Hi, On Mon, Oct 18, 2010 at 8:28 PM, Igor Filippov [Contr] <filipp...@mail.nih.gov> wrote: > Tim, > > Thanks, I can build my executable per your instructions and it runs > without segfaults, but doesn't seem to get the format plugins yet - the > output when I want to get SMILES for example is empty. > > I'm also looking at the page "Plugins -> Creating custom static > libraries" at http://openbabel.org/wiki/CMake > but it's so terse I cannot figure out how to use this information for a > project that does not use cmake itself. And I'm not a cmake expert at > all unfortunately...
You can build the doc/examples/static_executable exe using cmake and "make VERBOSE=1". This will print the commands used for compiling. For example: [100%] Building CXX object CMakeFiles/myexe.dir/myexe.cpp.o /usr/bin/c++ -u _ZTVN9OpenBabel9ACRFormatE -u _ZTVN9OpenBabel15ADFOutputFormatE -u _ZTVN9OpenBabel14ADFInputFormatE -u _ZTVN9OpenBabel11OBT41FormatE -u _ZTVN9OpenBabel13AlchemyFormatE -u _ZTVN9OpenBabel15AmberPrepFormatE -u _ZTVN9OpenBabel14OBAPIInterfaceE -u _ZTVN9OpenBabel15BallStickFormatE -u _ZTVN9OpenBabel9BGFFormatE -u _ZTVN9OpenBabel9BoxFormatE -u _ZTVN9OpenBabel11CacaoFormatE -u _ZTVN9OpenBabel11CacheFormatE -u _ZTVN9OpenBabel9CARFormatE -u _ZTVN9OpenBabel9CCCFormatE -u _ZTVN9OpenBabel13CHEM3D1FormatE -u _ZTVN9OpenBabel13CHEM3D2FormatE -u _ZTVN9OpenBabel20ChemDrawBinaryFormatE -u _ZTVN9OpenBabel14ChemDrawFormatE -u _ZTVN9OpenBabel13ChemKinFormatE -u _ZTVN9OpenBabel9CHTFormatE -u _ZTVN9OpenBabel9CIFFormatE -u _ZTVN9OpenBabel10CopyFormatE -u _ZTVN9OpenBabel11CRK2DFormatE -u _ZTVN9OpenBabel11CRK3DFormatE -u _ZTVN9OpenBabel9CSRFormatE -u _ZTVN9OpenBabel10CSSRFormatE -u _ZTVN9OpenBabel18DlpolyConfigFormatE -u _ZTVN9OpenBabel19DlpolyHISTORYFormatE -u _ZTVN9OpenBabel10DMolFormatE -u _ZTVN9OpenBabel9XXXFormatE -u _ZTVN9OpenBabel11FASTAFormatE -u _ZTVN9OpenBabel16FastSearchFormatE -u _ZTVN9OpenBabel10FCHKFormatE -u _ZTVN9OpenBabel10FEATFormatE -u _ZTVN9OpenBabel16FenskeZmatFormatE -u _ZTVN9OpenBabel13FHIainsFormatE -u _ZTVN9OpenBabel17FingerprintFormatE -u _ZTVN9OpenBabel24FreeFormFractionalFormatE -u _ZTVN9OpenBabel18GAMESSOutputFormatE -u _ZTVN9OpenBabel17GAMESSInputFormatE -u _ZTVN9OpenBabel14GAMESSUKFormatE -u _ZTVN9OpenBabel19GAMESSUKInputFormatE -u _ZTVN9OpenBabel20GAMESSUKOutputFormatE -u _ZTVN9OpenBabel20OBGaussianCubeFormatE -u _ZTVN9OpenBabel20GaussianOutputFormatE -u _ZTVN9OpenBabel19GaussianInputFormatE -u _ZTVN9OpenBabel26GaussianZMatrixInputFormatE -u _ZTVN9OpenBabel13GenBankFormatE -u _ZTVN9OpenBabel14GhemicalFormatE -u _ZTVN9OpenBabel14GROMOS96FormatE -u _ZTVN9OpenBabel10GULPFormatE -u _ZTVN9OpenBabel9HINFormatE -u _ZTVN9OpenBabel18JaguarOutputFormatE -u _ZTVN9OpenBabel17JaguarInputFormatE -u _ZTVN9OpenBabel10MCDLFormatE -u _ZTVN9OpenBabel9MDLFormatE -u _ZTVN9OpenBabel9MOLFormatE -u _ZTVN9OpenBabel9SDFFormatE -u _ZTVN9OpenBabel11mmCIFFormatE -u _ZTVN9OpenBabel14MacroModFormatE -u _ZTVN9OpenBabel9MNAFormatE -u _ZTVN9OpenBabel10MOL2FormatE -u _ZTVN9OpenBabel14OBMoldenFormatE -u _ZTVN9OpenBabel18MolproOutputFormatE -u _ZTVN9OpenBabel17MolproInputFormatE -u _ZTVN9OpenBabel15MolReportFormatE -u _ZTVN9OpenBabel11MOPACFormatE -u _ZTVN9OpenBabel15MOPACCARTFormatE -u _ZTVN9OpenBabel14MOPACINTFormatE -u _ZTVN9OpenBabel9MPDFormatE -u _ZTVN9OpenBabel10MPQCFormatE -u _ZTVN9OpenBabel15MPQCInputFormatE -u _ZTVN9OpenBabel9MSIFormatE -u _ZTVN9OpenBabel12OBMSMSFormatE -u _ZTVN9OpenBabel9NulFormatE -u _ZTVN9OpenBabel18NWChemOutputFormatE -u _ZTVN9OpenBabel17NWChemInputFormatE -u _ZTVN9OpenBabel18OBOpenDXCubeFormatE -u _ZTVN9OpenBabel12OutputFormatE -u _ZTVN9OpenBabel13PCModelFormatE -u _ZTVN9OpenBabel9PDBFormatE -u _ZTVN9OpenBabel11PDBQTFormatE -u _ZTVN9OpenBabel9PNGFormatE -u _ZTVN9OpenBabel12PovrayFormatE -u _ZTVN9OpenBabel9PQRFormatE -u _ZTVN9OpenBabel9PQSFormatE -u _ZTVN9OpenBabel11PWscfFormatE -u _ZTVN9OpenBabel17QChemOutputFormatE -u _ZTVN9OpenBabel16QChemInputFormatE -u _ZTVN9OpenBabel12ReportFormatE -u _ZTVN9OpenBabel14SmiReactFormatE -u _ZTVN9OpenBabel9RXNFormatE -u _ZTVN9OpenBabel11ShelXFormatE -u _ZTVN9OpenBabel9SMIFormatE -u _ZTVN9OpenBabel12CANSMIFormatE -u _ZTVN9OpenBabel9FIXFormatE -u _ZTVN9OpenBabel9SVGFormatE -u _ZTVN9OpenBabel10TextFormatE -u _ZTVN9OpenBabel12ThermoFormatE -u _ZTVN9OpenBabel12TinkerFormatE -u _ZTVN9OpenBabel11TitleFormatE -u _ZTVN9OpenBabel15TurbomoleFormatE -u _ZTVN9OpenBabel13UniChemFormatE -u _ZTVN9OpenBabel10VASPFormatE -u _ZTVN9OpenBabel13ViewMolFormatE -u _ZTVN9OpenBabel9XEDFormatE -u _ZTVN9OpenBabel9XTCFormatE -u _ZTVN9OpenBabel9XYZFormatE -u _ZTVN9OpenBabel9YOBFormatE -u _ZTVN9OpenBabel11ZINDOFormatE -u _ZTVN9OpenBabel17ChemDrawXMLFormatE -u _ZTVN9OpenBabel9CMLFormatE -u _ZTVN9OpenBabel14CMLReactFormatE -u _ZTVN9OpenBabel13PubChemFormatE -u _ZTVN9OpenBabel9XMLFormatE -u _ZTVN9OpenBabel9CanSmilesE -u _ZTVN9OpenBabel14CompoundFilterE -u _ZTVN9OpenBabel8MWFilterE -u _ZTVN9OpenBabel12SmartsFilterE -u _ZTVN9OpenBabel11TitleFilterE -u _ZTVN9OpenBabel17FormulaDescriptorE -u _ZTVN9OpenBabel7FPCountE -u _ZTVN9OpenBabel11InChIFilterE -u _ZTVN9OpenBabel16SmartsDescriptorE -u _ZTVN9OpenBabel12fingerprint2E -u _ZTVN9OpenBabel9PatternFPE -u _ZTVN9OpenBabel16OBForceFieldGaffE -u _ZTVN9OpenBabel20OBForceFieldGhemicalE -u _ZTVN9OpenBabel18OBForceFieldMMFF94E -u _ZTVN9OpenBabel15OBForceFieldUFFE -u _ZTVN9OpenBabel12OpAddInIndexE -u _ZTVN9OpenBabel11OpAddPolarHE -u _ZTVN9OpenBabel11OpCanonicalE -u _ZTVN9OpenBabel11OpConformerE -u _ZTVN9OpenBabel8OpFillUCE -u _ZTVN9OpenBabel8OpEnergyE -u _ZTVN9OpenBabel10OpMinimizeE -u _ZTVN9OpenBabel7OpGen2DE -u _ZTVN9OpenBabel7OpGen3DE -u _ZTVN9OpenBabel4Op2DE -u _ZTVN9OpenBabel6OpNewSE -u _ZTVN9OpenBabel15OpPartialChargeE -u _ZTVN9OpenBabel16OpReadConformersE -u _ZTVN9OpenBabel6OpSortE -u _ZTVN9OpenBabel8OpUniqueE -u _ZTVN9OpenBabel10OpExtraOutE -u _ZTVN9OpenBabel16GasteigerChargesE -u _ZTVN9OpenBabel13MMFF94ChargesE -u _ZTVN9OpenBabel10QEqChargesE -u _ZTVN9OpenBabel12QTPIEChargesE -static -I/usr/local/include/openbabel-2.0 -o CMakeFiles/myexe.dir/myexe.cpp.o -c /home/timvdm/openbabel-gitsvn/doc/examples/static_executable/myexe.cpp Linking CXX executable myexe /usr/bin/cmake -E cmake_link_script CMakeFiles/myexe.dir/link.txt --verbose=1 /usr/bin/c++ -u _ZTVN9OpenBabel9ACRFormatE -u _ZTVN9OpenBabel15ADFOutputFormatE -u _ZTVN9OpenBabel14ADFInputFormatE -u _ZTVN9OpenBabel11OBT41FormatE -u _ZTVN9OpenBabel13AlchemyFormatE -u _ZTVN9OpenBabel15AmberPrepFormatE -u _ZTVN9OpenBabel14OBAPIInterfaceE -u _ZTVN9OpenBabel15BallStickFormatE -u _ZTVN9OpenBabel9BGFFormatE -u _ZTVN9OpenBabel9BoxFormatE -u _ZTVN9OpenBabel11CacaoFormatE -u _ZTVN9OpenBabel11CacheFormatE -u _ZTVN9OpenBabel9CARFormatE -u _ZTVN9OpenBabel9CCCFormatE -u _ZTVN9OpenBabel13CHEM3D1FormatE -u _ZTVN9OpenBabel13CHEM3D2FormatE -u _ZTVN9OpenBabel20ChemDrawBinaryFormatE -u _ZTVN9OpenBabel14ChemDrawFormatE -u _ZTVN9OpenBabel13ChemKinFormatE -u _ZTVN9OpenBabel9CHTFormatE -u _ZTVN9OpenBabel9CIFFormatE -u _ZTVN9OpenBabel10CopyFormatE -u _ZTVN9OpenBabel11CRK2DFormatE -u _ZTVN9OpenBabel11CRK3DFormatE -u _ZTVN9OpenBabel9CSRFormatE -u _ZTVN9OpenBabel10CSSRFormatE -u _ZTVN9OpenBabel18DlpolyConfigFormatE -u _ZTVN9OpenBabel19DlpolyHISTORYFormatE -u _ZTVN9OpenBabel10DMolFormatE -u _ZTVN9OpenBabel9XXXFormatE -u _ZTVN9OpenBabel11FASTAFormatE -u _ZTVN9OpenBabel16FastSearchFormatE -u _ZTVN9OpenBabel10FCHKFormatE -u _ZTVN9OpenBabel10FEATFormatE -u _ZTVN9OpenBabel16FenskeZmatFormatE -u _ZTVN9OpenBabel13FHIainsFormatE -u _ZTVN9OpenBabel17FingerprintFormatE -u _ZTVN9OpenBabel24FreeFormFractionalFormatE -u _ZTVN9OpenBabel18GAMESSOutputFormatE -u _ZTVN9OpenBabel17GAMESSInputFormatE -u _ZTVN9OpenBabel14GAMESSUKFormatE -u _ZTVN9OpenBabel19GAMESSUKInputFormatE -u _ZTVN9OpenBabel20GAMESSUKOutputFormatE -u _ZTVN9OpenBabel20OBGaussianCubeFormatE -u _ZTVN9OpenBabel20GaussianOutputFormatE -u _ZTVN9OpenBabel19GaussianInputFormatE -u _ZTVN9OpenBabel26GaussianZMatrixInputFormatE -u _ZTVN9OpenBabel13GenBankFormatE -u _ZTVN9OpenBabel14GhemicalFormatE -u _ZTVN9OpenBabel14GROMOS96FormatE -u _ZTVN9OpenBabel10GULPFormatE -u _ZTVN9OpenBabel9HINFormatE -u _ZTVN9OpenBabel18JaguarOutputFormatE -u _ZTVN9OpenBabel17JaguarInputFormatE -u _ZTVN9OpenBabel10MCDLFormatE -u _ZTVN9OpenBabel9MDLFormatE -u _ZTVN9OpenBabel9MOLFormatE -u _ZTVN9OpenBabel9SDFFormatE -u _ZTVN9OpenBabel11mmCIFFormatE -u _ZTVN9OpenBabel14MacroModFormatE -u _ZTVN9OpenBabel9MNAFormatE -u _ZTVN9OpenBabel10MOL2FormatE -u _ZTVN9OpenBabel14OBMoldenFormatE -u _ZTVN9OpenBabel18MolproOutputFormatE -u _ZTVN9OpenBabel17MolproInputFormatE -u _ZTVN9OpenBabel15MolReportFormatE -u _ZTVN9OpenBabel11MOPACFormatE -u _ZTVN9OpenBabel15MOPACCARTFormatE -u _ZTVN9OpenBabel14MOPACINTFormatE -u _ZTVN9OpenBabel9MPDFormatE -u _ZTVN9OpenBabel10MPQCFormatE -u _ZTVN9OpenBabel15MPQCInputFormatE -u _ZTVN9OpenBabel9MSIFormatE -u _ZTVN9OpenBabel12OBMSMSFormatE -u _ZTVN9OpenBabel9NulFormatE -u _ZTVN9OpenBabel18NWChemOutputFormatE -u _ZTVN9OpenBabel17NWChemInputFormatE -u _ZTVN9OpenBabel18OBOpenDXCubeFormatE -u _ZTVN9OpenBabel12OutputFormatE -u _ZTVN9OpenBabel13PCModelFormatE -u _ZTVN9OpenBabel9PDBFormatE -u _ZTVN9OpenBabel11PDBQTFormatE -u _ZTVN9OpenBabel9PNGFormatE -u _ZTVN9OpenBabel12PovrayFormatE -u _ZTVN9OpenBabel9PQRFormatE -u _ZTVN9OpenBabel9PQSFormatE -u _ZTVN9OpenBabel11PWscfFormatE -u _ZTVN9OpenBabel17QChemOutputFormatE -u _ZTVN9OpenBabel16QChemInputFormatE -u _ZTVN9OpenBabel12ReportFormatE -u _ZTVN9OpenBabel14SmiReactFormatE -u _ZTVN9OpenBabel9RXNFormatE -u _ZTVN9OpenBabel11ShelXFormatE -u _ZTVN9OpenBabel9SMIFormatE -u _ZTVN9OpenBabel12CANSMIFormatE -u _ZTVN9OpenBabel9FIXFormatE -u _ZTVN9OpenBabel9SVGFormatE -u _ZTVN9OpenBabel10TextFormatE -u _ZTVN9OpenBabel12ThermoFormatE -u _ZTVN9OpenBabel12TinkerFormatE -u _ZTVN9OpenBabel11TitleFormatE -u _ZTVN9OpenBabel15TurbomoleFormatE -u _ZTVN9OpenBabel13UniChemFormatE -u _ZTVN9OpenBabel10VASPFormatE -u _ZTVN9OpenBabel13ViewMolFormatE -u _ZTVN9OpenBabel9XEDFormatE -u _ZTVN9OpenBabel9XTCFormatE -u _ZTVN9OpenBabel9XYZFormatE -u _ZTVN9OpenBabel9YOBFormatE -u _ZTVN9OpenBabel11ZINDOFormatE -u _ZTVN9OpenBabel17ChemDrawXMLFormatE -u _ZTVN9OpenBabel9CMLFormatE -u _ZTVN9OpenBabel14CMLReactFormatE -u _ZTVN9OpenBabel13PubChemFormatE -u _ZTVN9OpenBabel9XMLFormatE -u _ZTVN9OpenBabel9CanSmilesE -u _ZTVN9OpenBabel14CompoundFilterE -u _ZTVN9OpenBabel8MWFilterE -u _ZTVN9OpenBabel12SmartsFilterE -u _ZTVN9OpenBabel11TitleFilterE -u _ZTVN9OpenBabel17FormulaDescriptorE -u _ZTVN9OpenBabel7FPCountE -u _ZTVN9OpenBabel11InChIFilterE -u _ZTVN9OpenBabel16SmartsDescriptorE -u _ZTVN9OpenBabel12fingerprint2E -u _ZTVN9OpenBabel9PatternFPE -u _ZTVN9OpenBabel16OBForceFieldGaffE -u _ZTVN9OpenBabel20OBForceFieldGhemicalE -u _ZTVN9OpenBabel18OBForceFieldMMFF94E -u _ZTVN9OpenBabel15OBForceFieldUFFE -u _ZTVN9OpenBabel12OpAddInIndexE -u _ZTVN9OpenBabel11OpAddPolarHE -u _ZTVN9OpenBabel11OpCanonicalE -u _ZTVN9OpenBabel11OpConformerE -u _ZTVN9OpenBabel8OpFillUCE -u _ZTVN9OpenBabel8OpEnergyE -u _ZTVN9OpenBabel10OpMinimizeE -u _ZTVN9OpenBabel7OpGen2DE -u _ZTVN9OpenBabel7OpGen3DE -u _ZTVN9OpenBabel4Op2DE -u _ZTVN9OpenBabel6OpNewSE -u _ZTVN9OpenBabel15OpPartialChargeE -u _ZTVN9OpenBabel16OpReadConformersE -u _ZTVN9OpenBabel6OpSortE -u _ZTVN9OpenBabel8OpUniqueE -u _ZTVN9OpenBabel10OpExtraOutE -u _ZTVN9OpenBabel16GasteigerChargesE -u _ZTVN9OpenBabel13MMFF94ChargesE -u _ZTVN9OpenBabel10QEqChargesE -u _ZTVN9OpenBabel12QTPIEChargesE -static CMakeFiles/myexe.dir/myexe.cpp.o -o myexe -rdynamic /usr/local/lib/libopenbabel.so.4.0.0 -lm -ldl -lz -Wl,-Bstatic -Wl,-rpath,/usr/local/lib: > Igor > > > On Sat, 2010-10-16 at 10:23 -0400, Tim Vandermeersch wrote: >> On Fri, Oct 15, 2010 at 11:40 PM, Igor Filippov [Contr] >> <filipp...@mail.nih.gov> wrote: >> > It builds nicely on Fedora 12, x64 system. >> > Some points: >> > >> > 1) When building with -DBUILD_SHARED=no one needs to make sure static >> > zlib exists somewhere (libz.a) otherwise the error message which cmake >> > gives is somewhat confusing. >> > >> > 2) build/lib is full of dynamic libs (.so) even with BUILD_SHARED=no. >> > There is a static libopenbabel.a is build/src, which is great, but >> > linking against it gives the following error: >> > undefined reference to `OpenBabel::OBMol::FindChiralCenters()' >> > collect2: ld returned 1 exit status >> > >> > babel executable seems to be linked statically though so perhaps I'm not >> > linking correctly? >> >> Something like this should work: >> >> g++ -static myexe.cpp.o -o myexe /usr/local/lib/libopenbabel.a >> -Wl,-Bstatic -lm -lz >> >> I'll reply in a separate thread with more details on static building. >> The MinGW page (http://openbabel.org/wiki/Install_%28MinGW%29) is >> updated but it doesn't address handling