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
>>
>
>
>
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