Fwd: Problem restoring chado schema

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

Fwd: Problem restoring chado schema

Dave Clements, GMOD Help Desk-3
Hi Antonio,

I'm forwarding this to the main Chado list.  No one else has posted to
the Chado-seq-ad list for years.

What version of postgres are you running?  If it is version 9, then we
may have troubles.  It looks like R-tree support went away sometime
between version 8.1 and 9.  See
http://www.postgresql.org/docs/8.1/static/indexes-types.html
http://www.postgresql.org/docs/9/static/indexes-types.html

Also see this thread
http://gmod.827538.n3.nabble.com/Problem-with-the-function-create-point-when-I-try-to-restore-a-new-database-td1414635.html

Scott says
I've seen that before too, but have yet to spend much time figuring
out what is going on.  I assume that when this happens, some
range-based queries for GBrowse might be slower, but otherwise it
won't cause a problem.  I think the ultimate fix is to rewrite the
range queries to us GiST, but that means I (or somebody) will have to
take the time to learn how to use them appropriately.

Dave C

---------- Forwarded message ----------
From: Antonio Nhani Jr <[hidden email]>
Date: Thu, Oct 7, 2010 at 5:33 AM
Subject: [Gmod-chado-seq-ad] [SPAM] Problem restoring chado schema
To: [hidden email]


Hi,
I've just restored chado (Pg) database with the main backup (empty
database) and the following erros occured:

=========
ERROR:  function create_point(integer, integer) does not exist
LINE 1: SELECT box (create_point(0, $1), create_point($2,500000000))
                     ^
HINT:  No function matches the given name and argument types. You
might need to add explicit type casts.
QUERY:  SELECT box (create_point(0, $1), create_point($2,500000000))
CONTEXT:  SQL function "boxrange" during inlining
SQL statement "SELECT fk."group_id" FROM ONLY "frange"."featuregroup"
fk LEFT OUTER JOIN ONLY "public"."feature" pk ON ( pk."feature_id"
OPERATOR(pg_catalog.=) fk."group_id") WHERE pk."feature_id" IS NULL
AND (fk."group_id" IS NOT NULL)"
ERROR:  function create_point(integer, integer) does not exist
LINE 1: SELECT box (create_point(0, $1), create_point($2,500000000))
                     ^
HINT:  No function matches the given name and argument types. You
might need to add explicit type casts.
QUERY:  SELECT box (create_point(0, $1), create_point($2,500000000))
CONTEXT:  SQL function "boxrange" during inlining
SQL statement "SELECT fk."object_id" FROM ONLY "frange"."featuregroup"
fk LEFT OUTER JOIN ONLY "public"."feature" pk ON ( pk."feature_id"
OPERATOR(pg_catalog.=) fk."object_id") WHERE pk."feature_id" IS NULL
AND (fk."object_id" IS NOT NULL)"
ERROR:  function create_point(integer, integer) does not exist
LINE 1: SELECT box (create_point(0, $1), create_point($2,500000000))
                     ^
HINT:  No function matches the given name and argument types. You
might need to add explicit type casts.
QUERY:  SELECT box (create_point(0, $1), create_point($2,500000000))
CONTEXT:  SQL function "boxrange" during inlining
SQL statement "SELECT fk."srcfeature_id" FROM ONLY
"frange"."featuregroup" fk LEFT OUTER JOIN ONLY "public"."feature" pk
ON ( pk."feature_id" OPERATOR(pg_catalog.=) fk."srcfeature_id") WHERE
pk."feature_id" IS NULL AND (fk."srcfeature_id" IS NOT NULL)"
ERROR:  function create_point(integer, integer) does not exist
LINE 1: SELECT box (create_point(0, $1), create_point($2,500000000))
                     ^
HINT:  No function matches the given name and argument types. You
might need to add explicit type casts.
QUERY:  SELECT box (create_point(0, $1), create_point($2,500000000))
CONTEXT:  SQL function "boxrange" during inlining
SQL statement "SELECT fk."subject_id" FROM ONLY
"frange"."featuregroup" fk LEFT OUTER JOIN ONLY "public"."feature" pk
ON ( pk."feature_id" OPERATOR(pg_catalog.=) fk."subject_id") WHERE
pk."feature_id" IS NULL AND (fk."subject_id" IS NOT NULL)"

=========

Are they due to empty database?

Regards,

Antonio


Antonio Nhani Jr
Núcleo de Melhoramento e Biotecnologia
54 3316 5833 / 5829
Embrapa Trigo - Rod. BR 285 Km 294
99001-970 Passo Fundo/RS



------------------------------
Aviso de confidencialidade:

- Esta mensagem da Empresa Brasileira de Pesquisa Agropecuária
(Embrapa), empresa pública federal regida pelo disposto na Lei Federal
nº 5.851, de 7 de dezembro de 1972, é enviada exclusivamente a seu
destinatário e pode conter informações confidenciais, protegidas por
sigilo profissional. Sua utilização desautorizada é ilegal e sujeita o
infrator às penas da lei. Se você a recebeu indevidamente, queira, por
gentileza, reenviá-la ao emitente, esclarecendo o equívoco.

Confidentiality note:

- "This message from Empresa Brasileira de Pesquisa Agropecuária
(Embrapa), a government company established under Brazilian law
(5.851/72), is directed exclusively to its addressee and may contain
confidential data, protected under professional secrecy rules. Its
unauthorized use is illegal and may subject the transgressor to the
law's penalties. If you are not the addressee, please send it back,
elucidating the failure".

________________________________
View this message in context: Problem restoring chado schema
Sent from the gmod-chado-seq-ad mailing list archive at Nabble.com.

------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb
_______________________________________________
Gmod-chado-seq-ad mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-chado-seq-ad




--
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/GMOD_News
http://hinv.jp/biocuration2010/
http://gmod.org/wiki/Help_Desk_Feedback

------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2 & L3.
Spend less time writing and  rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
http://p.sf.net/sfu/beautyoftheweb
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema