> The same error message is reported in the "Stack trace" tab. Nothing else.
Strange. I just finsished downloading that (huge!) file and get the following error/stack trace: java.lang.ArrayIndexOutOfBoundsException: 511 at java.util.Arrays$ArrayList.set(Arrays.java:3385) at affymetrix.gcos.cdf.CDFFileData.readTextProbeSets(CDFFileData.java:500) at affymetrix.gcos.cdf.CDFFileData.readTextFormat(CDFFileData.java:298) at affymetrix.gcos.cdf.CDFFileData.open(CDFFileData.java:148) at affymetrix.gcos.cdf.CDFFileData.read(CDFFileData.java:687) at affymetrix.fusion.cdf.FusionCDFData.read(FusionCDFData.java:101) at net.sf.basedb.core.Affymetrix.checkIfReportersExists(Affymetrix.java:328) at net.sf.basedb.plugins.CdfFileReporterImporter.importFromCdf(CdfFileReporterImporter.java:488) at net.sf.basedb.plugins.CdfFileReporterImporter.run(CdfFileReporterImporter.java:197) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:110) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:506) at java.lang.Thread.run(Thread.java:619) The problem is with the following entry in the cdf file: [Unit4579024] Name=NONE Direction=1 NumAtoms=0 0 NumCells=510 UnitNumber=4579024 UnitType=0 NumberBlocks=1 It has 510 cells, but the code still tries to assign information to position 511 in the array. I don't know why or if this has been fixed in later versions of the SDK provided by Affymetrix. I have checked the code and it seems like in this particular case it only works if the number of cells is a multiple of 4 (eg. 508 or 512). In any case, it is not possible to simply replace the Affymetrix SDK that BASE uses with the new one since we have made some modifications to the code in the SDK to make it work with BASE. /Nicklas ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
