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

2016-04-13 Thread Greg Landrum 
On Wed, Apr 13, 2016 at 8:43 PM, Gianluca Sforna  wrote:

> On Wed, Apr 13, 2016 at 12:27 PM, Greg Landrum 
> wrote:
> > Wow, that's a "typing in the wrong buffer" bug.
> > Great catch.
>
> :)
>
> Another couple points.
> I noticed the RDKit_Overview.pdf file is not there anymore. Was it
> integrated in the main manual, moved somewhere else or just removed?
>

The information in the pdf and the odb source for it were pretty out of
date, they've been removed. Docs/Book/Overview.md and the other contents of
the Docs/Book directory are a better information source.


> Regarding PostgreSQL cartridge, I expected the build to fail since I
> knew it was ported to cmake; instead, the older recipe just worked, I
> don't know if this is intended or not.
>

I didn't see a reason to immediately remove the old cartridge build make
system and break things for people who are used to using it. It will be
deprecated and removed in a future release.


> Finally, Docs were not building anymore, it seems some stray char was
> left in a file, so I needed to apply this:
>

Fixed.

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

2016-04-13 Thread Gianluca Sforna 
On Wed, Apr 13, 2016 at 12:27 PM, Greg Landrum  wrote:
> Wow, that's a "typing in the wrong buffer" bug.
> Great catch.

:)

Another couple points.
I noticed the RDKit_Overview.pdf file is not there anymore. Was it
integrated in the main manual, moved somewhere else or just removed?

Regarding PostgreSQL cartridge, I expected the build to fail since I
knew it was ported to cmake; instead, the older recipe just worked, I
don't know if this is intended or not.

Finally, Docs were not building anymore, it seems some stray char was
left in a file, so I needed to apply this:

diff --git a/Docs/Book/Install.md b/Docs/Book/Install.md
index cd660cb..9c838f4 100644
--- a/Docs/Book/Install.md
+++ b/Docs/Book/Install.md
@@ -388,4 +388,4 @@ This document is copyright (C) 2012-2015 by Greg Landrum

 This work is licensed under the Creative Commons
Attribution-ShareAlike 3.0 License. To view a copy of this license,
visit  or send a
letter to Creative Commons, 543 Howard Street, 5th Floor, San
Francisco, California, 94105, USA.

-The intent of this license is similar to that of the RDKit itself. In
simple words: "Do whatever you want with it, but please give us some
credit."<9D>
+The intent of this license is similar to that of the RDKit itself. In
simple words: "Do whatever you want with it, but please give us some
credit."


Regards

G.



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

2016-04-13 Thread Greg Landrum 
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  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 
> wrote:
> > Hi Gianluca,
> >
> > On Tue, Apr 12, 2016 at 1:09 PM, Gianluca Sforna 
> 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
>
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Re: [Rdkit-devel] Beta of Q1 2016 release now up

2016-04-13 Thread Gianluca Sforna 
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  wrote:
> Hi Gianluca,
>
> On Tue, Apr 12, 2016 at 1:09 PM, Gianluca Sforna  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
>



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

2016-04-13 Thread Greg Landrum 
Hi Gianluca,

On Tue, Apr 12, 2016 at 1:09 PM, Gianluca Sforna  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
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Re: [Rdkit-devel] Beta of Q1 2016 release now up

2016-04-12 Thread Gianluca Sforna 
On Tue, Apr 12, 2016 at 11:51 AM, Gianluca Sforna  wrote:
> On Mon, Apr 11, 2016 at 1:20 PM, Greg Landrum  wrote:
>> This could be the issue fixed by this PR from Matt Swain:
>> https://github.com/rdkit/rdkit/pull/856
>
> Yeah, that's it. Thanks!

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  );




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

2016-04-12 Thread Gianluca Sforna 
On Mon, Apr 11, 2016 at 1:20 PM, Greg Landrum  wrote:
> This could be the issue fixed by this PR from Matt Swain:
> https://github.com/rdkit/rdkit/pull/856

Yeah, that's it. Thanks!



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

2016-04-11 Thread Greg Landrum 
Gianluca,

This could be the issue fixed by this PR from Matt Swain:
https://github.com/rdkit/rdkit/pull/856

-greg


On Mon, Apr 11, 2016 at 12:32 PM, Gianluca Sforna  wrote:

> On Thu, Apr 7, 2016 at 6:24 AM, Greg Landrum 
> wrote:
> > I have tagged a beta of the next RDKit release here:
> > https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_1b1
>
>
> Tried to rebuild the RPMs but got this right on cmake:
>
> -- Found INCHI: /usr/lib64/libinchi.so
> CMake Error at External/INCHI-API/CMakeLists.txt:64 (install):
>   install TARGETS given target "Inchi" which does not exist in this
>   directory.
>
>
> cmake invocation as follow:
>
> /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG
> -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG
> -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG
> -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr
> -DINCLUDE_INSTALL_DIR:PATH=/usr/include
> -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc
> -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64
> -DBUILD_SHARED_LIBS:BOOL=ON -D RDK_INSTALL_INTREE=OFF -D
> CMAKE_BUILD_TYPE=RelWithDebInfo -D RDK_BUILD_INCHI_SUPPORT:BOOL=ON -D
> RDK_BUILD_THREADSAFE_SSS:BOOL=ON -D RDK_BUILD_CAIRO_SUPPORT:BOOL=ON -D
> RDK_INSTALL_STATIC_LIBS:BOOL=OFF -D RDK_USE_FLEXBISON:BOOL=ON -D
> RDK_TEST_MULTITHREADED:BOOL=ON -D
> PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2 .
>
> I'll dig in it later, in the meanwhile if you have ideas they will be
> very welcome.
>
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Re: [Rdkit-devel] Beta of Q1 2016 release now up

2016-04-11 Thread Gianluca Sforna 
On Thu, Apr 7, 2016 at 6:24 AM, Greg Landrum  wrote:
> I have tagged a beta of the next RDKit release here:
> https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_1b1


Tried to rebuild the RPMs but got this right on cmake:

-- Found INCHI: /usr/lib64/libinchi.so
CMake Error at External/INCHI-API/CMakeLists.txt:64 (install):
  install TARGETS given target "Inchi" which does not exist in this
  directory.


cmake invocation as follow:

/usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG
-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr
-DINCLUDE_INSTALL_DIR:PATH=/usr/include
-DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc
-DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64
-DBUILD_SHARED_LIBS:BOOL=ON -D RDK_INSTALL_INTREE=OFF -D
CMAKE_BUILD_TYPE=RelWithDebInfo -D RDK_BUILD_INCHI_SUPPORT:BOOL=ON -D
RDK_BUILD_THREADSAFE_SSS:BOOL=ON -D RDK_BUILD_CAIRO_SUPPORT:BOOL=ON -D
RDK_INSTALL_STATIC_LIBS:BOOL=OFF -D RDK_USE_FLEXBISON:BOOL=ON -D
RDK_TEST_MULTITHREADED:BOOL=ON -D
PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python2 .

I'll dig in it later, in the meanwhile if you have ideas they will be
very welcome.

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