Re: [Rdkit-discuss] minGW fails to build rdkit

2016-12-21 Thread Yingfeng Wang 
Paolo,

Could you please let me know the version of your minGW and how you got or
built boost with minGW. I kept getting errors like "duplicate section" with
different size.

Thanks.

Yingfeng

On Tue, Dec 20, 2016 at 10:13 AM, Yingfeng Wang  wrote:

> Paolo,
>
> Thanks. I figure out this problem. The new cmake command is
>
> cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
> -DMSVC_RUNTIME_DLL=C:/Windows/System32/msvcr100.dll
> -DRDK_USE_BOOST_SERIALIZATION=OFF -DBOOST_ROOT=C:/boost
> -DCMAKE_INSTALL_PREFIX=C:/software/RDKit/install_2016_09_2
> -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_PYTHON_WRAPPERS=OFF -G "MinGW
> Makefiles" ..
>
> In comparison of the old command, I removed "" and replaced "\" by "/".
> The same error does not happen. Then I got a new error, "duplicate section"
> with different size when link to my boost library. I searched internet, and
> it looks this is a compiling problem when I build boost using minGW. I will
> update on you if I get some progress.
>
> Again, thank you very much for your help!
>
> Yingfeng
>
> On Tue, Dec 20, 2016 at 5:13 AM, Paolo Tosco  wrote:
>
>> Dear Yingfeng,
>>
>> I can build the latest RDKIt trunk from a MSYS2 shell using the following
>> cmake command:
>>
>> cmake -DEIGEN3_INCLUDE_DIR=/c/build/include/eigen3
>> -DBOOST_LIBRARYDIR=/mingw64/bin -DBOOST_ROOT=/mingw64
>> -DPYTHON_NUMPY_INCLUDE_PATH=/mingw64/include/python2.7
>> -DRDK_USE_BOOST_SERIALIZATION=OFF -G"MSYS Makefiles" ..
>>
>> I had to switch serialization off to avoid a bunch of errors while
>> building FilterCatalog; so far I haven't had time to investigate this
>> further.
>>
>> You should be able to succeed also from a CMD shell using
>> mingw32-make.exe.
>>
>> Make sure you start from a clean build directory before issuing the cmake
>> command.
>>
>> Cheers,
>> p.
>>
>>
>> On 12/20/16 04:47, Yingfeng Wang wrote:
>>
>> I try to use minGW to build rdkit_2016_09_2, which is from the following
>> link.
>>
>> https://github.com/rdkit/rdkit/archive/Release_2016_09_2.zip
>>
>> cmake command is
>>
>> cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
>> -DMSVC_RUNTIME_DLL="C:\Windows\System32\msvcr100.dll"
>>  -DBOOST_ROOT="C:\boost" 
>> -DCMAKE_INSTALL_PREFIX=C:\software\RDKit\install_2016_09_2
>> -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_PYTHON_WRAPPERS=OFF -G "MinGW
>> Makefiles" ..
>>
>> Error happens when running mingw32-make
>> Error message is given as follows.
>>
>> Scanning dependencies of target RDGeneral
>> [ 12%] Building CXX object Code/RDGeneral/CMakeFiles/RDGe
>> neral.dir/Invariant.cpp.obj
>> 'ccache' is not recognized as an internal or external command,
>> operable program or batch file.
>> Code\RDGeneral\CMakeFiles\RDGeneral.dir\build.make:62: recipe for target
>> 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.obj' failed
>> mingw32-make[2]: *** 
>> [Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.obj]
>> Error 1
>> CMakeFiles\Makefile2:494: recipe for target 
>> 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/all'
>> failed
>> mingw32-make[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error
>> 2
>> Makefile:159: recipe for target 'all' failed
>> mingw32-make: *** [all] Error 2
>>
>> By the way, the information of compiler is given in the following.
>>
>> C:\software\RDKit\rdkit-Release_2016_09_2\build>g++ -v
>> Reading specs from c:/mingw_win_build/bin/../lib/
>> gcc/i686-w64-mingw32/4.8.3/specs
>> COLLECT_GCC=g++
>> COLLECT_LTO_WRAPPER=c:/mingw_win_build/bin/../libexec/gcc/i6
>> 86-w64-mingw32/4.8.3
>> /lto-wrapper.exe
>> Target: i686-w64-mingw32
>> Configured with: ../gcc-4.8.3/configure --prefix=/opt/windows_32
>> --with-sysroot=/opt/windows_32 --libdir=/opt/windows_32/lib
>> --mandir=/opt/windows_32/man --infodir=/opt/windows_32/info --enable-shared
>> --disable-bootstrap --disable-multilib--with-arch=pentium3
>> --enable-threads=posix --enable-languages=c,c++ --enable-checking=release
>> --enable-libgomp --with-system-zlib 
>> --with-python-dir=/lib/python2.7/site-packages
>> --disable-libunwind-exceptions --enable-__cxa_atexit --enable-libssp
>> --with-gnu-ld --verbose --enable-java-home 
>> --with-java-home=/opt/windows_32/lib/jvm/jre
>> --with-jvm-root-dir=/opt/windows_32/lib/jvm
>> --with-jvm-jar-dir=/opt/windows_32/lib/jvm/jvm-exports
>> --with-arch-directory=amd64 --with-antlr-jar='/home/adrien
>> /projects/win-builds-1.5/slackware64-current/d/gcc/antlr-*.jar'
>> --disable-java-awt --disable-gtktest --build=x86_64-slackware-linux
>> --host=i686-w64-mingw32 --target=i686-w64-mingw32
>> Thread model: posix
>> gcc version 4.8.3 (GCC)
>>
>> Could you please give me any hints?
>>
>> Thank you very much in advance!
>>
>> Yingfeng
>>
>>
>> --
>> Developer Access Program for Intel Xeon Phi Processors
>> Access to Intel Xeon Phi processor-based developer platforms.
>> With one year of Intel Parallel Studio XE.
>> Training and support from

