ATdeveloper

Release timeline for BRB-ArrayTools

• 2013/9/12; v4.3.2 stable (R 3.0.2 and Bioc 2.13).
• 2013/6/12: v4.3.1 stable (R 3.0.1 and Bioc 2.12) Because changes in R 3.0.1, some Bioc packages compiled by R 3.0.1 may not work with R 3.0.0. Download link is here
• 2013/5/24: v4.3.0 stable (R 3.0.0 and Bioc 2.12)
• 2013/3/7: v4.3.0 beta3 (SOURCE website change, sorting of experiment worksheet). Downloaded from http://pub.emmes.com.
• 2012/11/28: v4.3.0 beta2
• 2012/8/15: v4.3.0 beta1
• 2012/1/24: v4.2.1 stable

Release timeline for R/Bioconductor

• 2013/9/25: R-3.0.2
• 2013/5/16: R-3.0.1
• 2013/4/3: R-3.0.0 and Bioconductor 2.12

Release Procedures (including check list for installer)

1. Misc Folder:
   • CGHTools
   • R installer
   • Rserve
   • Java installer
   • Microsoft C++ 2010 SP1 Redistribute packages, vcredist_x64.exe & vcredist_x86.exe
2. License file,
   • C:\Installer-2012\ArrayTools-Scripts\V4_3_And_CGH_1_3_RServe_Full\Setup Files\Compressed Files\Language Independent\OS Independent\License.doc. It is a text file.
   • C:\Installer-2012\CGHTools-Scripts\CGH_1_3_Rserve\Setup Files\Compressed Files\Language Independent\OS Independent\License.doc. It is a text file.
3. License agreement menu, About ArrayTools and About CGHTools menus.
4. Sample datasets.
5. ArrayTools: License.doc, Readme.doc.
6. ArrayTools\Updates: ArrayTools_CurrentVersion.txt.
7. ArrayTools\Doc: Manual.doc, ManualFrame.doc, Overview of Analysis Tools.doc, Plug-in Manual.doc, StatMethods.doc, Table of Contents.doc, FAQs.pdf.
8. CGHTools: LICENSE AGREEMENT.doc, Readme.doc
9. CGHTools\Updates: CGHTools_CurrentVersion.txt.
10. CGHTools\Doc: CGHManual.doc, CGHManualFrame.doc, Table of Contents.doc.
11. ArrayTools_UpdateVersion.txt, it will keep on the ArrayTools server.
12. http://linus.nci.nih.gov/~brb/news.html
13. Different ArrayTools installers.
    • There are 3 installers: Full, Individual and Update. Main release has no Update installers.
    • Individual installer has no R and no Java installers in the Misc folder. It will detect the required R version (or newer than the required R version). If no required R version or lower, the installation will abort.
    • Update installer has changed files between current and previous freeze folders.
14. The installers will keep a copy in K:\BRB\ARRAYTOOLS\archive\installers\. Alpha versions will not keep, only Beta versions and release versions will keep on K:.
15. YD puts the new release online:
    • Create a testing page: http://linus.nci.nih.gov/BRB-ArrayTools_test.html
    • Whats-new-v43b1.doc, Readme.doc, License.doc, Manual.doc
    • Java, R download links
    • Installers: Full, Individual, Update
    • ArrayTools_LatestVersion.txt (no more than 5 items)
    • Sending emails to users about new release need about 3 hours. Only Beta 1 and Stable versions need to send out user emails. Other Beta versions don't send to reduce user emails.

Trouble shooting

'This workbook is currently referenced by another workbook and cannot be closed' when I use VBAObjectManager

1. uninstall AT & CGHTools
2. use privilege manager to run installer
3. use privilege manager to open excel and run VBAObjectManager

Registrition

http://linus.nci.nih.gov/cgi-bin/brb/matchregistration.cgi?email=xxx.gmail.com
http://linus-stage.nci.nih.gov/cgi-bin/brb/matchregistration.cgi?email=xxx.gmail.com

How to Test

• Extreme number of arrays (eg 3, 10) This is used to test chunking, ...
• Extreme number of genes.
• Use non-default options.
• Analyze one project after another project to see if there is any memory issue.
• Use unreasonable entry like 1.5 if the value should be less than or equal to 1.
• Use long path name for project.
• Test on fresh machine (no R libraries installed).
• Data with lots of missing values.
• Test on a subset of arrays only.

Misc

• For an old project needs to be converted, the old project folder will be backed up with a new name 'XXXX_ArrayToolsOldProject'.

Good R writing habit

• Use indentaion.
• Use parenthesis if needed. For example, the following is bad

if (something) DoSomething
else DoAnother