Re: [base] MAGE-ML for ArrayExpress update, plug-ins

, by Henrik Bengtsson from Lund) continues to work in BASE 2.0 Thanks Charles On 16 janv. 06, at 13:40, Jari Häkkinen wrote: Hi Angela, BASE plug-ins ... we are slowly working on getting the web page up again. Meanwhile we urge those of you who have plug-ins to send them to us through http

Re: [base] Anybody install BASE under Tomcat?

? If I want to run BASE2.17 under tomcat, what I need to do? Reinstall the BASE, or just copy the corresponding folds to Tomcat? Any suggestions will be appreciated. Thanks a lot! Best Regards, Longfei -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL

[base] BASE2 and affymetrix

line to share with us, please use the mailing lists or add comments through http://lev.thep.lu.se/trac/base/ticket/150 Cheers, Jari -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46

Re: [base] 2 questions about Plugin configuration

Nicklas Nordborg wrote: Emmanuel Courcelle wrote: Hello Now using Base 2.1... I am trying to configure the Raw Data importer plugin, to upload and parse genepix-type files. 1/ Pb configuring this plugin -- I click Plugin/Configuration/New

Re: [base] how to import reporters ?

The reporter import button does appear because there is no plug-in configured for import of reporters. You need to create a configuration for the Reporter importer plug-in. We have compiled a getting started document that outlines the first steps with BASE 2,

[base] Browser compatibility

. The list of BASE team supported browsers is short: Firefox production releases 2 or later. Internet Explorer 7 or later. Jari -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46

Re: [base] long term future and support for BASE2

=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Häkkinen, PhD Complex Systems Division

Re: [base] Offline files

___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics

Re: [base] Offline files

PROTECTED] -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http

Re: [base] Offline files

Ah, even better ;-) Nicklas Nordborg wrote: Jari Häkkinen wrote: Hi all, Just a thought, I think the best choice to trigger a large import like this is to create a plug-in instead of adding extra tabs to the file browser. The plug-in should start by requesting the zip file/directory

Re: [base] Offline files

Micha Bayer wrote: Hi Jari, That sounds perfectly reasonable when you put it like this, but I was put off going down that route by a post to the list from Nicklas (http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg00228.html) where he says that it is best to not use a

Re: [base] Offline files

Jari Häkkinen wrote: Hi all, Just a thought, I think the best choice to trigger a large import like this is to create a plug-in instead of adding extra tabs to the file browser. The plug-in should start by requesting the zip file/directory to import. If the zip file

Re: [base] Offline files

] On Behalf Of Nicklas Nordborg Sent: 29 November 2006 14:40 To: BASE ML Subject: Re: [base] Offline files Jari Häkkinen wrote: Hi all, Just a thought, I think the best choice to trigger a large import like this is to create a plug

Re: [base] Offline files

clean. Jari Micha Bayer wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:basedb-users- [EMAIL PROTECTED] On Behalf Of Jari Häkkinen Sent: 30 November 2006 15:42 To: BASE ML Subject: Re: [base] Offline files There is a possibility to get access to the subversion repository

[base] BASE 2.1.1 released

A new minor release is available for download at http://base.thep.lu.se/wiki/DownloadPage A list of fixed item is available here http://base.thep.lu.se/query?status=closedmilestone=BASE+2.1.1order=id Jari -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL

Re: [base] walk thru

Hi, There is a getting started document available at http://base.thep.lu.se/chrome/site/doc/user/index.html Jari Gabe Dagani wrote: Greetings, Has anyone created a simple walkthru for setting up a simple experiment, uploading GPR, GPS, TIFF files into a project and doing some

Re: [base] Add new plates

A list of all core plug-ins with sample configuration files (also for plate importer) is available at http://base.thep.lu.se/chrome/site/doc/admin/plugin_configuration/coreplugins.html Jari Nicklas Nordborg wrote: Audrey Bihouee wrote: Hi everybody, A little question in BASE 2 : I'm very

Re: [base] Base and webservices

Hi, there is sample code available at http://baseplugins.thep.lu.se/wiki/se.lu.thep.webservices_clients that runs against the demo server. The code is written in Perl and R. The Perl can be used as a script or used to get BASE/R connectivity from an R environment. Jari Nicklas Nordborg

