TESTS: "system" on GenomeWideSNP_6 takes ~3.5 hours to complete

[HenrikBengtsson]

The redundancy tests for:

• testScripts/system/chipTypes/GenomeWideSNP_6/
  • 11.justSNPRMA.R (~1h20m)
  • 21.doASCRMAv2,AlleleSummation.R (~2h30m)
  • 21.doASCRMAv2,ArrayExplorer.R (~0h35m)
  • 21.doASCRMAv2,GCNorm.R (~0h20m)
  • 21.doASCRMAv2,extract.R (~0h04m)
  • 21.doASCRMAv2,plotACC.R (~0h05m)
  • 21.doASCRMAv2,plots.R (~0h08m)
  • 21.doASCRMAv2,singleArray.R (~0h30m)
  • 21.doASCRMAv2.R (~0h01m)

takes ~5.5 hours to complete. The data set is GSM337708 and consists of 14 CEL files. We should strip this down to processing of, say, 6 CEL files.

Also, can/should we move the justSNPRMA() test to testScripts/replication/?

[HenrikBengtsson]

Ah... have already cut down from 14 to 6 CEL files, cf. commit 0c9ec71 (was just running on an already downloaded data set).

[HenrikBengtsson]

Longest running test sets are now:

• 3h44m: testScripts/system/chipTypes/GenomeWideSNP_6/
• 2h17m: testScripts/replication/chipTypes/Mapping250K_Nsp/
• 1h53m: testScripts/system/chipTypes/Mapping250K_Nsp/
• 1h23m: testScripts/system/chipTypes/Mapping250K_Sty/
• 1h22m: testScripts/replication/chipTypes/GenomeWideSNP_6/
• 1h21m: testScripts/system/chipTypes/CytoScanHD_Array/
• 1h18m: testScripts/addons/chipTypes/Mapping250K_Nsp/

Note that the replication/ tests assume the system/ are already done, so if we run the former by themselves they might take much longer.