IMP build (r11272) on a MBP updated to Lion.
I got the latest version of IMP (svn co http://svn.salilab.org/imp/trunk) but I'm not able to compile it (Errors building: tools/imppy.sh).
Does anyone knows if it depends on the IMP version I'm trying to compile? Davide
> scons: *** [tools/imppy.sh] KeyError : 'kernel' > Traceback (most recent call last): > File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/scons-2.0.1/SCons/Action.py", line 1046, in execute > result = self.execfunction(target=target, source=rsources, env=env) > File "/usr/src/imp/r11272/scons_tools/imppy.py", line 61, in builder_script_file > if data.get(env).modules['kernel'].external: > KeyError: 'kernel' > scons: building terminated because of errors. > > > IMP configuration: > boost ='yes' > boostlibs ='' > boostversion ='104601' > boostlibsuffix ='-mt' > endian ='little' > boost_programoptions='yes' > boost_programoptionslibs='boost_program_options-mt' > build ='fast' > prefix ='/usr' > local ='True' > pythonpath ='/usr/src/imp/r11272' > libpath ='/opt/local/lib' > ldlibpath ='/usr/src/imp/r11272' > swigpath ='/usr/src/imp/r11272' > datapath ='/usr/src/imp/r11272' > cxxcompiler ='g++' > cxxflags='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wmissing-prototypes -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' > pythoncxxflags ='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wno-deprecated -Winit-self -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' > bincxxflags='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' > shliblinkflags =' -dynamiclib -headerpad_max_install_names' > arliblinkflags ='' > binlinkflags ='-headerpad_max_install_names' > pythonlinkflags =' -bundle -bundle -flat_namespace -undefined suppress -headerpad_max_install_names' > rpath ='True' > static ='False' > pythonsosuffix ='.so' > pkgconfig ='True' > path ="/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/opt/local/bin:/usr/local/git/bin:/Users/dbau/Work/scripts:/Users/dbau/Work/scripts/ucsf:/Users/dbau/Work/scripts/tools:/Users/dbau/Work/scripts/IMP:/Users/dbau/Scripts:/opt/local/bin:/usr/bin:/bin:/usr/local/git/bin:/usr/src/android-sdk-mac_x86/platforms:/usr/src/android-sdk-mac_x86/tools:/usr/src/android-sdk-mac_x86/platform-tools" > python ="python" > > > Enabled dependencies: Boost, Boost.ProgramOptions > > Disabled modules: em, core, container, saxs, multifit, modules, example_system_local, rmf, atom, em2d > > Disabled applications: rmf_tools, ligand_score, saxs_tools, Groel, nup84, multifit, em_tools, example_system, rnapii, foxs > > Errors building: > tools/imppy.sh
For some reason scons isn't finding most of the module source (at the bottom it thinks there are no modules it can build). Are you sure there is a directory modules/kernel?
On Oct 4, 2011, at 4:48 AM, Davide Baù wrote:
> Hi all, > > I have a problem trying to compile the latest IMP build (r11272) on a MBP updated to Lion. > > I got the latest version of IMP (svn co http://svn.salilab.org/imp/trunk) but I'm not able to compile it (Errors building: tools/imppy.sh). > > Does anyone knows if it depends on the IMP version I'm trying to compile? > Davide > >> scons: *** [tools/imppy.sh] KeyError : 'kernel' >> Traceback (most recent call last): >> File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/scons-2.0.1/SCons/Action.py", line 1046, in execute >> result = self.execfunction(target=target, source=rsources, env=env) >> File "/usr/src/imp/r11272/scons_tools/imppy.py", line 61, in builder_script_file >> if data.get(env).modules['kernel'].external: >> KeyError: 'kernel' >> scons: building terminated because of errors. >> >> >> IMP configuration: >> boost ='yes' >> boostlibs ='' >> boostversion ='104601' >> boostlibsuffix ='-mt' >> endian ='little' >> boost_programoptions='yes' >> boost_programoptionslibs='boost_program_options-mt' >> build ='fast' >> prefix ='/usr' >> local ='True' >> pythonpath ='/usr/src/imp/r11272' >> libpath ='/opt/local/lib' >> ldlibpath ='/usr/src/imp/r11272' >> swigpath ='/usr/src/imp/r11272' >> datapath ='/usr/src/imp/r11272' >> cxxcompiler ='g++' >> cxxflags='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wmissing-prototypes -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' >> pythoncxxflags ='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wno-deprecated -Winit-self -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' >> bincxxflags='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' >> shliblinkflags =' -dynamiclib -headerpad_max_install_names' >> arliblinkflags ='' >> binlinkflags ='-headerpad_max_install_names' >> pythonlinkflags =' -bundle -bundle -flat_namespace -undefined suppress -headerpad_max_install_names' >> rpath ='True' >> static ='False' >> pythonsosuffix ='.so' >> pkgconfig ='True' >> path ="/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/opt/local/bin:/usr/local/git/bin:/Users/dbau/Work/scripts:/Users/dbau/Work/scripts/ucsf:/Users/dbau/Work/scripts/tools:/Users/dbau/Work/scripts/IMP:/Users/dbau/Scripts:/opt/local/bin:/usr/bin:/bin:/usr/local/git/bin:/usr/src/android-sdk-mac_x86/platforms:/usr/src/android-sdk-mac_x86/tools:/usr/src/android-sdk-mac_x86/platform-tools" >> python ="python" >> >> >> Enabled dependencies: Boost, Boost.ProgramOptions >> >> Disabled modules: em, core, container, saxs, multifit, modules, example_system_local, rmf, atom, em2d >> >> Disabled applications: rmf_tools, ligand_score, saxs_tools, Groel, nup84, multifit, em_tools, example_system, rnapii, foxs >> >> Errors building: >> tools/imppy.sh > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Yes, the directory modules/kernel is present. I have tried to compile the same version on a linux machine. It does not compile either, but with a different error:
> g++ -o build/src/imp_misc_all.os -c -isystem /usr/src/imp/trunk -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wmissing-declarations -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations -fno-signed-zeros -freciprocal-math -fassociative-math -fvisibility=hidden -fPIC -DBOOST_ALL_NO_LIB -DIMPMISC_EXPORTS -DGCC_VISIBILITY -Ibuild/include -Ibuild/src build/src/imp_misc_all.cpp > scons: *** [build/src/imp_restrainer_all.os] Error 1 > /usr/src/imp/trunk/build/include/IMP/saxs/Score.h:30: Warning(401): Nothing known about base class 'RefCounted'. Ignored. > scons: building terminated because of errors.
