pneuvial / c3co

Inferring cancer cell clonality from copy-number data
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BUG FIX(?): Was it your intention to export the S4 classes? #14

Closed HenrikBengtsson closed 7 years ago

HenrikBengtsson commented 7 years ago

In commit 9395db, I just fixed:

diff --git a/NAMESPACE b/NAMESPACE
index ba237a4..bbdf326 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -15,6 +15,8 @@ export(mixSubclones)
 export(positiveFusedLasso)
 export(pvePlot)
 export(segmentData)
+exportClasses(c3coFit)
+exportClasses(posFused)
 exportMethods(Wplot)
 exportMethods(createZdf)
 exportMethods(showC3coFit)
diff --git a/R/AllClasses.R b/R/AllClasses.R
index 7241ce0..5a71bcd 100644
--- a/R/AllClasses.R
+++ b/R/AllClasses.R
@@ -22,8 +22,8 @@
 #'
 #' @exportClass posFused 
 setClass(
-  "posFused",
-  representation(
+  Class = "posFused",
+  representation = representation(
     S = "list",
     S0 = "list",
     W = "matrix",
@@ -43,11 +43,10 @@ setClass(
 #' 
 #' @slot fit A List of [\code{\linkS4class{posFused}}] objects.
 #' 
-#' @exportClass c3coClass
-#'
+#' @exportClass c3coFit
 setClass(
-  "c3coFit",
-  representation(
+  Class = "c3coFit",
+  representation = representation(
     bkp = "list",
     segDat = "list",
     fit = "list"
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
index c2baf0e..c234b4f 100644
--- a/R/AllGenerics.R
+++ b/R/AllGenerics.R
@@ -83,7 +83,7 @@ setMethod(
         rownames(W) <- rownamesW
pneuvial commented 7 years ago

Yes.