plugins yet. >> >> Tim >> >> > 3) The version is still set at 2.2.99 not 2.3.0 :) >> > >> > Thanks! >> > Igor >> > >> > >> > On Fri, 2010-10-15 at 16:56 -0400, Geoffrey Hutchison wrote: >> >> I have uploaded a source-code only version of the 2.3.0 release candidate >> >> 1. >> >> http://sourceforge.net/projects/openbabel/files/openbabel-snapshots/2010-10-15/openbabel-2.3.0rc1-20101015-r4206.tar.gz/download >> >> >> >> Please give this a try and see if there are glaring bugs, issues, etc. >> >> Over the next week, we will be working on fixing up the documentation the >> >> website, etc. >> >> >> >> Let us know what you think -- we look forward to a good release on Oct. >> >> 23rd. >> >> >> >> Thanks, >> >> -Geoff >> >> >> >> --- >> >> Prof. Geoffrey Hutchison >> >> Department of Chemistry >> >> University of Pittsburgh >> >> tel: (412) 648-0492 >> >> email: geo...@pitt.edu >> >> web: http://hutchison.chem.pitt.edu/ >> >> >> >> >> >> ------------------------------------------------------------------------------ >> >> Download new Adobe(R) Flash(R) Builder(TM) 4 >> >> The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly >> >> Flex(R) Builder(TM)) enable the development of rich applications that run >> >> across multiple browsers and platforms. Download your free trials today! >> >> http://p.sf.net/sfu/adobe-dev2dev >> >> _______________________________________________ >> >> OpenBabel-Devel mailing list >> >> OpenBabel-Devel@lists.sourceforge.net >> >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel >> > >> > >> > >> > ------------------------------------------------------------------------------ >> > Download new Adobe(R) Flash(R) Builder(TM) 4 >> > The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly >> > Flex(R) Builder(TM)) enable the development of rich applications that run >> > across multiple browsers and platforms. Download your free trials today! >> > http://p.sf.net/sfu/adobe-dev2dev >> > _______________________________________________ >> > OpenBabel-discuss mailing list >> > openbabel-disc...@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > > > > ------------------------------------------------------------------------------ Download new Adobe(R) Flash(R) Builder(TM) 4 The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly Flex(R) Builder(TM)) enable the development of rich applications that run across multiple browsers and platforms. Download your free trials today! http://p.sf.net/sfu/adobe-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
