From noreply at r-forge.r-project.org  Tue Jul  2 22:14:30 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  2 Jul 2013 22:14:30 +0200 (CEST)
Subject: [H5r-commits] r95 - / R src tests
Message-ID: <20130702201430.36CB0184D56@r-forge.r-project.org>

Author: extemporaneousb
Date: 2013-07-02 22:14:29 +0200 (Tue, 02 Jul 2013)
New Revision: 95

Modified:
   DESCRIPTION
   R/h5R.R
   src/h5_wrap.c
   tests/testMemory.R
Log:
Removed the malloc_trim code because it is not portable. 



Modified: DESCRIPTION
===================================================================
--- DESCRIPTION	2013-06-26 05:46:59 UTC (rev 94)
+++ DESCRIPTION	2013-07-02 20:14:29 UTC (rev 95)
@@ -1,7 +1,7 @@
 Package: h5r
 Type: Package
 Title: Interface to HDF5 Files
-Version: 1.4.5
+Version: 1.4.6
 Date: 2011-09-19
 Author: James Bullard
 Maintainer: James Bullard <jbullard at pacificbiosciences.com>

Modified: R/h5R.R
===================================================================
--- R/h5R.R	2013-06-26 05:46:59 UTC (rev 94)
+++ R/h5R.R	2013-07-02 20:14:29 UTC (rev 95)
@@ -120,10 +120,6 @@
   .myCall("h5R_get_object_count", .ePtr(h5File))
 }
 
-.mallocTrim <- function() {
-  .myCall("h5R_malloc_trim")
-}
-
 setMethod("getH5Group", c("H5Container", "character"), function(h5Obj, groupName) {
   if (is.null(x <- .myCall("h5R_get_group", .ePtr(h5Obj), groupName)))
     stop(paste("Group:", groupName, "cannot be opened."))

Modified: src/h5_wrap.c
===================================================================
--- src/h5_wrap.c	2013-06-26 05:46:59 UTC (rev 94)
+++ src/h5_wrap.c	2013-07-02 20:14:29 UTC (rev 95)
@@ -4,11 +4,6 @@
 #include <hdf5.h>
 #include <Rinternals.h>    
 #include <R.h>
-#ifdef __APPLE__
-#include <malloc/malloc.h>
-#else
-#include <malloc.h>
-#endif
 
 #define DEBUG 0
 #define MEMORYDEBUG 0
@@ -23,14 +18,6 @@
     hid_t id;
 } h5_holder;
 
-SEXP h5R_malloc_trim() {
-#ifdef __GLIBC__
-    return ScalarInteger(malloc_trim(0));
-#else
-    return ScalarInteger(-1);
-#endif
-}
-
 void h5R_finalizer(SEXP h5_obj) {
     h5_holder* h = (h5_holder*) R_ExternalPtrAddr(h5_obj);
     if (! h) {
@@ -63,9 +50,6 @@
     
     // This call is seemingly a noop.
     H5garbage_collect();
-
-    // Not sure if calling this here will be sufficient. 
-    h5R_malloc_trim();
 }
 
 SEXP _h5R_make_holder (hid_t id, int is_file) {

Modified: tests/testMemory.R
===================================================================
--- tests/testMemory.R	2013-06-26 05:46:59 UTC (rev 94)
+++ tests/testMemory.R	2013-07-02 20:14:29 UTC (rev 95)
@@ -27,13 +27,16 @@
 
 gc()
 
+## 7/2/2013 - malloc_trim commented out for CRAN submission.
+
+
 showPS()
 m <- .Call("h5R_allocate_gig")
 b <- 'bar' # from the post, "blocking the memory"
 rm(m)
 gcl()
 showPS()
-h5r:::.mallocTrim()
+# h5r:::.mallocTrim()
 showPS()
 
 m <- sapply(1:1000, function(a) {
@@ -43,7 +46,7 @@
 rm(m)
 gcl()
 showPS()
-h5r:::.mallocTrim()
+# h5r:::.mallocTrim()
 showPS()
 
 m <- sapply(1:100000, function(a) {
@@ -53,7 +56,7 @@
 rm(m)
 gcl()
 showPS()
-h5r:::.mallocTrim()
+# h5r:::.mallocTrim()
 showPS()
 
 m <- sapply(1:1000000, function(a) {
@@ -63,5 +66,5 @@
 rm(m)
 gcl()
 showPS()
-h5r:::.mallocTrim()
+# h5r:::.mallocTrim()
 showPS()


