Timeline



Dec 21, 2008:

5:01 PM Changeset [935] by Jari Häkkinen
Removing braches.
4:59 PM se.lu.thep.affymetrix edited by Jari Häkkinen
Added link to repository. (diff)

Dec 18, 2008:

5:05 PM se.lu.onk.CGHDataDumper edited by Jari Häkkinen
(diff)
5:03 PM PluginDownload edited by Jari Häkkinen
(diff)
4:07 PM PluginDownload edited by Jari Häkkinen
Update normalization package information (diff)
12:57 PM Ticket #120 (Create a normalization plug-in package.) closed by Jari Häkkinen
fixed: Released working plugins in 1.0. The remaining tickets moved to 1.1
12:56 PM Milestone Normalization package v1.0 completed
For more information see the [wiki:net.sf.basedb.normalizers
12:55 PM net.sf.basedb.normalizers edited by Jari Häkkinen
(diff)
12:54 PM net.sf.basedb.normalizers edited by Jari Häkkinen
Added raw download tag to package link. (diff)
12:53 PM normalization-plugins-1.0.tar.gz.MD5 attached to net.sf.basedb.normalizers by Jari Häkkinen
12:53 PM normalization-plugins-1.0.tar.gz attached to net.sf.basedb.normalizers by Jari Häkkinen
12:52 PM net.sf.basedb.normalizers edited by Jari Häkkinen
Preparing 1.0 release of net.sf.basedb.normalizers package. (diff)
12:48 PM Ticket #168 (MD5 sum should be automatically generated for a package) created by Jari Häkkinen
12:44 PM Changeset [934] by Jari Häkkinen
Tagging version 1.0 of the net.sf.basedb.normalizers.
12:41 PM Changeset [933] by Jari Häkkinen
Corrected spelling
12:40 PM Ticket #120 (Create a normalization plug-in package.) updated by Jari Häkkinen
(In [932]) Addresses #120.
12:40 PM Changeset [932] by Jari Häkkinen
Addresses #120.
12:30 PM Changeset [931] by Jari Häkkinen
Addresses #120. Preparing 1.0 release.
12:30 PM Ticket #120 (Create a normalization plug-in package.) updated by Jari Häkkinen
(In [931]) Addresses #120. Preparing 1.0 release.
12:30 PM Ticket #120 (Create a normalization plug-in package.) updated by Jari Häkkinen
Status, Owner changed
12:29 PM net.sf.basedb.normalizers edited by Jari Häkkinen
Preparing 1.0 release of net.sf.basedb.normalizers package. (diff)
12:18 PM Changeset [930] by Jari Häkkinen
Typo
12:15 PM Changeset [929] by Jari Häkkinen
Removing CubicSplineNormalization stub.
12:12 PM Changeset [928] by Jari Häkkinen
Fixes #167. Now using geometric mean
12:12 PM Ticket #167 ((net.sf.basedb.normalizers) Average normalizer should use geometric mean) closed by Jari Häkkinen
fixed: (In [928]) Fixes #167. Now using geometric mean
12:12 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by Jari Häkkinen
Summary changed
12:11 PM Changeset [927] by Jari Häkkinen
Refs #165.
12:11 PM Ticket #165 (Create quantile normalizer) updated by Jari Häkkinen
(In [927]) Refs #165.
11:14 AM Ticket #167 ((net.sf.basedb.normalizers) Average normalizer should use geometric mean) updated by Jari Häkkinen
Status, Owner changed
11:13 AM Ticket #167 ((net.sf.basedb.normalizers) Average normalizer should use geometric mean) created by Jari Häkkinen
The current version uses the arithmetic mean.

Dec 17, 2008:

11:24 PM Ticket #166 ((net.sf.basedb.normalizers) Automatic progression of version to source ...) created by Jari Häkkinen
The version of the plug-in is hard coded in the java source
11:23 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by Jari Häkkinen
Summary changed
11:22 PM Ticket #163 (Rank invariant normalization has a sorting bug) closed by Jari Häkkinen
fixed: The fix passes my test now (I found another issue in my own test code).
11:20 PM Ticket #165 (Create quantile normalizer) closed by Jari Häkkinen
fixed: (In [926]) Fixes #165. Simply renamed rank invariant to quantile and …
11:20 PM Changeset [926] by Jari Häkkinen
Fixes #165. Simply renamed rank invariant to quantile and made …
10:37 PM Ticket #119 (Create rank invariant normalizer) reopened by Jari Häkkinen
The normalizer is not the rank invariant normalizer but rather …
10:15 PM Ticket #165 (Create quantile normalizer) updated by Jari Häkkinen
Status changed
10:15 PM Ticket #165 (Create quantile normalizer) created by Jari Häkkinen
9:06 PM Changeset [925] by Jari Häkkinen
Improved README.
9:05 PM Changeset [924] by Jari Häkkinen

Dec 16, 2008:

