Timeline
Dec 21, 2008:
- 5:01 PM Changeset [935] by
- Removing braches.
- 4:59 PM se.lu.thep.affymetrix edited by
- Added link to repository. (diff)
Dec 18, 2008:
- 5:05 PM se.lu.onk.CGHDataDumper edited by
- (diff)
- 5:03 PM PluginDownload edited by
- (diff)
- 4:07 PM PluginDownload edited by
- Update normalization package information (diff)
- 12:57 PM Ticket #120 (Create a normalization plug-in package.) closed by
- 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
- (diff)
- 12:54 PM net.sf.basedb.normalizers edited by
- Added raw download tag to package link. (diff)
- 12:52 PM net.sf.basedb.normalizers edited by
- 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
- 12:44 PM Changeset [934] by
- Tagging version 1.0 of the net.sf.basedb.normalizers.
- 12:41 PM Changeset [933] by
- Corrected spelling
- 12:40 PM Ticket #120 (Create a normalization plug-in package.) updated by
- (In [932]) Addresses #120.
- 12:40 PM Changeset [932] by
- Addresses #120.
- 12:30 PM Changeset [931] by
- Addresses #120. Preparing 1.0 release.
- 12:30 PM Ticket #120 (Create a normalization plug-in package.) updated by
- (In [931]) Addresses #120. Preparing 1.0 release.
- 12:30 PM Ticket #120 (Create a normalization plug-in package.) updated by
-
Status, Owner changed
- 12:29 PM net.sf.basedb.normalizers edited by
- Preparing 1.0 release of net.sf.basedb.normalizers package. (diff)
- 12:18 PM Changeset [930] by
- Typo
- 12:15 PM Changeset [929] by
- Removing CubicSplineNormalization stub.
- 12:12 PM Changeset [928] by
- Fixes #167. Now using geometric mean
- 12:12 PM Ticket #167 ((net.sf.basedb.normalizers) Average normalizer should use geometric mean) closed by
- fixed: (In [928]) Fixes #167. Now using geometric mean
- 12:12 PM Ticket #118 (Create qQuantile normalizer (aka cubic-spline normalizer)) updated by
-
Summary changed
- 12:11 PM Changeset [927] by
- Refs #165.
- 12:11 PM Ticket #165 (Create quantile normalizer) updated by
- (In [927]) Refs #165.
- 11:14 AM Ticket #167 ((net.sf.basedb.normalizers) Average normalizer should use geometric mean) updated by
-
Status, Owner changed
- 11:13 AM Ticket #167 ((net.sf.basedb.normalizers) Average normalizer should use geometric mean) created by
- 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
- 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
-
Summary changed
- 11:22 PM Ticket #163 (Rank invariant normalization has a sorting bug) closed by
- 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
- fixed: (In [926]) Fixes #165. Simply renamed rank invariant to quantile and …
- 11:20 PM Changeset [926] by
- Fixes #165. Simply renamed rank invariant to quantile and made …
- 10:37 PM Ticket #119 (Create rank invariant normalizer) reopened by
- The normalizer is not the rank invariant normalizer but rather …
- 10:15 PM Ticket #165 (Create quantile normalizer) updated by
-
Status changed
- 10:15 PM Ticket #165 (Create quantile normalizer) created by
- 9:06 PM Changeset [925] by
- Improved README.
- 9:05 PM Changeset [924] by
Dec 16, 2008:
- 11:45 PM Ticket #164 (Improve documentation on how to upgrade the illumina plug-in package) created by
- 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
- (diff)
- 4:52 PM se.lu.onk.IlluminaSNPNormalization edited by
- (diff)
- 4:51 PM se.lu.onk.IlluminaSNPNormalization edited by
- (diff)
- 2:23 PM Changeset [923] by
- References #163 Disregard the last commit. This will do instead.
- 2:23 PM Ticket #163 (Rank invariant normalization has a sorting bug) updated by
- (In [923]) References #163 Disregard the last commit. This will do instead.
- 1:52 PM Changeset [922] by
- 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
- (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
-
Status changed
- 9:11 AM Changeset [921] by
- Preparing for future release 1.0
- 9:10 AM net.sf.basedb.ftp edited by
- Releasing FTP Server 1.0beta2 (diff)
- 9:05 AM Changeset [920] by
- Tagging release of FTP Server 1.0beta2
- 9:04 AM Changeset [919] by
- Preparing release of FTP Server 1.0beta2
Dec 15, 2008:
- 2:43 PM Changeset [918] by
- Removed stray lines.
