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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Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
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