11:45 PM Ticket #164 (Improve documentation on how to upgrade the illumina plug-in package) created by Jari Häkkinen
As the INSTALL doc now stands it is hard to know how an upgrade of the …
4:55 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
4:52 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
4:51 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
2:23 PM Changeset [923] by Martin Svensson
References #163 Disregard the last commit. This will do instead.
2:23 PM Ticket #163 (Rank invariant normalization has a sorting bug) updated by Martin Svensson
(In [923]) References #163 Disregard the last commit. This will do instead.
1:52 PM Changeset [922] by Martin Svensson
References #163 The sorting of spotdata should be stable now. Please …
1:52 PM Ticket #163 (Rank invariant normalization has a sorting bug) updated by Martin Svensson
(In [922]) References #163 The sorting of spotdata should be stable …
9:14 AM Ticket #163 (Rank invariant normalization has a sorting bug) updated by Martin Svensson
Status changed
9:11 AM Changeset [921] by Nicklas Nordborg
Preparing for future release 1.0
9:10 AM net.sf.basedb.ftp edited by Nicklas Nordborg
Releasing FTP Server 1.0beta2 (diff)
9:05 AM Changeset [920] by Nicklas Nordborg
Tagging release of FTP Server 1.0beta2
9:04 AM Changeset [919] by Nicklas Nordborg
Preparing release of FTP Server 1.0beta2

Dec 15, 2008:

2:43 PM Changeset [918] by Jari Häkkinen
Removed stray lines.
2:41 PM Ticket #163 (Rank invariant normalization has a sorting bug) created by Jari Häkkinen
I think the sorting is not stable for cases when there is a tie …

Dec 12, 2008:

9:35 AM Ticket #127 (Update to final release of Apache Mina FTP server) updated by Nicklas Nordborg
(In [917]) References #127: Update to final release of Apache Mina FTP …
9:35 AM Changeset [917] by Nicklas Nordborg
References #127: Update to final release of Apache Mina FTP server …

Dec 11, 2008:

10:21 PM Changeset [916] by Nicklas Nordborg
References #127: Update to final release of Apache Mina FTP server …
10:21 PM Ticket #127 (Update to final release of Apache Mina FTP server) updated by Nicklas Nordborg
(In [916]) References #127: Update to final release of Apache Mina FTP …
10:16 PM Ticket #127 (Update to final release of Apache Mina FTP server) updated by Nicklas Nordborg
(In [915]) References #127: Update to final release of Apache Mina FTP …
10:16 PM Changeset [915] by Nicklas Nordborg
References #127: Update to final release of Apache Mina FTP server I …

Dec 10, 2008:

11:39 PM Ticket #127 (Update to final release of Apache Mina FTP server) updated by Nicklas Nordborg
Status changed
Today 1.0-M4 (milestone 4) was released. According to the developers …
10:01 PM Ticket #162 (Upgrade to MeV 4.3) created by Nicklas Nordborg
Reports on the mailing lists indicate that MeV 4.3 has solved a lot of …
1:09 PM Changeset [914] by Nicklas Nordborg
Adding note about checking that the information on the download page …
1:07 PM PluginDownload edited by Nicklas Nordborg
(diff)
1:06 PM net.sf.basedb.illumina edited by Nicklas Nordborg
(diff)
1:05 PM Changeset [913] by Nicklas Nordborg
Preparing for future release 1.3
1:04 PM Milestone Illumina package v1.2 completed
See Illumina plug-ins package for BASE
1:02 PM net.sf.basedb.illumina edited by Nicklas Nordborg
Releasing Illumina package 1.2 (diff)
1:00 PM illumina-plugins-1.2.tar.gz attached to net.sf.basedb.illumina by Nicklas Nordborg
12:59 PM Changeset [912] by Nicklas Nordborg
Tagging Illumina package 1.2
12:59 PM Changeset [911] by Nicklas Nordborg
Preparing release of Illumina package 1.2

Dec 9, 2008:

1:26 PM Ticket #161 ((net.sf.basedb.normalizers) Automatic download of BASE API) created by Jari Häkkinen
The build process should detect whether the required BASE jars are …
1:05 PM net.sf.basedb.normalizers edited by Jari Häkkinen
Changing to GPL3 (diff)
1:01 PM Changeset [910] by Jari Häkkinen
Changing normalizer package license to GPL3.
11:38 AM Changeset [909] by Jari Häkkinen
Addresses #120.
11:38 AM Ticket #120 (Create a normalization plug-in package.) updated by Jari Häkkinen
(In [909]) Addresses #120.

