Nabble - Bio.net - Acedb

Acedb on OS X 10.5 (Leopard)

2008-01-24T08:13:11Z

The 4.9.39 binaries of xace and tace will work on Leopard...with a
little help.

You need to also install glib and gtk+. In the past I have done this
by using the fink project (http://www.finkproject.org/). However, the
version of glib available under fink doesn't meet the specifications
of what acedb needs. So, I tried installing MacPorts (http://
www.macports.org/) which has a similar raison d'etre to fink, and this
has a later version of glib.

So download MacPorts, use it to install glib, gtk+ and readline, and
then make one final tweak. Acedb will look in /usr/local/lib whereas
MacPorts installs to /opt/local/lib. So I just created a sym link at /
usr/local/lib to point to /opt/local/lib.

Regards,

Keith

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Bionet public archives and privacy

2007-11-15T01:48:04Z

All,

Please read the below from Don Gilbert who supervises/coordinates much of the
bionet archives.

I'm not aware of any issues for acedb but if you have concerns you should
probably contact me directly in the first instance.

Ed
--
------------------------------------------------------------------------
| Ed Griffiths, Acedb development, Informatics Group, |
| The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus |
| Hinxton, Cambridge CB10 1HH |
| |
| email: edgrif@... Tel: +44-1223-496844 Fax: +44-1223-494919 |
------------------------------------------------------------------------

---------- Forwarded message ----------
Date: Tue, 13 Nov 2007 17:18:49 -0500 (EST)
From: Don Gilbert <gilbertd@...>
To: biomail@...
Subject: [Biomail Site List] Update on Bionet public archives and privacy
concerns

Dear Bionet moderators,

As some contributors change their minds or learn after the fact
that any public discussions become Google'able and expose their
messages to searches by name, I and likely some of you, get
requests to edit/remove posts from the public archives at
www.bio.net

The consensus of comments from many folks on this
is summarized in this policy
http://www.bio.net/bionet/docs/biosci-termsofuse.html

A while back I brought this subject to your attention
http://www.bio.net/biomail/private/biomail/2006-July/000020.html

Please share your opinions among this moderators group. There is
not now software support for moderators to edit the Bionet group
archives. Somewhere down the road for Bionet, if new software
packages make this feasible, I would like to see moderators have
the option to handle these requests.

For now, you should direct requests for message removal/editing
to the above biosci-termsofuse.html document. If a Bionet
contributor's concerns extend beyond the fairly common
"just don't want my name in Google searches" to some
specific need or harm, I deal with these on a case by
case basis, thru e-mail to biosci-help@...

For instance, I handled a request from someone who posted many
messages with a personal address/phone to remove these when the
person started teaching prison inmates (who have web access).
I generally remove those post from people asking for
medical advice, etc. and off-topic posts.

I also have denied requests from people asking removal of their
messages, and replies by others quoting them, on subjects
of controversy where the discussion was pertinant to the
group. This included refusal in the face of legal action against
myself and Indiana U.

Generally if it is an appropriate message for a Bionet group,
this is a public message that should be preserved, and it will be
preserved in other Internet archives. Removing it from Bionet
archives doesn't solve problems of increased spam (spambots read
Usenet directly), and basically may only lower the
ranking in Google searchs of where the message is found
(e.g. all Bionet messages also make it into searchable Google
Groups archives).

Scientists have a public persona, with contact information and
views expressed in many venues. Googling our public discussions
is now part of our society. I occasionally look thru Bionet use logs,
and find for instance that Google searches from NSF.gov, which has
no reseachers in-house, only grant program officers and reviewers, is
often a search for people by name.

-- Don Gilbert

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Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.

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to Jhon: 139 error

2007-08-22T10:05:44Z

Hello Jhon,

I got error message "Error status = 139" while loading data into
acedb. Do you know what that means?

--------------------------------
--------------------------------
Best Regards,
Alveksei
<a href="http://www.diabetes.pocket-book.com/">diabetes weblog</a>

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to Jhon: 139 error

2007-08-22T09:57:55Z

Hello Jhon,

I got error message "Error status = 139" while loading data into
acedb. Do you know what that means?

