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 Changeset [932] by
- Addresses #120.
- 12:30 PM Changeset [931] by
- Addresses #120. Preparing 1.0 release.
- 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
- 12:11 PM Changeset [927] by
- Refs #165.
- 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
- 11:22 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) 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.
- 1:52 PM Changeset [922] by
- References #163 The sorting of spotdata should be stable now. Please …
- 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 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 …
- 10:16 PM Changeset [915] by
- References #127: Update to final release of Apache Mina FTP server I …
Dec 10, 2008:
- 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.
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)
- 10:58 PM Ticket #88 (extra values pass through) closed by
- wontfix
- 10:52 PM Ticket #75 (base2.xml genespring connection) closed by
- wontfix: Will not fix this. External contributions welcome.
- 10:48 PM Ticket #41 (Add data to output: sign flag, sign specific rank) closed by
- wontfix
- 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
- 10:53 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 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.
- 10:27 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.
- 8:49 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 …
- 6:32 PM Changeset [888] by
- fixing some make dependency
- 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
- 5:54 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 …
- 5:22 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.
- 4:04 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 …
- 3:45 PM Changeset [884] by
- Cleaning up JAVACCLASSPATH usage.
- 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 Changeset [881] by
- Addresses #157. Preparing release 2.1 of Center.
- 12:28 PM Changeset [880] by
- 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.
- 10:45 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)
- 10:06 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
Dec 4, 2008:
- 6:20 PM Changeset [874] by
- refs #71 Adding some targets for maintainer to check that everything …
- 6:08 PM Ticket #156 (Compilation fails in base2 test phase of 'make maintainer-check') created by
- Relates to ticket:63 With all the automagic download I thought a …
- 2:32 PM Ticket #155 (New error handling option for duplicated features when creating array ...) closed by
- wontfix: The duplication control/skipping is happening in the core and it can …
- 1:47 PM Ticket #155 (New error handling option for duplicated features when creating array ...) created by
- A bgx file contains array design information for Illumina arrays. The …
- 12:04 PM Ticket #154 (wenni compiling WeNNI.java requires -encoding option to the compiler) created by
- Since some of the strings in WeNNI.java contain international …
- 11:53 AM Changeset [873] by
- 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
- fixed: (In [873]) Fixes #151: Use two queries instead of one in …
Dec 3, 2008:
- 11:40 PM Changeset [872] by
- TODO is included in dist by default, so no need to add it explicitly
- 11:29 PM Changeset [871] by
- install-exec-local didn't respect DESTDIR. Copying code generated by …
- 11:19 PM Changeset [870] by
- calling tar through script 'missing'. refs #153.
- 11:05 PM Changeset [869] by
- Adding uninstall-plugin target Using install target for install-plugin …
- 10:43 PM Changeset [868] by
- JAVACFLAGS was a classpath! Correcting and introduced a proper …
- 10:40 PM Changeset [867] by
- Typo
- 7:40 PM Changeset [866] by
- simplify syntax of install-plugin targets by using install target
- 6:33 PM Changeset [865] by
- adding uninstall targets in base2. Should probably be added in other …
- 4:45 PM Changeset [864] by
- refs #153 - using autoreconf in bootstrap. Did not add '--force' …
- 4:04 PM se.lu.onk.IlluminaSNPNormalization edited by
- (diff)
- 3:53 PM se.lu.onk.IlluminaSNPNormalization edited by
- (diff)
- 3:51 PM se.lu.onk.IlluminaSNPNormalization edited by
- (diff)
- 3:47 PM se.lu.onk.IlluminaSNPNormalization edited by
- (diff)
Dec 2, 2008:
- 11:24 PM Changeset [863] by
- Addresses #50. Working on the Java wrapper.
