Re: [Rdkit-devel] Beta of Q1 2016 release now up

[Gianluca S. <gi...@gm...>]

I bisected with git the issue, it popped up after commit b76d1a9 last december.

I know almost nothing about flex & bison, but I noticed a suspicious
change in the diff, and indeed the following patch fixes the build:

 diff --git a/Code/GraphMol/SmilesParse/smiles.ll
b/Code/GraphMol/SmilesParse/smiles.ll
index 3a2346e..1f1cd27 100644
--- a/Code/GraphMol/SmilesParse/smiles.ll
+++ b/Code/GraphMol/SmilesParse/smiles.ll
@@ -1,4 +1,4 @@
-%setpropoption reentrant
+%option reentrant
 %option bison-bridge
 %option noyywrap

Was it correct?



On Wed, Apr 13, 2016 at 10:44 AM, Greg Landrum <gre...@gm...> wrote:
> Hi Gianluca,
>
> On Tue, Apr 12, 2016 at 1:09 PM, Gianluca Sforna <gi...@gm...> wrote:
>>
>>
>> But no joy still....
>>
>>
>> [ 36%] Building CXX object
>> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o
>> cd
>> /builddir/build/BUILD/rdkit-Release_2016_03_1b1/python2/Code/GraphMol/SmilesParse
>> && /usr/bin/c++   -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHR
>> EADED -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS
>> -I/usr/include/python2.7
>> -I/builddir/build/BUILD/rdkit-Release_2016_03_1b1/pyt
>> hon2/Code  -O2 -g -pipe -Wall -Werror=format-security
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong
>> --param=ssp-buffer-size=
>> 4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1
>> -m64 -mtune=generic  -mpopcnt -Wno-deprecated -Wno-unused-function -f
>> no-strict-aliasing -fPIC -Wall -Wextra -O2 -g -DNDEBUG -fPIC
>> -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o
>> CMakeFiles/SmilesParse.dir/lex.yys
>> marts.cpp.o -c
>> /builddir/build/BUILD/rdkit-Release_2016_03_1b1/python2/Code/GraphMol/SmilesParse/lex.yysmarts.cpp
>> smiles.ll:40:52: error: 'yyscan_t' has not been declared
>>  size_t setup_smiles_string(const std::string &text,yyscan_t yyscanner){
>>                                                     ^
>> smiles.ll: In function 'size_t setup_smiles_string(const string&, int)':
>> smiles.ll:49:46: error: too many arguments to function 'void*
>> yysmiles_alloc(yy_size_t)'
>>    buf = (char *) yysmiles_alloc(n ,yyscanner );
>>                                               ^
>>
>> /builddir/build/BUILD/rdkit-Release_2016_03_1b1/python2/Code/GraphMol/SmilesParse/lex.yysmiles.cpp:326:7:
>> note: declared here
>>  void *yysmiles_alloc (yy_size_t  );
>>        ^
>> smiles.ll:69:45: error: too many arguments to function
>> 'yy_buffer_state* yysmiles__scan_buffer(char*, yy_size_t)'
>>    b = yysmiles__scan_buffer(buf,n ,yyscanner);
>>                                              ^
>>
>> /builddir/build/BUILD/rdkit-Release_2016_03_1b1/python2/Code/GraphMol/SmilesParse/lex.yysmiles.cpp:322:17:
>> note: declared here
>>  YY_BUFFER_STATE yysmiles__scan_buffer (char *base,yy_size_t size  );
>
>
>
> Something odd is going on with the output of flex. The easiest way to "fix"
> this is just to avoid the problem by not running flex/bison yourself.
>
> If that would be ok, you can just change the cmake command line argment
> -D RDK_USE_FLEXBISON:BOOL=ON
> to
> -D RDK_USE_FLEXBISON:BOOL=OFF
>
> -greg
>



-- 
Gianluca Sforna

http://plus.google.com/+gianlucasforna - http://twitter.com/giallu
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