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

[Greg L. <gre...@gm...>]

Wow, that's a "typing in the wrong buffer" bug.
Great catch.

I will check in the fix in the next couple of minutes.

On Wed, Apr 13, 2016 at 12:09 PM, Gianluca Sforna <gi...@gm...> wrote:

> 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
> Tinker Garage - http://tinkergarage.it
>