I'm in the process of writing a few wrappers for loading and writing out files in the biom-format that happens to be in HDF5 format. The rhdf5 package is great, but in particular, the beginning of every file (as an example:https://github.com/biocore/biom-format/blob/master/examples/rich_sparse_otu_table_hdf5.biom ) has missing information that I can get running the command-line version of hdf5dump 

Running hdf5dump vs. 1.8.7 I'm able to see creation-date, format-url, format-version, etc (see below).

However, running h5read/ls/dump on the same object none of these categories/groups come up. My goal is to get the format-verson, etc groups that are not showing up. 

In particular rhdf5::hdf5dump function does not open the file unlike hdf5dump through terminal.

Example:

# in R

> h5dump("~/Desktop/rich_sparse_otu_table_hdf5.biom")
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
  #000: H5F.c line 1522 in H5Fopen(): unable to open file
    major: File accessability
    minor: Unable to open file
  #001: H5F.c line 1211 in H5F_open(): unable to open file: time = Tue Oct 28 00:27:02 2014
, name = '~/Desktop/rich_sparse_otu_table_hdf5.biom', tent_flags = 1
    major: File accessability
    minor: Unable to open file
  #002: H5FD.c line 1086 in H5FD_open(): open failed
    major: Virtual File Layer
    minor: Unable to initialize object
  #003: H5FDsec2.c line 348 in H5FD_sec2_open(): unable to open file: name = '~/Desktop/rich_sparse_otu_table_hdf5.biom', errno = 2, error message = 'No such file or directory', flags = 1, o_flags = 2
    major: File accessability
    minor: Unable to open file
HDF5: unable to open file
Error in h5checktypeOrOpenLoc(file) : 
Error in h5checktypeOrOpenLoc(). File '~/Desktop/rich_sparse_otu_table_hdf5.biom' is not a valid HDF5 file.

str(h5read("./rich_sparse_otu_table_hdf5.biom","/"))
List of 2
 $ observation:List of 4
  ..$ group-metadata: NULL
  ..$ ids           : chr [1:5(1d)] "GG_OTU_1" "GG_OTU_2" "GG_OTU_3" "GG_OTU_4" ...
  ..$ matrix        :List of 3
  .. ..$ data   : num [1:15(1d)] 1 5 1 2 3 1 1 4 2 2 ...
  .. ..$ indices: int [1:15(1d)] 2 0 1 3 4 5 2 3 5 0 ...
  .. ..$ indptr : int [1:6(1d)] 0 1 6 9 13 15
  ..$ metadata      :List of 1
  .. ..$ taxonomy: chr [1:7, 1:5] "k__Bacteria" "p__Proteobacteria" "c__Gammaproteobacteria" "o__Enterobacteriales" ...
 $ sample     :List of 4
  ..$ group-metadata: NULL
  ..$ ids           : chr [1:6(1d)] "Sample1" "Sample2" "Sample3" "Sample4" ...
  ..$ matrix        :List of 3
  .. ..$ data   : num [1:15(1d)] 5 2 1 1 1 1 1 1 1 2 ...
  .. ..$ indices: int [1:15(1d)] 1 3 1 3 4 0 2 3 4 1 ...
  .. ..$ indptr : int [1:7(1d)] 0 2 5 9 11 12 15
  ..$ metadata      :List of 4
  .. ..$ BODY_SITE           : chr [1:6(1d)] "gut" "gut" "gut" "skin" ...
  .. ..$ BarcodeSequence     : chr [1:6(1d)] "CGCTTATCGAGA" "CATACCAGTAGC" "CTCTCTACCTGT" "CTCTCGGCCTGT" ...
  .. ..$ Description         : chr [1:6(1d)] "human gut" "human gut" "human gut" "human skin" ...
  .. ..$ LinkerPrimerSequence: chr [1:6(1d)] "CATGCTGCCTCCCGTAGGAGT" "CATGCTGCCTCCCGTAGGAGT" "CATGCTGCCTCCCGTAGGAGT" "CATGCTGCCTCCCGTAGGAGT" ...

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] rhdf5_2.10.0         BiocInstaller_1.16.0
loaded via a namespace (and not attached):
[1] tools_3.1.0     zlibbioc_1.12.0

# Terminal 

./hdf5-1.8.7-mac-intel-x86_64-static/bin/h5dump ./rich_sparse_otu_table_hdf5.biom 
HDF5 "./rich_sparse_otu_table_hdf5.biom" {
GROUP "/" {
   ATTRIBUTE "creation-date" {
      DATATYPE  H5T_STRING {
            STRSIZE H5T_VARIABLE;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "2014-07-29T16:16:36.617320"
      }
   }
   ATTRIBUTE "format-url" {
      DATATYPE  H5T_STRING {
            STRSIZE H5T_VARIABLE;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "http://biom-format.org"
      }
   }
   ATTRIBUTE "format-version" {
      DATATYPE  H5T_STD_I64LE
      DATASPACE  SIMPLE { ( 2 ) / ( 2 ) }
      DATA {
      (0): 2, 1
      }
   }
   ATTRIBUTE "generated-by" {
      DATATYPE  H5T_STRING {
            STRSIZE H5T_VARIABLE;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "example"
      }
   }
   ATTRIBUTE "id" {
      DATATYPE  H5T_STRING {
            STRSIZE H5T_VARIABLE;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "No Table ID"
      }
   }
   ATTRIBUTE "nnz" {
      DATATYPE  H5T_STD_I64LE
      DATASPACE  SCALAR
      DATA {
      (0): 15
      }
   }
   ATTRIBUTE "shape" {
      DATATYPE  H5T_STD_I64LE
      DATASPACE  SIMPLE { ( 2 ) / ( 2 ) }
      DATA {
      (0): 5, 6
      }
   }
   ATTRIBUTE "type" {
      DATATYPE  H5T_STRING {
            STRSIZE H5T_VARIABLE;
            STRPAD H5T_STR_NULLTERM;
            CSET H5T_CSET_ASCII;
            CTYPE H5T_C_S1;
         }
      DATASPACE  SCALAR
      DATA {
      (0): "otu table"
      }
   }
.....

See the man page for h5read. The argument you're looking for is 'read.attributes'. By default attributes are not included with h5read.

?h5read

library(rhdf5)
fl = "min_sparse_otu_table_hdf5.biom"
withatts = h5read(fl, "/", read.attributes=TRUE)
withatts
attributes(withatts)