On 12.04 you do not need to add the PPA, PostgreSQL 9.1 is the
official package there. In addition, the official packages are also
provided by Martin Pitt, so the packages in the PPA and in the distro
are actually the same. It only make sense on 10.04 (and those that do
not ship with 9.1).
I suspect that the problem is in guc.c:
DefineCustomRealVariable(
"rdkit.tanimoto_threshold",
"Lower threshold of Tanimoto similarity",
"Molecules with similarity lower than
threshold are not similar by % operation",
&rdkit_tanimoto_smlar_limit,
0.5,
0.0,
1.0,
PGC_USERSET,
0,
#if PG_VERSION_NUM >= 90100
(GucRealCheckHook)TanimotoLimitAssign,
NULL,
#else
TanimotoLimitAssign,
#endif
NULL
);
PG_VERSION_NUM seems to be wrong on your installation which then calls
DefineCustomRealVariable with a different prototype which in turn
causes a segmentation fault on 9.1. The GUC code has changed between
9.0 and 9.1. You should try to debug what PG_VERSION_NUM compiles to
in your installation. Or you could remove the conditional entirely to
see if that causes the problem.
Adrian
On Wed, May 30, 2012 at 10:28 AM, George Papadatos <[email protected]> wrote:
> 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 <[email protected]> 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 <[email protected]> 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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