Re: [Rdkit-discuss] minGW fails to build rdkit

2016-12-20 Thread Paul Emsley 
On 20/12/16 15:13, Yingfeng Wang wrote:
> Paolo,
>
> Thanks. I figure out this problem. The new cmake command is
>
> cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ 
> -DMSVC_RUNTIME_DLL=C:/Windows/System32/msvcr100.dll 
> -DRDK_USE_BOOST_SERIALIZATION=OFF -DBOOST_ROOT=C:/boost 
> -DCMAKE_INSTALL_PREFIX=C:/software/RDKit/install_2016_09_2 
> -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_PYTHON_WRAPPERS=OFF -G "MinGW 
> Makefiles" ..
>
> In comparison of the old command, I removed "" and replaced "\" by 
> "/". The same error does not happen. Then I got a new error, 
> "duplicate section" with different size when link to my boost library. 
> I searched internet, and it looks this is a compiling problem when I 
> build boost using minGW. I will update on you if I get some progress.
>
>

I would try disabling ccache.

Paul.



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Re: [Rdkit-discuss] minGW fails to build rdkit

2016-12-20 Thread Yingfeng Wang 
Paolo,

Thanks. I figure out this problem. The new cmake command is

cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
-DMSVC_RUNTIME_DLL=C:/Windows/System32/msvcr100.dll
-DRDK_USE_BOOST_SERIALIZATION=OFF -DBOOST_ROOT=C:/boost
-DCMAKE_INSTALL_PREFIX=C:/software/RDKit/install_2016_09_2
-DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_PYTHON_WRAPPERS=OFF -G "MinGW
Makefiles" ..

In comparison of the old command, I removed "" and replaced "\" by "/". The
same error does not happen. Then I got a new error, "duplicate section"
with different size when link to my boost library. I searched internet, and
it looks this is a compiling problem when I build boost using minGW. I will
update on you if I get some progress.