- 11:22 PM Changeset [862] by
- Cleanup of the abstract super class. More to come …
- 11:21 PM Changeset [861] by
- Using BASE 2.9 API
- 9:31 PM Changeset [860] by
- adding tests for javac and jar - refs #153
- 9:31 PM Changeset [859] by
- adding tests for javac and jar - refs #153
- 4:33 PM Changeset [858] by
- Addresses #50. Working with BASE-plugin communication issues and …
- 3:57 PM Ticket #153 (Autoconf issues in se.lu.thep.WeNNI) created by
- Checks for used programs should be added jar, javac, tar, wget
- 9:05 AM Changeset [857] by
- Refs #50. AM_CONDITIONALs must be available for all build states.
- 8:55 AM Changeset [856] by
- Refs #50 and #63. All WeNNI build options now works. make distcheck …
- 7:39 AM Changeset [855] by
- Removed stray tabs
- 12:33 AM Ticket #53 (update INSTALL) closed by
- fixed: (In [854]) Fixes #53
- 12:33 AM Changeset [854] by
- Fixes #53
Dec 1, 2008:
- 11:59 PM Ticket #152 (Setting bindir in configure.ac destroys make distcheck) closed by
- fixed: (In [853]) Fixes #152. Added custom target 'install-plugin' that …
- 11:59 PM Changeset [853] by
- Fixes #152. Added custom target 'install-plugin' that parallels 'install'.
- 10:24 PM Changeset [852] by
- even some more typos - huuh
- 10:20 PM Changeset [851] by
- corrected some typos
- 10:13 PM Changeset [850] by
- forgot to save this file prior ci r849
- 10:01 PM Changeset [849] by
- defining state variable in config.h and when not in base1 mode slice …
- 9:23 PM Changeset [848] by
- Refs #50. Using proper PluginUtilities? URL for download
- 8:10 PM Changeset [847] by
- Renamed package to PluginUtilities?.
- 8:06 PM net.sf.basedb.pluginutilties created by
- First version of PluginUtilities? wiki page.
- 7:50 PM Ticket #152 (Setting bindir in configure.ac destroys make distcheck) created by
- Either create customized install directives or use --bindir for …
- 7:41 PM Changeset [846] by
- fixed so test can be run outside 'make check'
- 7:20 PM Changeset [845] by
- Correcting dangerous distclean directive that removed revision …
- 5:24 PM Changeset [844] by
- Addresses #50, #53. Automatic download of required components. Using …
- 10:35 AM Changeset [843] by
- Fixed indentation issues and outputting more information to user.
- 10:21 AM Changeset [842] by
- Typo
Nov 30, 2008:
- 12:46 AM Changeset [841] by
- avoid setting CPPFLAGS and friends in configure.ac and updating …
Nov 29, 2008:
- 10:23 PM Changeset [840] by
- added ACTION-IF-NOT-FOUND in AC_SEARCH_LIBS, in other words, configure …
- 10:12 PM Changeset [839] by
- removing warning - use C++ macro not C
- 2:28 AM Changeset [838] by
- typo
Nov 28, 2008:
- 8:12 PM Changeset [837] by
- removing annoying Automake warning that %-style pattern rules are a …
- 6:27 PM Changeset [836] by
- refs #63. Fixed vpath issues in test so make distcheck no works in …
- 6:03 PM Ticket #149 (Error: The query has already been executed (Illumina detection P-value ...) closed by
- invalid: I think this error has something to do with a mix of Illumina package …
- 5:55 PM Changeset [835] by
- Since changeset:834 there is no need to check for sed
- 4:36 PM Changeset [834] by
- Triggered by [826]. There were some problems with the Makefile.am, so …
- 2:15 PM Changeset [833] by
- Fixes #150: Fix layout of DetectionPValue.java
- 2:15 PM Ticket #150 (Fix layout of DetectionPValue.java) closed by
- fixed: (In [833]) Fixes #150: Fix layout of DetectionPValue.java
- 2:04 PM Ticket #151 (Use two queries instead of one in DetectionPValue.run() method) created by
- The plug-in uses a single query instance to get data from …
- 1:58 PM Ticket #150 (Fix layout of DetectionPValue.java) created by
- The layout in the file is a mess and seems to not follow any known …
- 1:36 PM Ticket #149 (Error: The query has already been executed (Illumina detection P-value ...) created by
- When trying to run plugin 'Illumina detection P-value calculation' I …
Nov 27, 2008:
- 11:32 PM Changeset [832] by
- Resetting svndigest:ignore property, testing of svndigest stats …
- 11:22 PM Changeset [831] by
- Removed bindir and cleaned up indentation.