From noreply at r-forge.r-project.org  Mon Jul  8 23:52:52 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon,  8 Jul 2013 23:52:52 +0200 (CEST)
Subject: [H5r-commits] r96 - / R inst tests
Message-ID: <20130708215252.80A2E18505B@r-forge.r-project.org>

Author: extemporaneousb
Date: 2013-07-08 23:52:52 +0200 (Mon, 08 Jul 2013)
New Revision: 96

Modified:
   DESCRIPTION
   R/h5R.R
   inst/CRAN_prepare_h5r.sh
   tests/Makefile
   tests/testCompound.R
   tests/testGetGroup.R
   tests/testReadPoints.R
   tests/testWrite.R
Log:
Fixed problem with .Call and registration for 3.1 check consistency. Also fixed a bug where createH5Dataset would ignore the dimensions and type argument -- thanks to d. alexander for the report.



Modified: DESCRIPTION
===================================================================
--- DESCRIPTION	2013-07-02 20:14:29 UTC (rev 95)
+++ DESCRIPTION	2013-07-08 21:52:52 UTC (rev 96)
@@ -1,7 +1,7 @@
 Package: h5r
 Type: Package
 Title: Interface to HDF5 Files
-Version: 1.4.6
+Version: 1.4.7
 Date: 2011-09-19
 Author: James Bullard
 Maintainer: James Bullard <jbullard at pacificbiosciences.com>

Modified: R/h5R.R
===================================================================
--- R/h5R.R	2013-07-02 20:14:29 UTC (rev 95)
+++ R/h5R.R	2013-07-08 21:52:52 UTC (rev 96)
@@ -49,13 +49,9 @@
 
 ## ##############################################################################
 ##
-## C-helper
+## C-helpers
 ##
 ## ##############################################################################
-.myCall <- function(nm, ...) {
-  .Call(nm, ..., PACKAGE = 'h5r')
-}
-
 H5File <- function(fileName, mode = 'r') {
   new("H5File", fileName, mode)
 }
@@ -117,21 +113,21 @@
 }
 
 .openObjects <- function(h5File) {
-  .myCall("h5R_get_object_count", .ePtr(h5File))
+  .Call("h5R_get_object_count", .ePtr(h5File))
 }
 
 setMethod("getH5Group", c("H5Container", "character"), function(h5Obj, groupName) {
-  if (is.null(x <- .myCall("h5R_get_group", .ePtr(h5Obj), groupName)))
+  if (is.null(x <- .Call("h5R_get_group", .ePtr(h5Obj), groupName)))
     stop(paste("Group:", groupName, "cannot be opened."))
   .H5Group(x, groupName)
 })
 
 setMethod("getH5Dim", "H5DataContainer", function(h5Obj) {
-  .myCall('h5R_get_dims', .ePtr(h5Obj))
+  .Call('h5R_get_dims', .ePtr(h5Obj))
 })
 
 setMethod("getH5Type", "H5DataContainer", function(h5Obj) {
-  .myCall("h5R_get_type", .ePtr(h5Obj))
+  .Call("h5R_get_type", .ePtr(h5Obj))
 })
 
 setMethod("initialize", c("H5File"), function(.Object, fileName, mode = c('r', 'w')) {
@@ -142,14 +138,14 @@
 
   mode <- match.arg(mode)
   if (! file.exists(fileName) && mode == 'w') {
-    .myCall("h5R_create", fileName)
+    .Call("h5R_create", fileName)
   }
   if (! file.exists(fileName)) {
     stop(paste("Unable to open file:", fileName, "does not exist."))
   }
   ## convert the fileName - essentially for ~. 
   fileName <- normalizePath(fileName)
-  x <- .myCall("h5R_open", fileName, if (mode == 'r') as.integer(0) else as.integer(1))
+  x <- .Call("h5R_open", fileName, if (mode == 'r') as.integer(0) else as.integer(1))
   if (is.null(x)) {
     stop(paste("Problem opening file:", fileName))
   }
@@ -160,14 +156,14 @@
 })
 
 setMethod("getH5Dataset", c("H5Container", "character"), function(h5Obj, datasetName, inMemory = FALSE) {
-  if (is.null(x <- .myCall("h5R_get_dataset", .ePtr(h5Obj), datasetName))) {
+  if (is.null(x <- .Call("h5R_get_dataset", .ePtr(h5Obj), datasetName))) {
     stop(paste("Dataset:", datasetName, "cannot be opened."))
   }
   return(.H5Dataset(x, datasetName, inMemory = inMemory))
 })
 
 setMethod("getH5Attribute", c("H5Obj", "character"), function(h5Obj, attrName) {
-  if (is.null(x <- .myCall("h5R_get_attr", .ePtr(h5Obj), attrName))) {
+  if (is.null(x <- .Call("h5R_get_attr", .ePtr(h5Obj), attrName))) {
     stop(paste("Attribute:", attrName, "cannot be opened."))
   }
   return(.H5Attribute(x, attrName, inMemory = TRUE))
@@ -177,38 +173,46 @@
 ## Writing.
 ##
 .flush <- function(h5Obj) {
-  .myCall("h5R_flush", .ePtr(h5Obj))
+  .Call("h5R_flush", .ePtr(h5Obj))
 }
 
 setMethod("writeH5Data", c("H5Dataset"), function(h5Obj, data, offsets, extents) {
   storage.mode(data) <- h5r:::.h5Types[getH5Type(h5Obj) + 1]
-  .myCall("h5R_write_slab", .ePtr(h5Obj), as.integer(offsets - 1), as.integer(extents), data)
+  .Call("h5R_write_slab", .ePtr(h5Obj), as.integer(offsets - 1), as.integer(extents),
+          data)
 })
 
-setMethod("createH5Dataset", c("H5Container", "character"), function(h5Obj, datasetName, data,
-                                                                     dims, dType = c("integer", "double", "character"),
-                                                                     chunkSizes = NA, overwrite = TRUE) {
+setMethod("createH5Dataset", c("H5Container", "character"),
+          function(h5Obj, datasetName, data,
+                   dims, dType = c("integer", "double", "character"),
+                   chunkSizes = NA, overwrite = TRUE) {
   if (h5DatasetExists(h5Obj, datasetName)) {
     if (! overwrite)
       stop(paste("Dataset:", datasetName, "already exists."))
     else
       deleteH5Obj(h5Obj, datasetName)
   }
-
   mData <- missing(data)
   mDims <- missing(dims)
   mType <- missing(dType)
   mChnk <- missing(chunkSizes)
 
   if (mData && (mDims || mType)) {
-    stop("Must specify either data or dimensions and type.")
+    stop("Must specify either data, dimensions and type, or all three.")
   }
 
-  if (mData && mType) {
-    storage.mode(data) <- dType
-  }
-  
-  if (! mData) { 
+  if (! mData) {
+    ## set the dType
+    if (! mType) {
+      storage.mode(data) <- match.arg(dType)
+    } else { 
+      dType <- storage.mode(data)
+    }
+    ## set the dims if they are given
+    if (! mDims) {
+      dim(data) <- dims
+    }
+    ## query and permute if needed
     if (is.null(dim(data))) {
       dims <- length(data)
     } else {
@@ -216,22 +220,20 @@
       dims <- dim(data)
       data <- aperm(data)
     }
-    dType <- storage.mode(data)
-  } else {
-    dType <- match.arg(dType)
   }
-  iType <- as.integer(match(dType, .h5Types) - 1)
 
+  ## set the H5 Type
+  iType <- as.integer(match(dType, .h5Types) - 1)
   if (is.na(iType)) {
     stop("Type is not resolveable.")
   }
-  dims  <- as.integer(dims)
-  if (mChnk)
-    chunkSizes <- rep(4096, length(dims))
-
-  h5Dataset <- .H5Dataset(.myCall("h5R_create_dataset", .ePtr(h5Obj), datasetName, iType, dims, as.integer(chunkSizes)),
-                          datasetName)
   
+  dims  <- as.integer(dims)
+  if (mChnk) {
+    chunkSizes <- rep(1, length(dims))
+  }
+  h5Dataset <- .H5Dataset(.Call("h5R_create_dataset", .ePtr(h5Obj), datasetName,
+                                  iType, dims, as.integer(chunkSizes)), datasetName)
   if (! mData) {
     if(! writeH5Data(h5Dataset, data,
                      as.integer(rep(1L, length(dims))),
@@ -251,7 +253,7 @@
       deleteH5Obj(h5Obj, groupName)
     }
   }
-  h5Group <- .H5Group(.myCall("h5R_create_group", .ePtr(h5Obj), groupName), groupName)
+  h5Group <- .H5Group(.Call("h5R_create_group", .ePtr(h5Obj), groupName), groupName)
   .flush(h5Obj)
   return(h5Group)
 })
@@ -289,14 +291,14 @@
 
