Hi, I'm using the RDKit PostgreSQL cartridge on the same Ubuntu architecture. I think it is a problem with the OpenSCG package, you should use the following repository instead: ppa:pitti/postgresql. He is also the official maintainer of the Ubuntu PostgreSQL packages; with those everything works as expected.
Adrian On Thu, Apr 26, 2012 at 23:31, Jan Holst Jensen <[email protected]> wrote: > Dear Greg, > > I can again reproduce the Postgres 9.1 issue, this time in a brand new > 64-bit VM. > > Ubuntu 10.04.2 x86_64 server installed from scratch. > gnome-desktop-environment installed, VMware tools installed. > > > jhje@ubuntu-x64-build:~$ cat /etc/issue > Ubuntu 10.04.2 LTS \n \l > > jhje@ubuntu-x64-build:~$ uname -a > Linux ubuntu-x64-build 2.6.32-28-server #55-Ubuntu SMP Mon Jan 10 > 23:57:16 UTC 2011 x86_64 GNU/Linux > jhje@ubuntu-x64-build:~$ > > > Packages build-essential, bison, flex, boost libraries, numpy, cmake > installed. > > RDKit_2012_03_1 builds (after the needed one-line patch to Wrap.h) and > all tests pass. > > Installed OpenSCG postgresql 9.1.3 package (latest postgres for Ubuntu > 10.04.2 is Pg 8.5, so not interesting). > > Set "trust" authentication for local connections in pg_hba.conf so rdkit > postgres test suite can run without prompting for password. > > > postgres@ubuntu-x64-build:~$ createuser jhje > Shall the new role be a superuser? (y/n) y > postgres@ubuntu-x64-build:~$ > > jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ . > /opt/postgres/9.1/pg91-openscg.env > jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make > ... builds with the usual 3-4 warnings ... > jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ > > jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ sudo su - > [sudo] password for jhje: > root@ubuntu-x64-build:~# cd /home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/ > root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# . > /opt/postgres/9.1/pg91-openscg.env > root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# make > install > /bin/mkdir -p '/opt/postgres/9.1/lib/postgresql' > /bin/mkdir -p '/opt/postgres/9.1/share/postgresql/extension' > /bin/sh > /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh > -c -m 755 rdkit.so '/opt/postgres/9.1/lib/postgresql/rdkit.so' > /bin/sh > /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh > -c -m 644 ./rdkit.control '/opt/postgres/9.1/share/postgresql/extension/' > /bin/sh > /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../config/install-sh > -c -m 644 ./rdkit--3.1.sql '/opt/postgres/9.1/share/postgresql/extension/' > root@ubuntu-x64-build:/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit# > > jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make installcheck > /opt/postgres/9.1/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress > --inputdir=. --psqldir='/opt/postgres/9.1/bin' > --dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91 > sfpgist slfpgist fps > (using postmaster on Unix socket, port 5432) > ============== dropping database "contrib_regression" ============== > NOTICE: database "contrib_regression" does not exist, skipping > DROP DATABASE > ============== creating database "contrib_regression" ============== > CREATE DATABASE > ALTER DATABASE > ============== running regression test queries ============== > test rdkit-91 ... FAILED (test process exited with exit > code 2) > test props ... FAILED > test btree ... FAILED > test molgist ... FAILED > test bfpgist-91 ... FAILED > test sfpgist ... FAILED > test slfpgist ... FAILED > test fps ... FAILED > > ====================== > 8 of 8 tests failed. > ====================== > > The differences that caused some tests to fail can be viewed in the > file "/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/regression.diffs". A > copy of the test summary that you see > above is saved in the file > "/home/jhje/RDKit_2012_03_1/Code/PgSQL/rdkit/regression.out". > > make: *** [installcheck] Error 1 > jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ > > > jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ less > regression.diffs > [... ...] > --- 4,9 ---- > -- > SET client_min_messages = warning; > \set ECHO none > ! FATAL: failed to initialize rdkit.dice_threshold to 0.5 > ! FATAL: failed to initialize rdkit.dice_threshold to 0.5 > ! connection to server was lost > > OK, this time around it is the dice_threshold instead of the > tanimoto_threshold that cannot be initialized, but still... > > Hmmm... 'less' is reporting a linking issue, but only when the postgres > environment has been loaded: > > jhje@ubuntu-x64-build:~$ less > Missing filename ("less --help" for help) > jhje@ubuntu-x64-build:~$ . /opt/postgres/9.1/pg91-openscg.env > jhje@ubuntu-x64-build:~$ less > less: Symbol `ospeed' has different size in shared object, consider > re-linking > Missing filename ("less --help" for help) > jhje@ubuntu-x64-build:~$ echo $LD_LIBRARY_PATH > /opt/postgres/9.1/lib: > jhje@ubuntu-x64-build:~$ > > Could a library conflict be what causes rdkit to abort ? > > Kind regards > -- Jan > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