[base] BASE 2.3.1 released

Hi all, Our best BASE so far is available for download at http://base.thep.lu.se/wiki/DownloadPage Happy BASEing, The Lund BASE team -- Jari Hakkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46

Re: [base] Unable to import root bioassay

Hi, You have probably not imported all probeset into the reporter table. Please make sure that ALL reporters are imported, that is check that the number of imported and updated reporters match the number of probesets in the affychip you use. Cheers, Jari [EMAIL PROTECTED] wrote: Dear

Re: [base] import of affymetrix data - which approach

Hi, The plier and rmaexpress plug-ins calculates the probeset expression values using information from the cel/cdf files. The plugins are presented on the BASE plugin site http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix How the expression values are calculated is presented elsewhere

[base] BASE 2.4 released

Hi all, We are happy to announce BASE 2.4. The packages are added to the download area, http://base.thep.lu.se/wiki/DownloadPage Please send feedback through the mailing lists. Happy BASEing The Lund BASE team - This

Re: [base] Base1PluginExecuter parameter xml

Why not use the clustering in the MeV plugin shipped with BASE? Jari Johan Enell wrote: Hj Bob, The clustering from Base1 will not work in Base2. Or more precisely, you will be able to run the plugin but you wont be able to se the result. The visualization page in Base1 was a

Re: [base] Error: Run Plugin: RMAExpress plug-in

Hi, jesse paquette wrote: Hello, I'm still trying to get through the 2.1 getting started document (http://base.thep.lu.se/chrome/site/doc/user/getting_started.html). Moving on to section 2d, Analysing an experiment step I. I'm getting an error when I try to run the RMAExpress plug-in

Re: [base] 2.4.2 = 2.4.3 - any database schema change?

There is no need to delete the database between upgrade in a stable release of BASE. Please read http://base.thep.lu.se/chrome/site/latest/html/admindoc/installation_upgrade/installation_upgrade.upgrade.html for upgrading instructions. Jari Dave Hau wrote: 2.4.3 release followed closely

Re: [base] Problems running Tab2Mage Importer, NOT sufficient Disk Space

Just for your information: Dominic Oyeniran wrote: This is a known issue and has been documented here: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt. Please scroll to the usage section right after the installation section. We prefer to use links

Re: [base] Tab2Mage Importer has problemsfinding AnnotationTypeCvImporter

However, given the performance improvement you should go for 2.4.4 Jari Nicklas Nordborg wrote: vegard nygaard wrote: When I briefly inspected what was created in BASE it looked OK despite the error messages in the log. The overview tab for the experiment crashed though, but it has done

Re: [base] migration from 1.2.16 to 2.3.2

Select 'Download BASE' at http://base1.thep.lu.se/ and download version 1.2.17b. Follow the instructions in the package to upgrade from 1.2.16 to 1.2.17b The 1.2.20/21 is a reference to the underlying database schema version and not the BASE application version. It is a little bit confusing.

[base] BASE 2.4.5 available for download

A new version of BASE is available for download at http://base.thep.lu.se/wiki/DownloadPage This release contains one fix removing a debug sleep statement. Server performance is improved when upgrading to this release. The Lund BASE team

Re: [base] regular expression and wildcards

Nicklas Nordborg wrote: vegard nygaard wrote: F633 Median not working but giving a funny error message: Error: For input string: F633 MEdian on line..., (The E's in the input has been uppercased!) That is because string like '1.23e-2' are not recognised as numbers unless the 'e' is first

Re: [base] regular expression and wildcards

I moved it to the BASE core ticketing system as http://base.thep.lu.se/ticket/811 Jari Nicklas Nordborg wrote: vegard nygaard wrote: Thanks for quick answers. I would like column mappings to support wildcards or regular expressions. Not a big thing, but I took the liberty to add it as a

Re: [base] Getting started with BASE2.4

Are you logged in as with administrator privileges? Only users with administrator privileges are allowed to use the Reporter map importer and thus configure it. There is no need to create this plug-in it comes with pre-installed with BASE. Jari Diana Bernal wrote: Dear BASE staff, I am

Re: [base] Java memory error

We cannot recreate this problem. We have used the CDF importer on BASE 2.5.0beta and 2.4.5 with no problems. One difference may be that we use jobagents (i.e., running jobs in a different thread than the core BASE application) but we did not experience any failures prior to switching to

