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Recent Releases of gdsfmt

gdsfmt - Bioconductor Release 3.16

CHANGES IN VERSION 1.34.0

UTILITIES

  • update the web links
  • update zlib to v1.12.2

- C
Published by zhengxwen over 3 years ago

gdsfmt - Bioconductor Release 3.15

CHANGES IN VERSION 1.32.0

UTILITIES

  • optimize using the utilities of the Matrix package for sparse matrices

CHANGES IN VERSION 1.28.1

UTILITIES

  • update according to gcc-11

- C
Published by zhengxwen about 4 years ago

gdsfmt - Bioconductor Release v3.13

CHANGES IN VERSION 1.28.0

NEW FEATURES

  • new function exist.gdsn()
  • new function is.sparse.gdsn()

UTILITIES

  • LZ4 updated to v1.9.3 from v1.9.2
  • XZ is updated to v5.2.5 from v5.2.4
  • apply.gdsn(): work around with factor variables if less-than-32-bit integers are stored
  • a new component 'is.sparse' in objdesp.gdsn()
  • options(gds.verbose=TRUE) to show additional information

- C
Published by zhengxwen about 5 years ago

gdsfmt - Bioconductor Release v3.11

CHANGES IN VERSION 1.24.1

NEW FEATURES

  • new option 'allow.error' in openfn.gds() for data recovery
  • new option 'log.only' in diagnosis.gds()
  • new C functions GDS_Node_Unload() and GDS_Node_Load() in R_GDS.h
  • new sparse array data types in GDS (SparseReal32, SparseReal64, SparseInt8, SparseInt16, SparseInt32, SparseInt64, SparseUInt8, SparseUInt16, SparseUInt32, SparseUInt64)
  • the opened gds file will be closed when the object is garbage collected

UTILITIES

  • 'show' option in print.gds.class() for array preview
  • zlib updated to v1.2.11 from v1.2.8
  • xz updated to v5.2.4 from v5.2.3
  • LZ4 updated to v1.9.2 from v1.7.5
  • showfile.gds() does not return the object of 'gds.class'
  • new 'nmax' and 'depth' in print.gdsn.class() and print.gds.class()

CHANGES IN VERSION 1.22.0

NEW FEATURES

  • a new function unload.gdsn() to unload a GDS node from memory

UTILITIES

  • add '#pragma GCC optimize("O3")' to some of C++ files when GCC is used
  • add the compiler information in system.gds()
  • change the file name "vignettes/gdsfmt_vignette.Rmd" to "vignettes/gdsfmt.Rmd", so vignette("gdsfmt") can work directly

BUG FIXES

  • avoid the segfault if the data type is not registered internally
  • use O_CLOEXEC (the close-on-exec flag) when open and create files to avoid potentially leaking file descriptors in forked processes

- C
Published by zhengxwen almost 6 years ago

gdsfmt - Bioconductor Release v3.9

UTILITIES * optimize the C implementation of 'packedreal8' using a look-up table

NEW FEATURES * new data types 'packedreal8u', 'packedreal16u', 'packedreal24u' and 'packedreal32u'

BUG FIXES * the compression method 'LZ4_RA.max' does not compress data * add.gdsn() fails if a factor variable has no level * add.gdsn(, storage=index.gdsn()) accepts the additional parameters from index.gdsn(), e.g., 'offset' and 'scale' for packedreal8

- C
Published by zhengxwen about 7 years ago

gdsfmt - Bioconductor Release v3.8

CHANGES IN VERSION 1.18.0

NEW FEATURES

  • new options 'recursive' and 'include.dirs' in ls.gdsn(): the listing recurses into child nodes

UTILITIES

  • replace BiocInstaller biocLite mentions with BiocManager
  • digest.gdsn() fails if the digest package is not installed
  • SIMD optimization in 2-bit array decoding with a logical vector of selection (3x speedup when there are lots of zeros)

BUG FIXES

  • bug fixed: put.attr.gdsn() fails to update the existing attribute

- C
Published by zhengxwen over 7 years ago

gdsfmt - Bioconductor Release v3.5

- C
Published by zhengxwen about 9 years ago

gdsfmt - gdsfmt_v1.7.17

The last version of gdsfmt before introducing lzma compression algorithm.

Installation from Github:

R library("devtools") install_github("zhengxwen/gdsfmt", ref="v1.7.17")

The install_github() approach requires that you build from source, i.e. make and compilers must be installed on your system -- see the R FAQ for your operating system; you may also need to install dependencies manually.

- C
Published by zhengxwen about 10 years ago

gdsfmt - Release v1.6.0 for BioC 3.2

NEW FEATURES - a new argument 'seldim' in assign.gdsn() - append.gdsn() allows appending data from a GDS node - add.gdsn() allows 'storage' to be a 'gdsn.class' object - put.attr.gdsn() allows 'val' to be a 'gdsn.class' object - a new function copyto.gdsn()

SIGNIFICANT USER-VISIBLE CHANGES - discontinue the support of SNPRelate (<= v0.9.*)

- C
Published by zhengxwen over 10 years ago

gdsfmt - The last version of gdsfmt on R-Forge

The R package gdsfmt will be submitted to Bioconductor. It is the last version on R-Forge before gdsfmt becomes a Bioconductor package formally.

- C
Published by zhengxwen over 11 years ago

gdsfmt - Release of gdsfmt_v1.1.2

Changes in v1.1.2: - minor fixes - support efficient random access of compressed data, which are composed of independent compressed blocks

- C
Published by zhengxwen over 11 years ago

gdsfmt - Major fix

The version 1.1.1.1 should be installed immediately, if you see the error like

Invalid Zip Deflate Stream operation 'Seek'!

- C
Published by zhengxwen over 11 years ago

gdsfmt - Formal release of gdsfmt v1.1.0

Full support big-endian systems

- C
Published by zhengxwen almost 12 years ago

gdsfmt - Formal release of gdsfmt v1.0.5

- C
Published by zhengxwen about 12 years ago