On Oct 4, 2011, at 4:48 PM, Daniel Russel wrote:
> For some reason scons isn't finding most of the module source (at the bottom it thinks there are no modules it can build). Are you sure there is a directory modules/kernel? > > On Oct 4, 2011, at 4:48 AM, Davide Baù wrote: > >> Hi all, >> >> I have a problem trying to compile the latest IMP build (r11272) on a MBP updated to Lion. >> >> I got the latest version of IMP (svn co http://svn.salilab.org/imp/trunk) but I'm not able to compile it (Errors building: tools/imppy.sh). >> >> Does anyone knows if it depends on the IMP version I'm trying to compile? >> Davide >> >>> scons: *** [tools/imppy.sh] KeyError : 'kernel' >>> Traceback (most recent call last): >>> File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/scons-2.0.1/SCons/Action.py", line 1046, in execute >>> result = self.execfunction(target=target, source=rsources, env=env) >>> File "/usr/src/imp/r11272/scons_tools/imppy.py", line 61, in builder_script_file >>> if data.get(env).modules['kernel'].external: >>> KeyError: 'kernel' >>> scons: building terminated because of errors. >>> >>> >>> IMP configuration: >>> boost ='yes' >>> boostlibs ='' >>> boostversion ='104601' >>> boostlibsuffix ='-mt' >>> endian ='little' >>> boost_programoptions='yes' >>> boost_programoptionslibs='boost_program_options-mt' >>> build ='fast' >>> prefix ='/usr' >>> local ='True' >>> pythonpath ='/usr/src/imp/r11272' >>> libpath ='/opt/local/lib' >>> ldlibpath ='/usr/src/imp/r11272' >>> swigpath ='/usr/src/imp/r11272' >>> datapath ='/usr/src/imp/r11272' >>> cxxcompiler ='g++' >>> cxxflags='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wmissing-prototypes -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' >>> pythoncxxflags ='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wno-deprecated -Winit-self -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' >>> bincxxflags='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' >>> shliblinkflags =' -dynamiclib -headerpad_max_install_names' >>> arliblinkflags ='' >>> binlinkflags ='-headerpad_max_install_names' >>> pythonlinkflags =' -bundle -bundle -flat_namespace -undefined suppress -headerpad_max_install_names' >>> rpath ='True' >>> static ='False' >>> pythonsosuffix ='.so' >>> pkgconfig ='True' >>> path ="/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/opt/local/bin:/usr/local/git/bin:/Users/dbau/Work/scripts:/Users/dbau/Work/scripts/ucsf:/Users/dbau/Work/scripts/tools:/Users/dbau/Work/scripts/IMP:/Users/dbau/Scripts:/opt/local/bin:/usr/bin:/bin:/usr/local/git/bin:/usr/src/android-sdk-mac_x86/platforms:/usr/src/android-sdk-mac_x86/tools:/usr/src/android-sdk-mac_x86/platform-tools" >>> python ="python" >>> >>> >>> Enabled dependencies: Boost, Boost.ProgramOptions >>> >>> Disabled modules: em, core, container, saxs, multifit, modules, example_system_local, rmf, atom, em2d >>> >>> Disabled applications: rmf_tools, ligand_score, saxs_tools, Groel, nup84, multifit, em_tools, example_system, rnapii, foxs >>> >>> Errors building: >>> tools/imppy.sh >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Your svn copy is somehow not updating properly then. Line 30 of Score.h is part of a comment in svn head. I'd "rm -rf" any directories that you haven't modified and do svn update again. Every once in a while svn gets confused.
On Oct 4, 2011, at 8:13 AM, Davide Baù wrote:
> Yes, the directory modules/kernel is present. > I have tried to compile the same version on a linux machine. It does not compile either, but with a different error: > >> g++ -o build/src/imp_misc_all.os -c -isystem /usr/src/imp/trunk -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wmissing-declarations -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations -fno-signed-zeros -freciprocal-math -fassociative-math -fvisibility=hidden -fPIC -DBOOST_ALL_NO_LIB -DIMPMISC_EXPORTS -DGCC_VISIBILITY -Ibuild/include -Ibuild/src build/src/imp_misc_all.cpp >> scons: *** [build/src/imp_restrainer_all.os] Error 1 >> /usr/src/imp/trunk/build/include/IMP/saxs/Score.h:30: Warning(401): Nothing known about base class 'RefCounted'. Ignored. >> scons: building terminated because of errors. > > > > On Oct 4, 2011, at 4:48 PM, Daniel Russel wrote: > >> For some reason scons isn't finding most of the module source (at the bottom it thinks there are no modules it can build). Are you sure there is a directory modules/kernel? >> >> On Oct 4, 2011, at 4:48 AM, Davide Baù wrote: >> >>> Hi all, >>> >>> I have a problem trying to compile the latest IMP build (r11272) on a MBP updated to Lion. >>> >>> I got the latest version of IMP (svn co http://svn.salilab.org/imp/trunk) but I'm not able to compile it (Errors building: tools/imppy.sh). >>> >>> Does anyone knows if it depends on the IMP version I'm trying to compile? >>> Davide >>> >>>> scons: *** [tools/imppy.sh] KeyError : 'kernel' >>>> Traceback (most recent call last): >>>> File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/scons-2.0.1/SCons/Action.py", line 1046, in execute >>>> result = self.execfunction(target=target, source=rsources, env=env) >>>> File "/usr/src/imp/r11272/scons_tools/imppy.py", line 61, in builder_script_file >>>> if data.get(env).modules['kernel'].external: >>>> KeyError: 'kernel' >>>> scons: building terminated because of errors. >>>> >>>> >>>> IMP configuration: >>>> boost ='yes' >>>> boostlibs ='' >>>> boostversion ='104601' >>>> boostlibsuffix ='-mt' >>>> endian ='little' >>>> boost_programoptions='yes' >>>> boost_programoptionslibs='boost_program_options-mt' >>>> build ='fast' >>>> prefix ='/usr' >>>> local ='True' >>>> pythonpath ='/usr/src/imp/r11272' >>>> libpath ='/opt/local/lib' >>>> ldlibpath ='/usr/src/imp/r11272' >>>> swigpath ='/usr/src/imp/r11272' >>>> datapath ='/usr/src/imp/r11272' >>>> cxxcompiler ='g++' >>>> cxxflags='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wmissing-prototypes -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' >>>> pythoncxxflags ='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wno-deprecated -Winit-self -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' >>>> bincxxflags='-isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations' >>>> shliblinkflags =' -dynamiclib -headerpad_max_install_names' >>>> arliblinkflags ='' >>>> binlinkflags ='-headerpad_max_install_names' >>>> pythonlinkflags =' -bundle -bundle -flat_namespace -undefined suppress -headerpad_max_install_names' >>>> rpath ='True' >>>> static ='False' >>>> pythonsosuffix ='.so' >>>> pkgconfig ='True' >>>> path ="/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/opt/local/bin:/usr/local/git/bin:/Users/dbau/Work/scripts:/Users/dbau/Work/scripts/ucsf:/Users/dbau/Work/scripts/tools:/Users/dbau/Work/scripts/IMP:/Users/dbau/Scripts:/opt/local/bin:/usr/bin:/bin:/usr/local/git/bin:/usr/src/android-sdk-mac_x86/platforms:/usr/src/android-sdk-mac_x86/tools:/usr/src/android-sdk-mac_x86/platform-tools" >>>> python ="python" >>>> >>>> >>>> Enabled dependencies: Boost, Boost.ProgramOptions >>>> >>>> Disabled modules: em, core, container, saxs, multifit, modules, example_system_local, rmf, atom, em2d >>>> >>>> Disabled applications: rmf_tools, ligand_score, saxs_tools, Groel, nup84, multifit, em_tools, example_system, rnapii, foxs >>>> >>>> Errors building: >>>> tools/imppy.sh >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Hi,