 setMethod("deleteH5Obj", c("H5Container"), function(h5Obj, h5ObjName) {
   if (h5ObjectExists(h5Obj, h5ObjName)) {
-    return(.myCall("h5R_delete_object", .ePtr(h5Obj), as.character(h5ObjName)) && .flush(h5Obj))
+    return(.Call("h5R_delete_object", .ePtr(h5Obj), as.character(h5ObjName)) && .flush(h5Obj))
   } else {
     return(FALSE)
   }
 })
 
 setMethod("deleteH5Attribute", c("H5Obj"), function(h5Obj, attrName) {
-  .myCall("h5R_delete_attribute", .ePtr(h5Obj), as.character(attrName)) && .flush(h5Obj)
+  .Call("h5R_delete_attribute", .ePtr(h5Obj), as.character(attrName)) && .flush(h5Obj)
 })
 
 ##
@@ -503,13 +505,13 @@
 }
 
 read1DSlabs <- function(h5Dataset, offsets, dims) {
-  .myCall("h5R_read_1d_slabs", .ePtr(h5Dataset), as.integer(offsets - 1), as.integer(dims))
+  .Call("h5R_read_1d_slabs", .ePtr(h5Dataset), as.integer(offsets - 1), as.integer(dims))
 }
 
 readSlab <- function(h5Dataset, offsets, dims) {
   if (! all((offsets + dims - 1) <= dim(h5Dataset)))
     stop("error invalid slice specification in readSlab.")
-  d <- .myCall("h5R_read_dataset", .ePtr(h5Dataset), as.integer(offsets - 1), as.integer(dims))
+  d <- .Call("h5R_read_dataset", .ePtr(h5Dataset), as.integer(offsets - 1), as.integer(dims))
   
   if (class(d) != 'list') ## compound datasets produce lists.
     dim(d) <- rev(dims)
@@ -524,22 +526,15 @@
   } else {
     stop("readPoints doesn't work on higher dimensional data.")
   }
-  .myCall("h5R_read_points", .ePtr(h5Dataset), as.integer(idxs - 1), as.integer(nr), as.integer(nc))
+  .Call("h5R_read_points", .ePtr(h5Dataset), as.integer(idxs - 1), as.integer(nr), as.integer(nc))
 }
 
 setMethod("readH5Data", "H5Dataset", function(h5Obj) {
-  ## nndims <- if (is.null(dim(h5Obj))) {
-  ##   length(h5Obj)
-  ## } else {
-  ##   dim(h5Obj)
-  ## }
-  ## .myCall('h5R_read_dataset', .ePtr(h5Obj), as.integer(rep(0, length(nndims))), as.integer(nndims));
-
-  .myCall('h5R_read_dataset_all', .ePtr(h5Obj))
+  .Call('h5R_read_dataset_all', .ePtr(h5Obj))
 })
 
 setMethod("readH5Data", "H5Attribute", function(h5Obj) {
-  .myCall('h5R_read_attr', .ePtr(h5Obj))
+  .Call('h5R_read_attr', .ePtr(h5Obj))
 })
 
 setMethod("show", "H5Obj", function(object) {
@@ -583,8 +578,8 @@
 ##
 
 ## construct a list of elements in the file.
-.listH5Contents <- function(h5Obj) .myCall("h5R_list_contents", .ePtr(h5Obj))
-listH5Attributes <- function(h5Obj) .myCall("h5R_list_attributes", .ePtr(h5Obj))
+.listH5Contents <- function(h5Obj) .Call("h5R_list_contents", .ePtr(h5Obj))
+listH5Attributes <- function(h5Obj) .Call("h5R_list_attributes", .ePtr(h5Obj))
 
 listH5Contents <- function(h5Obj) {
   contents <- .listH5Contents(h5Obj)
@@ -616,19 +611,19 @@
 })
 
 h5ObjectExists <- function(h5Obj, name) {
-  .myCall("h5R_dataset_exists", .ePtr(h5Obj), name)
+  .Call("h5R_dataset_exists", .ePtr(h5Obj), name)
 }
 
 h5GroupExists <- function(h5Obj, name) {
-  .myCall("h5R_dataset_exists", .ePtr(h5Obj), name)
+  .Call("h5R_dataset_exists", .ePtr(h5Obj), name)
 }
 
 h5DatasetExists <- function(h5Obj, name) {
-  .myCall("h5R_dataset_exists", .ePtr(h5Obj), name)
+  .Call("h5R_dataset_exists", .ePtr(h5Obj), name)
 }
 
 h5AttributeExists <- function(h5Obj, name) {
-  .myCall("h5R_attribute_exists", .ePtr(h5Obj), name)
+  .Call("h5R_attribute_exists", .ePtr(h5Obj), name)
 }
 