- 10:53 PM Changeset [830] by
- Deleting svndigest:ignore property to test svndigest stats counting.
- 9:44 PM Changeset [829] by
- Setting svndigest:ignore on copies of trunks to avoid multiple counting.
- 9:30 PM Ticket #54 (update README) closed by
- fixed: (In [828]) Fixes #54
- 9:30 PM Changeset [828] by
- Fixes #54
- 8:35 PM Ticket #55 (update ChangeLog) closed by
- fixed
- 4:03 PM PluginDownload edited by
- (diff)
- 4:02 PM PluginDownload edited by
- Moved WeNNI into 1.2 plug-in table. (diff)
- 12:39 AM Changeset [827] by
- Added check for SED and some more changelog entries.
- 12:32 AM Changeset [826] by
- Fixes #148.
- 12:32 AM Ticket #148 (BASE1 configuration: execname should be set automatically during build) closed by
- fixed: (In [826]) Fixes #148.
Nov 26, 2008:
- 11:42 PM Changeset [825] by
- Fixes #146.
- 11:42 PM Ticket #146 (Change references to lev.thep.lu.se to something more appropriate) closed by
- fixed: (In [825]) Fixes #146.
- 11:17 PM Ticket #145 (GPL3 for WeNNI) closed by
- fixed: (In [824]) Fixes #145.
- 11:17 PM Changeset [824] by
- Fixes #145.
- 5:43 PM se.lu.thep.WeNNI edited by
- fixing the query syntax (diff)
- 4:38 PM se.lu.thep.WeNNI edited by
- Updated the TODO list (diff)
- 4:28 PM Ticket #52 (Add educational material and use cases.) closed by
- wontfix
- 4:27 PM Ticket #148 (BASE1 configuration: execname should be set automatically during build) created by
- As it is now a default name is used. basedir or plugin dir shuold be …
- 4:25 PM Ticket #64 (configure does not find basefile.h) closed by
- fixed: Fixed in changeset:821
- 4:23 PM Changeset [823] by
- Addresses #53 and fixes #60.
- 4:23 PM Ticket #60 (explain how to run wenni (base1 version) against a base_devkit) closed by
- fixed: (In [823]) Addresses #53 and fixes #60.
- 4:20 PM Changeset [822] by
- Updated change information and default installation paths
Nov 25, 2008:
- 5:38 PM Changeset [821] by
- Build of stand-alone and base1 modes work. base2 still to be finalized.
- 5:29 PM Changeset [820] by
- Added note saying that repository checkout requires ./bootstrap.
Nov 24, 2008:
- 10:56 AM Changeset [819] by
- Changed u_int to unsigned int to make code pass compilation on my Mac …
Nov 23, 2008:
- 9:45 PM Ticket #147 (WeNNI for BASE2 should support the automatic plug-in installation ...) created by
- 8:46 PM Ticket #146 (Change references to lev.thep.lu.se to something more appropriate) created by
- 8:45 PM Ticket #145 (GPL3 for WeNNI) created by
Nov 21, 2008:
- 9:20 PM Changeset [818] by
- First commit of the AbstractRunBinaryPlugin? class. Still very …
- 9:17 PM Changeset [817] by
- Fixing typo.
- 9:24 AM Ticket #144 (R plug-in framework) created by
- A framework to support running R script should be created. This would …
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