- 2:41 PM Ticket #163 (Rank invariant normalization has a sorting bug) created by
- 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
- (In [917]) References #127: Update to final release of Apache Mina FTP …
- 9:35 AM Changeset [917] by
- References #127: Update to final release of Apache Mina FTP server …
Dec 11, 2008:
- 10:21 PM Changeset [916] by
- 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
- (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
- (In [915]) References #127: Update to final release of Apache Mina FTP …
- 10:16 PM Changeset [915] by
- 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
-
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
- Reports on the mailing lists indicate that MeV 4.3 has solved a lot of …
- 1:09 PM Changeset [914] by
- Adding note about checking that the information on the download page …
- 1:07 PM PluginDownload edited by
- (diff)
- 1:06 PM net.sf.basedb.illumina edited by
- (diff)
- 1:05 PM Changeset [913] by
- 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
- Releasing Illumina package 1.2 (diff)
- 12:59 PM Changeset [912] by
- Tagging Illumina package 1.2
- 12:59 PM Changeset [911] by
- 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
- The build process should detect whether the required BASE jars are …
- 1:05 PM net.sf.basedb.normalizers edited by
- Changing to GPL3 (diff)
- 1:01 PM Changeset [910] by
- Changing normalizer package license to GPL3.
- 11:38 AM Changeset [909] by
- Addresses #120.
- 11:38 AM Ticket #120 (Create a normalization plug-in package.) updated by
- (In [909]) Addresses #120.
Dec 8, 2008:
- 11:18 PM net.sf.basedb.normalizers edited by
- Updated TODO section (diff)
- 11:13 PM net.sf.basedb.normalizers edited by
- 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
-
Summary changed
- 11:01 PM Ticket #159 (Create a se.lu.onk.VirtualArray module) updated by
-
Milestone changed
- 11:01 PM Ticket #153 (Autoconf issues in se.lu.thep.WeNNI) updated by
-
Summary changed
- 11:00 PM Ticket #130 (Base1PluginExecuter/ReplicateError: errors are not catched properly ...) updated by
-
Summary changed
- 10:59 PM Ticket #97 (Remove Plier support from se.lu.thep.affymetrix) updated by
-
Component changed
- 10:59 PM Ticket #96 (Make the se.lu.thep.affymetrix plug-in compatible with the ...) updated by
-
Component changed
- 10:58 PM Ticket #88 (extra values pass through) closed by
- wontfix
- 10:58 PM Ticket #87 (AnnotationFilter (se.lu.onk.AnnotationFilter)) updated by
-
Summary changed
- 10:57 PM Ticket #86 (BasicReporter and BasicSpot (se.lu.onk.BaseFile)) updated by
-
Description, Summary changed
- 10:56 PM Ticket #85 (Pinbased normalization for VirtualArray data) updated by
-
Summary changed
- 10:56 PM Ticket #84 (Change parameter in ReplicateError (se.lu.onk.ReplicateError)) updated by
-
Summary changed
- 10:55 PM Ticket #80 (QQPlot) updated by
-
Component changed
- 10:54 PM Ticket #79 (Center on assay (se.lu.onk.Center)) updated by
-
Summary changed
- 10:53 PM Ticket #78 (Spike Lowess (se.lu.onk.lowess)) updated by
-
Component, Owner, Summary changed
- 10:52 PM Ticket #75 (base2.xml genespring connection) closed by
- wontfix: Will not fix this. External contributions welcome.
