[H5r-commits] r71 - / R

[noreply at r-forge.r-project.org]

Author: extemporaneousb
Date: 2011-11-18 21:12:27 +0100 (Fri, 18 Nov 2011)
New Revision: 71

Modified:
   DESCRIPTION
   NAMESPACE
   R/h5R.R
Log:
Redid the namespace and DESCRIPTION to better articulate the exports.

Modified: DESCRIPTION
===================================================================
--- DESCRIPTION	2011-10-21 23:17:38 UTC (rev 70)
+++ DESCRIPTION	2011-11-18 20:12:27 UTC (rev 71)
@@ -5,7 +5,8 @@
 Date: 2011-09-19
 Author: James Bullard
 Maintainer: <jbullard at pacificbiosciences.com>
-Depends: R (>= 2.10.0), methods, base
+Depends: R (>= 2.10.0), methods
+Imports: utils, methods
 Description: A package for interfacing with HDF5 files.
 License: LGPL
 

Modified: NAMESPACE
===================================================================
--- NAMESPACE	2011-10-21 23:17:38 UTC (rev 70)
+++ NAMESPACE	2011-11-18 20:12:27 UTC (rev 71)
@@ -1,7 +1,6 @@
 useDynLib(h5r)
 
-## Export everything lacking a leading .
-exportPattern("^[^\\.]")
+import(methods)
 
 exportClasses(H5Obj,
               H5File,
@@ -9,21 +8,48 @@
               H5Dataset,
               H5Attribute,
               H5DataContainer,
-              H5Container)
+              H5Container,
+              H5DataFrame,
+              hSlab)
 
-importMethodsFrom(methods, show)
+export(H5File,
+       read1DSlabs,
+       readSlab,
+       readPoints,
+       listH5Attributes,
+       listH5Contents,
+       h5ObjectExists,
+       h5GroupExists,
+       h5DatasetExists,
+       h5AttributeExists,
+       H5DataFrame,
+       writeH5DataFrame,
+       hSlab)
 
 exportMethods(getH5Group,
               getH5Dim,
               getH5Type,
               getH5Dataset,
               getH5Attribute,
+              writeH5Data,
+              createH5Dataset,
               createH5Group,
               createH5Attribute,
-              writeH5Data,
               deleteH5Obj,
               deleteH5Attribute,
+              "[",
               readH5Data,
               show,
+              dim,
+              length,
+              nrow,
               ncol,
-              nrow)
+              ls,
+              colnames,
+              "$",
+              "[[",
+              as.data.frame)
+              
+              
+            
+

Modified: R/h5R.R
===================================================================
--- R/h5R.R	2011-10-21 23:17:38 UTC (rev 70)
+++ R/h5R.R	2011-11-18 20:12:27 UTC (rev 71)
@@ -142,9 +142,8 @@
   if (! file.exists(fileName)) {
     stop(paste("Unable to open file:", fileName, "does not exist."))
   }
-
   ## convert the fileName - essentially for ~. 
-  fileName <- tools:::file_path_as_absolute(normalizePath(fileName))
+  fileName <- normalizePath(fileName)
   x <- .myCall("h5R_open", fileName, if (mode == 'r') as.integer(0) else as.integer(1))
   if (is.null(x)) {
     stop(paste("Problem opening file:", fileName))
@@ -536,7 +535,8 @@
 
 setMethod("show", "H5File", function(object) {
   callNextMethod(object)
-  cat("file:", object at fileName, "\n")
+  fname <- object at fileName
+  cat("file:", basename(fname), "\n")
 })
 
 setMethod("show", "H5Group", function(object) {