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 Changeset [932] by Jari Häkkinen
Addresses #120.
12:30 PM Changeset [931] by Jari Häkkinen
Addresses #120. Preparing 1.0 release.
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
12:11 PM Changeset [927] by Jari Häkkinen
Refs #165.
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
11:22 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) 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.
1:52 PM Changeset [922] by Martin Svensson
References #163 The sorting of spotdata should be stable now. Please …
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 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 …
10:16 PM Changeset [915] by Nicklas Nordborg
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 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.

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)
10:58 PM Ticket #88 (extra values pass through) closed by Jari Häkkinen
wontfix
10:52 PM Ticket #75 (base2.xml genespring connection) closed by Jari Häkkinen
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 Häkkinen
wontfix
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
10:53 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 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.
10:27 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.
8:49 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 …
6:32 PM Changeset [888] by Peter Johansson
fixing some make dependency
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
5:54 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 …
5:22 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.
4:04 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 …
3:45 PM Changeset [884] by Jari Häkkinen
Cleaning up JAVACCLASSPATH usage.
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 Changeset [881] by Jari Häkkinen
Addresses #157. Preparing release 2.1 of Center.
12:28 PM Changeset [880] by Jari Häkkinen
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.
10:45 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)
10:06 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:

6:20 PM Changeset [874] by Peter Johansson
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 Johansson
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 Nordborg
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 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 …

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.
11:05 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' …
4:04 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 Häkkinen
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 Changeset [859] by Peter Johansson
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 …
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
9:05 AM Changeset [857] by Jari Häkkinen
Refs #50. AM_CONDITIONALs must be available for all build states.
8:55 AM Changeset [856] by Jari Häkkinen
Refs #50 and #63. All WeNNI build options now works. make distcheck …
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

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 Changeset [848] by Jari Häkkinen
Refs #50. Using proper PluginUtilities? URL for download
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 …
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 …
6:03 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 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
2:04 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 …
1:36 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 …
Note: See TracTimeline for information about the timeline view.