Dec 8, 2008:

11:18 PM net.sf.basedb.normalizers edited by Jari Häkkinen
Updated TODO section (diff)
11:13 PM net.sf.basedb.normalizers edited by Jari Häkkinen
Added browse svn link (diff)
11:02 PM Ticket #160 (wenni and the underlying super class should be abortable (se.lu.thep.WeNNI)) updated by Jari Häkkinen
Summary changed
11:01 PM Ticket #159 (Create a se.lu.onk.VirtualArray module) updated by Jari Häkkinen
Milestone changed
11:01 PM Ticket #153 (Autoconf issues in se.lu.thep.WeNNI) updated by Jari Häkkinen
Summary changed
11:00 PM Ticket #130 (Base1PluginExecuter/ReplicateError: errors are not catched properly ...) updated by Jari Häkkinen
Summary changed
10:59 PM Ticket #97 (Remove Plier support from se.lu.thep.affymetrix) updated by Jari Häkkinen
Component changed
10:59 PM Ticket #96 (Make the se.lu.thep.affymetrix plug-in compatible with the ...) updated by Jari Häkkinen
Component changed
10:58 PM Ticket #88 (extra values pass through) closed by Jari Häkkinen
wontfix
10:58 PM Ticket #87 (AnnotationFilter (se.lu.onk.AnnotationFilter)) updated by Jari Häkkinen
Summary changed
10:57 PM Ticket #86 (BasicReporter and BasicSpot (se.lu.onk.BaseFile)) updated by Jari Häkkinen
Description, Summary changed
10:56 PM Ticket #85 (Pinbased normalization for VirtualArray data) updated by Jari Häkkinen
Summary changed
10:56 PM Ticket #84 (Change parameter in ReplicateError (se.lu.onk.ReplicateError)) updated by Jari Häkkinen
Summary changed
10:55 PM Ticket #80 (QQPlot) updated by Jari Häkkinen
Component changed
10:54 PM Ticket #79 (Center on assay (se.lu.onk.Center)) updated by Jari Häkkinen
Summary changed
10:53 PM Ticket #78 (Spike Lowess (se.lu.onk.lowess)) updated by Jari Häkkinen
Component, Owner, Summary changed
10:52 PM Ticket #75 (base2.xml genespring connection) closed by Jari Häkkinen
wontfix: Will not fix this. External contributions welcome.
10:51 PM Ticket #74 (unmappable character for encoding UTF8 Copyright (C) Jari Häkkinen ...) updated by Jari Häkkinen
Summary changed
10:50 PM Ticket #71 (write HowToRelease document for se.lu.thep.WeNNI) updated by Jari Häkkinen
Summary changed
10:50 PM Ticket #70 (Add releasing procedure to se.lu.thep.affymetrix) updated by Jari Häkkinen
Component changed
10:49 PM Ticket #50 (create a BASE2 plug-in for se.lu.thep.WeNNI) updated by Jari Häkkinen
Component, Summary changed
10:49 PM Ticket #43 (Add request for proper default permissions (se.lu.thep.affymetrix).) updated by Jari Häkkinen
Component changed
10:49 PM Ticket #41 (Add data to output: sign flag, sign specific rank) updated by Jari Häkkinen
Milestone changed
10:48 PM Ticket #41 (Add data to output: sign flag, sign specific rank) closed by Jari Häkkinen
wontfix
10:47 PM Ticket #39 (create reporter list (se.lu.onk.ztest)) updated by Jari Häkkinen
Summary changed
10:44 PM Ticket #130 (Base1PluginExecuter/ReplicateError: errors are not catched properly ...) updated by Jari Häkkinen
Milestone changed
10:43 PM Ticket #97 (Remove Plier support from se.lu.thep.affymetrix) updated by Jari Häkkinen
Component changed
10:43 PM Ticket #96 (Make the se.lu.thep.affymetrix plug-in compatible with the ...) updated by Jari Häkkinen
Component changed
10:43 PM Ticket #88 (extra values pass through) updated by Jari Häkkinen
Milestone, Owner, Component changed
10:42 PM Ticket #87 (AnnotationFilter (se.lu.onk.AnnotationFilter)) updated by Jari Häkkinen
Owner, Component, Milestone changed
10:42 PM Ticket #86 (BasicReporter and BasicSpot (se.lu.onk.BaseFile)) updated by Jari Häkkinen