 

Modified: inst/CRAN_prepare_h5r.sh
===================================================================
--- inst/CRAN_prepare_h5r.sh	2013-07-02 20:14:29 UTC (rev 95)
+++ inst/CRAN_prepare_h5r.sh	2013-07-08 21:52:52 UTC (rev 96)
@@ -2,6 +2,7 @@
 
 SOURCE=h5r
 TARGET=scratch/h5r-CRAN
+RCMD=/home/UNIXHOME/jbullard/projects/software/R/common/R-3.1-install/bin/R
 
 rm -rf $TARGET
 rsync -av $SOURCE/ $TARGET/
@@ -21,10 +22,10 @@
 echo 'PKG_LIBS = -lm -L$(LIB_HDF5)$(R_ARCH)/lib -lhdf5 -lsz -lz' >> $TARGET/src/Makevars.win
 
 # 4. build
-R CMD build $TARGET
+$RCMD CMD build $TARGET
 
 BUILT_TARGET=h5r_`cat $TARGET/DESCRIPTION | grep Version | sed 's/Version: //g'`.tar.gz
 
 # 5. check
-R CMD check --as-cran --timings --install-args="--no-lock --preclean" $BUILT_TARGET
+$RCMD CMD check --as-cran --timings --install-args="--no-lock --preclean" $BUILT_TARGET
 

Modified: tests/Makefile
===================================================================
--- tests/Makefile	2013-07-02 20:14:29 UTC (rev 95)
+++ tests/Makefile	2013-07-08 21:52:52 UTC (rev 96)
@@ -1,15 +1,18 @@
 
+export RCMD=R-devel
+
 clean : 
-	rm -f *.Rout *.h5
+	rm -f *.Rout *.h5 .Rhistory
 
 all :
-	R CMD BATCH --no-save testRead.R &
-	R CMD BATCH --no-save testReadPoints.R &
-	R CMD BATCH --no-save testWrite.R &
-	R CMD BATCH --no-save testErrors.R & 
-	R CMD BATCH --no-save testGetGroup.R &
+	${RCMD} CMD BATCH --no-save testRead.R &
+	${RCMD} CMD BATCH --no-save testReadPoints.R &
+	${RCMD} CMD BATCH --no-save testWrite.R &
+	${RCMD} CMD BATCH --no-save testErrors.R & 
+	${RCMD} CMD BATCH --no-save testGetGroup.R &
+	${RCMD} CMD BATCH --no-save testCompound.R & 
 
 valgrind:
-	R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < testGetGroup.R
+	${RCMD} -d "valgrind --tool=memcheck --leak-check=full" --vanilla < testGetGroup.R
 
 

Modified: tests/testCompound.R
===================================================================
--- tests/testCompound.R	2013-07-02 20:14:29 UTC (rev 95)
+++ tests/testCompound.R	2013-07-08 21:52:52 UTC (rev 96)
@@ -21,4 +21,6 @@
      all(as.data.frame(d[1:10]) == as.data.frame(d[10:1])[10:1,]))
 }
 
+TH(action = 'print')
+TH(action = 'throw')
 

Modified: tests/testGetGroup.R
===================================================================
--- tests/testGetGroup.R	2013-07-02 20:14:29 UTC (rev 95)
+++ tests/testGetGroup.R	2013-07-08 21:52:52 UTC (rev 96)
@@ -1,14 +1,22 @@
 require(h5r)
 
-##
-## The tests.
-##
+source('tinyTestHarness.R')
+TH <- TestHarness()
+
 file <- system.file("h5_files", "ex_1.h5", package = 'h5r')
 f <- H5File(file)
 
-gc()
-v <- replicate(1000, {
-  getH5Group(f, "group_1")
+TH('get group', {
+  ## Not quite sure how to really do this right, I don't expect the
+  ## memory to always go back to the original state.
+  g = gc()
+  v <- replicate(1000, {
+    getH5Group(f, "group_1")
+  })
+  rm(v)
+  gc()
+  TRUE
 })
-rm(v)
-lapply(1:5, function(i) gc())
+
+TH(action = 'print')
+TH(action = 'throw')

