Timeline



Jun 18, 2007:

11:15 AM WikiStart edited by Peter Johansson
(diff)

Jun 15, 2007:

9:45 AM WikiStart edited by Jari Häkkinen
Added login information for ticket submitters. (diff)

Jun 14, 2007:

10:30 AM Changeset [341] by Peter Johansson
update copyright

Jun 13, 2007:

6:39 PM Changeset [340] by Peter Johansson
fixes #65 version number in plugin_WeNNI.base is generated …
6:39 PM Ticket #65 (version number in BASE1 plugin is not updated automatically) closed by Peter Johansson
fixed: (In [340]) fixes #65 version number in plugin_WeNNI.base is generated …
5:14 PM Ticket #65 (version number in BASE1 plugin is not updated automatically) created by Peter Johansson
4:28 PM Changeset [339] by Jari Häkkinen
Added comment (recommendation) on using presence filter in BASE 1.
11:27 AM Changeset [338] by Peter Johansson
using ac macro fully rather than bashing

Jun 12, 2007:

7:01 PM DeveloperPage edited by Peter Johansson
(diff)
6:58 PM Ticket #61 (change structure of tags) closed by Peter Johansson
fixed
6:56 PM se.lu.thep.affymetrix edited by Peter Johansson
(diff)
6:55 PM SubversionCheckout edited by Peter Johansson
(diff)
6:53 PM Changeset [337] by Peter Johansson
reorganizing tag file structure refs #61
6:11 PM Changeset [336] by Peter Johansson
adding javacflags in configure
3:11 PM Changeset [335] by Peter Johansson
slimming down files refs #50
11:18 AM Changeset [334] by Peter Johansson
first compilable version refs #50
9:32 AM Changeset [333] by Peter Johansson
improved Makefile.am refs #50

Jun 11, 2007:

4:49 PM Changeset [332] by Peter Johansson
class is BASE2 specific and should be in that directory
4:47 PM Changeset [331] by Peter Johansson
initial commit for abstract plugin support class for running external …
4:38 PM Changeset [330] by Peter Johansson
clean removes entire .build file structure

Jun 8, 2007:

3:00 PM Changeset [329] by Peter Johansson
overriding autotools variable bindir, so bins are installed in …

Jun 7, 2007:

6:25 PM Ticket #59 (--with-gsl configure option) closed by Peter Johansson
fixed: (In [328]) cleaning up and adding --with-gsl option fixes #59
6:25 PM Changeset [328] by Peter Johansson
cleaning up and adding --with-gsl option fixes #59
5:03 PM Changeset [327] by Peter Johansson
refs #58 variable INSTALLDIR is set in configure and propagated out to …

Jun 5, 2007:

9:07 AM Ticket #62 (make check does not work) closed by Peter Johansson
fixed
9:01 AM WikiStart edited by Peter Johansson
(diff)

Jun 1, 2007:

4:55 PM Changeset [326] by Peter Johansson
fixes #325 make check works
4:37 PM Changeset [325] by Peter Johansson
refs #62 make check now works in base1 mode

May 31, 2007:

7:21 PM Ticket #64 (configure does not find basefile.h) created by Peter Johansson
Even though configure does not find basefile.h the pre-processor …
7:16 PM Ticket #57 (--with-base configure option [default /usr/local/base]) closed by Peter Johansson
fixed: (In [324]) fixes #57. --enable-base=X where X is either base1 base2 or …
7:16 PM Changeset [324] by Peter Johansson
fixes #57. --enable-base=X where X is either base1 base2 or stand-alone.
1:10 PM Ticket #63 (make distcheck should work) created by Peter Johansson
1:10 PM Ticket #62 (make check does not work) created by Peter Johansson
12:51 PM Changeset [323] by Peter Johansson
minor fixes
11:52 AM Changeset [322] by Peter Johansson
fixed typo
11:23 AM Changeset [321] by Peter Johansson
improved flags to local c++_tools

May 30, 2007:

12:15 AM Ticket #61 (change structure of tags) created by Peter Johansson
How? Add the package name to the path. What do you mean? Well, for …
12:07 AM DeveloperPage edited by Peter Johansson
(diff)

May 29, 2007:

11:30 PM WikiStart edited by Peter Johansson
(diff)
4:57 PM Ticket #51 (add configure options to WeNNI) closed by Peter Johansson
fixed: (In [320]) fixes #51. configure option state {base1, base2, …
4:57 PM Changeset [320] by Peter Johansson
fixes #51. configure option state {base1, base2, stand-alone} where …
4:37 PM Ticket #60 (explain how to run wenni (base1 version) against a base_devkit) created by Peter Johansson
3:54 PM Ticket #59 (--with-gsl configure option) created by Peter Johansson
3:53 PM Ticket #58 (--base-plugindir configure option) created by Peter Johansson
In BASE2 default is <--with-base>/www/plugins Files are installed in …
3:52 PM Ticket #57 (--with-base configure option [default /usr/local/base]) created by Peter Johansson
12:09 PM Ticket #49 (Rename wiki:onk.lu.se.ZTest to wiki:se.lu.onk.ZTest) closed by Jari Häkkinen
fixed
12:09 PM DeveloperPage edited by Jari Häkkinen
(diff)
12:07 PM DeveloperPage edited by Jari Häkkinen
Renaming onk.lu.se.ZTest (diff)
12:05 PM PluginDownload edited by Jari Häkkinen
Renaming onk.lu.se.ZTest (diff)
12:04 PM poolSD.png attached to se.lu.onk.ZTest by Jari Häkkinen
12:04 PM zscore.png attached to se.lu.onk.ZTest by Jari Häkkinen
12:03 PM probability.png attached to se.lu.onk.ZTest by Jari Häkkinen
12:03 PM normsdist.2.png attached to se.lu.onk.ZTest by Jari Häkkinen
12:03 PM normsdist.png attached to se.lu.onk.ZTest by Jari Häkkinen
11:59 AM se.lu.onk.ZTest created by Jari Häkkinen
Renaming onk.lu.se.ZTest
1:17 AM Changeset [319] by Peter Johansson
empty WeNNI.java and some minor changes in configure.ac stolen from yat

May 28, 2007:

11:37 PM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) created by Peter Johansson
I can see no reason why this component should be an outlier. The …
11:33 PM Ticket #55 (update ChangeLog) created by Peter Johansson
and make it look good in wiki
11:32 PM Ticket #54 (update README) created by Peter Johansson
and make it look good in wiki
11:32 PM Ticket #53 (update INSTALL) created by Peter Johansson
and make it look good in wiki
11:30 PM Changeset [318] by Peter Johansson
adding Makefile.am for base2 dir
11:27 PM Changeset [317] by Peter Johansson
wikized README et al and corrected configure.ac
11:18 PM Changeset [316] by Peter Johansson
replaced todo items with a reference to todo list in wiki
11:14 PM Ticket #52 (Add educational material and use cases.) created by Peter Johansson
11:10 PM Changeset [315] by Peter Johansson
changed structure again. NNIFileConverter is moved to bin, which means …
10:46 PM Changeset [314] by Peter Johansson
updating copyrights in modified files and added some Makefile.am
10:35 PM Changeset [313] by Peter Johansson
new file structure for BASE2
9:55 PM Ticket #48 (Rename wiki:WeNNI to wiki:se.lu.thep.wenni) closed by Peter Johansson
invalid: Published homepage is http://lev.thep.lu.se/trac/baseplugins/wiki/WeNNI
8:02 PM Ticket #51 (add configure options to WeNNI) created by Peter Johansson
Thre cases should be supported * ./configure --stand-alone -- skip …
7:55 PM Ticket #50 (create a BASE2 plug-in for se.lu.thep.WeNNI) created by Peter Johansson
6:23 PM Changeset [312] by Peter Johansson
removed imports not needed and added dependency in Makefile. Inherited …
5:42 PM Changeset [311] by Peter Johansson
creating a base class for plier and rma

May 25, 2007:

1:27 PM Changeset [310] by Peter Johansson
oops now we can compile again. sorry about that
12:59 PM Changeset [309] by Peter Johansson
changed name of the package in copyrights. It is no longer RMAExpress

May 24, 2007:

7:24 PM Changeset [308] by Peter Johansson
bumping version number
6:47 PM Ticket #45 (PLIER - Probe Logaritmic Intensity ERror) closed by Peter Johansson
fixed
5:39 PM Ticket #46 (RMAExpress wiki page) closed by Jari Häkkinen
fixed
5:39 PM Ticket #49 (Rename wiki:onk.lu.se.ZTest to wiki:se.lu.onk.ZTest) created by Jari Häkkinen
5:37 PM Ticket #48 (Rename wiki:WeNNI to wiki:se.lu.thep.wenni) created by Jari Häkkinen
5:36 PM PluginDownload edited by Jari Häkkinen
Renaming onk.lu.se.MergBioAssay? (diff)
5:34 PM mergebioassay_182.zip attached to se.lu.onk.MergeBioAssay by Jari Häkkinen
5:33 PM se.lu.onk.MergeBioAssay created by Jari Häkkinen
Renaming onk.lu.se.MergBioAssay?
5:25 PM PluginDownload edited by Jari Häkkinen
Renaming onk.lu.se.Smooth (diff)
5:24 PM smooth_179.zip attached to se.lu.onk.Smooth by Jari Häkkinen
revision 179
5:23 PM se.lu.onk.Smooth created by Jari Häkkinen
Renaming onk.lu.se.Smooth
5:18 PM PluginDownload edited by Jari Häkkinen
Renaming BatchDataImporter? (diff)
5:16 PM uk.ac.scri.batchimporter created by Jari Häkkinen
Renaming BatchDataImporter?
5:11 PM SubversionCheckout edited by Peter Johansson
(diff)
5:09 PM PluginDownload edited by Jari Häkkinen
Renaming WebServices? page (diff)
5:03 PM se.lu.thep.affymetrix edited by Peter Johansson
added info on how to check out tagged release (diff)
4:59 PM PluginDownload edited by Jari Häkkinen
affymetrix 0.6 release. (diff)
4:49 PM DeveloperPage edited by Jari Häkkinen
(diff)
4:47 PM SubversionCheckout edited by Jari Häkkinen
(diff)
4:47 PM se.lu.thep.affymetrix edited by Peter Johansson
changed doc links to tagged version (diff)
4:40 PM se.lu.thep.affymetrix edited by Jari Häkkinen
(diff)
4:37 PM se.lu.thep.affymetrix edited by Jari Häkkinen
New release to download. (diff)
4:32 PM base_affymetrix_plugin-0.6-src.tar.gz.MD5 attached to se.lu.thep.affymetrix by Jari Häkkinen
4:31 PM base_affymetrix_plugin-0.6-src.tar.gz attached to se.lu.thep.affymetrix by Jari Häkkinen
4:31 PM base_affymetrix_plugin-0.6.tar.gz.MD5 attached to se.lu.thep.affymetrix by Jari Häkkinen
4:31 PM base_affymetrix_plugin-0.6.tar.gz attached to se.lu.thep.affymetrix by Jari Häkkinen
4:28 PM Changeset [307] by Jari Häkkinen
Tagging se.lu.thep.affymetrix release 0.6
4:26 PM Changeset [306] by Jari Häkkinen
Setting up tagging hierarchy.
4:18 PM Changeset [305] by Jari Häkkinen
Added fixed items to list.
4:11 PM Changeset [304] by Jari Häkkinen
Bumped version number.
4:10 PM Changeset [303] by Jari Häkkinen
Improved speed.
4:07 PM Changeset [302] by Peter Johansson
changed to log2 base
4:05 PM Changeset [301] by Jari Häkkinen
Added clarification on result scale.
3:57 PM Changeset [300] by Peter Johansson
Result from plier is now logarithmized prior imported to BASE
3:25 PM Changeset [299] by Jari Häkkinen
Wiki page changed.

May 23, 2007:

3:56 PM Changeset [298] by Jari Häkkinen
Fixing broken sed substitution.
3:56 PM Changeset [297] by Jari Häkkinen
Fixing copyright year.
2:48 PM Changeset [296] by Peter Johansson
removing debug ''
2:40 PM Changeset [295] by Jari Häkkinen
Added Plier class name to instructions.
2:34 PM Changeset [294] by Peter Johansson
typo
2:31 PM Changeset [293] by Peter Johansson
improved text on PLIER
1:46 PM Changeset [292] by Jari Häkkinen
Fixing precompiled dependency.
11:25 AM Ticket #21 (Make installation from the packaged source distribution work) closed by Jari Häkkinen
fixed: (In [291]) Fixes #21.
11:25 AM Changeset [291] by Jari Häkkinen
Fixes #21.
11:04 AM Changeset [290] by Jari Häkkinen
Got rid of deprecation warning.

May 22, 2007:

5:33 PM Changeset [289] by Peter Johansson
improved dependencies
5:33 PM Changeset [288] by Peter Johansson
typo
4:39 PM Changeset [287] by Jari Häkkinen
Removed explicit version number.
3:20 PM Changeset [286] by Jari Häkkinen
Fixes #42.
3:20 PM Ticket #42 (Add sample extended-properties.xml and configuration files needed for ...) closed by Jari Häkkinen
fixed: (In [286]) Fixes #42.
2:51 PM Changeset [285] by Jari Häkkinen
Addresses #42.
2:51 PM Changeset [284] by Jari Häkkinen
Spell checked.
2:08 PM Ticket #19 (RMA plugin should check that cel files are assigned to correct cdf.) closed by Jari Häkkinen
duplicate: This is an issue for the BASE team, http://base.thep.lu.se/ticket/372.
1:56 PM Ticket #47 (A new release of RMAExpress was released 25 March 2007.) closed by Jari Häkkinen
fixed: The new releaseis tested and works. There is a minor glitch compiling …
1:52 PM Changeset [283] by Jari Häkkinen
Removed stray \!
1:45 PM Changeset [282] by Jari Häkkinen
Improved text.
11:35 AM Changeset [281] by Jari Häkkinen
Updated confusing numbering.
11:30 AM Changeset [280] by Jari Häkkinen
Removed my email address. Updated RMAExpress information to release …
11:29 AM Changeset [279] by Jari Häkkinen
Removed my email address, and updated link to new demo server location.
9:39 AM Changeset [278] by Peter Johansson
fixing a few typos
9:38 AM se.lu.thep.affymetrix created by Peter Johansson
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