Owner, Component, Milestone changed
10:42 PM Ticket #85 (Pinbased normalization for VirtualArray data) updated by Jari Häkkinen
Owner, Component, Milestone changed
10:41 PM Ticket #84 (Change parameter in ReplicateError (se.lu.onk.ReplicateError)) updated by Jari Häkkinen
Owner, Component, Milestone changed
10:41 PM Ticket #82 (COPA) updated by Jari Häkkinen
Owner, Component, Milestone changed
10:41 PM Ticket #81 (Merge on genesymbol) updated by Jari Häkkinen
Owner, Component, Milestone changed
10:40 PM Ticket #80 (QQPlot) updated by Jari Häkkinen
Owner, Component, Milestone changed
10:40 PM Ticket #79 (Center on assay (se.lu.onk.Center)) updated by Jari Häkkinen
Owner, Component, Milestone changed
10:40 PM Ticket #78 (Spike Lowess (se.lu.onk.lowess)) updated by Jari Häkkinen
Component, Milestone changed
10:39 PM Ticket #77 (Update information about webservice) updated by Jari Häkkinen
Owner, Status, Description changed
10:38 PM Ticket #70 (Add releasing procedure to se.lu.thep.affymetrix) updated by Jari Häkkinen
Component changed
10:38 PM Ticket #50 (create a BASE2 plug-in for se.lu.thep.WeNNI) updated by Jari Häkkinen
Component changed
10:38 PM Ticket #43 (Add request for proper default permissions (se.lu.thep.affymetrix).) updated by Jari Häkkinen
Component changed
10:37 PM Ticket #43 (Add request for proper default permissions (se.lu.thep.affymetrix).) updated by Jari Häkkinen
Summary changed
10:36 PM Ticket #41 (Add data to output: sign flag, sign specific rank) updated by Jari Häkkinen
Owner, Component changed
10:35 PM Ticket #39 (create reporter list (se.lu.onk.ztest)) updated by Jari Häkkinen
Owner, Component changed
10:34 PM Ticket #96 (Make the se.lu.thep.affymetrix plug-in compatible with the ...) updated by Jari Häkkinen
Summary changed
10:30 PM Ticket #50 (create a BASE2 plug-in for se.lu.thep.WeNNI) updated by Jari Häkkinen
(In [908]) Addresses #50. Running nni with phony weights.
10:30 PM Changeset [908] by Jari Häkkinen
Addresses #50. Running nni with phony weights.
10:07 PM Changeset [907] by Peter Johansson
using ACLOCAL_AMFLAGS requires Automake 1.10
10:01 PM Changeset [906] by Jari Häkkinen
Some external binary will output result to stdout ... optionally …
9:31 PM Changeset [905] by Peter Johansson
WeNNI.java should be included in dist
9:19 PM Changeset [904] by Peter Johansson
installing jars with chmod 644
9:11 PM Changeset [903] by Peter Johansson
Style is everything
4:49 PM Changeset [902] by Peter Johansson
timestamp of downloaded jar file will be old. Fixing deps to reflect …
4:25 PM Changeset [901] by Peter Johansson
improve dependency
10:56 AM Changeset [900] by Jari Häkkinen
Refs #159
10:56 AM Ticket #159 (Create a se.lu.onk.VirtualArray module) updated by Jari Häkkinen
(In [900]) Refs #159
10:53 AM Changeset [899] by Jari Häkkinen
Address #159. Renaming BASE1 plugin definition and minor changes to …
10:50 AM Changeset [898] by Jari Häkkinen
Adding URL.
10:48 AM Changeset [897] by Jari Häkkinen
Correcting URL
10:42 AM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by Jari Häkkinen
(In [896]) Refs #56. Removing branches and tags directories since they …
10:42 AM Changeset [896] by Jari Häkkinen
Refs #56. Removing branches and tags directories since they will never …
10:39 AM Changeset [895] by Jari Häkkinen
Addresses #56 and #159. Creating VirtualArray module.
10:39 AM Tickets #159,​56 batch updated by Jari Häkkinen
(In [895]) Addresses #56 and #159. Creating VirtualArray module.
10:27 AM Changeset [894] by Jari Häkkinen
Adding missing svn property.