--------------------------------
--------------------------------
Best Regards,
Alveksei
<a href="http://www.diabetes.pocket-book.com/">diabetes weblog</a>
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Re: aql error 810, Inconsistent value types

2007-03-14T11:25:43Z

Hi jean,

> f is type float
> g is type tag
>
> it means that in m[2] you had something heterogeneous
> the only way i see to produce that is that the model
> allowed either float or tag at this position

Aha! You nailed it. I have

?Locus Location Map ?Map #map_position

?map_position Position Float
Ends Left Float
Right Float

Changing the query to this fixes the problem:

select l, m, p
from s in class sequence where exists_tag s->dna_homol,
l in s->probe->locus,
m in l->map,
p in m[Position]

> 1) do you have a suggestion to improve the error message

How about
"Value type was 'tag' and now the field evaluates to type 'float' in row 19822"

Thanks for the help!!
- Dave

> From mieg@... Wed Mar 14 12:29:04 2007
>
> >What does this error message mean?
> >
> >// AQL error 810 around: 'l, m, p from s in'
> >// ^
> >// Inconsistent value types in table column 3
> >// Value type was 'g' and now the field evaluates to type 'f' in row 19822
> >
> >What are value types g and f?
> >
> f is type float
> g is type tag
>
> it means that in m[2] you had something heterogeneous
> the only way i see to produce that is that the model
> allowed either float or tag at this position
>
> either you did a read-model during the lifetime of the database
> this does not erase the data, the dumper still works
> the purpose of this is that we do not lose data in acedb
> by reading a wrong model, we just loose access via queries
> (direct query, table maker, aql, aceperl)
> but the dumper survives
>
> or the schema is complex and you should select on m[1]
> to be sure that m[2] is a float
>
> Maybe te schema is
>
> ?Sequence Map #map_info
>
> #map_info Position float
> Neighbours Left ?Sequence
> Right ?Sequence
>
>
> .ace file:
>
> Sequence s1
> Map 2 Position 3.2
>
> Sequence s2
> Map 4 Neighbours Left s1
>
>
> ==
>
> not the aql query will give a float 3.2 for s1
> and a tag Left (type 'g') for s2
>
> Table maker is this case would have imposed 'float'
> and just export a void cell,
> aql reports a detailled error message, which is nice,
> although a bit cryptic, sorry
>
> 1) do you have a suggestion to improve the error message
> 2) the solu is to select on m[1]==Position
> or on selecting p from m.Position or maybe m[Position]
> (i am never sure of the aql syntax, but something like this
> works)
> naming tags is more secure than offsets if you access
> constructed types, and more robust if the schema changes in the
> future and gets enriched
>
>
>
> Please let me know if the explanation is clear enough
>
>
> >This comes from the following aql query, explorable at
> >http://grain.jouy.inra.fr/cgi-bin/ace/custom/aqlInterface/graingenes :
> >
> >select l, m, p
> >from s in class sequence where exists_tag s->dna_homol,
> > l in s->probe->locus,
> > m in l->map,
> > p in m[2]
> >
> >
> >I routinely aql out every map position in the database using a different
> >query, but it gets them all with no errors, so this is strange.
> >
> >This is using ace4_9t.
> >
> >- Dave

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Re: aql error 810, Inconsistent value types

2007-03-14T10:28:59Z

>What does this error message mean?
>
>// AQL error 810 around: 'l, m, p from s in'
>// ^
>// Inconsistent value types in table column 3
>// Value type was 'g' and now the field evaluates to type 'f' in row 19822
>
>What are value types g and f?
>
f is type float
g is type tag

it means that in m[2] you had something heterogeneous
the only way i see to produce that is that the model
allowed either float or tag at this position

either you did a read-model during the lifetime of the database
this does not erase the data, the dumper still works
the purpose of this is that we do not lose data in acedb
by reading a wrong model, we just loose access via queries
(direct query, table maker, aql, aceperl)
but the dumper survives

or the schema is complex and you should select on m[1]
to be sure that m[2] is a float

Maybe te schema is

?Sequence Map #map_info

#map_info Position float
Neighbours Left ?Sequence
Right ?Sequence

.ace file:

Sequence s1
Map 2 Position 3.2

Sequence s2
Map 4 Neighbours Left s1

==

not the aql query will give a float 3.2 for s1
and a tag Left (type 'g') for s2

Table maker is this case would have imposed 'float'
and just export a void cell,
aql reports a detailled error message, which is nice,
although a bit cryptic, sorry

1) do you have a suggestion to improve the error message
2) the solu is to select on m[1]==Position
or on selecting p from m.Position or maybe m[Position]
(i am never sure of the aql syntax, but something like this
works)
naming tags is more secure than offsets if you access
constructed types, and more robust if the schema changes in the
future and gets enriched

