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 <gia...@gmail.com> 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 <greg.land...@gmail.com>
> wrote:
> > Hi Gianluca,
> >
> > On Tue, Apr 12, 2016 at 1:09 PM, Gianluca Sforna <gia...@gmail.com>
> 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
>
------------------------------------------------------------------------------
Find and fix application performance issues faster with Applications Manager
Applications Manager provides deep performance insights into multiple tiers of
your business applications. It resolves application problems quickly and
reduces your MTTR. Get your free trial!
https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
_______________________________________________
Rdkit-devel mailing list
Rdkit-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-devel