Dec 7, 2008:

9:05 PM Ticket #160 (wenni and the underlying super class should be abortable (se.lu.thep.WeNNI)) created by Jari Häkkinen
Implement the plug-in abort functionality available in BASE in WeNNI. …
8:50 PM Changeset [893] by Jari Häkkinen
Addresses #50. Adapting to PluginUtilities interface changes.
8:50 PM Ticket #50 (create a BASE2 plug-in for se.lu.thep.WeNNI) updated by Jari Häkkinen
(In [893]) Addresses #50. Adapting to PluginUtilities interface changes.
8:49 PM Changeset [892] by Jari Häkkinen
Improved dependency checking on pluginutilities.
8:46 PM Changeset [891] by Jari Häkkinen
Changed interface and added debug code.
12:57 PM Changeset [890] by Jari Häkkinen
Added debug code.

Dec 5, 2008:

11:59 PM Changeset [889] by Peter Johansson
experienced some problems when changing from normal build to VPATH …
7:49 PM Ticket #156 (Compilation fails in base2 test phase of 'make maintainer-check') updated by Peter Johansson
Replying to jari: > Replying to peter: > > Ok, …
6:32 PM Changeset [888] by Peter Johansson
fixing some make dependency
6:28 PM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by Jari Häkkinen
Description changed
6:26 PM Ticket #159 (Create a se.lu.onk.VirtualArray module) updated by Jari Häkkinen
Status changed
6:26 PM Ticket #159 (Create a se.lu.onk.VirtualArray module) created by Jari Häkkinen
Relates to ticket:56 Split se.lu.onk into smaller modules. Change to GPL3.
6:23 PM Ticket #34 (move base.css) closed by Jari Häkkinen
wontfix: This will resolve as a side effect of fixing ticket:56
5:58 PM Ticket #158 (README in PluginUtilities refers to AbstractRunBinary.jar) updated by Jari Häkkinen
The PluginUtilities is still very immature and will undergo major …
5:54 PM se.lu.thep.WeNNI edited by Jari Häkkinen
Added link to project statistics. (diff)
5:52 PM se.lu.onk.BaseFile edited by Jari Häkkinen
Updated link to project statistics. (diff)
5:51 PM se.lu.onk.ReplicateError edited by Jari Häkkinen
Update link to project statistics. (diff)
5:50 PM se.lu.onk.MergeBioAssay edited by Jari Häkkinen
Update link to project statistics. (diff)
5:50 PM se.lu.onk.Center edited by Jari Häkkinen
Update link to project statistics. (diff)
5:45 PM Changeset [887] by Jari Häkkinen
Fixes #154. configure now supports setting of java source files encoding.
5:45 PM Ticket #154 (wenni compiling WeNNI.java requires -encoding option to the compiler) closed by Jari Häkkinen
fixed: (In [887]) Fixes #154. configure now supports setting of java source …
5:23 PM Ticket #156 (Compilation fails in base2 test phase of 'make maintainer-check') updated by Jari Häkkinen
Replying to peter: > Ok, now `./configure --enable-debug …
5:22 PM Ticket #158 (README in PluginUtilities refers to AbstractRunBinary.jar) created by Peter Johansson
README refers to AbstractRunBinary but I only see …
5:06 PM Ticket #63 (make distcheck should work) closed by Peter Johansson
fixed: (In [886]) typo that fixes #63. 'make mainatianer-check' now works here.
5:06 PM Changeset [886] by Peter Johansson
typo that fixes #63. 'make mainatianer-check' now works here.
4:48 PM Ticket #156 (Compilation fails in base2 test phase of 'make maintainer-check') updated by Peter Johansson
Ok, now ./configure --enable-debug && make also works for me. Two …
4:04 PM Changeset [885] by Jari Häkkinen
Use rather that '.' in classpath.
4:03 PM Ticket #156 (Compilation fails in base2 test phase of 'make maintainer-check') closed by Jari Häkkinen
fixed: Ah, I got it! it downloads the pre-version PluginUtilities from …
3:46 PM Ticket #156 (Compilation fails in base2 test phase of 'make maintainer-check') updated by Jari Häkkinen
The problem must be that the compiling happens in a directory where …
3:45 PM Changeset [884] by Jari Häkkinen
Cleaning up JAVACCLASSPATH usage.
3:33 PM Ticket #156 (Compilation fails in base2 test phase of 'make maintainer-check') updated by Jari Häkkinen
Description, Summary changed
Ok, trying 'make maintainer-check' actually fails with your falure …
3:18 PM Ticket #156 (Compilation fails in base2 test phase of 'make maintainer-check') updated by Jari Häkkinen
Does your software environment fulfil the requirements stated in the …
12:57 PM PluginDownload edited by Jari Häkkinen
Added se.lu.onk.Center to the list pf plugins. (diff)
12:56 PM Center-2.1.tgz.MD5 attached to se.lu.onk.Center by Jari Häkkinen
12:56 PM Center-2.1.tgz attached to se.lu.onk.Center by Jari Häkkinen
12:55 PM se.lu.onk.Center created by Jari Häkkinen
Adding se.lu.onk.Center page.
12:41 PM Ticket #157 (Create a se.lu.onk.Center module) closed by Jari Häkkinen
fixed: (In [883]) Fixes #157. Bumping version number to 2.2pre
12:41 PM Changeset [883] by Jari Häkkinen
Fixes #157. Bumping version number to 2.2pre
12:40 PM Changeset [882] by Jari Häkkinen
Tagging version 2.1 of se.lu.onk.Center
12:39 PM Ticket #157 (Create a se.lu.onk.Center module) updated by Jari Häkkinen
(In [881]) Addresses #157. Preparing release 2.1 of Center.
12:39 PM Changeset [881] by Jari Häkkinen
Addresses #157. Preparing release 2.1 of Center.
12:28 PM Changeset [880] by Jari Häkkinen
Addresses #157.
12:28 PM Ticket #157 (Create a se.lu.onk.Center module) updated by Jari Häkkinen
(In [880]) Addresses #157.
11:28 AM Changeset [879] by Jari Häkkinen
Changed documentation to document the Center plug-in
11:27 AM Changeset [878] by Jari Häkkinen
Spell checked.
11:27 AM Changeset [877] by Jari Häkkinen
Spell checked.
11:15 AM Changeset [876] by Jari Häkkinen
Correcting typo.
10:53 AM Changeset [875] by Jari Häkkinen
Addresses #157 and #56. Creating se.lu.onk.Center.
10:53 AM Tickets #157,​56 batch updated by Jari Häkkinen
(In [875]) Addresses #157 and #56. Creating se.lu.onk.Center.
10:45 AM se.lu.onk.MergeBioAssay edited by Jari Häkkinen
Removed features section, added link to svndigest statistics. (diff)
10:42 AM se.lu.onk.MergeBioAssay edited by Jari Häkkinen
Added license note (diff)
10:07 AM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by Jari Häkkinen
Description changed
10:07 AM Ticket #157 (Create a se.lu.onk.Center module) updated by Jari Häkkinen
Status changed
10:06 AM Ticket #157 (Create a se.lu.onk.Center module) created by Jari Häkkinen
Relates to ticket:56 Split se.lu.onk into smaller modules Change to GPL3