[base] BASE 2.5 released

Hi all, We are happy to announce the release of BASE 2.5. The packages are added to the download area, http://base.thep.lu.se/wiki/DownloadPage Please send feedback through the mailing lists. Happy BASEing The Lund BASE team

[base] BASE 2.5.1 released

A new version of BASE is available for download at http://base.thep.lu.se/wiki/DownloadPage Fixed issues are listed at http://base.thep.lu.se/query?status=closedmilestone=BASE+2.5.1 The Lund BASE team - This SF.net email

Re: [base] APT version 0.2 released

Nice work. I've successfully tested the apt-summarize plug-in. I do not have any genotype data so I have to leave that for someone else to test. I miss a short description of the two plug-ins. How to use them and what to expect from them. Specifically the genotyoe plug-in requires some

Re: [base] BASE2 backups

Hi, We are working on a backup scheme here in Lund. We'll send a note when we have something that at least works. Then we can all improve our backup strategy ;-) Why use svn? Do you need to track changes to files? For the userfiles directory a simple rsync should be fine, it is incremental

Re: [base] Luminex data

There is support for Illumina using the Illumina plug-in package, http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina. Illumina is bead-based and maybe a similar package can be created for Luminex? So, BASE supports bead based data but luminex is currently not directly supported. Jari

Re: [base] Which import plugins are available in BASE?

Good Morning All, I have a lot of Affymetrix array data that I would like to analyze together. The zip that contains these files is very big and I can't upload it to BASE to use Batch Data Importer to import it into my experiment. There is a known issue with files larger than 2GB,

Re: [base] lowess normalisation

The problem is now being fixed, http://base.thep.lu.se/ticket/1077. Unfortunately this problem affects all versions of BASE2 and everyone are recommended to upgrade to the future 2.7.2 (or later). The problem is localized and 2.7.2 will be released later today or at latest tomorrow. More

[base] BASE 2.7.2 released. Important bug fix included!

Hi all, We have released BASE 2.7.2. The release includes important bug fixes in the LOWESS plug-in shipped as a part of the BASE package. Some other improvement are also included in the release. It is highly recommended at all BASE installations where LOWESS is used as a part of their analysis

Re: [base] How to connect to FTP server

Hi, In ftp/config.xml the nio-listener tag there is a port property set to 2121. I think this sets the port number. See http://baseplugins.thep.lu.se/browser/extensions/net.sf.basedb.ftp/trunk/ftp-config.xml#L29 Jari Pawel Sztromwasser wrote: Hi all, I have just upgraded to the latest

Re: [base] high-throughput transcriptome sequencing data

Hi Bob, Sorry for not commenting your thoughs on storing sequencing data in BASE. We have discussed it here and will be looking into it later. This will become an issue for us also since we have sequencing equipment generating huge quantities of data. So far we are only getting friendly with

Re: [base] batchimport example spreadsheet seems corrupted

Micha Bayer wrote: Hi, I have been trying to look at the example file for the batch import but it seems corrupted. I am trying to open it in OpenOffice 2.3.0 and the file does load but then Calc instantly hangs. The file is created with OpenOffice 2.4 and works. I downloaded it and could

Re: [base] problem attaching files to raw bioassays using the batch importer -- BASE 2.8.4

Are the raw data files visible to the plug-in? If you upload the files with ftp they are not automatically assigned to a project. You need to set the parameter defining how the plug-in should find existing items referenced in the file. If this is not the problem, can you try to only map the

Re: [base] problem attaching files to raw bioassays using the batch importer -- BASE 2.8.4

I have not encountered any problems with attaching files earlier. I decided to play around with partially filled import files. I succeeded in creating a file that fails to attach files even though the importer reports success. BASE 2.8.4 and my 2.9pre test version both fails but the resolution

Re: [base] Getting Internal File Name

There is an ftp-server extension for BASE, http://baseplugins.thep.lu.se/wiki/net.sf.basedb.ftp Maybe this can help? It should be possible to get Perl to download files using ftp. And the names are the native names, i.e. no translation is needed to the internal name. Jari Offord, Victoria

[base] Changing default permission setting for a project

The default project permission for items created with an active projects is 'RUWD'. Can I change this default to a simple 'R'? It is of course possible to restrict all project members credential to 'R' individually, but I would prefer to set the project credentials for new items to 'R'.

