@@ -57,17 +57,17 @@ importFrom(mvtnorm, dmvnorm)

 importFrom(ellipse, ellipse)

 importFrom(ff, ffdf, physical.ff, physical.ffdf, ffrowapply)

-

 ## It is important not to import these classes from oligoClasses

 ## Doing so causes the following errors:

 ## N.AA(container)[index, ] <- someMatrix

 ##Error in function (classes, fdef, mtable)  :

 ##  unable to find an inherited method for function "medianA.AA<-", for signature "CNSet", "ff_matrix"

 ##importClassesFrom(oligoClasses, ffdf, ff_matrix)

+importClassesFrom(oligoClasses, ff_matrix)

 ## Important to export these classes

 ##exportClasses(ff_or_matrix, ff_matrix, ffdf)

-exportClasses(ff_or_matrix)

+##exportClasses(ff_or_matrix)

 exportMethods(lines)

 exportMethods(CA, CB)

 export(crlmm,

@@ -85,13 +85,13 @@ export(constructIlluminaCNSet)

 export(totalCopynumber)

 export(cnrma, cnrma2)

 exportMethods(A, B, nuA, nuB, phiA, phiB, corr, tau2, Ns, medians, mads)

-export(genotypeSummary,

-       shrinkSummary,

+##export(genotypeSummary,

+##       shrinkSummary,

 ##       estimateCnParameters,

 ##       shrinkGenotypeSummaries,

 ##       summarizeSnps,

 ##       constructIlluminaAssayData,

-       ACN, C1, C2, C3)

+##       ACN, C1, C2, C3)

 ## For debugging

 ## exportPattern("^[^\\.]")

@@ -1,5 +1,3 @@

 setOldClass("ellipse")

-setOldClass("ff_matrix")

 setOldClass("ffdf")

-##setClassUnion("ff_or_matrix", c("ff_matrix", "matrix", "ffdf"))

 setClassUnion("ff_or_matrix", c("ff_matrix", "matrix"))