Timeline


and

Dec 18, 2008:

5:05 PM se.lu.onk.CGHDataDumper edited by jari
(diff)
5:03 PM PluginDownload edited by jari
(diff)
4:07 PM PluginDownload edited by jari
Update normalization package information (diff)
12:57 PM Ticket #120 (Create a normalization plug-in package.) closed by jari
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
(diff)
12:54 PM net.sf.basedb.normalizers edited by jari
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
12:53 PM normalization-plugins-1.0.tar.gz attached to net.sf.basedb.normalizers by jari
12:52 PM net.sf.basedb.normalizers edited by jari
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
12:44 PM Changeset [934] by jari
Tagging version 1.0 of the net.sf.basedb.normalizers.
12:41 PM Changeset [933] by jari
Corrected spelling
12:40 PM Changeset [932] by jari
Addresses #120.
12:30 PM Changeset [931] by jari
Addresses #120. Preparing 1.0 release.
12:29 PM net.sf.basedb.normalizers edited by jari
Preparing 1.0 release of net.sf.basedb.normalizers package. (diff)
12:18 PM Changeset [930] by jari
Typo
12:15 PM Changeset [929] by jari
Removing CubicSplineNormalization? stub.
12:12 PM Changeset [928] by jari
Fixes #167. Now using geometric mean
12:12 PM Ticket #167 ((net.sf.basedb.normalizers) Average normalizer should use geometric mean) closed by jari
fixed: (In [928]) Fixes #167. Now using geometric mean
12:11 PM Changeset [927] by jari
Refs #165.
11:13 AM Ticket #167 ((net.sf.basedb.normalizers) Average normalizer should use geometric mean) created by jari
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
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 jari
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
fixed: (In [926]) Fixes #165. Simply renamed rank invariant to quantile and …
11:20 PM Changeset [926] by jari
Fixes #165. Simply renamed rank invariant to quantile and made …
10:37 PM Ticket #119 (Create rank invariant normalizer) reopened by jari
The normalizer is not the rank invariant normalizer but rather …
10:15 PM Ticket #165 (Create quantile normalizer) created by jari
9:06 PM Changeset [925] by jari
Improved README.
9:05 PM Changeset [924] by jari

Dec 16, 2008:

11:45 PM Ticket #164 (Improve documentation on how to upgrade the illumina plug-in package) created by jari
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
References #163 Disregard the last commit. This will do instead.
1:52 PM Changeset [922] by martin
References #163 The sorting of spotdata should be stable now. Please …
9:11 AM Changeset [921] by nicklas
Preparing for future release 1.0
9:10 AM net.sf.basedb.ftp edited by nicklas
Releasing FTP Server 1.0beta2 (diff)
9:05 AM Changeset [920] by nicklas
Tagging release of FTP Server 1.0beta2
9:04 AM Changeset [919] by nicklas
Preparing release of FTP Server 1.0beta2

Dec 15, 2008:

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

Dec 12, 2008:

9:35 AM Changeset [917] by nicklas
References #127: Update to final release of Apache Mina FTP server …

Dec 11, 2008:

10:21 PM Changeset [916] by nicklas
References #127: Update to final release of Apache Mina FTP server …
10:16 PM Changeset [915] by nicklas
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 nicklas
Reports on the mailing lists indicate that MeV 4.3 has solved a lot of …
1:09 PM Changeset [914] by nicklas
Adding note about checking that the information on the download page …
1:07 PM PluginDownload edited by nicklas
(diff)
1:06 PM net.sf.basedb.illumina edited by nicklas
(diff)
1:05 PM Changeset [913] by nicklas
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
Releasing Illumina package 1.2 (diff)
1:00 PM illumina-plugins-1.2.tar.gz attached to net.sf.basedb.illumina by nicklas
12:59 PM Changeset [912] by nicklas
Tagging Illumina package 1.2
12:59 PM Changeset [911] by nicklas
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
The build process should detect whether the required BASE jars are …
1:05 PM net.sf.basedb.normalizers edited by jari
Changing to GPL3 (diff)
1:01 PM Changeset [910] by jari
Changing normalizer package license to GPL3.
11:38 AM Changeset [909] by jari
Addresses #120.

Dec 8, 2008:

11:18 PM net.sf.basedb.normalizers edited by jari
Updated TODO section (diff)
11:13 PM net.sf.basedb.normalizers edited by jari
Added browse svn link (diff)
10:58 PM Ticket #88 (extra values pass through) closed by jari
wontfix
10:52 PM Ticket #75 (base2.xml genespring connection) closed by jari
wontfix: Will not fix this. External contributions welcome.
10:48 PM Ticket #41 (Add data to output: sign flag, sign specific rank) closed by jari
wontfix
10:30 PM Changeset [908] by jari
Addresses #50. Running nni with phony weights.
10:07 PM Changeset [907] by peter
using ACLOCAL_AMFLAGS requires Automake 1.10
10:01 PM Changeset [906] by jari
Some external binary will output result to stdout ... optionally …
9:31 PM Changeset [905] by peter
WeNNI.java should be included in dist
9:19 PM Changeset [904] by peter
installing jars with chmod 644
9:11 PM Changeset [903] by peter
Style is everything
4:49 PM Changeset [902] by peter
timestamp of downloaded jar file will be old. Fixing deps to reflect …
4:25 PM Changeset [901] by peter
improve dependency
10:56 AM Changeset [900] by jari
Refs #159
10:53 AM Changeset [899] by jari
Address #159. Renaming BASE1 plugin definition and minor changes to …
10:50 AM Changeset [898] by jari
Adding URL.
10:48 AM Changeset [897] by jari
Correcting URL
10:42 AM Changeset [896] by jari
Refs #56. Removing branches and tags directories since they will never …
10:39 AM Changeset [895] by jari
Addresses #56 and #159. Creating VirtualArray? module.
10:27 AM Changeset [894] by jari
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
Implement the plug-in abort functionality available in BASE in WeNNI. …
8:50 PM Changeset [893] by jari
Addresses #50. Adapting to PluginUtilities? interface changes.
8:49 PM Changeset [892] by jari
Improved dependency checking on pluginutilities.
8:46 PM Changeset [891] by jari
Changed interface and added debug code.
12:57 PM Changeset [890] by jari
Added debug code.

Dec 5, 2008:

11:59 PM Changeset [889] by peter
experienced some problems when changing from normal build to VPATH …
6:32 PM Changeset [888] by peter
fixing some make dependency
6:26 PM Ticket #159 (Create a se.lu.onk.VirtualArray module) created by jari
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
wontfix: This will resolve as a side effect of fixing ticket:56
5:54 PM se.lu.thep.WeNNI edited by jari
Added link to project statistics. (diff)
5:52 PM se.lu.onk.BaseFile edited by jari
Updated link to project statistics. (diff)
5:51 PM se.lu.onk.ReplicateError edited by jari
Update link to project statistics. (diff)
5:50 PM se.lu.onk.MergeBioAssay edited by jari
Update link to project statistics. (diff)
5:50 PM se.lu.onk.Center edited by jari
Update link to project statistics. (diff)
5:45 PM Changeset [887] by jari
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
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 peter
README refers to AbstractRunBinary but I only see …
5:06 PM Ticket #63 (make distcheck should work) closed by peter
fixed: (In [886]) typo that fixes #63. 'make mainatianer-check' now works here.
5:06 PM Changeset [886] by peter
typo that fixes #63. 'make mainatianer-check' now works here.
4:04 PM Changeset [885] by jari
Use rather that '.' in classpath.
4:03 PM Ticket #156 (Compilation fails in base2 test phase of 'make maintainer-check') closed by jari
fixed: Ah, I got it! it downloads the pre-version PluginUtilities? from …
3:45 PM Changeset [884] by jari
Cleaning up JAVACCLASSPATH usage.
12:57 PM PluginDownload edited by jari
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
12:56 PM Center-2.1.tgz attached to se.lu.onk.Center by jari
12:55 PM se.lu.onk.Center created by jari
Adding se.lu.onk.Center page.
12:41 PM Ticket #157 (Create a se.lu.onk.Center module) closed by jari
fixed: (In [883]) Fixes #157. Bumping version number to 2.2pre
12:41 PM Changeset [883] by jari
Fixes #157. Bumping version number to 2.2pre
12:40 PM Changeset [882] by jari
Tagging version 2.1 of se.lu.onk.Center
12:39 PM Changeset [881] by jari
Addresses #157. Preparing release 2.1 of Center.
12:28 PM Changeset [880] by jari
Addresses #157.
11:28 AM Changeset [879] by jari
Changed documentation to document the Center plug-in
11:27 AM Changeset [878] by jari
Spell checked.
11:27 AM Changeset [877] by jari
Spell checked.
11:15 AM Changeset [876] by jari
Correcting typo.
10:53 AM Changeset [875] by jari
Addresses #157 and #56. Creating se.lu.onk.Center.
10:45 AM se.lu.onk.MergeBioAssay edited by jari
Removed features section, added link to svndigest statistics. (diff)
10:42 AM se.lu.onk.MergeBioAssay edited by jari
Added license note (diff)
10:06 AM Ticket #157 (Create a se.lu.onk.Center module) created by jari
Relates to ticket:56 Split se.lu.onk into smaller modules Change to GPL3