Re: [base] Experiment overview loads very slowly

Hi all, The 2.11 release will target performance issues. The next release is 2.10 but we have not set a dead line for the 2.10 release yet. However, a hopefully performance boosted BASE 2.11 should be out during the spring, until then we have to live with some slow BASE clicks. I agree with

Re: [base] JEP plugins

Hi Louise, Maybe you should look into the http://baseplugins.thep.lu.se/wiki/net.sf.basedb.normalizers package for inspiration on how to create a plug-in for your needs. Jari Nicklas Nordborg wrote: Louise Donnison wrote: Hi We have some raw bioassays in an experiment and I am trying

Re: [base] BASE on 64-bit machine

I am running BASE on a 64-bit mac but my mysql server is a 32-bit binary (java is 64-bit). I have no problems to report related to the bitness but then again I am not completely in the 64-bit domain. Jari michael watson (IAH-C) wrote: Dear All Quick question with a quick answer I expect

Re: [base] Errors while creating bead summary Illumina data

Hi, As you describe it it seems like you have bead level data in your data files. The Illumina package for BASE expects bead summary data, i.e., the average for each bead type (together with some other numbers as described in

Re: [base] can you give spot images a css class?

Hi Chad, The requested class will appear in BASE. We missed it for the 2.10 release but the request is now added to the ticketing system, http://base.thep.lu.se/ticket/1242 Cheers, Jari Chad Matsalla wrote: Greetings! I'm using base-2.9.2 on tomcat 6.0.18 in Geronimo 2.1.3. We use

Re: [base] Affymetrix Power Tools Error

Hi, The problem seems to be in the apt-probeset-summarize program as you point out. Have you tried to run the same analysis outside of BASE? What is the outcome of that? Cheers, Jari philipp-1.kai...@novartis.com wrote: Hi, I am trying to get BASE 2.9.2 working with the APT 0.2 plugin

Re: [base] Affymetrix Power Tools Error

Klybeckstrasse 141 CH-4057 Basel Switzerland Phone: +41 61 6962720 Fax: +41 61 6963373 Email : philipp-1.kai...@novartis.com Jari Häkkinen j...@thep.lu.se 04.03.2009 15:37 Please respond to BASE ML basedb-users@lists.sourceforge.net To BASE ML basedb-users@lists.sourceforge.net cc

Re: [base] File types assigned when extracting an archive

I notice that I closed the ticket. Maybe we should reopen it and put it out BASE 3 milestone? Disclaimer: There is NO plans to start on a BASE 3 in the foreseeable future. Jari Nicklas Nordborg wrote: This was requested some time ago. There is a ticket at http://base.thep.lu.se/ticket/978

[base] New version of MultiExperiment Viewer, MeV, extension for BASE released

A new version of the MeV extension for BASE was released yesterday and already improved today! The new extension is based on the latest MeV (4.3.02) and supports expression data analysis from BASE with simple clicks. MeV web page http://www.tm4.org/mev.html MeV BASE extension web page

Re: [base] BASE and methylation data.

Hi Lavinia, I apologize the delayed response but I needed to check whether we anticipate this need for our own purposes. The good news is that our lab will be interested in getting methylation array support into BASE, the bad news is that we have no real time line for BASE methylation

Re: [base] Item name when using batch importer

Hi Klemens, When using the batch importers you must create the names for all items yourself. We use a spreadsheet that follows the naming convention adopted in BASE. See the attached file that we use at our facility. Cheers, Jari Klemens Vierlinger wrote: Hi everyone, I quite like the

Re: [base] normalization and ratios between 2 bioassays

YANNICK wrote: Hi BASE2 users! I am using BASE 2.11 and have some questions. I want to calculate Ratios from 2 bioassays organized as following: - 1st bioassay = control - 2nd = treatment Labellings are performed as following: Cy5= pool of all samples extracts. Same in all arrays (serves

Re: [base] Tab2Mage export

Hi, It is a while since Paulo asked the below question. I have added a ticket on this to the plug-in dev site, http://baseplugins.thep.lu.se/ticket/209 This means that we are going to look into creating a submission tool. It will probably target GEO submission since there are work done on

Re: [base] quantile normalization questions

Yannick Lippi wrote: __SECOND QUESTION: R/G quantile normalization Jari said: Obviously R-G quantile is not supported since the methods in net.sf.basedb.normalizers only work on ratios. - i am not expert on java developping.. but what does mean: methods in net.sf.basedb.normalizers only