Please let me know if the explanation is clear enough

>This comes from the following aql query, explorable at
>http://grain.jouy.inra.fr/cgi-bin/ace/custom/aqlInterface/graingenes :
>
>select l, m, p
>from s in class sequence where exists_tag s->dna_homol,
> l in s->probe->locus,
> m in l->map,
> p in m[2]
>
>
>I routinely aql out every map position in the database using a different
>query, but it gets them all with no errors, so this is strange.
>
>This is using ace4_9t.
>
>- Dave
>
>- - - - - - - - - - - - - - - - - - - -
>David E. Matthews, PhD USDA-ARS Plant Genome Database Curator
>Cornell University Email: matthews@...
>Department of Plant Breeding Phone: +1-607-255-9951
>409 Bradfield Hall Fax: +1-607-255-6683
>Ithaca, New York 14853, USA GrainGenes: http://wheat.pw.usda.gov
>
>_______________________________________________
>Acedb mailing list
>Acedb@...
>http://www.bio.net/biomail/listinfo/acedb

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aql error 810, Inconsistent value types

2007-03-13T20:08:06Z

What does this error message mean?

// AQL error 810 around: 'l, m, p from s in'
// ^
// Inconsistent value types in table column 3
// Value type was 'g' and now the field evaluates to type 'f' in row 19822

What are value types g and f?

This comes from the following aql query, explorable at
http://grain.jouy.inra.fr/cgi-bin/ace/custom/aqlInterface/graingenes :

select l, m, p
from s in class sequence where exists_tag s->dna_homol,
l in s->probe->locus,
m in l->map,
p in m[2]

I routinely aql out every map position in the database using a different
query, but it gets them all with no errors, so this is strange.

This is using ace4_9t.

- Dave

- - - - - - - - - - - - - - - - - - - -
David E. Matthews, PhD USDA-ARS Plant Genome Database Curator
Cornell University Email: matthews@...
Department of Plant Breeding Phone: +1-607-255-9951
409 Bradfield Hall Fax: +1-607-255-6683
Ithaca, New York 14853, USA GrainGenes: http://wheat.pw.usda.gov

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Acedb bug....

2006-10-14T05:46:32Z

All,

Following a report by a user at Sanger I have found a serious bug has been
introduced into the way acedb parses in data, the bug has been in the code for
several years so its surprising it has not come to light before.

The problem can be summarised as follows, if you parse in the following file:

//------start--------
CDS : "R09E10.1"

Sequence : "Eds_sequence"
CDS_child "R09E10.1" 11111 22222

Sequence : "R09E10"
-D CDS_child "R09E10.1" 11111 22222
CDS_child "R09E10.1" 33333 44444
//------------end-----

You end up with "R09E10" looking like this:

Sequence R09E10
SMap S_Child CDS_child R09E10.1

i.e. you have lost the new coordinates from your change.

There is a work around in that if you do the deletion and addition in two stages
then all will be fine:

Sequence : "R09E10"
-D CDS_child "R09E10.1" 11111 22222

Sequence : "R09E10"
CDS_child "R09E10.1" 33333 44444

I am urgently looking to find when this problem was introduced and to fix it.

Ed
--
------------------------------------------------------------------------
| Ed Griffiths, Acedb development, Informatics Group, |
| The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus |
| Hinxton, Cambridge CB10 1HH |
| |
| email: edgrif@... Tel: +44-1223-496844 Fax: +44-1223-494919 |
------------------------------------------------------------------------

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BIRD: Deadline Extension: Sepptember 22 2006

2006-09-16T03:59:40Z

*CALL FOR PAPERS*

*&*

*CALL FOR POSTERS*

* *

* *

*1st International Conference*

*on*

* *

*Bioinformatics Research and Development*

* B I R D '07***

*http://www.birdconf.org* <http://www.birdconf.org/>**

* *

*Berlin**, Germany***

*March 12-14, 2007*

*Keynote Talk:*

* *

*Josef Penninger*
Institute of Molecular Biotechnology (IMBA)

http://www.imba.oeaw.ac.at/index.php?id=115

*Scope of the conference:*

* *

The primary focus of BIRD '07 is to provide researchers and users in the
field of bioinformatics a forum in which to interact about new research
directions, developments, and software/web services.

It encompasses the methods of solving biological, medical, or chemical
problems by computer science, machine learning, or information
processing tools.