Modified: tests/testReadPoints.R
===================================================================
--- tests/testReadPoints.R	2013-07-02 20:14:29 UTC (rev 95)
+++ tests/testReadPoints.R	2013-07-08 21:52:52 UTC (rev 96)
@@ -1,24 +1,41 @@
 require(h5r)
 
-h5 <- H5File("test.h5", 'w')
+source("tinyTestHarness.R")
 
-createH5Attribute(h5, "e", 10:1)
-createH5Attribute(h5, "d", c("jome?", "jeosfmdlmf", "s"))
+TH <- TestHarness()
+h5 <- H5File("test-read-points.h5", 'w')
 
-d <- createH5Dataset(h5, "jim", cbind(c('jime ', 'joe', 'mikey'),
-                                      c('jime 2 ', 'joe 2', 'mikey 2')))
-d[]
+TH('create h5 attribute', {
+  createH5Attribute(h5, "e", 10:1)
+  all(getH5Attribute(h5, "e")[] == 10:1)
+})
 
-writeH5Data(d, c("johnson", "jodhsd"), c(1,0), c(2, 1))
+TH('create h5 attribute 2', {
+  strings <- c("ACGTACGT", "GGGGGGGGGGGGGGGG", "CCGCGCGCG")
+  createH5Attribute(h5, "d", strings)
+  all(getH5Attribute(h5, "d")[] == strings)
+})
 
-m <- createH5Dataset(h5, "mm", cbind(rnorm(1000), rnorm(1000)))
-m[1:10, 2]
-                
+indta <- cbind(c(' xx ', '$$$$$$$$$$$', '||||'),
+               c(' jjjj', '"$"', '"""""""'))
 
-d1 <- createH5Dataset(h5, "jon", runif(100000))
-p <- readPoints(d1, ss <- sample(1:length(d1), size = 1000, replace = T))
-all(p == d1[ss])
+TH('create dataset', {
+  d <- createH5Dataset(h5, "d1", indta)
+  all(d[] == indta)
+})
 
+TH('write data', {
+  ndta <- cbind("yyy", "xxx")
+  writeH5Data(d, ndta, c(1,1), dim(ndta))
+  indta[1,] <- ndta
+  all(getH5Dataset(h5, "d1")[] == indta)
+})
 
-d2 <- createH5Dataset(h5, "jodf", paste(runif(200010)))
-d2[sample(1:length(d2), size = 1000)]
+TH('read points', {
+  d1 <- createH5Dataset(h5, "d3", runif(100000))
+  p <- readPoints(d1, ss <- sample(1:length(d1), size = 1000, replace = T))
+  all(p == d1[ss])
+})
+
+TH(action = 'print')
+TH(action = 'throw')

Modified: tests/testWrite.R
===================================================================
--- tests/testWrite.R	2013-07-02 20:14:29 UTC (rev 95)
+++ tests/testWrite.R	2013-07-08 21:52:52 UTC (rev 96)
@@ -73,5 +73,29 @@
   deleteH5Attribute(g1, "jim")
 })
 
+gt <- createH5Group(h5, "grp-type")
+
+TH("dataset type create 1", {
+  d <- createH5Dataset(gt, "d-type-1", matrix(rnorm(200, 100, sd = 10), ncol = 10), dType = "integer",
+                       chunk = c(10, 10))
+  dd <- getH5Dataset(gt, "d-type-1")
+  all(dim(dd) == c(20, 10)) && storage.mode(dd[]) == 'integer'
+})
+
+TH("dataset type create 2", {
+  d <- createH5Dataset(gt, "d-type-2", rnorm(200, 100, sd = 10), dType = "integer",
+                       dim = c(10, 20), chunk = c(10, 10))
+  dd <- getH5Dataset(gt, "d-type-2")
+  all(dim(dd) == c(10, 20)) && storage.mode(dd[]) == 'integer'
+})
+
+TH("dataset type 3", {
+  d <- createH5Dataset(gt, "d-type-3", rnorm(200, 100, sd = 10), dType = "character",
+                       dim = c(10, 20), chunk = c(10, 10))
+  dd <- getH5Dataset(gt, "d-type-3")
+  all(dim(dd) == c(10, 20)) && storage.mode(dd[]) == 'character'
+})
+
 TH(action = 'print')
+TH(action = 'throw')