On 2012-04-27 11:02, Adrian Schreyer wrote:
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
Hi Adrian,
Thanks for the pointer! This solves it for my Ubuntu 10.04.2 server.
And Greg - I could successfully build and run the cartridge on a plain
vanilla Ubuntu 11.10; see below.
On Linux Mint 12 I wasn't able to get this solution to work. The ppa
repositories conflict with the packages on Linux Mint. Even though I
pinned the ppa repository to have a higher priority than Ubuntu packages
- here in /etc/apt/preferences:
Package: *
Pin: release o=linuxmint
Pin-Priority: 700
Package: *
Pin: origin packages.linuxmint.com
Pin-Priority: 700
Package: *
Pin: origin ppa.launchpad.net
Pin-Priority: 650
Package: *
Pin: release o=Ubuntu
Pin-Priority: 600
This only resulted in postgresql-common being installed from
ppa.launchpad.net - the postgres server package was still being
installed from the Ubuntu archives and I still have the rdkit install
failure. I think I will just note that Linux Mint doesn't play nice with
RDKit and move on :-).
Cheers
-- Jan
________________________
Ubuntu 11.10 x64 basic server install in VMware 7.1.5.
add packages
gnome-desktop-environment xinit build-essential
install
vmware-tools
add packages
cmake flex bison libboost-dev libboost-regex-dev
libboost-python-dev python-numpy
Build RDKit_2012_03_1 - all tests pass.
add packages
postgresql-9.1 postgresql-server-dev-9.1
run "createuser jhje" as the postgres user - make the new user a superuser
cd to the rdkit cartridge dir - as the "jhje" user.
run "make"
run "make install"
run "make installcheck" - all tests pass.
_________________________
Ubuntu 10.04.2 server with OpenSCG Postgres 9.1 installed. The rdkit
cartridge was failing to install.
I stopped the OpenSCG Postgres 9.1 service. Then added the following to
/etc/apt/sources.list:
deb http://ppa.launchpad.net/pitti/postgresql/ubuntu lucid main
deb-src http://ppa.launchpad.net/pitti/postgresql/ubuntu lucid main
apt-get update
apt-get install postgresql-9.1 postgresql-server-dev-9.1
Re-built the rdkit cartridge using the new 9.1 postgres package.
jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ export
RDBASE=/home/jhje/RDKit_2012_03_1/
jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ export
LD_LIBRARY_PATH=/home/jhje/RDKit_2012_03_1/lib/
jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make clean
rm -f rdkit.so librdkit.a
rm -f rdkit_io.o mol_op.o bfp_op.o sfp_op.o rdkit_gist.o low_gist.o
guc.o cache.o adapter.o
rm -f rdkit--3.1.sql
rm -rf results/ regression.diffs regression.out tmp_check/ log/
jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make
... bla bla bla ...
jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ sudo make install
[sudo] password for jhje:
/bin/mkdir -p '/usr/lib/postgresql/9.1/lib'
/bin/mkdir -p '/usr/share/postgresql/9.1/extension'
/bin/sh
/usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh
-c -m 755 rdkit.so '/usr/lib/postgresql/9.1/lib/rdkit.so'
/bin/sh
/usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh
-c -m 644 ./rdkit.control '/usr/share/postgresql/9.1/extension/'
/bin/sh
/usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../config/install-sh
-c -m 644 ./rdkit--3.1.sql '/usr/share/postgresql/9.1/extension/'
jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$ make installcheck
/usr/lib/postgresql/9.1/lib/pgxs/src/makefiles/../../src/test/regress/pg_regress
--inputdir=. --psqldir='/usr/lib/postgresql/9.1/bin'
--dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91
sfpgist slfpgist fps
(using postmaster on Unix socket, default port)
============== 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 ... ok
test props ... ok
test btree ... ok
test molgist ... ok
test bfpgist-91 ... ok
test sfpgist ... ok
test slfpgist ... ok
test fps ... ok
=====================
All 8 tests passed.
=====================
jhje@ubuntu-x64-build:~/RDKit_2012_03_1/Code/PgSQL/rdkit$
jhje@ubuntu-x64-build:~$ ldd /usr/lib/postgresql/9.1/lib/rdkit.so
linux-vdso.so.1 => (0x00007fff2f1bc000)
libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x00007f7581515000)
libm.so.6 => /lib/libm.so.6 (0x00007f7581292000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007f758107a000)
libc.so.6 => /lib/libc.so.6 (0x00007f7580cf7000)
/lib64/ld-linux-x86-64.so.2 (0x00007f7581c0d000)
jhje@ubuntu-x64-build:~$
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