Changes in version 2.24.0: NEW FEATURES o Removed bundled HDF5 library - rhdf5 now depends on Rhdf5lib. This updates the version of HDF5 to 1.8.19. o Functions H5Ldelete() and h5delete() added to provide mechanisms for removing items from HDF files. o Added argument `native` to many functions, which allows data to be treated as row-major rather than column-major, improving portability with other programming languages. o Added function H5Sunlimited() allowing creation of extensible datasets - thanks to Brad Friedman BUG FIXES o Datasets can now be subset using `[` and a range of values e.g. did[,1:5]. o Writing a data.frame that contains factors and setting DataFrameAsCompound=FALSE now works. o Many functions that would leave open file handles after exiting under error conditions have been fixed. o Performance improvements in h5read(). Changes in version 2.20.0: NEW FEATURES o Indexing into spaces with more than .Machine$integer.max elements is supported using numeric (rather than integer) indexing; this provides exact indexing into spaces with about 51 bits of precision. o Zero-length indexing is now supported (returning zero-length slabs). BUG FIXES o Using bit64conversion = "double" would always warn about loss of precision, but now only warns when precision is actually lost. Changes in version 2.18.0: NEW FEATURES o The low-level functions H5Pset_libver_bounds and H5Pget_libver_bounds is implemented. Creating files that can only be read by library versions 1.8 or later allows the usage of large attributes and improves performance. USER VISIBLE CHANGES o Per default all HDF5 files will be created with version 1.8 as lower bound. That means the created files can only be read with HDF5 library versions >= 1.8. This changes allows the usage of large attributes and leads to performance improvements. If one wants to create a file that is readable with the earliest version of HDF5, one has to call H5Fcreate with fapl=h5default("H5P"). o Warning messages from the package C code can now be suppressed by the R-function suppressWarnings(). Changes in version 2.16.0: NEW FEATURES o New access of HDF5 files by file, group and dataset handles. HDF5 groups and datasets can be read and written by the $-operator (e.g. h5f$A) and the [-operator can be used for partial reading and writing of datasets (e.g. h5d[3,,]). o New low level general library function H5Dget_create_plist implemented. o Removed #include from external C code. To be compatible with newest C-compilers and current R-devel Changes in version 2.14.0: NEW FEATURES o improved handling of error messages: HDF5 error messages are simplified and forwarded to R. o When reading integer valued data, especially 64-integers and unsigned 32-bit integers, overflow values are now replaced by NA's and a warning is thrown in this case. o When coercing HDF5-integers to R-double, a warning is displayed when integer precision is lost. o New low level general library function H5Dget_storage_size implemented. BUG FIXES o Memory allocation on heap instead of stack for reading large datasets (Thanks to a patch from Jimmy Jia). o Some bugs have been fixed for reading large 64-bit integers and unsigned 32-bit integers. o A bug was fixed for reading HDF5 files containing soft links. Changes in version 2.12.0: NEW FEATURES o Filenames are expanded with normalizePaths. o New function h5set_extent implemented. o New low level function H5Sset_extent_simple implemented. BUG FIXES o Segmentation fault while writing data type names for uncommitted data types. Changes in version 2.10.0: NEW FEATURES o Added support for HDF5 property lists. o Added property list arguments to H5Dcreate and H5Dopen. o New function h5readAttributes implemented that reads all HDF5 attributes of one object. o New function h5version implemented. o fillValue parameter added to h5createDataset. o New low level general library functions H5Lcreate_external, H5Fis_hdf5, H5Fget_filesize, H5Fget_name, H5Pcreate, H5Pcopy, H5Pget_class, H5Pclose, H5Pclose_class, H5Pset_char_encoding, H5Pset_create_intermediate_group, H5Pset_chunk_cache, H5Pset_layout, H5Pset_chunk, H5Pget_chunk, H5Pset_deflate, H5Pset_fill_value, H5Pset_fill_time, H5Pset_alloc_time, H5Pequal implemented. o Support for parallel Make (make -j) USER VISIBLE CHANGES o A warning is shown in high level function (h5read, h5write and others), if an open HDF5 handle already exists for the specified filename. BUG FIXES o Error in h5write for 0-length objects, as a consequence of automatic determining chunk size o missing size parameter message in h5createDataset now correctly display o checking for open file identifiers in h5read and h5ls now only searches for file names in open files, groups and datasets. o assignment has now correct pointer target type (void *) in H5Pset_fill_value Changes in version 2.8.0: NEW FEATURES o New function h5version implemented. o New low level general library functions H5open, H5close, H5garbage_collect, H5get_libversion, and H5Dset_extent implemented. USER VISIBLE CHANGES o h5createDataset automatically uses chunking and compression. o Added a warning if chunk size is equal to dimensions for large compressed datasets. BUG FIXES o C-stack overflow when reading large fixed-length strings. o error in i/o with chunksize or blocksize parameters. o compiling errors due to missing int return value. Changes in version 2.6.0: NEW FEATURES o support for logical added o support for reading attributes added (use read.attributes=TRUE) o enabeled compression for data.frame in h5write USER VISIBLE CHANGES o Use BiocStyles for package vignette Changes in version 2.4.0: NEW FEATURES o support for reading 64-bit integers added o support for reading variable length strings added o support for reading scalar objects added USER VISIBLE CHANGES o NEWS.Rd added o display of chunksize.pdf as a vignette avoided