I have done a svn update after deleting the whole dir. I now get a different error (same on Linux and on Mac): > Checking for ExampleLib with variables...(cached) no > Checking for ExampleLib with pkg-config...no > The lib argument must be given as a list. It was not for ExampleLib
And from the config.log files (Linux and Mac respectively):
On Linux: > g++ -o .sconf_temp/conftest_39.o -c -isystem /usr/src/imp/trunk -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wmissing-declarations -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations -fno-signed-zeros -freciprocal-math -fassociative-math -DBOOST_ALL_NO_LIB -Ibuild/include -Ibuild/src .sconf_temp/conftest_39.cpp > .sconf_temp/conftest_39.cpp:3:36: fatal error: btBulletDynamicsCommon.h: No such file or directory > compilation terminated. > scons: Configure: no > > > file /usr/src/imp/trunk/scons_tools/dependency/__init__.py,line 224: > Configure(confdir = .sconf_temp) > scons: Configure: Checking for ExampleLib with variables... > scons: Configure: (cached) no > > scons: Configure: Checking for ExampleLib with pkg-config... > pkg-config --exists 'examplelib' > scons: Configure: no
On Mac: > g++ -o .sconf_temp/conftest_34.o -c -isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wmissing-prototypes -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations -DBOOST_ALL_NO_LIB -Ibuild/include -Ibuild/src .sconf_temp/conftest_34.cpp > .sconf_temp/conftest_34.cpp:3:36: error: btBulletDynamicsCommon.h: No such file or directory > .sconf_temp/conftest_34.cpp: In function 'int main()': > .sconf_temp/conftest_34.cpp:7: error: 'btBroadphaseInterface' was not declared in this scope > .sconf_temp/conftest_34.cpp:7: error: 'broadphase' was not declared in this scope > .sconf_temp/conftest_34.cpp:7: error: expected type-specifier before 'btDbvtBroadphase' > .sconf_temp/conftest_34.cpp:7: error: expected `;' before 'btDbvtBroadphase' > .sconf_temp/conftest_34.cpp:3:36: error: btBulletDynamicsCommon.h: No such file or directory > .sconf_temp/conftest_34.cpp: In function 'int main()': > .sconf_temp/conftest_34.cpp:7: error: 'btBroadphaseInterface' was not declared in this scope > .sconf_temp/conftest_34.cpp:7: error: 'broadphase' was not declared in this scope > .sconf_temp/conftest_34.cpp:7: error: expected type-specifier before 'btDbvtBroadphase' > .sconf_temp/conftest_34.cpp:7: error: expected `;' before 'btDbvtBroadphase' > lipo: can't figure out the architecture type of: /var/tmp//ccheyZks.out > scons: Configure: no > > > file /usr/src/imp/imp-r11272/scons_tools/dependency/__init__.py,line 224: > Configure(confdir = .sconf_temp) > scons: Configure: Checking for ExampleLib with variables... > scons: Configure: (cached) no > > scons: Configure: Checking for ExampleLib with pkg-config... > pkg-config --exists 'examplelib' > scons: Configure: no
Davide
OK, that looks better. A there were some changes with how dependencies were set up to support more involved libraries. You probably have a library of your own which still has the unupdated example dependency code. You should simply comment out references to ExampleLib in your module SConscript.
On Wed, Oct 5, 2011 at 2:34 AM, Davide Baù davide.bau@gmail.com wrote:
> Hi, > > I have done a svn update after deleting the whole dir. I now get a > different error (same on Linux and on Mac): > > Checking for ExampleLib with variables...(cached) no > > Checking for ExampleLib with pkg-config...no > > The lib argument must be given as a list. It was not for ExampleLib > > And from the config.log files (Linux and Mac respectively): > > On Linux: > > g++ -o .sconf_temp/conftest_39.o -c -isystem /usr/src/imp/trunk -Wall > -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align > -fno-operator-names -Wmissing-declarations -Wundef -Woverloaded-virtual -O3 > -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only > -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store > -Wno-unused -funsafe-loop-optimizations -fno-signed-zeros -freciprocal-math > -fassociative-math -DBOOST_ALL_NO_LIB -Ibuild/include -Ibuild/src > .sconf_temp/conftest_39.cpp > > .sconf_temp/conftest_39.cpp:3:36: fatal error: btBulletDynamicsCommon.h: > No such file or directory > > compilation terminated. > > scons: Configure: no > > > > > > file /usr/src/imp/trunk/scons_tools/dependency/__init__.py,line 224: > > Configure(confdir = .sconf_temp) > > scons: Configure: Checking for ExampleLib with variables... > > scons: Configure: (cached) no > > > > scons: Configure: Checking for ExampleLib with pkg-config... > > pkg-config --exists 'examplelib' > > scons: Configure: no > > On Mac: > > g++ -o .sconf_temp/conftest_34.o -c -isystem /opt/local/include -Os > -fno-common -arch i386 -arch x86_64 -Wall -Wextra -Wno-deprecated > -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names > -Wmissing-prototypes -Wundef -Woverloaded-virtual -O3 > -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only > -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store > -Wno-unused -funsafe-loop-optimizations -DBOOST_ALL_NO_LIB -Ibuild/include > -Ibuild/src .sconf_temp/conftest_34.cpp > > .sconf_temp/conftest_34.cpp:3:36: error: btBulletDynamicsCommon.h: No > such file or directory > > .sconf_temp/conftest_34.cpp: In function 'int main()': > > .sconf_temp/conftest_34.cpp:7: error: 'btBroadphaseInterface' was not > declared in this scope > > .sconf_temp/conftest_34.cpp:7: error: 'broadphase' was not declared in > this scope > > .sconf_temp/conftest_34.cpp:7: error: expected type-specifier before > 'btDbvtBroadphase' > > .sconf_temp/conftest_34.cpp:7: error: expected `;' before > 'btDbvtBroadphase' > > .sconf_temp/conftest_34.cpp:3:36: error: btBulletDynamicsCommon.h: No > such file or directory > > .sconf_temp/conftest_34.cpp: In function 'int main()': > > .sconf_temp/conftest_34.cpp:7: error: 'btBroadphaseInterface' was not > declared in this scope > > .sconf_temp/conftest_34.cpp:7: error: 'broadphase' was not declared in > this scope > > .sconf_temp/conftest_34.cpp:7: error: expected type-specifier before > 'btDbvtBroadphase' > > .sconf_temp/conftest_34.cpp:7: error: expected `;' before > 'btDbvtBroadphase' > > lipo: can't figure out the architecture type of: /var/tmp//ccheyZks.out > > scons: Configure: no > > > > > > file /usr/src/imp/imp-r11272/scons_tools/dependency/__init__.py,line 224: > > Configure(confdir = .sconf_temp) > > scons: Configure: Checking for ExampleLib with variables... > > scons: Configure: (cached) no > > > > scons: Configure: Checking for ExampleLib with pkg-config... > > pkg-config --exists 'examplelib' > > scons: Configure: no > > > Davide > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev >
You're right. I had some references to ExampleLib in a local library. That solved the issue on my Mac but not on my linux machine (updated to revision 11289 on both machines):
> g++ -o modules/benchmark/bin/benchmark_knn -Wl,-rpath=/usr/src/imp/imp-r11289 modules/benchmark/bin/benchmark_knn.o -Lbuild/lib -L. -limp_benchmark -limp_domino -limp_display -limp_em -limp_atom -limp_con > tainer -limp_core -limp_statistics -limp -limp_algebra -limp_cgal -limp_base -limp_compatibility -lCGAL -lgmp -lmpfr -lgmpxx -lboost_thread -lpthread -lmscons: *** [modules/benchmark/bin/benchmark_domino_container.o] Error 1scons: building terminated because of errors.