Dec 4, 2008:

7:32 PM Ticket #155 (New error handling option for duplicated features when creating array ...) updated by Nicklas Nordborg
No it is not possible. And it doesn't matter. There can only be one …
6:20 PM Changeset [874] by Peter Johansson
refs #71 Adding some targets for maintainer to check that everything …
6:20 PM Tickets #156,​71 batch updated by Peter Johansson
(In [874]) refs #71 Adding some targets for maintainer to check that …
6:08 PM Ticket #156 (Compilation fails in base2 test phase of 'make maintainer-check') created by Peter Johansson
Relates to ticket:63 With all the automagic download I thought a …
5:07 PM Ticket #155 (New error handling option for duplicated features when creating array ...) updated by Jari Häkkinen
Is it possible to call the core importer twice, first with the …
2:32 PM Ticket #155 (New error handling option for duplicated features when creating array ...) closed by Nicklas Nordborg
wontfix: The duplication control/skipping is happening in the core and it can …
1:59 PM Ticket #155 (New error handling option for duplicated features when creating array ...) updated by johan
For clarity. The additional error handling option would be to skip the …
1:49 PM HumanHT-12_V3_0_R1_11283641_A.bgx attached to Ticket #155 by johan
BGX file for Illumina Human HT12 bead chip
1:47 PM Ticket #155 (New error handling option for duplicated features when creating array ...) created by johan
A bgx file contains array design information for Illumina arrays. The …
1:22 PM Ticket #71 (write HowToRelease document for se.lu.thep.WeNNI) updated by Peter Johansson
I think it is doable. Let me try and I come back to this later today.
12:04 PM Ticket #154 (wenni compiling WeNNI.java requires -encoding option to the compiler) updated by Jari Häkkinen
Status, Owner changed
12:04 PM Ticket #154 (wenni compiling WeNNI.java requires -encoding option to the compiler) created by Jari Häkkinen
Since some of the strings in WeNNI.java contain international …
11:53 AM Changeset [873] by Nicklas Nordborg
Fixes #151: Use two queries instead of one in DetectionPValue.run() method
11:53 AM Ticket #151 (Use two queries instead of one in DetectionPValue.run() method) closed by Nicklas Nordborg
fixed: (In [873]) Fixes #151: Use two queries instead of one in …
8:42 AM Ticket #71 (write HowToRelease document for se.lu.thep.WeNNI) updated by Jari Häkkinen
Replying to peter: > Replying to jari: > > …

Dec 3, 2008:

11:40 PM Changeset [872] by Peter Johansson
TODO is included in dist by default, so no need to add it explicitly
11:29 PM Changeset [871] by Peter Johansson
install-exec-local didn't respect DESTDIR. Copying code generated by …
11:19 PM Changeset [870] by Peter Johansson
calling tar through script 'missing'. refs #153.
11:19 PM Ticket #153 (Autoconf issues in se.lu.thep.WeNNI) updated by Peter Johansson
(In [870]) calling tar through script 'missing'. refs #153.
11:05 PM Changeset [869] by Peter Johansson
Adding uninstall-plugin target Using install target for install-plugin …
10:43 PM Changeset [868] by Jari Häkkinen
JAVACFLAGS was a classpath! Correcting and introduced a proper …
10:40 PM Changeset [867] by Jari Häkkinen
Typo
7:40 PM Changeset [866] by Peter Johansson
simplify syntax of install-plugin targets by using install target
6:33 PM Changeset [865] by Peter Johansson
adding uninstall targets in base2. Should probably be added in other …
4:45 PM Changeset [864] by Peter Johansson
refs #153 - using autoreconf in bootstrap. Did not add '--force' …
4:45 PM Ticket #153 (Autoconf issues in se.lu.thep.WeNNI) updated by Peter Johansson
(In [864]) refs #153 - using autoreconf in bootstrap. Did not add …
4:04 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
3:53 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
3:51 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
3:47 PM se.lu.onk.IlluminaSNPNormalization edited by markus
(diff)
2:38 PM Ticket #153 (Autoconf issues in se.lu.thep.WeNNI) updated by Peter Johansson
The problem is the bootstrap. I forgot that we have such an old …
12:58 PM Ticket #153 (Autoconf issues in se.lu.thep.WeNNI) updated by Jari Häkkinen
And now I get, with no changes made except rerunning bootstrap and …
11:21 AM Ticket #153 (Autoconf issues in se.lu.thep.WeNNI) updated by Jari Häkkinen
I get […] and JAR is not set. The new m4 directory is not …