Re: [base] Illumina plugin

Hi, Olivier Lefevre wrote: I am not having much luck installing that plugin. It wants you to run updatedb.sh. When I do that it says Building database, which is alarming in and of itself since that suggests it is rebuilding the db from scratch, which begs the question of whether it is

Re: [base] Cloning a BASE instance

Before starting to clone BASE you could try to reset list settings with File - Reset list settings ... select memory and database in the pop-up. BASE stores uploaded or generated files as files in the filesystem. The database keep tracks of file locations. There is no information in files

Re: [base] Cloning a BASE instance

The steps I send covers my needs in that I do not use a secondary storage area, user files area is covered in my previous posting, and installed plug-ins are backed up by normal computer backups. But you are right, for a full clone you should also copy your complete BASE installation and the

Re: [base] Can't find getting started guide

Hi, The document you are looking for is obsolete, try the getting started section link at http://base.thep.lu.se instead. If you really want the outdated document you'll find it at http://base.thep.lu.se/browser/trunk/doc/historical/user/getting_started.html You'll need to download the file

Re: [base] Can't export data to Tmev

Nicklas Nordborg wrote: Daniel Octavio Palenzuela Gardon wrote: By other side, when we try to launch Mev in the Tools column when viewing bioassay sets of an experiment, there is a file with extension …TDMS.TXT that it`s suppose to be save in raw data, but when we do browse, there isn’t

Re: [base] Size limit of online file edit

I can confirm Pawels problem. I run Firefox 3.5.3 on Mac OS X 10.6.1 (Snowleopard). My 63k file is now only 32k. Jari Nicklas Nordborg wrote: Pawel Sztromwasser wrote: I just tested it again (FF3.5.3). Here is how to reproduce: - upload a text file which is larger then 8kb - memorize

Re: [base] Size limit of online file edit

Jari Häkkinen wrote: I can confirm Pawels problem. I run Firefox 3.5.3 on Mac OS X 10.6.1 (Snowleopard). My 63k file is now only 32k. And redoing edit saves a 16k file, redoing the edit saves a 8k file, and another edit will not halve the size but a 7.99k file is saved. Jari

Re: [base] Size limit of online file edit

Nicklas Nordborg wrote: I downloaded and installed Tomcat 6.0.16 and got the same problem. It works with Tomcat 6.0.20. And our production server runs 6.0.16. So, it is time to upgrade. Jari -- Come build with us!

Re: [base] File path derivations

Offord, Victoria wrote: I gather that the 2009 is the year and the 02 refers to the date the file was uploaded. How are the other numbers/values created as I wanted to add folders/directories from a program I am running which creates reults files for the data stored in BASE and wanted to keep

Re: [base] MEV Launcher suggestions

tropy wrote: Nicklas Nordborg wrote: tr...@valdelsa.net wrote: 1. Log2 ratio transform MeV behaved (still behaves) inconsistently with data it read from TDMS with respect to logging data or not. In some cases MeV auto-logged data and in some other cases it did not. When we began to

Re: [base] MEV Launcher suggestions

Jari Häkkinen wrote: MeV behaved (still behaves) inconsistently with data it read from TDMS The above line was meant to say MeV behaved (still behaves?) inconsistently with data it read from TDMS ... The question mark because I have not actually checked it. It may be that the issues

Re: [base] Data truncation: Data too long

Hi, There is already a property Gene Symbol but maybe this won't cut it for you? Jari On 1/12/10 4:25 PM, flap...@free.fr wrote: Hello, I'm using the base-2.14.1 and I'm trying to import a genepix GAL file. I've add in the file named extended-properties.xml, this :

Re: [base] FW: tab2mage and magetab

Hi, Was this mail was intended for the mailing list? Jari On 2/21/10 12:34 AM, alaa gaber wrote: HI, I am asking 1-if the base2 uses a tab2mage format 2-i have a problem in converting tab2mage into mage-tab format 3-displaying both in base2 4-can base2 understand perl language my

Re: [base] FW: tab2mage and magetab

On 2/21/10 12:34 AM, alaa gaber wrote: 4-can base2 understand perl language Not directly, BASE is written in Java. You can write plug-ins using Perl or other languages. See plug-in developer documents for more details and browse plug-ins in http://baseplugins.thep.lu.se where several plug-ins