I don't know if it depends on CGAL which is installed anyway. Davide
On Oct 5, 2011, at 5:39 PM, Daniel Russel wrote:
> OK, that looks better. A there were some changes with how dependencies were set up to support more involved libraries. You probably have a library of your own which still has the unupdated example dependency code. You should simply comment out references to ExampleLib in your module SConscript. > > On Wed, Oct 5, 2011 at 2:34 AM, Davide Baù davide.bau@gmail.com wrote: > Hi, > > I have done a svn update after deleting the whole dir. I now get a different error (same on Linux and on Mac): > > Checking for ExampleLib with variables...(cached) no > > Checking for ExampleLib with pkg-config...no > > The lib argument must be given as a list. It was not for ExampleLib > > And from the config.log files (Linux and Mac respectively): > > On Linux: > > g++ -o .sconf_temp/conftest_39.o -c -isystem /usr/src/imp/trunk -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wmissing-declarations -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations -fno-signed-zeros -freciprocal-math -fassociative-math -DBOOST_ALL_NO_LIB -Ibuild/include -Ibuild/src .sconf_temp/conftest_39.cpp > > .sconf_temp/conftest_39.cpp:3:36: fatal error: btBulletDynamicsCommon.h: No such file or directory > > compilation terminated. > > scons: Configure: no > > > > > > file /usr/src/imp/trunk/scons_tools/dependency/__init__.py,line 224: > > Configure(confdir = .sconf_temp) > > scons: Configure: Checking for ExampleLib with variables... > > scons: Configure: (cached) no > > > > scons: Configure: Checking for ExampleLib with pkg-config... > > pkg-config --exists 'examplelib' > > scons: Configure: no > > On Mac: > > g++ -o .sconf_temp/conftest_34.o -c -isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wmissing-prototypes -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations -DBOOST_ALL_NO_LIB -Ibuild/include -Ibuild/src .sconf_temp/conftest_34.cpp > > .sconf_temp/conftest_34.cpp:3:36: error: btBulletDynamicsCommon.h: No such file or directory > > .sconf_temp/conftest_34.cpp: In function 'int main()': > > .sconf_temp/conftest_34.cpp:7: error: 'btBroadphaseInterface' was not declared in this scope > > .sconf_temp/conftest_34.cpp:7: error: 'broadphase' was not declared in this scope > > .sconf_temp/conftest_34.cpp:7: error: expected type-specifier before 'btDbvtBroadphase' > > .sconf_temp/conftest_34.cpp:7: error: expected `;' before 'btDbvtBroadphase' > > .sconf_temp/conftest_34.cpp:3:36: error: btBulletDynamicsCommon.h: No such file or directory > > .sconf_temp/conftest_34.cpp: In function 'int main()': > > .sconf_temp/conftest_34.cpp:7: error: 'btBroadphaseInterface' was not declared in this scope > > .sconf_temp/conftest_34.cpp:7: error: 'broadphase' was not declared in this scope > > .sconf_temp/conftest_34.cpp:7: error: expected type-specifier before 'btDbvtBroadphase' > > .sconf_temp/conftest_34.cpp:7: error: expected `;' before 'btDbvtBroadphase' > > lipo: can't figure out the architecture type of: /var/tmp//ccheyZks.out > > scons: Configure: no > > > > > > file /usr/src/imp/imp-r11272/scons_tools/dependency/__init__.py,line 224: > > Configure(confdir = .sconf_temp) > > scons: Configure: Checking for ExampleLib with variables... > > scons: Configure: (cached) no > > > > scons: Configure: Checking for ExampleLib with pkg-config... > > pkg-config --exists 'examplelib' > > scons: Configure: no > > > Davide > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
I think the linux errors are elsewhere in the output (you are probably using -j n with n>1 and so different build commands and errors are woven together).
On Oct 6, 2011, at 3:49 AM, Davide Baù wrote:
> You're right. I had some references to ExampleLib in a local library. That solved the issue on my Mac but not on my linux machine (updated to revision 11289 on both machines): > >> g++ -o modules/benchmark/bin/benchmark_knn -Wl,-rpath=/usr/src/imp/imp-r11289 modules/benchmark/bin/benchmark_knn.o -Lbuild/lib -L. -limp_benchmark -limp_domino -limp_display -limp_em -limp_atom -limp_con >> tainer -limp_core -limp_statistics -limp -limp_algebra -limp_cgal -limp_base -limp_compatibility -lCGAL -lgmp -lmpfr -lgmpxx -lboost_thread -lpthread -lmscons: *** [modules/benchmark/bin/benchmark_domino_container.o] Error 1scons: building terminated because of errors. > > I don't know if it depends on CGAL which is installed anyway. > Davide > > > > > On Oct 5, 2011, at 5:39 PM, Daniel Russel wrote: > >> OK, that looks better. A there were some changes with how dependencies were set up to support more involved libraries. You probably have a library of your own which still has the unupdated example dependency code. You should simply comment out references to ExampleLib in your module SConscript. >> >> On Wed, Oct 5, 2011 at 2:34 AM, Davide Baù davide.bau@gmail.com wrote: >> Hi, >> >> I have done a svn update after deleting the whole dir. I now get a different error (same on Linux and on Mac): >> > Checking for ExampleLib with variables...(cached) no >> > Checking for ExampleLib with pkg-config...no >> > The lib argument must be given as a list. It was not for ExampleLib >> >> And from the config.log files (Linux and Mac respectively): >> >> On Linux: >> > g++ -o .sconf_temp/conftest_39.o -c -isystem /usr/src/imp/trunk -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wmissing-declarations -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations -fno-signed-zeros -freciprocal-math -fassociative-math -DBOOST_ALL_NO_LIB -Ibuild/include -Ibuild/src .sconf_temp/conftest_39.cpp >> > .sconf_temp/conftest_39.cpp:3:36: fatal error: btBulletDynamicsCommon.h: No such file or directory >> > compilation terminated. >> > scons: Configure: no >> > >> > >> > file /usr/src/imp/trunk/scons_tools/dependency/__init__.py,line 224: >> > Configure(confdir = .sconf_temp) >> > scons: Configure: Checking for ExampleLib with variables... >> > scons: Configure: (cached) no >> > >> > scons: Configure: Checking for ExampleLib with pkg-config... >> > pkg-config --exists 'examplelib' >> > scons: Configure: no >> >> On Mac: >> > g++ -o .sconf_temp/conftest_34.o -c -isystem /opt/local/include -Os -fno-common -arch i386 -arch x86_64 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wmissing-prototypes -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations -DBOOST_ALL_NO_LIB -Ibuild/include -Ibuild/src .sconf_temp/conftest_34.cpp >> > .sconf_temp/conftest_34.cpp:3:36: error: btBulletDynamicsCommon.h: No such file or directory >> > .sconf_temp/conftest_34.cpp: In function 'int main()': >> > .sconf_temp/conftest_34.cpp:7: error: 'btBroadphaseInterface' was not declared in this scope >> > .sconf_temp/conftest_34.cpp:7: error: 'broadphase' was not declared in this scope >> > .sconf_temp/conftest_34.cpp:7: error: expected type-specifier before 'btDbvtBroadphase' >> > .sconf_temp/conftest_34.cpp:7: error: expected `;' before 'btDbvtBroadphase' >> > .sconf_temp/conftest_34.cpp:3:36: error: btBulletDynamicsCommon.h: No such file or directory >> > .sconf_temp/conftest_34.cpp: In function 'int main()': >> > .sconf_temp/conftest_34.cpp:7: error: 'btBroadphaseInterface' was not declared in this scope >> > .sconf_temp/conftest_34.cpp:7: error: 'broadphase' was not declared in this scope >> > .sconf_temp/conftest_34.cpp:7: error: expected type-specifier before 'btDbvtBroadphase' >> > .sconf_temp/conftest_34.cpp:7: error: expected `;' before 'btDbvtBroadphase' >> > lipo: can't figure out the architecture type of: /var/tmp//ccheyZks.out >> > scons: Configure: no >> > >> > >> > file /usr/src/imp/imp-r11272/scons_tools/dependency/__init__.py,line 224: >> > Configure(confdir = .sconf_temp) >> > scons: Configure: Checking for ExampleLib with variables... >> > scons: Configure: (cached) no >> > >> > scons: Configure: Checking for ExampleLib with pkg-config... >> > pkg-config --exists 'examplelib' >> > scons: Configure: no >> >> >> Davide >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
I have re-run scones without the -j option. It seems that it's a problem with domino?
Davide
> g++ -o modules/benchmark/bin/benchmark_domino_container.o -c -isystem /usr/src/imp/imp-r11289 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef - > Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop- > optimizations -fno-signed-zeros -freciprocal-math -fassociative-math -DBOOST_ALL_NO_LIB -Ibuild/include -Ibuild/src modules/benchmark/bin/benchmark_domino_container.cpp > modules/benchmark/bin/benchmark_domino_container.cpp: In function 'int main(int, char**)': > modules/benchmark/bin/benchmark_domino_container.cpp:43:5: error: 'RMF' has not been declared > modules/benchmark/bin/benchmark_domino_container.cpp:43:19: error: expected ';' before 'file' > modules/benchmark/bin/benchmark_domino_container.cpp:45:5: error: 'RMF' has not been declared > modules/benchmark/bin/benchmark_domino_container.cpp:45:29: error: expected ';' before 'ds' > modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: 'HDF5AssignmentContainer' was not declared in this scope > modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: template argument 1 is invalid > modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: invalid type in declaration before '(' token > modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: expected type-specifier before 'HDF5AssignmentContainer' > modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: expected ')' before 'HDF5AssignmentContainer' > modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: invalid conversion from 'int*' to 'int' > modules/benchmark/bin/benchmark_domino_container.cpp:47:7: error: base operand of '->' is not a pointer > modules/benchmark/bin/benchmark_domino_container.cpp:48:21: error: 'HDF5AssignmentContainer' cannot appear in a constant-expression > modules/benchmark/bin/benchmark_domino_container.cpp:48:65: error: no matching function for call to 'benchmark_table(int&, const char [14])' > modules/benchmark/bin/benchmark_domino_container.cpp:51:5: error: 'RMF' has not been declared > modules/benchmark/bin/benchmark_domino_container.cpp:51:19: error: expected ';' before 'file' > modules/benchmark/bin/benchmark_domino_container.cpp:53:5: error: 'RMF' has not been declared > modules/benchmark/bin/benchmark_domino_container.cpp:53:29: error: expected ';' before 'ds' > modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: 'HDF5AssignmentContainer' was not declared in this scope > modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: template argument 1 is invalid > modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: invalid type in declaration before '(' token > modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: expected type-specifier before 'HDF5AssignmentContainer' > modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: expected ')' before 'HDF5AssignmentContainer' > modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: invalid conversion from 'int*' to 'int' > modules/benchmark/bin/benchmark_domino_container.cpp:55:7: error: base operand of '->' is not a pointer > modules/benchmark/bin/benchmark_domino_container.cpp:56:21: error: 'HDF5AssignmentContainer' cannot appear in a constant-expression > modules/benchmark/bin/benchmark_domino_container.cpp:56:56: error: no matching function for call to 'benchmark_table(int&, const char [5])' > modules/benchmark/bin/benchmark_domino_container.cpp:60:21: error: 'HDF5AssignmentContainer' was not declared in this scope > modules/benchmark/bin/benchmark_domino_container.cpp:60:68: error: no matching function for call to 'benchmark_table(IMP::base::PointerIMP::domino::PackedAssignmentContainer&, const char [17])' > modules/benchmark/bin/benchmark_domino_container.cpp:64:21: error: 'HDF5AssignmentContainer' was not declared in this scope > modules/benchmark/bin/benchmark_domino_container.cpp:64:66: error: no matching function for call to 'benchmark_table(IMP::base::PointerIMP::domino::ListAssignmentContainer&, const char [15])' > scons: *** [modules/benchmark/bin/benchmark_domino_container.o] Error 1 > scons: building terminated because of errors.
