Hi
Thanks a lot Nikolas I have been following that tutorial for installation.
Abhik Seal
Indiana University Bloomington
Department of Chemical Informatics
[email protected]
*OSDD CHEMINFORMATICS*
+18123699097
http://mypage.iu.edu/~abseal/index.htm
On Thu, Jul 18, 2013 at 3:14 PM, Nikolas Fechner <[email protected]> wrote:
> Hi Abhik,
> since OSX Lion postgresql is apparently integrated within the OS. Browsing
> around this it seems that this integration is causing a lot of trouble. I
> was able to complete the "make" and "make install" steps for the rdkit
> cartridge by simply creating an alias
> for the missing /usr/bin/postgres to use the OSX
> integrated /usr/bin/postgres_real instead. However, being no postgres user
> myself, I did not manage to get the "make installcheck" working and it
> seems that the cartridge has been build and the problem is on the postgres
> side.
>
> There is a step-by-step tutorial for an earlier OSX version on
> http://silicos-it.com/cookbook/configuring_osx_for_chemoinformatics/configuring_osx_for_chemoinformatics.html#postgresql
> -
> maybe that works for you.
> I am on 10.8.4 and it seems that there subtle differences between the OSX
> versions with respect to postgres.
>
> Sorry for not being of more help,
> Nikolas
>
> On Jul 18, 2013, at 12:56 AM, Abhik Seal <[email protected]> wrote:
>
> Hi Nikolas,
>
> Now i am running into this error
>
> abhikseal/usr/local/Cellar/RDKit_2013_03_2/Code/PgSQL/rdkit$make
> c++ -arch x86_64 -pipe -Os -g -Wall -Wno-deprecated-declarations -Wall
> -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement
> -Wendif-labels -Wformat-security -fno-strict-aliasing -fwrapv -bundle
> -multiply_defined suppress -o rdkit.so rdkit_io.o mol_op.o bfp_op.o
> sfp_op.o rdkit_gist.o low_gist.o guc.o cache.o adapter.o -L/usr/lib -arch
> x86_64 -pipe -Os -g -Wall -Wno-deprecated-declarations
> -Wl,-dead_strip_dylibs -L/usr/local/Cellar/RDKit_2013_03_2/lib
> -Wl,-rpath,'/usr/local/Cellar/RDKit_2013_03_2/lib' -lChemTransforms
> -lFileParsers -lSmilesParse -lFingerprints -lSubgraphs -lSubstructMatch
> -lDescriptors -lPartialCharges -lGraphMol -lDataStructs -lRDGeometryLib
> -lRDGeneral -pthread -bundle_loader /usr/bin/postgres
> clang: warning: argument unused during compilation: '-pthread'
> ld: file not found: /usr/bin/postgres
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> make: *** [rdkit.so] Error 1
>
>
>
>
>
>
> Abhik Seal
> Indiana University Bloomington
> Department of Chemical Informatics
> [email protected]
> *OSDD CHEMINFORMATICS*
> +18123699097
> http://mypage.iu.edu/~abseal/index.htm
>
>
> On Wed, Jul 17, 2013 at 2:25 AM, Nikolas Fechner <[email protected]>wrote:
>
>> **
>> Dear Abhik,
>> the error you see is probably related to Apple changing the path names
>> for mountain lion. At several places a simple workaround is suggested (e.g.
>> http://code.google.com/p/modwsgi/issues/detail?id=298), which is to
>> create a symbolic link to use the default xctoolchain instead.
>>
>> sudo ln -s
>> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/
>> /Applications/Xcode.app/Contents/Developer/Toolchains/OSX10.8.xctoolchain
>>
>> Maybe that helps.
>>
>>
>> Kind regards,
>>
>> Nikolas
>>
>> On July 17, 2013 at 1:33 AM Abhik Seal <[email protected]> wrote:
>> Hi All,
>>
>> I have installed Rdkit using homebrew and after installing it i was
>> trying to install the Postgresql cartridge in Mac and now it is throwing an
>> unique error related to Xcode tools . Is any libraries missing.
>>
>> usr/local/Cellar/RDKit_2013_03_2/Code/PgSQL/rdkit$make
>>
>>
>> /Applications/Xcode.app/Contents/Developer/Toolchains/OSX10.8.xctoolchain/usr/bin/cc
>> -I/usr/local/Cellar/boost/1.53.0/ -I/usr/local/Cellar/RDKit_2013_03_2/Code
>> -DRDKITVER='"007000"' -I. -I. -I/usr/include/postgresql/server
>> -I/usr/include/postgresql/internal -I/usr/include/libxml2 -fPIC -c -o
>> rdkit_io.o rdkit_io.c
>> make:
>> /Applications/Xcode.app/Contents/Developer/Toolchains/OSX10.8.xctoolchain/usr/bin/cc:
>> No such file or directory
>> make: *** [rdkit_io.o] Error 1
>>
>> Any help on this ?
>>
>>
>>
>> Abhik Seal
>> Indiana University Bloomington
>> Department of Chemical Informatics
>> [email protected]
>> *OSDD CHEMINFORMATICS*
>> +18123699097
>> http://mypage.iu.edu/~abseal/index.htm
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> See everything from the browser to the database with AppDynamics
>> Get end-to-end visibility with application monitoring from AppDynamics
>> Isolate bottlenecks and diagnose root cause in seconds.
>> Start your free trial of AppDynamics Pro today!
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Rdkit-discuss mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
> ------------------------------------------------------------------------------
> See everything from the browser to the database with AppDynamics
> Get end-to-end visibility with application monitoring from AppDynamics
> Isolate bottlenecks and diagnose root cause in seconds.
> Start your free trial of AppDynamics Pro today!
>
> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk_______________________________________________
> Rdkit-discuss mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
>
------------------------------------------------------------------------------
See everything from the browser to the database with AppDynamics
Get end-to-end visibility with application monitoring from AppDynamics
Isolate bottlenecks and diagnose root cause in seconds.
Start your free trial of AppDynamics Pro today!
http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
_______________________________________________
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
