Hi Michael,
That second set of errors seems to be due to an error in the code (one I'm
somewhat surprised hasn't caused problems before).
The most straightforward fix is to add the line:
using boost::uint32_t;
at around line 35 of $RDBASE/Code/GraphMol/Fingerprints/Fingerprints.cpp
Best,
-greg
On Wed, Feb 5, 2014 at 11:53 PM, Michael Mysinger <[email protected]>wrote:
>
> Hello All,
>
> I just tried without cygwin in the path to skip bison and flex. Now I get
> this error, much later in the build:
>
> ...
> Linking CXX executable testDescriptors.exe
> [ 69%] Built target testDescriptors
> Scanning dependencies of target Fingerprints
> [ 69%] Building CXX object
> Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.di
> r/Fingerprints.cpp.obj
> Fingerprints.cpp
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol/Conformer.h(112) :
> warning C426
> 7: 'return' : conversion from 'size_t' to 'unsigned int', possible loss of
> data
> c:\build\x64\rdkit\rdkit_2013_09_2\code\graphmol\ROMol.h(297) : warning
> C4267: '
> return' : conversion from 'size_t' to 'unsigned int', possible loss of data
> c:\build\x64\rdkit\rdkit_2013_09_2\code\datastructs\SparseBitVect.h(73) :
> warnin
> g C4267: 'return' : conversion from 'size_t' to 'unsigned int', possible
> loss of
> data
> c:\build\x64\rdkit\rdkit_2013_09_2\code\datastructs\SparseBitVect.h(74) :
> warnin
> g C4267: 'return' : conversion from 'size_t' to 'unsigned int', possible
> loss of
> data
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 16) : error C2146: syntax error : missing ';' before identifier 'hashBond'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 16) : error C4430: missing type specifier - int assumed. Note: C++ does
> not supp
> ort default-int
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 16) : error C2923: 'std::vector' :
> 'RDKit::`anonymous-namespace'::uint32_t' is n
> ot a valid template type argument for parameter '_Ty'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprin
> ts.cpp(116) : see declaration of 'RDKit::`anonymous-namespace'::uint32_t'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 17) : error C2923: 'std::vector' :
> 'RDKit::`anonymous-namespace'::uint32_t' is n
> ot a valid template type argument for parameter '_Ty'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprin
> ts.cpp(116) : see declaration of 'RDKit::`anonymous-namespace'::uint32_t'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 17) : error C2061: syntax error : identifier 'uint32_t'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 18) : error C4430: missing type specifier - int assumed. Note: C++ does
> not supp
> ort default-int
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 20) : error C2146: syntax error : missing ';' before identifier 'res'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 20) : error C2065: 'res' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 21) : error C2065: 'useBondOrder' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 23) : error C2065: 'res' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 25) : error C2065: 'res' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 28) : error C2065: 'res' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 30) : error C2146: syntax error : missing ';' before identifier 'iv1'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 30) : error C2065: 'iv1' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 31) : error C2146: syntax error : missing ';' before identifier 'iv2'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 31) : error C2065: 'iv2' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 32) : error C2146: syntax error : missing ';' before identifier 'deg1'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 32) : error C2065: 'deg1' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 33) : error C2146: syntax error : missing ';' before identifier 'deg2'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 33) : error C2065: 'deg2' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 35) : error C2065: 'iv1' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 35) : error C2065: 'iv2' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 36) : error C2065: 'iv1' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 36) : error C2065: 'iv2' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 37) : error C2065: 'deg1' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 37) : error C2065: 'deg2' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 38) : error C2065: 'iv1' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 38) : error C2065: 'iv2' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 39) : error C2065: 'deg1' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 39) : error C2065: 'deg2' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 40) : error C2065: 'deg1' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 40) : error C2065: 'deg2' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 44) : error C2065: 'res' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 44) : error C2065: 'res' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 44) : error C2065: 'iv1' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 44) : error C2065: 'iv2' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 44) : error C2065: 'deg1' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 44) : error C2065: 'deg2' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 44) : error C2065: 'bondDegree' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 46) : error C2065: 'res' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 48) : error C2146: syntax error : missing ';' before identifier
> 'canonicalPathHa
> sh'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 48) : error C4430: missing type specifier - int assumed. Note: C++ does
> not supp