> Enabled dependencies: CGAL, Boost.ProgramOptions, Boost.Thread, Boost > Disabled dependencies: Bullet, HDF5, OpenCV21, ANN, Boost.FileSystem, modeller, FFTW3, GSL, OpenCV22 > > Enabled modules: em, kernel, scratch, domino, misc, statistics, container, saxs, system, parallel, example, benchmark, core, algebra, cgal, restrainer, example_system_local, base, atom, compatibility, display > Disabled modules: rmf, RMF, multifit, bullet, gsl, modeller, em2d > > Enabled applications: saxs_tools, em_tools, foxs > Disabled applications: rmf_tools, ligand_score, nup84, multifit, example_system, rnapii > > Enabled systems: Groel > > Errors building: > modules/benchmark/bin/benchmark_domino_container.o
On Oct 6, 2011, at 5:27 PM, Daniel Russel wrote: > I think the linux errors are elsewhere in the output (you are probably using -j n with n>1 and so different build commands and errors are woven together). > > On Oct 6, 2011, at 3:49 AM, Davide Baù wrote: > >> You're right. I had some references to ExampleLib in a local library. That solved the issue on my Mac but not on my linux machine (updated to revision 11289 on both machines): >> >>> g++ -o modules/benchmark/bin/benchmark_knn -Wl,-rpath=/usr/src/imp/imp-r11289 modules/benchmark/bin/benchmark_knn.o -Lbuild/lib -L. -limp_benchmark -limp_domino -limp_display -limp_em -limp_atom -limp_con >>> tainer -limp_core -limp_statistics -limp -limp_algebra -limp_cgal -limp_base -limp_compatibility -lCGAL -lgmp -lmpfr -lgmpxx -lboost_thread -lpthread -lmscons: *** [modules/benchmark/bin/benchmark_domino_container.o] Error 1scons: building terminated because of errors. >> >> I don't know if it depends on CGAL which is installed anyway. >> Davide
It looks like that benchmark doesn't properly disable itself when you don't have hdf5 installed. You can safetly ignore it for now (just use -k with scons). On Oct 7, 2011, at 1:50 AM, Davide Baù wrote:
> I have re-run scones without the -j option. It seems that it's a problem with domino? > > Davide > >> g++ -o modules/benchmark/bin/benchmark_domino_container.o -c -isystem /usr/src/imp/imp-r11289 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef - >> Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop- >> optimizations -fno-signed-zeros -freciprocal-math -fassociative-math -DBOOST_ALL_NO_LIB -Ibuild/include -Ibuild/src modules/benchmark/bin/benchmark_domino_container.cpp >> modules/benchmark/bin/benchmark_domino_container.cpp: In function 'int main(int, char**)': >> modules/benchmark/bin/benchmark_domino_container.cpp:43:5: error: 'RMF' has not been declared >> modules/benchmark/bin/benchmark_domino_container.cpp:43:19: error: expected ';' before 'file' >> modules/benchmark/bin/benchmark_domino_container.cpp:45:5: error: 'RMF' has not been declared >> modules/benchmark/bin/benchmark_domino_container.cpp:45:29: error: expected ';' before 'ds' >> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: 'HDF5AssignmentContainer' was not declared in this scope >> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: template argument 1 is invalid >> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: invalid type in declaration before '(' token >> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: expected type-specifier before 'HDF5AssignmentContainer' >> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: expected ')' before 'HDF5AssignmentContainer' >> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: invalid conversion from 'int*' to 'int' >> modules/benchmark/bin/benchmark_domino_container.cpp:47:7: error: base operand of '->' is not a pointer >> modules/benchmark/bin/benchmark_domino_container.cpp:48:21: error: 'HDF5AssignmentContainer' cannot appear in a constant-expression >> modules/benchmark/bin/benchmark_domino_container.cpp:48:65: error: no matching function for call to 'benchmark_table(int&, const char [14])' >> modules/benchmark/bin/benchmark_domino_container.cpp:51:5: error: 'RMF' has not been declared >> modules/benchmark/bin/benchmark_domino_container.cpp:51:19: error: expected ';' before 'file' >> modules/benchmark/bin/benchmark_domino_container.cpp:53:5: error: 'RMF' has not been declared >> modules/benchmark/bin/benchmark_domino_container.cpp:53:29: error: expected ';' before 'ds' >> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: 'HDF5AssignmentContainer' was not declared in this scope >> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: template argument 1 is invalid >> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: invalid type in declaration before '(' token >> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: expected type-specifier before 'HDF5AssignmentContainer' >> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: expected ')' before 'HDF5AssignmentContainer' >> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: invalid conversion from 'int*' to 'int' >> modules/benchmark/bin/benchmark_domino_container.cpp:55:7: error: base operand of '->' is not a pointer >> modules/benchmark/bin/benchmark_domino_container.cpp:56:21: error: 'HDF5AssignmentContainer' cannot appear in a constant-expression >> modules/benchmark/bin/benchmark_domino_container.cpp:56:56: error: no matching function for call to 'benchmark_table(int&, const char [5])' >> modules/benchmark/bin/benchmark_domino_container.cpp:60:21: error: 'HDF5AssignmentContainer' was not declared in this scope >> modules/benchmark/bin/benchmark_domino_container.cpp:60:68: error: no matching function for call to 'benchmark_table(IMP::base::PointerIMP::domino::PackedAssignmentContainer&, const char [17])' >> modules/benchmark/bin/benchmark_domino_container.cpp:64:21: error: 'HDF5AssignmentContainer' was not declared in this scope >> modules/benchmark/bin/benchmark_domino_container.cpp:64:66: error: no matching function for call to 'benchmark_table(IMP::base::PointerIMP::domino::ListAssignmentContainer&, const char [15])' >> scons: *** [modules/benchmark/bin/benchmark_domino_container.o] Error 1 >> scons: building terminated because of errors. > > >> Enabled dependencies: CGAL, Boost.ProgramOptions, Boost.Thread, Boost >> Disabled dependencies: Bullet, HDF5, OpenCV21, ANN, Boost.FileSystem, modeller, FFTW3, GSL, OpenCV22 >> >> Enabled modules: em, kernel, scratch, domino, misc, statistics, container, saxs, system, parallel, example, benchmark, core, algebra, cgal, restrainer, example_system_local, base, atom, compatibility, display >> Disabled modules: rmf, RMF, multifit, bullet, gsl, modeller, em2d >> >> Enabled applications: saxs_tools, em_tools, foxs >> Disabled applications: rmf_tools, ligand_score, nup84, multifit, example_system, rnapii >> >> Enabled systems: Groel >> >> Errors building: >> modules/benchmark/bin/benchmark_domino_container.o > > > > <config.log> > > > On Oct 6, 2011, at 5:27 PM, Daniel Russel wrote: >> I think the linux errors are elsewhere in the output (you are probably using -j n with n>1 and so different build commands and errors are woven together). >> >> On Oct 6, 2011, at 3:49 AM, Davide Baù wrote: >> >>> You're right. I had some references to ExampleLib in a local library. That solved the issue on my Mac but not on my linux machine (updated to revision 11289 on both machines): >>> >>>> g++ -o modules/benchmark/bin/benchmark_knn -Wl,-rpath=/usr/src/imp/imp-r11289 modules/benchmark/bin/benchmark_knn.o -Lbuild/lib -L. -limp_benchmark -limp_domino -limp_display -limp_em -limp_atom -limp_con >>>> tainer -limp_core -limp_statistics -limp -limp_algebra -limp_cgal -limp_base -limp_compatibility -lCGAL -lgmp -lmpfr -lgmpxx -lboost_thread -lpthread -lmscons: *** [modules/benchmark/bin/benchmark_domino_container.o] Error 1scons: building terminated because of errors. >>> >>> I don't know if it depends on CGAL which is installed anyway. >>> Davide > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Hi,
I still have the same compilation error even using the -k option.
