Hi Jan,
I followed your advice and I added the new repo, however the problem still
persists:
georgep@george-VB:~$ sudo apt-get install postgresql
postgresql-server-dev-all
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
comerr-dev dctrl-tools krb5-multidev libgssrpc4 libkadm5clnt-mit8
libkadm5srv-mit8 libkdb5-6 libkrb5-dev libpq-dev postgresql-9.1
postgresql-client-9.1 postgresql-client-common postgresql-common
postgresql-server-dev-9.1
Suggested packages:
debtags krb5-doc krb5-user postgresql-doc-9.2 oidentd ident-server
locales-all postgresql-doc-9.1
The following NEW packages will be installed
comerr-dev dctrl-tools krb5-multidev libgssrpc4 libkadm5clnt-mit8
libkadm5srv-mit8 libkdb5-6 libkrb5-dev libpq-dev postgresql postgresql-9.1
postgresql-client-9.1 postgresql-client-common
postgresql-common postgresql-server-dev-9.1 postgresql-server-dev-all
0 upgraded, 16 newly installed, 0 to remove and 8 not upgraded.
Need to get 40.8 kB/7,258 kB of archives.
After this operation, 21.7 MB of additional disk space will be used.
Do you want to continue [Y/n]? y
WARNING: The following packages cannot be authenticated!
libpq-dev postgresql-client-common postgresql-common postgresql
postgresql-server-dev-all
Install these packages without verification [y/N]? y
*Get:1 http://ppa.launchpad.net/pitti/postgresql/ubuntu/ precise/main
postgresql all 9.1+130~precise [40.8 kB]*
Fetched 40.8 kB in 0s (650 kB/s)
Preconfiguring packages ...
Selecting previously unselected package libgssrpc4.
(Reading database ... 222988 files and directories currently installed.)
Unpacking libgssrpc4 (from
.../libgssrpc4_1.10+dfsg~beta1-2ubuntu0.1_i386.deb) ...
Selecting previously unselected package libkadm5clnt-mit8.
Unpacking libkadm5clnt-mit8 (from
.../libkadm5clnt-mit8_1.10+dfsg~beta1-2ubuntu0.1_i386.deb) ...
Selecting previously unselected package libkdb5-6.
Unpacking libkdb5-6 (from
.../libkdb5-6_1.10+dfsg~beta1-2ubuntu0.1_i386.deb) ...
Selecting previously unselected package libkadm5srv-mit8.
Unpacking libkadm5srv-mit8 (from
.../libkadm5srv-mit8_1.10+dfsg~beta1-2ubuntu0.1_i386.deb) ...
Selecting previously unselected package dctrl-tools.
Unpacking dctrl-tools (from .../dctrl-tools_2.18ubuntu1_i386.deb) ...
Selecting previously unselected package comerr-dev.
Unpacking comerr-dev (from .../comerr-dev_2.1-1.42-1ubuntu2_i386.deb) ...
Selecting previously unselected package krb5-multidev.
Unpacking krb5-multidev (from
.../krb5-multidev_1.10+dfsg~beta1-2ubuntu0.1_i386.deb) ...
Selecting previously unselected package libkrb5-dev.
Unpacking libkrb5-dev (from
.../libkrb5-dev_1.10+dfsg~beta1-2ubuntu0.1_i386.deb) ...
Selecting previously unselected package libpq-dev.
Unpacking libpq-dev (from .../libpq-dev_9.2~beta1-1~precise_i386.deb) ...
Selecting previously unselected package postgresql-client-common.
Unpacking postgresql-client-common (from
.../postgresql-client-common_130~precise_all.deb) ...
Selecting previously unselected package postgresql-client-9.1.
Unpacking postgresql-client-9.1 (from
.../postgresql-client-9.1_9.1.3-2_i386.deb) ...
Selecting previously unselected package postgresql-common.
Unpacking postgresql-common (from
.../postgresql-common_130~precise_all.deb) ...
Adding 'diversion of /usr/bin/pg_config to /usr/bin/pg_config.libpq-dev by
postgresql-common'
Selecting previously unselected package postgresql-9.1.
Unpacking postgresql-9.1 (from .../postgresql-9.1_9.1.3-2_i386.deb) ...
Selecting previously unselected package postgresql.
Unpacking postgresql (from .../postgresql_9.1+130~precise_all.deb) ...
Selecting previously unselected package postgresql-server-dev-9.1.
Unpacking postgresql-server-dev-9.1 (from
.../postgresql-server-dev-9.1_9.1.3-2_i386.deb) ...
Selecting previously unselected package postgresql-server-dev-all.
Unpacking postgresql-server-dev-all (from
.../postgresql-server-dev-all_130~precise_all.deb) ...
Processing triggers for man-db ...
Processing triggers for doc-base ...
Processing 1 added doc-base file...
Processing triggers for install-info ...
Processing triggers for ureadahead ...