The conceptual level of the methods range from theoretical approaches
through the design of algorithms, models, and information processing
systems through to the development of software packages and web services.

The program committee seeks contributions, which topics include, but are
not limited to:

* *

* Algebraic Biology
* Databases & Data Integration
* Drug Design
* Ontologies & Textmining
* Evolution and Phylogenetics
* Genomics
* Gene and Splice Site Recognition
* Machine Learning and Data Analysis
* Gene Expression/Regulation & Microarrays
* MicroRNA and RNAi
* Molecular Diagnostics and Treatment Support
* Molecular Dynamics
* Pathways, Networks, Systems Biology
* Phylogenetics & Molecular Evolution
* Protein & RNA Structure and Function
* Proteomics
* Sequence Analysis & Alignment
* SNPs and Haplotyping
* Systems Biology and Modelling

* *

*General Chair:*

Roland Wagner, FAW, University of Linz, Austria

*Program Chair:*

Sepp Hochreiter, University of Linz, Austria

* *

*Program Committee (Steering):*

Amos Bairoch, Swiss Institute of Bioinformatics, Switzerland

Pierre Baldi, University of California, Irvine, USA

Philip E. Bourne, UCSD, USA

Cornelius Frömmel, Georg-August-Universität Göttingen, Germany

David Gilbert, University of Glasgow, UK

Amarnath Gupta, SDSC of the University of California San Diego, USA

Knut Reinert, FU Berlin, Germany

Hershel Safer, Weizmann Institute of Science, Israel

Erik Sonnhammer, Stockholm University, Sweden

and about 200 other PC-members

* *

*Paper and Poster Submission Details:
*Authors are invited to submit original research contributions or
experience reports in English.
Paper registration and electronic submission will start in August 2006.

Submitted papers will be carefully evaluated based on originality,
significance, technical soundness, and clarity of exposition.

*Papers:*
Please submit your paper as PDF file only. Paper submissions in LNCS format
(http://www.springer.de/comp/lncs/authors.html) would be highly
appreciated.
In order to avoid problems in viewing and printing your paper, please,
only use embedded fonts. Please, do not use language extensions
(e.g., Chinese language support) neither in texts nor in figures.
The submitted manuscript should closely reflect the final paper as it will
appear in the Proceedings.
Papers should not exceed 15 pages in LNCS format.
Any submission that exceeds length limits or deviates from formatting
requirements may be rejected without review.

*Posters:*
Please submit an extended abstract or short paper version of your poster
as PDF file only.

*Important Dates:*

* Submission of Full Papers: September 22, 2006
* Noification of Acceptance: November 20, 2006
* Camera-ready Copies of papers: December 20, 2006

For further inquiries, please contact the BIRD Conference Organisation
Office (office@... <mailto:office@...>)

All accepted conference papers will be published in "Lecture Notes in
Bioinformatics" (LNBI) by Springer Verlag.

All accepted poster will be published by the Austrian Computer Society.

--
Univ. Prof. Dr. Roland Wagner
Director of the Institute of Applied Knowledgeprocessing (FAW)
Director of the Institute "integriert studieren"

Tel.: +43 676 84673210
Fax: +43 732 24689308
rrwagner@...

sec1: Monika Neubauer
Tel.: +43 676 84673212
Fax.:+43 732 2468 9308
mneubauer@...

sec2: Barbara Arrer
Tel: +43 732 2468 9232
Fax:+43 732 2468 9322
barbara.arrer@...

http://www.faw.uni-linz.ac.at
http://www.integriert-studieren.jku.at
http://www.dexa.org
http://www.icchp.org

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acedb 4.9 news.

2006-03-30T06:06:48Z

All,

I tried to post this a couple of days ago but it seems not to have go through.

Time moves on and the GTK graphics toolkit that acedb 4.9.* uses has moved on a
lot. Currently acedb 4.9 is compiled against GTK version 1.2 and the latest
stable version of GTK is version 2.6. GTK 1.2 is now not regularly installed
except as the libraries on our systems and it makes sense to move on.

I am proposing to do the following:

1) Make a special download link for the current development release of acedb
which will remain parmanently on our website as acedb/GKT1, the code will be
available as both statically and dynamically linked versions.

2) From now on make versions of acedb that are linked against GTK version 2.6.
This is the most stable current version of gtk (see www.gtk.org). I will make
dynamically linked versions but not statically linked. Making the statically
linked versions is painful and the binaries produced exceed the filesize limit
for our external website so that they are only available via ftp.