Davide
On Oct 7, 2011, at 5:26 PM, Daniel Russel wrote:
> It looks like that benchmark doesn't properly disable itself when you don't have hdf5 installed. You can safetly ignore it for now (just use -k with scons). > On Oct 7, 2011, at 1:50 AM, Davide Baù wrote: > >> I have re-run scones without the -j option. It seems that it's a problem with domino? >> >> Davide >> >>> g++ -o modules/benchmark/bin/benchmark_domino_container.o -c -isystem /usr/src/imp/imp-r11289 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef - >>> Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop- >>> optimizations -fno-signed-zeros -freciprocal-math -fassociative-math -DBOOST_ALL_NO_LIB -Ibuild/include -Ibuild/src modules/benchmark/bin/benchmark_domino_container.cpp >>> modules/benchmark/bin/benchmark_domino_container.cpp: In function 'int main(int, char**)': >>> modules/benchmark/bin/benchmark_domino_container.cpp:43:5: error: 'RMF' has not been declared >>> modules/benchmark/bin/benchmark_domino_container.cpp:43:19: error: expected ';' before 'file' >>> modules/benchmark/bin/benchmark_domino_container.cpp:45:5: error: 'RMF' has not been declared >>> modules/benchmark/bin/benchmark_domino_container.cpp:45:29: error: expected ';' before 'ds' >>> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: 'HDF5AssignmentContainer' was not declared in this scope >>> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: template argument 1 is invalid >>> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: invalid type in declaration before '(' token >>> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: expected type-specifier before 'HDF5AssignmentContainer' >>> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: expected ')' before 'HDF5AssignmentContainer' >>> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: invalid conversion from 'int*' to 'int' >>> modules/benchmark/bin/benchmark_domino_container.cpp:47:7: error: base operand of '->' is not a pointer >>> modules/benchmark/bin/benchmark_domino_container.cpp:48:21: error: 'HDF5AssignmentContainer' cannot appear in a constant-expression >>> modules/benchmark/bin/benchmark_domino_container.cpp:48:65: error: no matching function for call to 'benchmark_table(int&, const char [14])' >>> modules/benchmark/bin/benchmark_domino_container.cpp:51:5: error: 'RMF' has not been declared >>> modules/benchmark/bin/benchmark_domino_container.cpp:51:19: error: expected ';' before 'file' >>> modules/benchmark/bin/benchmark_domino_container.cpp:53:5: error: 'RMF' has not been declared >>> modules/benchmark/bin/benchmark_domino_container.cpp:53:29: error: expected ';' before 'ds' >>> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: 'HDF5AssignmentContainer' was not declared in this scope >>> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: template argument 1 is invalid >>> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: invalid type in declaration before '(' token >>> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: expected type-specifier before 'HDF5AssignmentContainer' >>> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: expected ')' before 'HDF5AssignmentContainer' >>> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: invalid conversion from 'int*' to 'int' >>> modules/benchmark/bin/benchmark_domino_container.cpp:55:7: error: base operand of '->' is not a pointer >>> modules/benchmark/bin/benchmark_domino_container.cpp:56:21: error: 'HDF5AssignmentContainer' cannot appear in a constant-expression >>> modules/benchmark/bin/benchmark_domino_container.cpp:56:56: error: no matching function for call to 'benchmark_table(int&, const char [5])' >>> modules/benchmark/bin/benchmark_domino_container.cpp:60:21: error: 'HDF5AssignmentContainer' was not declared in this scope >>> modules/benchmark/bin/benchmark_domino_container.cpp:60:68: error: no matching function for call to 'benchmark_table(IMP::base::PointerIMP::domino::PackedAssignmentContainer&, const char [17])' >>> modules/benchmark/bin/benchmark_domino_container.cpp:64:21: error: 'HDF5AssignmentContainer' was not declared in this scope >>> modules/benchmark/bin/benchmark_domino_container.cpp:64:66: error: no matching function for call to 'benchmark_table(IMP::base::PointerIMP::domino::ListAssignmentContainer&, const char [15])' >>> scons: *** [modules/benchmark/bin/benchmark_domino_container.o] Error 1 >>> scons: building terminated because of errors. >> >> >>> Enabled dependencies: CGAL, Boost.ProgramOptions, Boost.Thread, Boost >>> Disabled dependencies: Bullet, HDF5, OpenCV21, ANN, Boost.FileSystem, modeller, FFTW3, GSL, OpenCV22 >>> >>> Enabled modules: em, kernel, scratch, domino, misc, statistics, container, saxs, system, parallel, example, benchmark, core, algebra, cgal, restrainer, example_system_local, base, atom, compatibility, display >>> Disabled modules: rmf, RMF, multifit, bullet, gsl, modeller, em2d >>> >>> Enabled applications: saxs_tools, em_tools, foxs >>> Disabled applications: rmf_tools, ligand_score, nup84, multifit, example_system, rnapii >>> >>> Enabled systems: Groel >>> >>> Errors building: >>> modules/benchmark/bin/benchmark_domino_container.o >> >> >> >> <config.log> >> >> >> On Oct 6, 2011, at 5:27 PM, Daniel Russel wrote: >>> I think the linux errors are elsewhere in the output (you are probably using -j n with n>1 and so different build commands and errors are woven together). >>> >>> On Oct 6, 2011, at 3:49 AM, Davide Baù wrote: >>> >>>> You're right. I had some references to ExampleLib in a local library. That solved the issue on my Mac but not on my linux machine (updated to revision 11289 on both machines): >>>> >>>>> g++ -o modules/benchmark/bin/benchmark_knn -Wl,-rpath=/usr/src/imp/imp-r11289 modules/benchmark/bin/benchmark_knn.o -Lbuild/lib -L. -limp_benchmark -limp_domino -limp_display -limp_em -limp_atom -limp_con >>>>> tainer -limp_core -limp_statistics -limp -limp_algebra -limp_cgal -limp_base -limp_compatibility -lCGAL -lgmp -lmpfr -lgmpxx -lboost_thread -lpthread -lmscons: *** [modules/benchmark/bin/benchmark_domino_container.o] Error 1scons: building terminated because of errors. >>>> >>>> I don't know if it depends on CGAL which is installed anyway. >>>> Davide >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
The k option just makes it continue after the errors and build everything else since that error is in a file you probably don't care about. Anyway, that error should be fixed if you svn update now.