Setting up libgssrpc4 (1.10+dfsg~beta1-2ubuntu0.1) ...
Setting up libkadm5clnt-mit8 (1.10+dfsg~beta1-2ubuntu0.1) ...
Setting up libkdb5-6 (1.10+dfsg~beta1-2ubuntu0.1) ...
Setting up libkadm5srv-mit8 (1.10+dfsg~beta1-2ubuntu0.1) ...
Setting up dctrl-tools (2.18ubuntu1) ...
Setting up comerr-dev (2.1-1.42-1ubuntu2) ...
Setting up krb5-multidev (1.10+dfsg~beta1-2ubuntu0.1) ...
Setting up libkrb5-dev (1.10+dfsg~beta1-2ubuntu0.1) ...
Setting up libpq-dev (9.2~beta1-1~precise) ...
Setting up postgresql-client-common (130~precise) ...
Setting up postgresql-client-9.1 (9.1.3-2) ...
update-alternatives: using /usr/share/postgresql/9.1/man/man1/psql.1.gz to
provide /usr/share/man/man1/psql.1.gz (psql.1.gz) in auto mode.
Setting up postgresql-common (130~precise) ...
Building PostgreSQL dictionaries from installed myspell/hunspell packages...
en_au
en_gb
en_us
en_za
Setting up postgresql-9.1 (9.1.3-2) ...
Creating new cluster (configuration: /etc/postgresql/9.1/main, data:
/var/lib/postgresql/9.1/main)...
Moving configuration file /var/lib/postgresql/9.1/main/postgresql.conf to
/etc/postgresql/9.1/main...
Moving configuration file /var/lib/postgresql/9.1/main/pg_hba.conf to
/etc/postgresql/9.1/main...
Moving configuration file /var/lib/postgresql/9.1/main/pg_ident.conf to
/etc/postgresql/9.1/main...
Configuring postgresql.conf to use port 5432...
update-alternatives: using
/usr/share/postgresql/9.1/man/man1/postmaster.1.gz to provide
/usr/share/man/man1/postmaster.1.gz (postmaster.1.gz) in auto mode.
* Starting PostgreSQL 9.1 database server
[ OK ]
Setting up postgresql (9.1+130~precise) ...
Setting up postgresql-server-dev-9.1 (9.1.3-2) ...
Setting up postgresql-server-dev-all (130~precise) ...
Processing triggers for libc-bin ...
ldconfig deferred processing now taking place
Again, *all* the tests fail as do the "create extension" attempts.
I even tried explicit postgresql-9.1 and postgresql-9.2 (beta version) but
with the same sad results.
Do I do something wrong here, like still installing the default postgresql
packages and not the "good" ones?
Regards,
George
On 29 May 2012 23:27, George Papadatos <gpapada...@gmail.com> wrote:
> Hi Jan,
>
> Many thanks for the reply.
> Yes, I used apt-get and the default repositories to install postgresql on
> a Ubuntu 12.04.
> I'll follow your guidelines and the new repos tomorrow and I'll let you
> know.
>
> Many thanks again,
>
> George
>
>
> On 29 May 2012 23:15, Jan Holst Jensen <j...@biochemfusion.com> wrote:
>
>> On 2012-05-29 17:45, George Papadatos wrote:
>>
>> Hi RDKitters,
>>
>> Today I tried to install the RDKit and cartridge to a brand new Ubuntu
>> 12.04 32-bit running on a Virtual Box.
>>
>> [...]
>>
>> Then when I tried to install the extension:
>> georgep@george-VB:~$ psql -c 'CREATE EXTENSION rdkit' gpdb
>> FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5
>> FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5
>> connection to server was lost
>>
>> or even:
>> georgep@george-VB:~/local/rdkit/rdkit_trunk/Code/PgSQL/rdkit$ psql gpdb
>> psql (9.1.3)
>> Type "help" for help.
>>
>> gpdb=# create extension "rdkit";
>> FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5
>> FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5
>> The connection to the server was lost. Attempting reset: Succeeded.
>> gpdb=# show rdkit.tanimoto_threshold;
>> ERROR: unrecognized configuration parameter "rdkit.tanimoto_threshold"
>>
>>
>> Any ideas would be much appreciated!
>>
>>
>> Hi George,
>>
>> Sounds exactly like the behavior I described in this thread:
>>
>>
>> http://sourceforge.net/mailarchive/forum.php?thread_name=CAD4fdRRHdpqDRCWd5AjEzDWJia5WM6zsq%3DosvVmb%3DYHe%3DpmR7A%40mail.gmail.com&forum_name=rdkit-discuss
>>
>> My issue seemed to be related to the OpenSCG version of PostgreSQL and
>> for my purposes the issue was solved by using Martin Pitt's postgres
>> packages instead. However, on one machine, a Linux Mint box, I never got it
>> working. Are you using all plain vanilla packages from Ubuntu 12.04 ?
>>
>> Cheers
>> -- Jan
>>
>
>
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