Dec 2, 2008:

11:24 PM Changeset [863] by Jari Häkkinen
Addresses #50. Working on the Java wrapper.
11:24 PM Ticket #50 (create a BASE2 plug-in for se.lu.thep.WeNNI) updated by Jari Häkkinen
(In [863]) Addresses #50. Working on the Java wrapper.
11:22 PM Changeset [862] by Jari Häkkinen
Cleanup of the abstract super class. More to come …
11:21 PM Changeset [861] by Jari Häkkinen
Using BASE 2.9 API
9:31 PM Changeset [860] by Peter Johansson
adding tests for javac and jar - refs #153
9:31 PM Ticket #153 (Autoconf issues in se.lu.thep.WeNNI) updated by Peter Johansson
(In [860]) adding tests for javac and jar - refs #153
9:31 PM Changeset [859] by Peter Johansson
adding tests for javac and jar - refs #153
9:31 PM Ticket #153 (Autoconf issues in se.lu.thep.WeNNI) updated by Peter Johansson
(In [859]) adding tests for javac and jar - refs #153
4:33 PM Changeset [858] by Jari Häkkinen
Addresses #50. Working with BASE-plugin communication issues and …
4:33 PM Ticket #50 (create a BASE2 plug-in for se.lu.thep.WeNNI) updated by Jari Häkkinen
(In [858]) Addresses #50. Working with BASE-plugin communication …
3:57 PM Ticket #153 (Autoconf issues in se.lu.thep.WeNNI) created by Jari Häkkinen
Checks for used programs should be added jar, javac, tar, wget
12:36 PM Ticket #71 (write HowToRelease document for se.lu.thep.WeNNI) updated by Peter Johansson
Replying to jari: > There are three states ... probably …
11:29 AM Ticket #151 (Use two queries instead of one in DetectionPValue.run() method) updated by Nicklas Nordborg
Status changed
9:06 AM Ticket #63 (make distcheck should work) updated by Jari Häkkinen
Owner, Status changed
9:05 AM Changeset [857] by Jari Häkkinen
Refs #50. AM_CONDITIONALs must be available for all build states.
9:05 AM Ticket #50 (create a BASE2 plug-in for se.lu.thep.WeNNI) updated by Jari Häkkinen
(In [857]) Refs #50. AM_CONDITIONALs must be available for all build …
9:04 AM Ticket #71 (write HowToRelease document for se.lu.thep.WeNNI) updated by Jari Häkkinen
There are three states ... probably three different make distchecks …
8:55 AM Changeset [856] by Jari Häkkinen
Refs #50 and #63. All WeNNI build options now works. make distcheck …
8:55 AM Tickets #50,​63 batch updated by Jari Häkkinen
(In [856]) Refs #50 and #63. All WeNNI build options now works. make …
7:39 AM Changeset [855] by Jari Häkkinen
Removed stray tabs
12:33 AM Ticket #53 (update INSTALL) closed by Jari Häkkinen
fixed: (In [854]) Fixes #53
12:33 AM Changeset [854] by Jari Häkkinen
Fixes #53
12:00 AM Ticket #53 (update INSTALL) updated by Jari Häkkinen
Status, Owner changed

Dec 1, 2008:

11:59 PM Ticket #152 (Setting bindir in configure.ac destroys make distcheck) closed by Jari Häkkinen
fixed: (In [853]) Fixes #152. Added custom target 'install-plugin' that …
11:59 PM Changeset [853] by Jari Häkkinen
Fixes #152. Added custom target 'install-plugin' that parallels 'install'.
10:24 PM Changeset [852] by Peter Johansson
even some more typos - huuh
10:20 PM Changeset [851] by Peter Johansson
corrected some typos
10:13 PM Changeset [850] by Peter Johansson
forgot to save this file prior ci r849
10:01 PM Changeset [849] by Peter Johansson
defining state variable in config.h and when not in base1 mode slice …
9:23 PM Ticket #152 (Setting bindir in configure.ac destroys make distcheck) updated by Jari Häkkinen
Owner, Status changed
9:23 PM Changeset [848] by Jari Häkkinen
Refs #50. Using proper PluginUtilities URL for download
9:23 PM Ticket #50 (create a BASE2 plug-in for se.lu.thep.WeNNI) updated by Jari Häkkinen
(In [848]) Refs #50. Using proper PluginUtilities URL for download
8:55 PM Ticket #71 (write HowToRelease document for se.lu.thep.WeNNI) updated by Jari Häkkinen
When this ticket is fixed remember these things from configre.ac …
8:10 PM Changeset [847] by Jari Häkkinen
Renamed package to PluginUtilities.
8:06 PM net.sf.basedb.pluginutilties created by Jari Häkkinen
First version of PluginUtilities wiki page.
7:50 PM Ticket #152 (Setting bindir in configure.ac destroys make distcheck) created by Jari Häkkinen
Either create customized install directives or use --bindir for …
7:41 PM Changeset [846] by Peter Johansson
fixed so test can be run outside 'make check'
7:20 PM Changeset [845] by Jari Häkkinen
Correcting dangerous distclean directive that removed revision …
5:24 PM Changeset [844] by Jari Häkkinen
Addresses #50, #53. Automatic download of required components. Using …
5:24 PM Tickets #50,​53 batch updated by Jari Häkkinen
(In [844]) Addresses #50, #53. Automatic download of required …
10:35 AM Changeset [843] by Jari Häkkinen
Fixed indentation issues and outputting more information to user.
10:21 AM Changeset [842] by Jari Häkkinen
Typo

