[ome-devel] Cvs install broken
Ilya Goldberg
igg at nih.gov
Fri May 5 23:36:16 BST 2006
Thanks for sorting that out.
Added 1.45 to the invalid list, 1.41 to the valid list when module
checking.
http://cvs.openmicroscopy.org.uk/horde/chora/diff.php?f=/OME/src/
perl2/OME/Install/PerlModuleTask.pm&r1=1.60&r2=1.61&ty=h&num=10
-I
On May 4, 2006, at 3:30 PM, kris wrote:
> Downgrading to 1.41 did the trick..
>
> Thx,
> Kgk
>
>
> On Thu, 2006-05-04 at 11:13 +0100, Chris Allan wrote:
>> For what it's worth, I had no problem installing from CVS with
>> DBD::Pg 1.41 a little while ago.
>>
>> Ciao.
>>
>> -Chris
>>
>> On 4 May 2006, at 00:35, kris wrote:
>>
>>> I also ran into the omeis problem, but a make clean worked
>>> to clear that up.
>>>
>>> My DBD::Pg is 1.45 so I will be downgrading. However, on CPAN I
>>> notice
>>> that there is 1.47 from 19 Mar 06, while 1.45 is from Feb 06.
>>> The version 1.32 mentioned is from Feb 04 and 1.22 doesn't
>>> seem available anymore.
>>>
>>> Postgresql is 7.4
>>>
>>>
>>> On Wed, 2006-05-03 at 19:24 -0400, Ilya Goldberg wrote:
>>>> This one is probably my fault. I don't know why it wants a
>>>> Makefile.in in omeis/t/, but not for any other sub-directory.
>>>> You can cd src/C/omeis, then run ./autogen.sh, then make, and it
>>>> should work.
>>>> You did your update with the -dP flags? These create and prune
>>>> directories as needed. A fresh checkout should have worked also.
>>>>
>>>> The DB thing is a new one. What version of postgres and DBD::Pg
>>>> are
>>>> you using?
>>>> -I
>>>>
>>>> On May 3, 2006, at 11:46 AM, Curtis Rueden wrote:
>>>>
>>>>> Hi Kris,
>>>>>
>>>>> I've seen similar DBD::Pg::db errors before. It seems various
>>>>> versions
>>>>> of DBD::Pg (including some of the latest ones) are broken with
>>>>> respect
>>>>> to OME. On our Debian systems, DBD::Pg 1.32 definitely works (I am
>>>>> fairly sure 1.22 also works). Alternately, you can refrain from
>>>>> installing DBD::Pg manually or with your package manager, and
>>>>> instead
>>>>> allow the OME installer to download and install its preferred
>>>>> version,
>>>>> which I believe should work.
>>>>>
>>>>> I was planning to test my claims with the latest OME from CVS
>>>>> today, but
>>>>> ran into an error of my own much earlier (included below, in case
>>>>> anyone
>>>>> else knows what's wrong).
>>>>>
>>>>> -Curtis
>>>>>
>>>>> -------------------
>>>>> Core Binary Setup
>>>>> -------------------
>>>>>
>>>>> (All verbose information logged in /var/tmp/OME/install/
>>>>> BinaryBuilds.log)
>>>>>
>>>>> Installing OMEIS
>>>>> \_ Configuring [FAILURE].
>>>>>
>>>>>
>>>>> Errors executing task: Unable to configure module, see
>>>>> BinaryBuilds.log
>>>>> for details. at (eval 36) line 1
>>>>>
>>>>> at ./install.pl line 81
>>>>> main::run_tasks() called at ./install.pl line 265
>>>>>
>>>>> -------------------
>>>>> curtis at skyking:~/OME$ tail /var/tmp/OME/install/BinaryBuilds.log
>>>>> checking for strdup... yes
>>>>> checking for strerror... yes
>>>>> checking for strstr... yes
>>>>> configure: creating ./config.status
>>>>> config.status: creating Makefile
>>>>> config.status: creating zoom/Makefile
>>>>> config.status: creating zoom/lib/Makefile
>>>>> config.status: error: cannot find input file: t/Makefile.in
>>>>> "
>>>>>
>>>>>
>>>>> kris wrote:
>>>>>
>>>>>> Database woes when installing from CVS...
>>>>>>
>>>>>>
>>>>>> ---CUT----
>>>>>>
>>>>>> # cat /var/tmp/OME/install/CoreDatabaseTablesTask.log
>>>>>> Creating OME PostgreSQL SUPERUSER (ome)
>>>>>> ERROR LOADING CLASS "OME::LookupTable" -- OUTPUT: "DBD::Pg::db do
>>>>>> failed: ERROR: could not determine data type of parameter $1
>>>>>> "
>>>>>>
>>>>>> --------------------
>>>>>> Database Bootstrap
>>>>>> --------------------
>>>>>>
>>>>>> (All verbose information logged
>>>>>> in /var/tmp/OME/install/CoreDatabaseTablesTask.log)
>>>>>>
>>>>>> Finding DB configuration in installation environment [FOUND
>>>>>> EXISTING].
>>>>>> Database connection information
>>>>>> N.B.: The database host must already be installed and running.
>>>>>> It must already be configured for accepting the connection
>>>>>> specified here, or a superuser connection from user "postgres".
>>>>>> Database Delegate Class: OME::Database::PostgresDelegate
>>>>>> Database Name: ome
>>>>>> Host: undefined (local)
>>>>>> Port: undefined (default)
>>>>>> Username for DB connection: undefined (process owner)
>>>>>>
>>>>>> Are these values correct ? [y/n]:
>>>>>> Creating OME PostgreSQL SUPERUSER (ome)[SUCCESS].
>>>>>> Creating Apache PostgreSQL SUPERUSER (www-data)[SUCCESS].
>>>>>> Creating Admin PostgreSQL SUPERUSER (kgk)[SUCCESS].
>>>>>> Checking database
>>>>>> Creating PostgreSQL database ome... [Done.]
>>>>>> Fixing OID/INTEGER compatability bug...WARNING: changing return
>>>>>> type of
>>>>>> function plpgsql_call_handler from "opaque" to "language_handler"
>>>>>> [Done.]
>>>>>> Loading the database schema
>>>>>> \__ OME::LookupTable NOTICE: CREATE TABLE / PRIMARY KEY will
>>>>>> create
>>>>>> implicit index "lookup_tables_pkey" for table "lookup_tables"
>>>>>> DBD::Pg::db do failed: ERROR: could not determine data type of
>>>>>> parameter $1
>>>>>> [FAILURE].
>>>>>>
>>>>>>
>>>>>> Errors executing task: Error loading class "OME::LookupTable",
>>>>>> see
>>>>>> CoreDatabaseTablesTask.log details. at (eval 202) line 1
>>>>>>
>>>>>> at install.pl line 81
>>>>>> main::run_tasks() called at install.pl line 265
>>>>>> # Looks like your test died before it could output anything.
>>>>>> arno:/home/kgk/work/ome/OME-CVS#
>>>>>> m /var/tmp/OME/install/CoreDatabaseTablesTask.log
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> ome-devel mailing list
>>>>> ome-devel at lists.openmicroscopy.org.uk
>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>>>>
>>> --
>>> Kristian Kvilekval
>>> kris at cs.ucsb.edu http://www.cs.ucsb.edu/~kris w:805-893-2526 h:
>>> 504-9756
>>>
>>> _______________________________________________
>>> ome-devel mailing list
>>> ome-devel at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
> --
> Kristian Kvilekval
> kris at cs.ucsb.edu http://www.cs.ucsb.edu/~kris w:805-893-2526 h:
> 504-9756
>
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
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