Releases: zhengxwen/gdsfmt
Releases · zhengxwen/gdsfmt
Bioconductor Release 3.16
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
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
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()
andGDS_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()
andprint.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
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 leveladd.gdsn(, storage=index.gdsn())
accepts the additional parameters fromindex.gdsn()
, e.g., 'offset' and 'scale' for packedreal8
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
Bioconductor Release v3.5
v1.12.0 typo
gdsfmt_v1.7.17
The last version of gdsfmt before introducing lzma compression algorithm.
Installation from Github:
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.
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 nodeadd.gdsn()
allows 'storage' to be a 'gdsn.class' objectput.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.*)
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.