Again, thank you very much for your help!

Yingfeng

On Tue, Dec 20, 2016 at 5:13 AM, Paolo Tosco  wrote:

> Dear Yingfeng,
>
> I can build the latest RDKIt trunk from a MSYS2 shell using the following
> cmake command:
>
> cmake -DEIGEN3_INCLUDE_DIR=/c/build/include/eigen3
> -DBOOST_LIBRARYDIR=/mingw64/bin -DBOOST_ROOT=/mingw64
> -DPYTHON_NUMPY_INCLUDE_PATH=/mingw64/include/python2.7
> -DRDK_USE_BOOST_SERIALIZATION=OFF -G"MSYS Makefiles" ..
>
> I had to switch serialization off to avoid a bunch of errors while
> building FilterCatalog; so far I haven't had time to investigate this
> further.
>
> You should be able to succeed also from a CMD shell using mingw32-make.exe.
>
> Make sure you start from a clean build directory before issuing the cmake
> command.
>
> Cheers,
> p.
>
>
> On 12/20/16 04:47, Yingfeng Wang wrote:
>
> I try to use minGW to build rdkit_2016_09_2, which is from the following
> link.
>
> https://github.com/rdkit/rdkit/archive/Release_2016_09_2.zip
>
> cmake command is
>
> cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
> -DMSVC_RUNTIME_DLL="C:\Windows\System32\msvcr100.dll"
>  -DBOOST_ROOT="C:\boost" -DCMAKE_INSTALL_PREFIX=C:\
> software\RDKit\install_2016_09_2 -DRDK_BUILD_INCHI_SUPPORT=ON
> -DRDK_BUILD_PYTHON_WRAPPERS=OFF -G "MinGW Makefiles" ..
>
> Error happens when running mingw32-make
> Error message is given as follows.
>
> Scanning dependencies of target RDGeneral
> [ 12%] Building CXX object Code/RDGeneral/CMakeFiles/
> RDGeneral.dir/Invariant.cpp.obj
> 'ccache' is not recognized as an internal or external command,
> operable program or batch file.
> Code\RDGeneral\CMakeFiles\RDGeneral.dir\build.make:62: recipe for target
> 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.obj' failed
> mingw32-make[2]: *** [Code/RDGeneral/CMakeFiles/
> RDGeneral.dir/Invariant.cpp.obj] Error 1
> CMakeFiles\Makefile2:494: recipe for target 
> 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/all'
> failed
> mingw32-make[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error 2
> Makefile:159: recipe for target 'all' failed
> mingw32-make: *** [all] Error 2
>
> By the way, the information of compiler is given in the following.
>
> C:\software\RDKit\rdkit-Release_2016_09_2\build>g++ -v
> Reading specs from c:/mingw_win_build/bin/../lib/
> gcc/i686-w64-mingw32/4.8.3/specs
> COLLECT_GCC=g++
> COLLECT_LTO_WRAPPER=c:/mingw_win_build/bin/../libexec/gcc/
> i686-w64-mingw32/4.8.3
> /lto-wrapper.exe
> Target: i686-w64-mingw32
> Configured with: ../gcc-4.8.3/configure --prefix=/opt/windows_32
> --with-sysroot=/opt/windows_32 --libdir=/opt/windows_32/lib
> --mandir=/opt/windows_32/man --infodir=/opt/windows_32/info --enable-shared
> --disable-bootstrap --disable-multilib--with-arch=pentium3
> --enable-threads=posix --enable-languages=c,c++ --enable-checking=release
> --enable-libgomp --with-system-zlib 
> --with-python-dir=/lib/python2.7/site-packages
> --disable-libunwind-exceptions --enable-__cxa_atexit --enable-libssp
> --with-gnu-ld --verbose --enable-java-home 
> --with-java-home=/opt/windows_32/lib/jvm/jre
> --with-jvm-root-dir=/opt/windows_32/lib/jvm 
> --with-jvm-jar-dir=/opt/windows_32/lib/jvm/jvm-exports
> --with-arch-directory=amd64 --with-antlr-jar='/home/
> adrien/projects/win-builds-1.5/slackware64-current/d/gcc/antlr-*.jar'
> --disable-java-awt --disable-gtktest --build=x86_64-slackware-linux
> --host=i686-w64-mingw32 --target=i686-w64-mingw32
> Thread model: posix
> gcc version 4.8.3 (GCC)
>
> Could you please give me any hints?
>
> Thank you very much in advance!
>
> Yingfeng
>
>
> --
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today.http://sdm.link/intel
>
>
>
> ___
> Rdkit-discuss mailing 
> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based