I intend to start this process at the end of April. Please let me have any
comments/problems etc before then.

thanks, Ed
--
------------------------------------------------------------------------
| Ed Griffiths, Acedb development, Informatics Group, |
| The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus |
| Hinxton, Cambridge CB10 1HH |
| |
| email: edgrif@... Tel: +44-1223-496844 Fax: +44-1223-494919 |
------------------------------------------------------------------------

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2006-02-24T09:11:54Z

subscribe

can i subscribe to that list

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Re: acediff bug

2006-02-24T08:20:04Z

following up on the below bug report, here is a quick patch which makes
all -D lines appear first in the acediff output
The resulting diff file is still more heavy than it should be (ie it can
say "-D somedata" on one line and later add the same data back in the
object), but at least this prevents data loss...

On a side note, gcc 4.0 and later doesn't support -fwritable-strings, so
I had to remove this switch from wmake/LINUX_GTK2_4_DEF to compile
anything. This seems ok for acediff, but I'm not sure how this would
affect the rest of the code. Is this OK, or is it necessary to use gcc 3
to compile acedb?

Nicolas Thierry-Mieg wrote:

> hi all,
>
> I've run into what looks like a bug in acediff.
> This happens with all versions I've tested, ie today's daily build and
> the current supported build, both with dynamically linked binaries. I've
> also tested the current supported static build, same result.
> All of this, on linux (FC4, kernel 2.6.14-1.1656_FC4 on a pentium4 system)
>
> Here is a tiny example to illustrate the problem:
> $ more wspec/models.wrm
> ?Interaction Bait UNIQUE ?Text
> Prey UNIQUE ?Text
> fns
>
> $ more test1.ace
> Interaction : "test1"
> Bait "bait1"
> Prey "prey1"
>
> $ more test2.ace
> Interaction : "test1"
> Bait "bait1"
> Prey "prey1"
> fns
>
> $ ace.supported/acediff test1.ace test2.ace
> reading file 1 - 4 lines read - sorting file 1
> reading file 2 - 6 lines read - sorting file 2
> performing diff - sorting diff
> // acediff difference from test1.ace to test2.ace
>
> Interaction "test1"
> Prey "prey1"
> fns
> -D Prey "prey1"
>
> // end of file
>
>
> As you can see, acediff adds the Prey, then deletes it. After parsing
> the acediff output, I've obviously lost my Prey info.
>
>
> Funny thing is, if you replace "fns" with "Fns" it's OK...
> But if you use a different tag you get strange behaviours.
> eg, using "a_A", acediff also kills the Bait!
> As far as I can tell (but I haven't tested it much), it works OK when
> the tag starts with an uppercase letter.
>
> Is something wrong with my files or ace binaries??
>
> A+
> nicolas
>
>

--
------------------------------------------------------------
Problems with my digital signature? visit:
http://igc.services.cnrs.fr/Doc/General/trust.html
--------------------
Nicolas Thierry-Mieg
Laboratoire LSR-IMAG, BP 53, 38041 Grenoble Cedex 9, France
tel : (33/0)4-76-63-55-79, fax : (33/0)4-76-63-55-50
------------------------------------------------------------

diff -Naur ACEDB-source.daily.060224/wace/acediff.c ACEDB-source.daily.060224.patched/wace/acediff.c
--- ACEDB-source.daily.060224/wace/acediff.c 2003-06-24 01:30:10.000000000 +0200
+++ ACEDB-source.daily.060224.patched/wace/acediff.c 2006-02-24 17:09:35.000000000 +0100
@@ -337,7 +337,7 @@
and advance consumed input streams */
if (cmpClass < 0 || (cmpClass == 0 && cmpData < 0))
{
- if (fprintf (out, "%8d %s -D %s\n",
+ if (fprintf (out, "%08d %s -D %s\n",
lineA, Text(obNameA), Text(dataA)) == 0)
aceDiffAbort("IO error") ;
getLine (inA, &lineA, obNameA, dataA) ;

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smime.p7s (5K) Download Attachment

Protein subclass

2006-02-23T07:31:45Z

hi all,

I am trying to define a subclass named Protein, but this doesn't work
with any tested xace versions (current supported or daily)
Is this forbidden? If yes, shouldn't xace/tace complain when it reads
the models?