On Oct 8, 2011, at 1:57 AM, Davide Baù wrote:
> Hi, > > I still have the same compilation error even using the -k option. > > Davide > > > > On Oct 7, 2011, at 5:26 PM, Daniel Russel wrote: > >> It looks like that benchmark doesn't properly disable itself when you don't have hdf5 installed. You can safetly ignore it for now (just use -k with scons). >> On Oct 7, 2011, at 1:50 AM, Davide Baù wrote: >> >>> I have re-run scones without the -j option. It seems that it's a problem with domino? >>> >>> Davide >>> >>>> g++ -o modules/benchmark/bin/benchmark_domino_container.o -c -isystem /usr/src/imp/imp-r11289 -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef - >>>> Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop- >>>> optimizations -fno-signed-zeros -freciprocal-math -fassociative-math -DBOOST_ALL_NO_LIB -Ibuild/include -Ibuild/src modules/benchmark/bin/benchmark_domino_container.cpp >>>> modules/benchmark/bin/benchmark_domino_container.cpp: In function 'int main(int, char**)': >>>> modules/benchmark/bin/benchmark_domino_container.cpp:43:5: error: 'RMF' has not been declared >>>> modules/benchmark/bin/benchmark_domino_container.cpp:43:19: error: expected ';' before 'file' >>>> modules/benchmark/bin/benchmark_domino_container.cpp:45:5: error: 'RMF' has not been declared >>>> modules/benchmark/bin/benchmark_domino_container.cpp:45:29: error: expected ';' before 'ds' >>>> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: 'HDF5AssignmentContainer' was not declared in this scope >>>> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: template argument 1 is invalid >>>> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: invalid type in declaration before '(' token >>>> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: expected type-specifier before 'HDF5AssignmentContainer' >>>> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: expected ')' before 'HDF5AssignmentContainer' >>>> modules/benchmark/bin/benchmark_domino_container.cpp:46:5: error: invalid conversion from 'int*' to 'int' >>>> modules/benchmark/bin/benchmark_domino_container.cpp:47:7: error: base operand of '->' is not a pointer >>>> modules/benchmark/bin/benchmark_domino_container.cpp:48:21: error: 'HDF5AssignmentContainer' cannot appear in a constant-expression >>>> modules/benchmark/bin/benchmark_domino_container.cpp:48:65: error: no matching function for call to 'benchmark_table(int&, const char [14])' >>>> modules/benchmark/bin/benchmark_domino_container.cpp:51:5: error: 'RMF' has not been declared >>>> modules/benchmark/bin/benchmark_domino_container.cpp:51:19: error: expected ';' before 'file' >>>> modules/benchmark/bin/benchmark_domino_container.cpp:53:5: error: 'RMF' has not been declared >>>> modules/benchmark/bin/benchmark_domino_container.cpp:53:29: error: expected ';' before 'ds' >>>> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: 'HDF5AssignmentContainer' was not declared in this scope >>>> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: template argument 1 is invalid >>>> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: invalid type in declaration before '(' token >>>> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: expected type-specifier before 'HDF5AssignmentContainer' >>>> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: expected ')' before 'HDF5AssignmentContainer' >>>> modules/benchmark/bin/benchmark_domino_container.cpp:54:5: error: invalid conversion from 'int*' to 'int' >>>> modules/benchmark/bin/benchmark_domino_container.cpp:55:7: error: base operand of '->' is not a pointer >>>> modules/benchmark/bin/benchmark_domino_container.cpp:56:21: error: 'HDF5AssignmentContainer' cannot appear in a constant-expression >>>> modules/benchmark/bin/benchmark_domino_container.cpp:56:56: error: no matching function for call to 'benchmark_table(int&, const char [5])' >>>> modules/benchmark/bin/benchmark_domino_container.cpp:60:21: error: 'HDF5AssignmentContainer' was not declared in this scope >>>> modules/benchmark/bin/benchmark_domino_container.cpp:60:68: error: no matching function for call to 'benchmark_table(IMP::base::PointerIMP::domino::PackedAssignmentContainer&, const char [17])' >>>> modules/benchmark/bin/benchmark_domino_container.cpp:64:21: error: 'HDF5AssignmentContainer' was not declared in this scope >>>> modules/benchmark/bin/benchmark_domino_container.cpp:64:66: error: no matching function for call to 'benchmark_table(IMP::base::PointerIMP::domino::ListAssignmentContainer&, const char [15])' >>>> scons: *** [modules/benchmark/bin/benchmark_domino_container.o] Error 1 >>>> scons: building terminated because of errors. >>> >>> >>>> Enabled dependencies: CGAL, Boost.ProgramOptions, Boost.Thread, Boost >>>> Disabled dependencies: Bullet, HDF5, OpenCV21, ANN, Boost.FileSystem, modeller, FFTW3, GSL, OpenCV22 >>>> >>>> Enabled modules: em, kernel, scratch, domino, misc, statistics, container, saxs, system, parallel, example, benchmark, core, algebra, cgal, restrainer, example_system_local, base, atom, compatibility, display >>>> Disabled modules: rmf, RMF, multifit, bullet, gsl, modeller, em2d >>>> >>>> Enabled applications: saxs_tools, em_tools, foxs >>>> Disabled applications: rmf_tools, ligand_score, nup84, multifit, example_system, rnapii >>>> >>>> Enabled systems: Groel >>>> >>>> Errors building: >>>> modules/benchmark/bin/benchmark_domino_container.o >>> >>> >>> >>> <config.log> >>> >>> >>> On Oct 6, 2011, at 5:27 PM, Daniel Russel wrote: >>>> I think the linux errors are elsewhere in the output (you are probably using -j n with n>1 and so different build commands and errors are woven together). >>>> >>>> On Oct 6, 2011, at 3:49 AM, Davide Baù wrote: >>>> >>>>> You're right. I had some references to ExampleLib in a local library. That solved the issue on my Mac but not on my linux machine (updated to revision 11289 on both machines): >>>>> >>>>>> g++ -o modules/benchmark/bin/benchmark_knn -Wl,-rpath=/usr/src/imp/imp-r11289 modules/benchmark/bin/benchmark_knn.o -Lbuild/lib -L. -limp_benchmark -limp_domino -limp_display -limp_em -limp_atom -limp_con >>>>>> tainer -limp_core -limp_statistics -limp -limp_algebra -limp_cgal -limp_base -limp_compatibility -lCGAL -lgmp -lmpfr -lgmpxx -lboost_thread -lpthread -lmscons: *** [modules/benchmark/bin/benchmark_domino_container.o] Error 1scons: building terminated because of errors. >>>>> >>>>> I don't know if it depends on CGAL which is installed anyway. >>>>> Davide >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Hi,
I have tried several things and updated to revision 11334 but still no luck. Using the -k option, the compilation continues but the imppy.sh script generated does not works properly (python tools/imppy.sh aborts complaining about a syntax error in imply.sh). I will roll back to an earlier version for the moment.
Davide
On Oct 8, 2011, at 3:46 PM, Daniel Russel wrote:
> The k option just makes it continue after the errors and build everything else since that error is in a file you probably don't care about. Anyway, that error should be fixed if you svn update now.
Sorry, I made a mistake in my previous email. The imppy.sh script generated works properly using the -k option.
Davide
> Hi, > > I have tried several things and updated to revision 11334 but still no luck. Using the -k option, the compilation continues but the imppy.sh script generated does not works properly (python tools/imppy.sh aborts complaining about a syntax error in imply.sh). I will roll back to an earlier version for the moment. > > Davide > > On Oct 8, 2011, at 3:46 PM, Daniel Russel wrote: > >> The k option just makes it continue after the errors and build everything else since that error is in a file you probably don't care about. Anyway, that error should be fixed if you svn update now.
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Daniel Russel -
Davide Baù