- 10:51 PM Ticket #74 (unmappable character for encoding UTF8 Copyright (C) Jari Häkkinen ...) updated by
-
Summary changed
- 10:50 PM Ticket #71 (write HowToRelease document for se.lu.thep.WeNNI) updated by
-
Summary changed
- 10:50 PM Ticket #70 (Add releasing procedure to se.lu.thep.affymetrix) updated by
-
Component changed
- 10:49 PM Ticket #50 (create a BASE2 plug-in for se.lu.thep.WeNNI) updated by
-
Component, Summary changed
- 10:49 PM Ticket #43 (Add request for proper default permissions (se.lu.thep.affymetrix).) updated by
-
Component changed
- 10:49 PM Ticket #41 (Add data to output: sign flag, sign specific rank) updated by
-
Milestone changed
- 10:48 PM Ticket #41 (Add data to output: sign flag, sign specific rank) closed by
- wontfix
- 10:47 PM Ticket #39 (create reporter list (se.lu.onk.ztest)) updated by
-
Summary changed
- 10:44 PM Ticket #130 (Base1PluginExecuter/ReplicateError: errors are not catched properly ...) updated by
-
Milestone changed
- 10:43 PM Ticket #97 (Remove Plier support from se.lu.thep.affymetrix) updated by
-
Component changed
- 10:43 PM Ticket #96 (Make the se.lu.thep.affymetrix plug-in compatible with the ...) updated by
-
Component changed
- 10:43 PM Ticket #88 (extra values pass through) updated by
-
Component, Milestone, Owner changed
- 10:42 PM Ticket #87 (AnnotationFilter (se.lu.onk.AnnotationFilter)) updated by
-
Owner, Component, Milestone changed
- 10:42 PM Ticket #86 (BasicReporter and BasicSpot (se.lu.onk.BaseFile)) updated by
-
Owner, Component, Milestone changed
- 10:42 PM Ticket #85 (Pinbased normalization for VirtualArray data) updated by
-
Owner, Component, Milestone changed
- 10:41 PM Ticket #84 (Change parameter in ReplicateError (se.lu.onk.ReplicateError)) updated by
-
Owner, Component, Milestone changed
- 10:41 PM Ticket #82 (COPA) updated by
-
Owner, Component, Milestone changed
- 10:41 PM Ticket #81 (Merge on genesymbol) updated by
-
Owner, Component, Milestone changed
- 10:40 PM Ticket #80 (QQPlot) updated by
-
Owner, Component, Milestone changed
- 10:40 PM Ticket #79 (Center on assay (se.lu.onk.Center)) updated by
-
Owner, Component, Milestone changed
- 10:40 PM Ticket #78 (Spike Lowess (se.lu.onk.lowess)) updated by
-
Component, Milestone changed
- 10:39 PM Ticket #77 (Update information about webservice) updated by
-
Owner, Status, Description changed
- 10:38 PM Ticket #70 (Add releasing procedure to se.lu.thep.affymetrix) updated by
-
Component changed
- 10:38 PM Ticket #50 (create a BASE2 plug-in for se.lu.thep.WeNNI) updated by
-
Component changed
- 10:38 PM Ticket #43 (Add request for proper default permissions (se.lu.thep.affymetrix).) updated by
-
Component changed
- 10:37 PM Ticket #43 (Add request for proper default permissions (se.lu.thep.affymetrix).) updated by
-
Summary changed
- 10:36 PM Ticket #41 (Add data to output: sign flag, sign specific rank) updated by
-
Component, Owner changed
- 10:35 PM Ticket #39 (create reporter list (se.lu.onk.ztest)) updated by
-
Owner, Component changed
- 10:34 PM Ticket #96 (Make the se.lu.thep.affymetrix plug-in compatible with the ...) updated by
-
Summary changed
- 10:30 PM Ticket #50 (create a BASE2 plug-in for se.lu.thep.WeNNI) updated by
- (In [908]) Addresses #50. Running nni with phony weights.
- 10:30 PM Changeset [908] by
- Addresses #50. Running nni with phony weights.
- 10:07 PM Changeset [907] by
- using ACLOCAL_AMFLAGS requires Automake 1.10
- 10:01 PM Changeset [906] by
- Some external binary will output result to stdout ... optionally …
- 9:31 PM Changeset [905] by
- WeNNI.java should be included in dist
- 9:19 PM Changeset [904] by
- installing jars with chmod 644
- 9:11 PM Changeset [903] by
- Style is everything
- 4:49 PM Changeset [902] by
- timestamp of downloaded jar file will be old. Fixing deps to reflect …
- 4:25 PM Changeset [901] by
- improve dependency
- 10:56 AM Changeset [900] by
- Refs #159
- 10:56 AM Ticket #159 (Create a se.lu.onk.VirtualArray module) updated by
- (In [900]) Refs #159
- 10:53 AM Changeset [899] by
- Address #159. Renaming BASE1 plugin definition and minor changes to …
- 10:50 AM Changeset [898] by
- Adding URL.
- 10:48 AM Changeset [897] by
- Correcting URL
- 10:42 AM Ticket #56 (rename component onk.lu.se to be se.lu.onk -- split into several packages) updated by
- (In [896]) Refs #56. Removing branches and tags directories since they …
- 10:42 AM Changeset [896] by
- Refs #56. Removing branches and tags directories since they will never …
- 10:39 AM Changeset [895] by
- Addresses #56 and #159. Creating VirtualArray module.
- 10:39 AM Tickets #159,56 batch updated by
- (In [895]) Addresses #56 and #159. Creating VirtualArray module.
- 10:27 AM Changeset [894] by
- 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
- Implement the plug-in abort functionality available in BASE in WeNNI. …
- 8:50 PM Changeset [893] by
- Addresses #50. Adapting to PluginUtilities interface changes.
- 8:50 PM Ticket #50 (create a BASE2 plug-in for se.lu.thep.WeNNI) updated by
- (In [893]) Addresses #50. Adapting to PluginUtilities interface changes.