Here is a small example to illustrate:

######################################
$ more models.wrm
?Ligand Protein
Sugar

######################################
$ more subclasses.wrm
Class Prot
Visible
Is_a_subclass_of Ligand
Filter Protein

Class Protein
Visible
Is_a_subclass_of Ligand
Filter Protein

Class Sugar
Visible
Is_a_subclass_of Ligand
Filter Sugar

######################################
$ more test.ace
Ligand : "lig1"
Protein

Ligand : "lig2"
Sugar

######################################

Initializing the database works fine
When parsing test.ace, no errors

object lig2 is OK, and shows up in class Sugar
but lig1 is NOT in class Protein (ace says that class Protein is empty),
although it does show up fine in class Prot.

thanks
nicolas

--
------------------------------------------------------------
Nicolas Thierry-Mieg
Laboratoire LSR-IMAG, BP 53, 38041 Grenoble Cedex 9, France
tel : (33/0)4-76-63-55-79, fax : (33/0)4-76-63-55-50
------------------------------------------------------------

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acediff bug

2006-02-16T08:55:49Z

hi all,

I've run into what looks like a bug in acediff.
This happens with all versions I've tested, ie today's daily build and
the current supported build, both with dynamically linked binaries. I've
also tested the current supported static build, same result.
All of this, on linux (FC4, kernel 2.6.14-1.1656_FC4 on a pentium4 system)

Here is a tiny example to illustrate the problem:
$ more wspec/models.wrm
?Interaction Bait UNIQUE ?Text
Prey UNIQUE ?Text
fns

$ more test1.ace
Interaction : "test1"
Bait "bait1"
Prey "prey1"

$ more test2.ace
Interaction : "test1"
Bait "bait1"
Prey "prey1"
fns

$ ace.supported/acediff test1.ace test2.ace
reading file 1 - 4 lines read - sorting file 1
reading file 2 - 6 lines read - sorting file 2
performing diff - sorting diff
// acediff difference from test1.ace to test2.ace

Interaction "test1"
Prey "prey1"
fns
-D Prey "prey1"

// end of file

As you can see, acediff adds the Prey, then deletes it. After parsing
the acediff output, I've obviously lost my Prey info.

Funny thing is, if you replace "fns" with "Fns" it's OK...
But if you use a different tag you get strange behaviours.
eg, using "a_A", acediff also kills the Bait!
As far as I can tell (but I haven't tested it much), it works OK when
the tag starts with an uppercase letter.

Is something wrong with my files or ace binaries??

A+
nicolas

--
------------------------------------------------------------
Nicolas Thierry-Mieg
Laboratoire LSR-IMAG, BP 53, 38041 Grenoble Cedex 9, France
tel : (33/0)4-76-63-55-79, fax : (33/0)4-76-63-55-50
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Re: What AceDB "Error status = 139" means?

2006-02-14T11:28:03Z

Nicolas,

No error appears after setting up ulimit -s unlimited, and
everything looks fine. Thank you very much!!

Jing

On Tue, 14 Feb 2006, Nicolas Thierry-Mieg wrote:

>
> bash is fine
>
> ...
> ulimit -a
> to see your current limits
>
> then eg to set the stack size to max, type:
> ulimit -s unlimited
>
>
> this will only change the limits for your current shell, hence you
> should call tace from it
>
> when satisfied you can put the correct ulimit commands in your
> .bash_profile to make the changes affect every new shell
>
>
> try setting every value to unlimited, at least the memory related ones
> (except core, which you can set to 0 since you probably don't read core
> dumps anyways)

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ulimit ["Error status = 139"]

2006-02-14T09:04:57Z

Hi Jing,

> I checked the ulimit on my server
> (see bellow) but not sure what that means? what is the current size that
> I am having? - Could you give me a hint?

In bash, say "ulimit -a".
On greengenes this gives me:

$ ulimit -a
time(seconds) unlimited
file(blocks) unlimited
data(kbytes) unlimited
stack(kbytes) 8192
coredump(blocks) 0
nofiles(descriptors) 64
memory(kbytes) unlimited

This reminds me, a few months ago I had to reset the limit on descriptors
(the number of files open at the same time) in order to load GrainGenes.
User acedb's .cshrc has this:

# dem 8nov05: The default 64 descriptors isn't enough for loading ACEDB now.
unlimit descriptors

This is because GG's database/ directory has so many files, which isn't
your problem.

If your problem is running out of stack space there might be a message in
the system log, /var/adm/messages or wherever it is in baumwolle.

- Dave

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Re: What AceDB "Error status = 139" means?