Re: [Rdkit-discuss] minGW fails to build rdkit

2016-12-20 Thread Paolo Tosco 

Dear Yingfeng,

I can build the latest RDKIt trunk from a MSYS2 shell using the 
following cmake command:


cmake -DEIGEN3_INCLUDE_DIR=/c/build/include/eigen3 
-DBOOST_LIBRARYDIR=/mingw64/bin -DBOOST_ROOT=/mingw64 
-DPYTHON_NUMPY_INCLUDE_PATH=/mingw64/include/python2.7 
-DRDK_USE_BOOST_SERIALIZATION=OFF -G"MSYS Makefiles" ..


I had to switch serialization off to avoid a bunch of errors while 
building FilterCatalog; so far I haven't had time to investigate this 
further.


You should be able to succeed also from a CMD shell using mingw32-make.exe.

Make sure you start from a clean build directory before issuing the 
cmake command.


Cheers,
p.

On 12/20/16 04:47, Yingfeng Wang wrote:
I try to use minGW to build rdkit_2016_09_2, which is from the 
following link.


https://github.com/rdkit/rdkit/archive/Release_2016_09_2.zip

cmake command is

cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ 
-DMSVC_RUNTIME_DLL="C:\Windows\System32\msvcr100.dll" 
 -DBOOST_ROOT="C:\boost" 
-DCMAKE_INSTALL_PREFIX=C:\software\RDKit\install_2016_09_2 
-DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_PYTHON_WRAPPERS=OFF -G "MinGW 
Makefiles" ..


Error happens when running mingw32-make
Error message is given as follows.

Scanning dependencies of target RDGeneral
[ 12%] Building CXX object 
Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.obj

'ccache' is not recognized as an internal or external command,
operable program or batch file.
Code\RDGeneral\CMakeFiles\RDGeneral.dir\build.make:62: recipe for 
target 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.obj' failed
mingw32-make[2]: *** 
[Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.obj] Error 1
CMakeFiles\Makefile2:494: recipe for target 
'Code/RDGeneral/CMakeFiles/RDGeneral.dir/all' failed

mingw32-make[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error 2
Makefile:159: recipe for target 'all' failed
mingw32-make: *** [all] Error 2

By the way, the information of compiler is given in the following.

C:\software\RDKit\rdkit-Release_2016_09_2\build>g++ -v
Reading specs from 
c:/mingw_win_build/bin/../lib/gcc/i686-w64-mingw32/4.8.3/specs

COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=c:/mingw_win_build/bin/../libexec/gcc/i686-w64-mingw32/4.8.3
/lto-wrapper.exe
Target: i686-w64-mingw32
Configured with: ../gcc-4.8.3/configure --prefix=/opt/windows_32 
--with-sysroot=/opt/windows_32 --libdir=/opt/windows_32/lib 
--mandir=/opt/windows_32/man --infodir=/opt/windows_32/info 
--enable-shared --disable-bootstrap 
--disable-multilib--with-arch=pentium3 --enable-threads=posix 
--enable-languages=c,c++ --enable-checking=release --enable-libgomp 
--with-system-zlib --with-python-dir=/lib/python2.7/site-packages 
--disable-libunwind-exceptions --enable-__cxa_atexit --enable-libssp 
--with-gnu-ld --verbose --enable-java-home 
--with-java-home=/opt/windows_32/lib/jvm/jre 
--with-jvm-root-dir=/opt/windows_32/lib/jvm 
--with-jvm-jar-dir=/opt/windows_32/lib/jvm/jvm-exports 
--with-arch-directory=amd64 
--with-antlr-jar='/home/adrien/projects/win-builds-1.5/slackware64-current/d/gcc/antlr-*.jar' 
--disable-java-awt --disable-gtktest --build=x86_64-slackware-linux 
--host=i686-w64-mingw32 --target=i686-w64-mingw32

