Hello Greg,
Thanks for the swift reply. I got sidelined by the flu, but I did finally get
RDKit to compile and install with VS 2008 SDK. Still testing it fully now.
For the record, I'm not sure if I put the "using boost" line you suggested in
the right spot. But when I put it just after the includes, I also had to
include the same line in $RDBASE/Code/GraphMol/Fingerprints/test1.cpp.
Thanks again for your swift help,
Michael
On Wednesday, February 5, 2014 7:58 PM, Greg Landrum <[email protected]>
wrote:
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
>
>
>
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