@@ -1,21 +1,21 @@

 Package: Streamer

 Type: Package

 Title: Enabling stream processing of large files

-Version: 1.3.11

+Version: 1.3.12

 Author: Martin Morgan, Nishant Gopalakrishnan

 Maintainer: Martin Morgan <mtmorgan@fhcrc.org>

 Description: Large data files can be difficult to work with in R,

-  where data generally resides in memory. This package encourages a

-  style of programming where data is 'streamed' from disk into R via a

-  `producer' and through a series of `consumers' that, typically

-  reduce the original data to a manageable size. The package provides

-  useful Producer and Consumer stream components for operations such

-  as data input, sampling, indexing, and transformation; see

-  package?Streamer for details.

+    where data generally resides in memory. This package encourages a

+    style of programming where data is 'streamed' from disk into R via

+    a `producer' and through a series of `consumers' that, typically

+    reduce the original data to a manageable size. The package

+    provides useful Producer and Consumer stream components for

+    operations such as data input, sampling, indexing, and

+    transformation; see package?Streamer for details.

 License: Artistic-2.0

 LazyLoad: yes

-Imports: methods, graph, parallel, BiocGenerics

-Suggests: RUnit, Rsamtools (>= 1.5.53)

+Imports: methods, graph, RBGL, parallel, BiocGenerics

+Suggests: RUnit, Rsamtools (>= 1.5.53), Rgraphviz

 biocViews: Infrastructure, DataImport

 Collate: 

   AllGenerics.R 

@@ -23,7 +23,7 @@ Collate:

   ConnectionProducer-classes.R RawInput-class.R Seq-class.R

   Downsample-class.R FunctionProducerConsumer-classes.R

   ParallelParam-classes.R Team-class.R Team-methods.R Reducer-class.R

-  Utility-classes.R ParallelConnector-class.R TConnector-class.R

-  YConnector-class.R

-  lapply-methods.R stream-methods.R

+  DAGParam-class.R DAGParam-methods.R DAGTeam-class.R

+  Utility-classes.R

+  lapply-methods.R stream-methods.R plot-methods.R

   zzz.R

@@ -9,16 +9,27 @@ importClassesFrom(BiocGenerics, connection)

 ## only exported on unix

 ## importFrom(parallel, mccollect, mcparallel)

-importFrom(graph, graphBAM)

+importClassesFrom(graph, graphNEL)

-importMethodsFrom(graph, degree)

+importFrom(graph, ftM2graphNEL)

+

+importMethodsFrom(graph, numNodes, numEdges, nodes, edges, inEdges)

+

+importFrom(RBGL, tsort)

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

 exportMethods(lapply, sapply)

-exportClasses(Streamer,

-              Producer, RawInput, Seq, 

-              Consumer, RawToChar, Rev, Reducer, Team, Downsample,

-              Stream, ConnectionProducer, ParallelConnector,

-              TConnector, YConnector)

+exportClasses(

+    Streamer,

+    Stream,

+    Producer,

+        RawInput, Seq,

+        FunctionProducer,

+        ConnectionProducer,

+    Consumer,

+        RawToChar, Rev, Downsample, Reducer,

+        FunctionConsumer,

+        Team, ParallelParam, MulticoreParam,

+        DAGTeam, DAGParam)