Dec 4, 2008:

6:20 PM Changeset [874] by peter
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 peter
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 nicklas
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 johan
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 jari
Since some of the strings in WeNNI.java contain international …
11:53 AM Changeset [873] by nicklas
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
fixed: (In [873]) Fixes #151: Use two queries instead of one in …

Dec 3, 2008:

11:40 PM Changeset [872] by peter
TODO is included in dist by default, so no need to add it explicitly
11:29 PM Changeset [871] by peter
install-exec-local didn't respect DESTDIR. Copying code generated by …
11:19 PM Changeset [870] by peter
calling tar through script 'missing'. refs #153.
11:05 PM Changeset [869] by peter
Adding uninstall-plugin target Using install target for install-plugin …
10:43 PM Changeset [868] by jari
JAVACFLAGS was a classpath! Correcting and introduced a proper …
10:40 PM Changeset [867] by jari
Typo
7:40 PM Changeset [866] by peter
simplify syntax of install-plugin targets by using install target
6:33 PM Changeset [865] by peter
adding uninstall targets in base2. Should probably be added in other …
4:45 PM Changeset [864] by peter
refs #153 - using autoreconf in bootstrap. Did not add '--force' …
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)

Dec 2, 2008:

11:24 PM Changeset [863] by jari
Addresses #50. Working on the Java wrapper.
11:22 PM Changeset [862] by jari
Cleanup of the abstract super class. More to come …
11:21 PM Changeset [861] by jari
Using BASE 2.9 API
9:31 PM Changeset [860] by peter
adding tests for javac and jar - refs #153
9:31 PM Changeset [859] by peter
adding tests for javac and jar - refs #153
4:33 PM Changeset [858] by jari
Addresses #50. Working with BASE-plugin communication issues and …
3:57 PM Ticket #153 (Autoconf issues in se.lu.thep.WeNNI) created by jari
Checks for used programs should be added jar, javac, tar, wget
9:05 AM Changeset [857] by jari
Refs #50. AM_CONDITIONALs must be available for all build states.
8:55 AM Changeset [856] by jari
Refs #50 and #63. All WeNNI build options now works. make distcheck …
7:39 AM Changeset [855] by jari
Removed stray tabs
12:33 AM Ticket #53 (update INSTALL) closed by jari
fixed: (In [854]) Fixes #53
12:33 AM Changeset [854] by jari
Fixes #53

Dec 1, 2008:

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

Nov 30, 2008:

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

Nov 29, 2008:

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

Nov 28, 2008:

8:12 PM Changeset [837] by peter
removing annoying Automake warning that %-style pattern rules are a …
6:27 PM Changeset [836] by peter
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 jari
invalid: I think this error has something to do with a mix of Illumina package …
5:55 PM Changeset [835] by jari
Since changeset:834 there is no need to check for sed
4:36 PM Changeset [834] by peter
Triggered by [826]. There were some problems with the Makefile.am, so …
2:15 PM Changeset [833] by nicklas
Fixes #150: Fix layout of DetectionPValue.java
2:15 PM Ticket #150 (Fix layout of DetectionPValue.java) closed by nicklas
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 nicklas
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
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 base
When trying to run plugin 'Illumina detection P-value calculation' I …

Nov 27, 2008:

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

Nov 26, 2008:

11:42 PM Changeset [825] by jari
Fixes #146.
11:42 PM Ticket #146 (Change references to lev.thep.lu.se to something more appropriate) closed by jari
fixed: (In [825]) Fixes #146.
11:17 PM Ticket #145 (GPL3 for WeNNI) closed by jari
fixed: (In [824]) Fixes #145.
11:17 PM Changeset [824] by jari
Fixes #145.
5:43 PM se.lu.thep.WeNNI edited by peter
fixing the query syntax (diff)
4:38 PM se.lu.thep.WeNNI edited by jari
Updated the TODO list (diff)
4:28 PM Ticket #52 (Add educational material and use cases.) closed by jari
wontfix
4:27 PM Ticket #148 (BASE1 configuration: execname should be set automatically during build) created by jari
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 jari
fixed: Fixed in changeset:821
4:23 PM Changeset [823] by jari
Addresses #53 and fixes #60.
4:23 PM Ticket #60 (explain how to run wenni (base1 version) against a base_devkit) closed by jari
fixed: (In [823]) Addresses #53 and fixes #60.
4:20 PM Changeset [822] by jari
Updated change information and default installation paths

Nov 25, 2008:

5:38 PM Changeset [821] by jari
Build of stand-alone and base1 modes work. base2 still to be finalized.
5:29 PM Changeset [820] by jari
Added note saying that repository checkout requires ./bootstrap.

Nov 24, 2008:

10:56 AM Changeset [819] by jari
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 jari
8:46 PM Ticket #146 (Change references to lev.thep.lu.se to something more appropriate) created by jari
8:45 PM Ticket #145 (GPL3 for WeNNI) created by jari

Nov 21, 2008:

9:20 PM Changeset [818] by jari
First commit of the AbstractRunBinaryPlugin? class. Still very …
9:17 PM Changeset [817] by jari
Fixing typo.
9:24 AM Ticket #144 (R plug-in framework) created by jari
A framework to support running R script should be created. This would …

Nov 19, 2008:

3:50 PM Changeset [816] by martin
References #143 Removed unnecessary comments.
3:49 PM Changeset [815] by martin
Fixes #143 Illumina plug-in package installer requests wrong permissions
3:49 PM Ticket #143 (Illumina plug-in package installer requests wrong permissions) closed by martin
fixed: (In [815]) Fixes #143 Illumina plug-in package installer requests …
2:22 PM Ticket #143 (Illumina plug-in package installer requests wrong permissions) created by martin
If only using the permissions requested by the plug-in, the jobs will …
11:08 AM Changeset [814] by nicklas
References #142. Removed problematic character. For historical reasons …
9:37 AM Changeset [813] by martin
Fixes #142 Illumina installer plugin cannot be installed in some cases
9:37 AM Ticket #142 (Illumina installer plugin cannot be installed in some cases) closed by martin
fixed: (In [813]) Fixes #142 Illumina installer plugin cannot be installed in …
8:22 AM Ticket #142 (Illumina installer plugin cannot be installed in some cases) created by martin
Installing Illumina plugin installer fails when either doing it …
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