Hi, aroma.affymetrix v2.10.0 and friends has been released and is available on CRAN (where the package is hosted). Update by:
source("http://aroma-project.org/hbLite.R"); hbInstall("aroma.affymetrix"); This release is mainly about bug fixes, internal cleanups and some minor speedups. Cheers, Henrik - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Updates to aroma.affymetrix - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Version: 2.10.0 [2013-08-04] o CLEANUP: The formal package dependancy on Bioconductor packages 'aroma.light' and 'affxparser' has been relaxed so the package can be installed without them. o CLEANUP: Package now only imports matrixStats, R.oo, R.filesets and aroma.apd. o CLEANUP: Removed since-long defunct methods. Made deprecated methods defunct. o Bumped version for CRAN submission. o Updated package dependences. o Package passes all redundancy tests. Version: 2.9.7 [2013-07-28] o ROBUSTNESS: byPath() for DChipDcpSet was not decleared static. o BUG FIX: In certain cases, calls to static method byPath() would be affected by the NextMethod() '...' bug reported in R-devel thread "Do *not* pass '...' to NextMethod() - it'll do it for you; missing documentation, a bug or just me?" on 2012-10-16. Version: 2.9.6 [2013-07-03] o Added argument 'flavor' or doRMA() making it easier to replicate the results of other packages, e.g. doRMA(..., flavor="oligo"). Version: 2.9.5 [2013-06-02] o ROBUSTNESS: Now more methods are creating/writing signals atomically. o BUG FIX: Since v2.9.0, doFIRMA() would give "Exception: Unknown arguments: .onUnknownArgs" in the alternative splicing step. o BUG FIX: calculateConfidenceScores() for CrlmmModel used defunct method isHeterozygote() instead of isHeterozygous(). o BUG FIX: Certain methods could throw 'Error in UseMethod("getChecksum") : no applicable method for 'getChecksum' applied to an object of class "list"' if (and only if) R.cache package was not attached. The same bug was fixed on aroma.core v2.9.2 recently. Version: 2.9.4 [2013-05-30] o Now it's possible to call aroma.affymetrix::doRMA() without first loading package. Same for all other doNnn() methods, e.g. doCRMAv2(), doFIRMA() and doGCRMA(). Version: 2.9.3 [2013-05-25] o SPEEDUP: Replaced all rm() calls with NULL assignments. Version: 2.9.2 [2013-05-22] o CLEANUP: Now using getChecksum() instead of (internal) R.filesets::digest2() with identical results. o CLEANUP: Now getIdentifier() for CnagCfhFile utilizes getChecksum() for the GenericDataFile class. Version: 2.9.1 [2013-05-20] o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Updates to aroma.core - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Version: 2.10.0 [2013-08-03] o Bumped version for CRAN submission. o Updated package dependences. o Package passes all redundancy tests. Version: 2.9.7 [2013-07-20] o CLEANUP: Replaced all internal x11() with dev.new() calls. o CLEANUP: Moved more packages from Depends to Imports. o Updated package dependences. Version: 2.9.6 [2013-06-01] o Added findFilesTodo() for AromaTransform. Version: 2.9.5 [2013-05-30] o DOCUMENTATION: Now help("doCBS") documents all doCBS() methods. o Now it's possible to call aroma.core::doCBS() without loading package. o Turned doCBS() into a default method, cf. aroma.affymetrix::doRMA(). Version: 2.9.4 [2013-05-25] o SPEEDUP: Replaced all rm() calls with NULL assignments. Version: 2.9.3 [2013-05-22] o CLEANUP: Now using getChecksum() instead of (internal) R.filesets::digest2() with identical results. Version: 2.9.2 [2013-05-22] o BUG FIX: extractRawCopyNumbers() for CopyNumberChromosomalModel would throw 'Error in UseMethod("getChecksum") : no applicable method for 'getChecksum' applied to an object of class "list"' if (and only if) R.cache package was not attached. Thanks Yadav Sapkota at University of Alberta for reporting on this. Version: 2.9.1 [2013-05-20] o CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long. o CRAN POLICY: Now all Rd example lines are at most 100 characters long. -- -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.