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An unofficial fork of the R rhdf5 package developed by Bernd Fischer and Gregoire Pau. This fork is based on rhdf5 version 2.10.0
Home Page: http://www.bioconductor.org/packages/release/bioc/html/rhdf5.html
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> library(rhdf5 )
> test2 = h5read(" tmp/Daily.h5" , " y2014" , bit64conversion = " bit64" )
Attaching package bit
package : bit (c ) 2008 - 2012 Jens Oehlschlaegel (GPL - 2 )
creators : bit bitwhich
coercion : as.logical as.integer as.bit as.bitwhich which
operator : ! & | xor != ==
querying : print length any all min max range sum summary
bit access : length <- [ [<- [[ [[<-
for more help type ?bit
Attaching package : ‘bit ’
The following object is masked from ‘package : base ’:
xor
Attaching package bit64
package : bit64 (c ) 2011 - 2012 Jens Oehlschlaegel (GPL - 2 with commercial restrictions )
creators : integer64 seq :
coercion : as.integer64 as.vector as.logical as.integer as.double as.character as.bin
logical operator : ! & | xor != == < < = > = >
arithmetic operator : + - * / %/% %% ^
math : sign abs sqrt log log2 log10
math : floor ceiling trunc round
querying : is.integer64 is.vector [is.atomic } [length ] is.na format print
aggregation : any all min max range sum prod
cumulation : diff cummin cummax cumsum cumprod
access : length <- [ [<- [[ [[<-
combine : c rep cbind rbind as.data.frame
for more help type ?bit64
Attaching package : ‘bit64 ’
The following object is masked from ‘package : bit ’:
still.identical
The following objects are masked from ‘package : base ’:
: , %in% , is.double , match , order , rank
Error : segfault from C stack overflow
Not setting bit64conversion="bit64" will avoid this segfault
It's not implemented in the original package. Reading a hdf5 file with python datetime data field will result a warning and that data field been set to NA.
The function h5read can not properly import int64 data from HDF5 files, even when its parameter bit64conversion has been explicitly specified as "bit64" as suggested by the function's warning output, it will still force convert int64 data to int32 (R only has int32 for integer type, but int64 is supported by bit64 package, which rhdf5 package is capable of using. )