2006-02-14T08:21:49Z

> alright, how about stack size limits etc...?
> if you have very large objects I think this could be a problem

That sounds in the right track! I do have very large objects and that's
where the problem starts to appear ... I checked the ulimit on my server
(see bellow) but not sure what that means? what is the current size that
I am having? - Could you give me a hint? By the way, I run tace under
bash, shall I try other shell?

Thank you.

Jing

=====================
baumwolle:/usr/bin$ more ulimit
#!/bin/ksh -p
#
#ident "@(#)alias.sh 1.2 00/02/15 SMI"
#
# Copyright (c) 1995 by Sun Microsystems, Inc.
#
cmd=`basename $0`
$cmd "$@"
=====================

On Tue, 14 Feb 2006, Nicolas Thierry-Mieg wrote:

> alright, how about stack size limits etc...?
> if you have very large objects I think this could be a problem
>
> (on bash, the relevant command is ulimit; on csh it's limit)
>
>
>
> Jing Yu wrote:
> >> have you tried
> >>loading the data with tace instead of xace?
> >
> >
> > Yes. The error message was given from tace. :(
> >
> > Jing
> >
> > On Tue, 14 Feb 2006, Nicolas Thierry-Mieg wrote:
> >
> >
> >>hello
> >>
> >>this is a long shot, but just in case it's gtk-related: have you tried
> >>loading the data with tace instead of xace?
> >>
> >>good luck
> >>nicolas
> >>
> >>Jing Yu wrote:
> >>
> >>>Hello,
> >>>
> >>>I got error message "Error status = 139" while loading data into
> >>>acedb. Does anyone know what that means?
> >>>
> >>>- The error message never appears when I load each data independently into
> >>>an empty database, but will appear when load them together or added
> >>>more data into a database that with large part of data existing.
> >>>
> >>>- I've tried ace_4.9f, ace_4.9p, etc.;
> >>>- The systems so far I've tried are:
> >>> 1. SunOS baumwolle 5.10 Generic sun4u sparc SUNW,Ultra-4
> >>> 2. SunOS algodon 5.8 Generic_108528-21 sun4u sparc SUNW,Ultra-60
> >>> 3. Linux ceres 2.2.16-22smp
> >>>
> >>>And they all gave me the same error message. And my dataset is not very
> >>>large yet, much smaller than that of graingenes (8 block*.wrm files of
> >>>mine compare to 69 block*.wrm files of graingenes, with the same size of
> >>>each block*.wrm in /database).
> >>>
> >>>Can anyone help me on this? Thank you very much.
> >>>
> >>>
> >>>Jing
> >>>
> >>>
>
> --
> ------------------------------------------------------------
> Problems with my digital signature? visit:
> http://igc.services.cnrs.fr/Doc/General/trust.html
> --------------------
> Nicolas Thierry-Mieg
> Laboratoire LSR-IMAG, BP 53, 38041 Grenoble Cedex 9, France
> tel : (33/0)4-76-63-55-79, fax : (33/0)4-76-63-55-50
> ------------------------------------------------------------
>

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Re: What AceDB "Error status = 139" means?

2006-02-14T06:45:00Z

> have you tried
> loading the data with tace instead of xace?

Yes. The error message was given from tace. :(

Jing

On Tue, 14 Feb 2006, Nicolas Thierry-Mieg wrote:

> hello
>
> this is a long shot, but just in case it's gtk-related: have you tried
> loading the data with tace instead of xace?
>
> good luck
> nicolas
>
> Jing Yu wrote:
> > Hello,
> >
> > I got error message "Error status = 139" while loading data into
> > acedb. Does anyone know what that means?
> >
> > - The error message never appears when I load each data independently into
> > an empty database, but will appear when load them together or added
> > more data into a database that with large part of data existing.
> >
> > - I've tried ace_4.9f, ace_4.9p, etc.;
> > - The systems so far I've tried are:
> > 1. SunOS baumwolle 5.10 Generic sun4u sparc SUNW,Ultra-4
> > 2. SunOS algodon 5.8 Generic_108528-21 sun4u sparc SUNW,Ultra-60
> > 3. Linux ceres 2.2.16-22smp
> >
> > And they all gave me the same error message. And my dataset is not very
> > large yet, much smaller than that of graingenes (8 block*.wrm files of
> > mine compare to 69 block*.wrm files of graingenes, with the same size of
> > each block*.wrm in /database).
> >
> > Can anyone help me on this? Thank you very much.
> >
> >
> > Jing
> >
> >
> > _______________________________________________
> > Acedb mailing list
> > Acedb@...
> > http://www.bio.net/biomail/listinfo/acedb
>
> --
> ------------------------------------------------------------
> Problems with my digital signature? visit:
> http://igc.services.cnrs.fr/Doc/General/trust.html
> --------------------
> Nicolas Thierry-Mieg
> Laboratoire LSR-IMAG, BP 53, 38041 Grenoble Cedex 9, France
> tel : (33/0)4-76-63-55-79, fax : (33/0)4-76-63-55-50
> ------------------------------------------------------------
>