> ort default-int
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 48) : error C2086: 'int RDKit::`anonymous-namespace'::uint32_t' :
> redefinition
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprin
> ts.cpp(116) : see declaration of 'RDKit::`anonymous-namespace'::uint32_t'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 51) : error C2923: 'std::vector' :
> 'RDKit::`anonymous-namespace'::uint32_t' is n
> ot a valid template type argument for parameter '_Ty'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprin
> ts.cpp(116) : see declaration of 'RDKit::`anonymous-namespace'::uint32_t'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 51) : error C4430: missing type specifier - int assumed. Note: C++ does
> not supp
> ort default-int
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 53) : error C2146: syntax error : missing ';' before identifier 'best'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 53) : error C2065: 'best' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 63) : error C2065: 'best' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 65) : error C2065: 'best' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 66) : error C2065: 'best' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 68) : error C2065: 'best' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 78) : error C2146: syntax error : missing ';' before identifier 'res'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 78) : error C2065: 'res' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 78) : error C2065: 'best' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 80) : error C2065: 'res' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(1
> 81) : error C2065: 'best' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(2
> 02) : error C2065: 'best' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(2
> 08) : error C2065: 'best' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(2
> 10) : error C2065: 'best' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(2
> 23) : error C2065: 'res' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(2
> 23) : error C2065: 'best' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(2
> 27) : error C2065: 'best' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(2
> 31) : error C2065: 'res' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(2
> 32) : error C2065: 'res' : undeclared identifier
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(2
> 82) : warning C4805: '|' : unsafe mix of type 'int' and type 'bool' in
> operation
>
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(3
> 26) : error C2923: 'std::vector' :
> 'RDKit::`anonymous-namespace'::uint32_t' is n
> ot a valid template type argument for parameter '_Ty'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprin
> ts.cpp(116) : see declaration of 'RDKit::`anonymous-namespace'::uint32_t'
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(4
> 64) : warning C4267: 'argument' : conversion from 'size_t' to 'const
> RDKit::UINT
> ', possible loss of data
>
> C:\build\x64\rdkit\RDKit_2013_09_2\Code\GraphMol\Fingerprints\Fingerprints.cpp(8
> 35) : warning C4267: 'argument' : conversion from 'size_t' to 'const
> RDKit::UINT
> ', possible loss of data
> NMAKE : fatal error U1077: 'C:\PROGRA~2\MICROS~1.0\VC\bin\amd64\cl.exe' :
> return
>
> code '0x2'
> Stop.
> NMAKE : fatal error U1077: '"C:\Program Files (x86)\Microsoft Visual
> Studio 9.0\
> VC\Bin\amd64\nmake.exe"' : return code '0x2'
> Stop.
> NMAKE : fatal error U1077: '"C:\Program Files (x86)\Microsoft Visual
> Studio 9.0\
> VC\Bin\amd64\nmake.exe"' : return code '0x2'
> Stop.
>
> Any ideas here?
>
> Thanks,
> Michael Mysinger
>
>
>
> On Wednesday, February 5, 2014 12:53 PM, Michael Mysinger <
> [email protected]> wrote:
>
> Hello Greg,
>
> I have the smarts.tab.cpp.cmake and lex.yysmarts.cpp.cmake not the
> versions with the cmake extension.
>
> What is the exact bison command it is trying to run, so I can test it
> indepentantly?
>
> I also again tried to build without using the nmake target, like so:
> > cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=""
> -DCMAKE_MAKE_PROGRAM="nmake" -DBOOST_ROOT=c:/boost -G"Visual Studio 9 2008
> Win64" ..
>
> But configure fails with a long string of errors like:
>
> -- The C compiler identification is unknown
> -- The CXX compiler identification is unknown
> -- Check if the system is big endian
> -- Searching 16 bit integer
> -- Looking for sys/types.h
> CMake Error at C:/Program Files (x86)/CMake
> 2.8/share/cmake-2.8/Modules/CMakeCIn
> formation.cmake:37 (get_filename_component):
> get_filename_component called with incorrect number of arguments
> Call Stack (most recent call first):
> CMakeLists.txt:3 (PROJECT)
>
> Looking around, the get_filename_component seems to be a common but
> correctable error when still targeting VS Express/SDK 2008. This is likely
> a fixable bug.
>
> Thanks,
> Michael
>
>
> On Monday, February 3, 2014 8:46 PM, Greg Landrum <
> [email protected]> wrote:
> Minor correction:
>
> On Tue, Feb 4, 2014 at 5:38 AM, Greg Landrum <[email protected]>wrote:.
>
>
> Can you please confirm that in $RDBASE/Code/GraphMol/SmilesParse you have
> the files:
> lex.yysmarts.cpp.cmake and, hopefully, lex.yysmarts.cpp?
>
>
> Those files should also be there, but the ones that are relevant here are
> smarts.tab.cpp.cmake and smarts.tab.cpp
>
> Best,
> -greg
>
>
>
>
> ------------------------------------------------------------------------------
> Managing the Performance of Cloud-Based Applications
> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
> Read the Whitepaper.
>
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>
>
>
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Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
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