Nov 30, 2008:

12:46 AM Changeset [841] by Peter Johansson
avoid setting CPPFLAGS and friends in configure.ac and updating …

Nov 29, 2008:

10:23 PM Changeset [840] by Peter Johansson
added ACTION-IF-NOT-FOUND in AC_SEARCH_LIBS, in other words, configure …
10:12 PM Changeset [839] by Peter Johansson
removing warning - use C++ macro not C
2:28 AM Changeset [838] by Peter Johansson
typo

Nov 28, 2008:

8:12 PM Changeset [837] by Peter Johansson
removing annoying Automake warning that %-style pattern rules are a …
6:27 PM Changeset [836] by Peter Johansson
refs #63. Fixed vpath issues in test so make distcheck no works in …
6:27 PM Ticket #63 (make distcheck should work) updated by Peter Johansson
(In [836]) refs #63. Fixed vpath issues in test so make distcheck no …
6:03 PM Ticket #149 (Error: The query has already been executed (Illumina detection P-value ...) closed by Jari Häkkinen
invalid: I think this error has something to do with a mix of Illumina package …
5:55 PM Changeset [835] by Jari Häkkinen
Since changeset:834 there is no need to check for sed
4:36 PM Ticket #63 (make distcheck should work) updated by Peter Johansson
(In [834]) Triggered by [826]. There were some problems with the …
4:36 PM Changeset [834] by Peter Johansson
Triggered by [826]. There were some problems with the Makefile.am, so …
2:15 PM Changeset [833] by Nicklas Nordborg
Fixes #150: Fix layout of DetectionPValue.java
2:15 PM Ticket #150 (Fix layout of DetectionPValue.java) closed by Nicklas Nordborg
fixed: (In [833]) Fixes #150: Fix layout of DetectionPValue.java
2:06 PM Ticket #150 (Fix layout of DetectionPValue.java) updated by Nicklas Nordborg
Status changed
2:04 PM Ticket #151 (Use two queries instead of one in DetectionPValue.run() method) created by Nicklas Nordborg
The plug-in uses a single query instance to get data from …
1:58 PM Ticket #150 (Fix layout of DetectionPValue.java) created by Nicklas Nordborg
The layout in the file is a mess and seems to not follow any known …
1:55 PM Ticket #149 (Error: The query has already been executed (Illumina detection P-value ...) updated by Nicklas Nordborg
The stacktrace doesn't make sense. It doesn't match the 1.0 or the 1.1 …
1:37 PM Ticket #149 (Error: The query has already been executed (Illumina detection P-value ...) updated by base
net.sf.basedb.core.BaseException: The query has already been executed. …
1:36 PM Ticket #149 (Error: The query has already been executed (Illumina detection P-value ...) created by base
When trying to run plugin 'Illumina detection P-value calculation' I …

Nov 27, 2008:

11:32 PM Changeset [832] by Jari Häkkinen
Resetting svndigest:ignore property, testing of svndigest stats …
11:22 PM Changeset [831] by Jari Häkkinen
Removed bindir and cleaned up indentation.
10:53 PM Changeset [830] by Jari Häkkinen
Deleting svndigest:ignore property to test svndigest stats counting.
9:44 PM Changeset [829] by Jari Häkkinen
Setting svndigest:ignore on copies of trunks to avoid multiple counting.
9:30 PM Ticket #54 (update README) closed by Jari Häkkinen
fixed: (In [828]) Fixes #54
9:30 PM Changeset [828] by Jari Häkkinen
Fixes #54
8:35 PM Ticket #55 (update ChangeLog) closed by Jari Häkkinen
fixed
4:03 PM PluginDownload edited by Jari Häkkinen
(diff)
4:02 PM PluginDownload edited by Jari Häkkinen
Moved WeNNI into 1.2 plug-in table. (diff)
12:39 AM Changeset [827] by Jari Häkkinen
Added check for SED and some more changelog entries.
12:32 AM Changeset [826] by Jari Häkkinen
Fixes #148.
12:32 AM Ticket #148 (BASE1 configuration: execname should be set automatically during build) closed by Jari Häkkinen
fixed: (In [826]) Fixes #148.
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