Merge RGLab:devel into k-motwani:devel-phylo

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: flowWorkspace
 Type: Package
 Title: Infrastructure for representing and interacting with gated and ungated cytometry data sets.
-Version: 4.9.1
+Version: 4.13.0
 Date: 2011-06-10
 Author: Greg Finak, Mike Jiang
 Maintainer: Greg Finak <[email protected]>, Mike Jiang <[email protected]>
@@ -11,15 +11,13 @@ Description: This package is designed to facilitate comparison of automated
     gating from flowJo using the flowCore functionality. Gating hierarchies,
     groups of samples, compensation, and transformation are performed so that
     the output matches the flowJo analysis.
-License: file LICENSE
-License_restricts_use: yes
+License: AGPL-3.0-only 
+License_restricts_use: no 
 LazyLoad: yes
 Imports:
     Biobase,
     BiocGenerics,
     cytolib (>= 2.3.9),
-    lattice,
-    latticeExtra,
     XML,
     ggplot2,
     graph,
@@ -34,14 +32,9 @@ Imports:
     Rgraphviz,
     data.table,
     dplyr,
-    Rcpp,
     scales,
     matrixStats,
-    RcppParallel,
     RProtoBufLib,
-    digest,
-	aws.s3,
-	aws.signature,
     flowCore(>= 2.1.1),
 	ncdfFlow(>= 2.25.4),
 	DelayedArray,
@@ -54,11 +47,10 @@ Collate:
     'GatingHierarchy_Methods.R'
     'GatingSet_Methods.R'
     'GatingSetList_Methods.R'
-    'RcppExports.R'
     'filterObject_Methods.R'
     'add_Methods.R'
     'copyNode.R'
-    'cytoctx.R'
+    'cpp11.R'
     'deprecated.R'
     'flow_trans.R'
     'getDescendants.R'
@@ -83,9 +75,9 @@ Suggests:
     parallel,
     CytoML,
     openCyto
-LinkingTo: Rcpp, BH(>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib (>= 2.3.7),Rhdf5lib, RcppArmadillo, RcppParallel(>= 4.4.2-1)
+LinkingTo: cpp11, BH(>= 1.62.0-1), RProtoBufLib(>= 1.99.4), cytolib (>= 2.3.7),Rhdf5lib
 VignetteBuilder: knitr
 biocViews: ImmunoOncology, FlowCytometry, DataImport, Preprocessing, DataRepresentation
 SystemRequirements: GNU make, C++11
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1

NAMESPACE

@@ -63,7 +63,6 @@ export(cf_swap_colnames)
 export(cf_unlock)
 export(cf_write_disk)
 export(cf_write_h5)
-export(cf_write_tile)
 export(char2booleanFilter)
 export(checkRedundantNodes)
 export(convert_backend)
@@ -86,8 +85,6 @@ export(cs_lock)
 export(cs_set_cytoframe)
 export(cs_swap_colnames)
 export(cs_unlock)
-export(ctx_to_list)
-export(cytoctx)
 export(cytoframe_to_flowFrame)
 export(cytoset)
 export(cytoset_to_flowSet)
@@ -219,7 +216,6 @@ export(isGated)
 export(isHidden)
 export(isNcdf)
 export(isNegated)
-export(is_tiledb_support)
 export(load_cytoframe)
 export(load_cytoframe_from_fcs)
 export(load_cytoset)
@@ -230,13 +226,10 @@ export(logicleGml2_trans)
 export(logicle_trans)
 export(logtGml2_trans)
 export(merge_list_to_gs)
-export(moveNode)
 export(openWorkspace)
-export(plotGate)
 export(pop.MFI)
 export(pop_add)
 export(prettyAxis)
-export(print.cytoctx)
 export(realize_view)
 export(recompute)
 export(save_cytoset)
@@ -323,18 +316,9 @@ importFrom(Biobase,sampleNames)
 importFrom(BiocGenerics,"rownames<-")
 importFrom(BiocGenerics,duplicated)
 importFrom(BiocGenerics,rownames)
-importFrom(Rcpp,evalCpp)
-importFrom(RcppParallel,RcppParallelLibs)
 importFrom(Rgraphviz,agread)
 importFrom(S4Vectors,coolcat)
-importFrom(aws.s3,delete_object)
-importFrom(aws.s3,get_bucket)
-importFrom(aws.s3,get_bucket_df)
-importFrom(aws.s3,put_object)
-importFrom(aws.s3,save_object)
-importFrom(aws.signature,read_credentials)
 importFrom(cytolib,cytolib_LdFlags)
-importFrom(digest,digest)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,do)
@@ -347,8 +331,6 @@ importFrom(graph,"edgeRenderInfo<-")
 importFrom(graph,"nodeRenderInfo<-")
 importFrom(graph,addEdge)
 importFrom(graph,graphNEL)
-importFrom(lattice,barchart)
-importFrom(latticeExtra,ggplot2like)
 importFrom(matrixStats,colMedians)
 importFrom(scales,format_format)
 importFrom(scales,trans_new)

R/AllClasses.R

@@ -9,7 +9,6 @@ NULL
 #' flowWorkspace-package
 #' flowWorkspace
 #' @docType package
-#' @importFrom Rcpp evalCpp
 #' @importFrom cytolib cytolib_LdFlags
 #' @title Import and replicate flowJo workspaces and gating schemes using flowCore.
 #' @description Import flowJo workspaces into R. Generate the flowJo gating hierarchy and gates using flowCore functionality. Transform and compensate data in accordance with flowJo settings. Plot gates, gating hierarchies,  population statistics, and compare flowJo vs flowCore population summaries.
@@ -21,7 +20,7 @@ NULL
 #'     Date: \tab 2011-03-04\cr
 #'     License: \tab Artistic 2.0 \cr
 #'     LazyLoad: \tab yes\cr
-#'     Depends: \tab R (>= 2.16.0),Rcpp (>= 0.9.9)\cr
+#'     Depends: \tab R (>= 2.16.0)\cr
 #'   }
 #' @author Greg Finak, Mike Jiang
 #' @references \url{http://www.rglab.org/}