- 8:49 PM Changeset [892] by
- Improved dependency checking on pluginutilities.
- 8:46 PM Changeset [891] by
- Changed interface and added debug code.
- 12:57 PM Changeset [890] by
- Added debug code.
Dec 5, 2008:
- 11:59 PM Changeset [889] by
- 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
- Replying to jari: > Replying to peter: > > Ok, …
- 6:32 PM Changeset [888] by
- 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
-
Description changed
- 6:26 PM Ticket #159 (Create a se.lu.onk.VirtualArray module) updated by
-
Status changed
- 6:26 PM Ticket #159 (Create a se.lu.onk.VirtualArray module) created by
- Relates to ticket:56 Split se.lu.onk into smaller modules. Change to GPL3.
- 6:23 PM Ticket #34 (move base.css) closed by
- 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
- The PluginUtilities is still very immature and will undergo major …
- 5:54 PM se.lu.thep.WeNNI edited by
- Added link to project statistics. (diff)
- 5:52 PM se.lu.onk.BaseFile edited by
- Updated link to project statistics. (diff)
- 5:51 PM se.lu.onk.ReplicateError edited by
- Update link to project statistics. (diff)
- 5:50 PM se.lu.onk.MergeBioAssay edited by
- Update link to project statistics. (diff)
- 5:50 PM se.lu.onk.Center edited by
- Update link to project statistics. (diff)
- 5:45 PM Changeset [887] by
- 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
- 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
- Replying to peter: > Ok, now `./configure --enable-debug …
- 5:22 PM Ticket #158 (README in PluginUtilities refers to AbstractRunBinary.jar) created by
- README refers to AbstractRunBinary but I only see …
- 5:06 PM Ticket #63 (make distcheck should work) closed by
- fixed: (In [886]) typo that fixes #63. 'make mainatianer-check' now works here.
- 5:06 PM Changeset [886] by
- 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
-
Ok, now
./configure --enable-debug && makealso works for me. Two … - 4:04 PM Changeset [885] by
- Use rather that '.' in classpath.
- 4:03 PM Ticket #156 (Compilation fails in base2 test phase of 'make maintainer-check') closed by
- 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
- The problem must be that the compiling happens in a directory where …
- 3:45 PM Changeset [884] by
- Cleaning up JAVACCLASSPATH usage.
- 3:33 PM Ticket #156 (Compilation fails in base2 test phase of 'make maintainer-check') updated by
-
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
- Does your software environment fulfil the requirements stated in the …
- 12:57 PM PluginDownload edited by
- Added se.lu.onk.Center to the list pf plugins. (diff)
- 12:55 PM se.lu.onk.Center created by
- Adding se.lu.onk.Center page.
- 12:41 PM Ticket #157 (Create a se.lu.onk.Center module) closed by
- fixed: (In [883]) Fixes #157. Bumping version number to 2.2pre
- 12:41 PM Changeset [883] by
- Fixes #157. Bumping version number to 2.2pre
- 12:40 PM Changeset [882] by
- Tagging version 2.1 of se.lu.onk.Center
- 12:39 PM Ticket #157 (Create a se.lu.onk.Center module) updated by
- (In [881]) Addresses #157. Preparing release 2.1 of Center.
- 12:39 PM Changeset [881] by
- Addresses #157. Preparing release 2.1 of Center.
- 12:28 PM Changeset [880] by
- Addresses #157.
- 12:28 PM Ticket #157 (Create a se.lu.onk.Center module) updated by
- (In [880]) Addresses #157.
- 11:28 AM Changeset [879] by
- Changed documentation to document the Center plug-in
- 11:27 AM Changeset [878] by
- Spell checked.
- 11:27 AM Changeset [877] by
- Spell checked.
- 11:15 AM Changeset [876] by
- Correcting typo.
- 10:53 AM Changeset [875] by
- Addresses #157 and #56. Creating se.lu.onk.Center.
- 10:53 AM Tickets #157,56 batch updated by
- (In [875]) Addresses #157 and #56. Creating se.lu.onk.Center.
- 10:45 AM se.lu.onk.MergeBioAssay edited by
- Removed features section, added link to svndigest statistics. (diff)
- 10:42 AM se.lu.onk.MergeBioAssay edited by
- 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
-
Description changed
- 10:07 AM Ticket #157 (Create a se.lu.onk.Center module) updated by
-
Status changed
- 10:06 AM Ticket #157 (Create a se.lu.onk.Center module) created by
- Relates to ticket:56 Split se.lu.onk into smaller modules Change to GPL3
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