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| -rw-r--r-- | var/spack/repos/builtin/packages/r-ff/package.py | 47 |
1 files changed, 45 insertions, 2 deletions
diff --git a/var/spack/repos/builtin/packages/r-ff/package.py b/var/spack/repos/builtin/packages/r-ff/package.py index d7fcd5184b..8e0552852f 100644 --- a/var/spack/repos/builtin/packages/r-ff/package.py +++ b/var/spack/repos/builtin/packages/r-ff/package.py @@ -7,17 +7,60 @@ from spack import * class RFf(RPackage): - """memory-efficient storage of large data on disk and - fast access functions.""" + """Memory-Efficient Storage of Large Data on Disk and Fast Access Functions + + The ff package provides data structures that are stored on disk but behave + (almost) as if they were in RAM by transparently mapping only a section + (pagesize) in main memory - the effective virtual memory consumption per + ff object. ff supports R's standard atomic data types 'double', 'logical', + 'raw' and 'integer' and non-standard atomic types boolean (1 bit), quad (2 + bit unsigned), nibble (4 bit unsigned), byte (1 byte signed with NAs), + ubyte (1 byte unsigned), short (2 byte signed with NAs), ushort (2 byte + unsigned), single (4 byte float with NAs). For example 'quad' allows + efficient storage of genomic data as an 'A','T','G','C' factor. The + unsigned types support 'circular' arithmetic. There is also support for + close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and custom + close-to-atomic types. ff not only has native C-support for vectors, + matrices and arrays with flexible dimorder (major column-order, major + row-order and generalizations for arrays). There is also a ffdf class not + unlike data.frames and import/export filters for csv files. ff objects + store raw data in binary flat files in native encoding, and complement this + with metadata stored in R as physical and virtual attributes. ff objects + have well-defined hybrid copying semantics, which gives rise to certain + performance improvements through virtualization. ff objects can be stored + and reopened across R sessions. ff files can be shared by multiple ff R + objects (using different data en/de-coding schemes) in the same process + or from multiple R processes to exploit parallelism. A wide choice of + finalizer options allows to work with 'permanent' files as well as + creating/removing 'temporary' ff files completely transparent to the user. + On certain OS/Filesystem combinations, creating the ff files works without + notable delay thanks to using sparse file allocation. Several access + optimization techniques such as Hybrid Index Preprocessing and + Virtualization are implemented to achieve good performance even with large + datasets, for example virtual matrix transpose without touching a single + byte on disk. Further, to reduce disk I/O, 'logicals' and non-standard + data types get stored native and compact on binary flat files i.e. + logicals take up exactly 2 bits to represent TRUE, FALSE and NA. Beyond + basic access functions, the ff package also provides compatibility + functions that facilitate writing code for ff and ram objects and support + for batch processing on ff objects (e.g. as.ram, as.ff, ffapply). ff + interfaces closely with functionality from package 'bit': chunked looping, + fast bit operations and coercions between different objects that can store + subscript information ('bit', 'bitwhich', ff 'boolean', ri range index, hi + hybrid index). This allows to work interactively with selections of large + datasets and quickly modify selection criteria. Further high-performance + enhancements can be made available upon request.x """ homepage = "http://ff.r-forge.r-project.org/" url = "https://cloud.r-project.org/src/contrib/ff_2.2-13.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/ff" + version('4.0.4', sha256='22ecf1811263f27c9fd9f7e13e77f97dcbc0b8ae6f59b76dbaed77569c13d2e5') version('2.2-14', sha256='1c6307847275b1b8ad9e2ffdce3f4df3c9d955dc2e8a45e3fd7bfd2b0926e2f0') version('2.2-13', sha256='8bfb08afe0651ef3c23aaad49208146d5f929af5af12a25262fe7743fa346ddb') depends_on('r@2.10.1:', type=('build', 'run')) depends_on('r-bit@1.1-13:', type=('build', 'run')) + depends_on('r-bit@4.0.0:', when='@4.0.4:', type=('build', 'run')) patch('utk_platform_macros.hpp.patch', when='target=aarch64:') |