Re: [base] base help

Hi, This question was asked the other day on the BASE user mailing list (http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg01954.html) and Nicklas responded to it. The problem is that user qouta is too low. Your BASE administrator must increase the quota or you must delete

Re: [base] help

On 5/28/10 5:43 AM, Irina Maltseva wrote: I followed the installation instruction on http://base.thep.lu.se/chrome/site/doc/html/admindoc/installation_upgrade/installation_upgrade.html and change the user to ‘root’ in base.config file. I've created base2 and dynamic.base2 on mysql server

Re: [base] Handling RNA-Seq and ChIP-Seq data

Hi, We are currently working on how to incorporate sequence data in BASE. We now have in-house sequencing capacity and need to manage all data generated. We have not formalized our ideas yet but we'll post whatever we will are planning to do in another mail/ticket in very near future. We

Re: [base] Handling RNA-Seq and ChIP-Seq data

Hi, On 2010-10-18 20.35, Adam Halstead wrote: Thanks for your response Jari. I understand support for next generation sequencing data is currently being developed by the BASE developers - is there a beta version we can look at? Do you need help developing this functionality? What kind of

Re: [base] Error running RMAExpress plug-in

Have you followed the instructions in the README http://baseplugins.thep.lu.se/browser/plugins/base2/se.lu.thep.affymetrix/tags/0.7/README Do you have an CDF file attached to the design? Jari On 2010-12-06 07.56, Irina 264 wrote: I am trying to run the RMAExpress plug-in to import

Re: [base] Base 1.2 plugin - Virtual Array -1.1

Are you sure that all prerequisites are met? The plug-in configuration and the Base1PluginExecutor should be shared appropriately. Also, Virtual array works only on 2-channel data. Jari On 2011-03-10 17.25, Thomas Person wrote: Thanks! That change allows installation but once I atmpt to

Re: [base] Error: GC overhead limit exceeded

Can the problem be that the jobagent does not get enough memory? CATALINA OPTS will only influence the BASE core server and if there are separate jobagent processed then these may need an increased memory setting? I may be completely off here but just a thought. Jari On 2011-05-23 08.27,

Re: [base] Dealing wiht duplicate spots

On 2011-11-22 09.43, Nicklas Nordborg wrote: On 2011-11-21 21:32, Nantel Andre wrote: We don't have any regular users yet since we are still figuring out how it works. I am doing everything from my administrator account. Have you created a file format configuration for the files you are

Re: [base] BASE database

Hi, The procedure to upgrade from 1.2 to latest BASE is uncharted territory for us. We switched from 1.2 when BASE 2.6 was current. One path forward may be as outlined below. Each BASE 2 and newer distribution contains upgrade instructions. Please read them. Please report if you succeed and

Re: [base] BASE database

We have realized that migration from BASE 1.2 to BASE 2/3 is only supported from a BASE 1.2 server running MySQL. We do think that adding support for other database engines is possible but we have not tested it and will not actively work on extending migration support beyond what can be found

Re: [base] Base 3.2 installation on Mac OS 10.6 server

On 2013-09-12 16:47, Laurent TROXLER wrote: Yes, I can axes to Tomcat Home page and login as root. There I can see that base2 is uploaded. There isn't any obvious error on the web interface. To answer to Jari, I am working presently directly on the server to avoid any internet problem. Ok.

Re: [base] Base 3.2 installation on Mac OS 10.6 server

On 2013-09-11 10:57, Laurent Troxler wrote: going through the log files here is what I can get: system.log: repeating those two lines Sep 11 10:32:00 seridi java[85937]: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. Sep 11 10:32:02 seridi

Re: [base] Anyone have a cloud-deployable image with BASE?

Hi, There is no cloud-deployable BASE available and there is no plans for one either. The demo server has moved and the redirect seems to be broken. I have sent a mail to the network administrator of the previous facilities asking them to restore the redirect. The demo server is located at

Re: [base] basedb-users Digest, Vol 70, Issue 1

On 2015-03-12 09:24, Jari Häkkinen wrote: One source for the problem is that the underlying RMAExpressConsole program doesn't handle ST arrays, or maybe treats ST arrays differently. I meant to say that problem may be with RMAExpressConsole but I don't know. Jari