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What AceDB "Error status = 139" means?

2006-02-13T09:30:31Z

Hello,

I got error message "Error status = 139" while loading data into
acedb. Does anyone know what that means?

- The error message never appears when I load each data independently into
an empty database, but will appear when load them together or added
more data into a database that with large part of data existing.

- I've tried ace_4.9f, ace_4.9p, etc.;
- The systems so far I've tried are:
1. SunOS baumwolle 5.10 Generic sun4u sparc SUNW,Ultra-4
2. SunOS algodon 5.8 Generic_108528-21 sun4u sparc SUNW,Ultra-60
3. Linux ceres 2.2.16-22smp

And they all gave me the same error message. And my dataset is not very
large yet, much smaller than that of graingenes (8 block*.wrm files of
mine compare to 69 block*.wrm files of graingenes, with the same size of
each block*.wrm in /database).

Can anyone help me on this? Thank you very much.

Jing

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[Acedb-soft] AceDB on Windows

2005-11-24T06:08:19Z

Hi,

I got a person with problems using the Wormbase WS149 database with AceDB on
Windows.
When he tries to dump all objects from Wormpep, AceDB dies and throws a memory
allocation error:
like:
(Memory allocation failure when acedb requested 301989888 bytes, acedb has
already allocared 1134799304 bytes)

Now that wouldn't be too unusual if the machine wouldn't be a 3GB RAM windows
2003 server with a 4GB paging file. So the free memory is there, it just cannot
allocate it. As far as I remember there was some kind of slight issue with
allocating more than 2GB in one chunk in Windows, but 1.4 GB should be fine.

On a 32bit i686 GNU/Linux machine it needs to allocate 1501MB to dump all
objects and does so without any errors.

thanks,

Michael

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[Acedb-soft] BIRCH: ACEDB organizes software documentation

2005-10-24T11:34:02Z

Readers of this group may be interested in knowing that the
BIRCH bioinformatics platform employs ACEDB as the
database manager for all software documentation files,
giving the user a one-stop view of all documentation for
all programs.
The Python program htmldoc.py automatically creates
web pages from the birchdb database. Web pages organize
programs by Category, Package, and also a Program Index.
A tutorial with screenshots showing how local documentation
is merged with core BIRCH documentation is found at

http://home.cc.umanitoba.ca/~psgendb/birchadmin/addprog/localdocs.html

Below is a more general description of the most recent
release of BIRCH

---------------------------------------------------------------
The word 'system' implies many parts working together in a coordinated fashion.
While installing programs and databases can be a major effort, transforming them
from a mere collection into an integrated system is far more difficult.

The BIRCH system (http://home.cc.umanitoba.ca/~psgendb) makes it easy to find and use
almost any program, data or document. The core distribution includes software for DNA,
protein, and molecular marker data.

For end users:

* The GDE graphic interface [Smith et al., 1994] makes it easy to create ad
hoc data pipelines using output from one program as input for another.
* Locally-installed programs and databases can be added transparently,
without re-compiling GDE.
* Web documentation from the BIRCH core and local documents are unified in a
single database.
* Tutorials are task-oriented, rather than program-oriented.

For the sysadmin:

* Install wizard automates installation, configuration and updates.
* Local customizations automatically re-integrated into BIRCH during updates.
* Central configuration: everything works the same for all users.
* OS-independent datafiles, documentation and scripts are installed separately from
OS-dependent binaries. BIRCH automatically finds the binaries for each host (eg.
Solaris, Linux)
* All components are freely-available software.
* Scaleable from a single PC to a campus-wide system

Web applications are awkward to use and are intractable to automation for large projects.
When BIRCH is installed along with desktop and office applications, the result is a
seamless system on a single desktop. Because BIRCH is network-centric, any user can do
any task from anywhere.

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