Thread model: posix
gcc version 4.8.3 (GCC)

Could you please give me any hints?

Thank you very much in advance!

Yingfeng


--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today.http://sdm.link/intel


___
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Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
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[Rdkit-discuss] minGW fails to build rdkit

2016-12-19 Thread Yingfeng Wang 
I try to use minGW to build rdkit_2016_09_2, which is from the following
link.

https://github.com/rdkit/rdkit/archive/Release_2016_09_2.zip

cmake command is

cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++
-DMSVC_RUNTIME_DLL="C:\Windows\System32\msvcr100.dll"
 -DBOOST_ROOT="C:\boost"
-DCMAKE_INSTALL_PREFIX=C:\software\RDKit\install_2016_09_2
-DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_PYTHON_WRAPPERS=OFF -G "MinGW
Makefiles" ..

Error happens when running mingw32-make
Error message is given as follows.

Scanning dependencies of target RDGeneral
[ 12%] Building CXX object
Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.obj
'ccache' is not recognized as an internal or external command,
operable program or batch file.
Code\RDGeneral\CMakeFiles\RDGeneral.dir\build.make:62: recipe for target
'Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.obj' failed
mingw32-make[2]: ***
[Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.obj] Error 1
CMakeFiles\Makefile2:494: recipe for target
'Code/RDGeneral/CMakeFiles/RDGeneral.dir/all' failed
mingw32-make[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error 2
Makefile:159: recipe for target 'all' failed
mingw32-make: *** [all] Error 2

By the way, the information of compiler is given in the following.

C:\software\RDKit\rdkit-Release_2016_09_2\build>g++ -v
Reading specs from
c:/mingw_win_build/bin/../lib/gcc/i686-w64-mingw32/4.8.3/specs
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=c:/mingw_win_build/bin/../libexec/gcc/i686-w64-mingw32/4.8.3
/lto-wrapper.exe
Target: i686-w64-mingw32
Configured with: ../gcc-4.8.3/configure --prefix=/opt/windows_32
--with-sysroot=/opt/windows_32 --libdir=/opt/windows_32/lib
--mandir=/opt/windows_32/man --infodir=/opt/windows_32/info --enable-shared
--disable-bootstrap --disable-multilib--with-arch=pentium3
--enable-threads=posix --enable-languages=c,c++ --enable-checking=release
--enable-libgomp --with-system-zlib
--with-python-dir=/lib/python2.7/site-packages
--disable-libunwind-exceptions --enable-__cxa_atexit --enable-libssp
--with-gnu-ld --verbose --enable-java-home
--with-java-home=/opt/windows_32/lib/jvm/jre
--with-jvm-root-dir=/opt/windows_32/lib/jvm
--with-jvm-jar-dir=/opt/windows_32/lib/jvm/jvm-exports
--with-arch-directory=amd64
--with-antlr-jar='/home/adrien/projects/win-builds-1.5/slackware64-current/d/gcc/antlr-*.jar'
--disable-java-awt --disable-gtktest --build=x86_64-slackware-linux
--host=i686-w64-mingw32 --target=i686-w64-mingw32
Thread model: posix
gcc version 4.8.3 (GCC)

Could you please give me any hints?

Thank you very much in advance!

Yingfeng
--
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today.http://sdm.link/intel___
Rdkit-discuss mailing list
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