https://github.com/cran/ff
Tip revision: 573fcb991d9bd71ddf53ed4f303d3fd7921e3332 authored by Jens Oehlschlägel on 12 January 2024, 15:10:03 UTC
version 4.0.12
version 4.0.12
Tip revision: 573fcb9
NEWS
CHANGES IN ff VERSION 4.0.12
BUG FIXES
o .Last.lib replaced by .onDetach
CHANGES IN ff VERSION 4.0.11
BUG FIXES
o registered S3 "as.hi.("
CHANGES IN ff VERSION 4.0.10
BUG FIXES
o removed -Wformat-security warnings
format string is not a string literal (potentially insecure)
CHANGES IN ff VERSION 4.0.9
BUG FIXES
o removed -Wstrict-prototypes compiler warnings
CHANGES IN ff VERSION 4.0.8
BUG FIXES
o renewed .configure using recent autoconf
will no longer check for gcc under clang
CHANGES IN ff VERSION 4.0.7
BUG FIXES
o corrected invalid email of Christian Gläser
o get.ff, getset.ff and set.ff no longer throw an error
when accessing more than one element (found and fixed by
Michael Chirico and Jan Wijffels)
CHANGES IN ff VERSION 4.0.5
BUG FIXES
o as of R 4.1.2 memory.limit() is no longer supported
and its use has been removed from ff if favor of a constant
(thanks to Alexander Grueneberg).
Adjust options("ffbatchbytes") and options("ffmaxbytes")
as suitable for your available memory.
o ff no longer recreates the 'clone' generic hence
clone(ff) properly dispatches to clone.ff
instead of clone.default
CHANGES IN ff VERSION 4.0.4
BUG FIXES
o test that fail under any MACOS
have been disabled under that platform
CHANGES IN ff VERSION 4.0.3
USER VISIBLE CHANGES
o now aarch64 is supported (thanks to Terje Kvernes)
BUG FIXES
o test that fail under r-oldrel-macos-x86_64
have been disabled under that platform
CHANGES IN ff VERSION 4.0.2
BUG FIXES
o now DESCRIPTION URL points to github
CHANGES IN ff VERSION 4.0.1
BUG FIXES
o ffindexget no longer allocates batchsizes lager than vector length
(realized via fixes to bbatch() in package 'bit')
CHANGES IN ff VERSION 4.0.0
BUG FIXES
o all calls to data.frame now use 'stringsAsFactors = TRUE' in order to cope with the new defaults in R-4.0.0
CHANGES IN ff VERSION 2.2.16
USER VISIBLE CHANGES
o license has been extendend from GPL-2 to GPL-2 | GPL-3
o since template ffdfs now can be created with zero rows,
read.table.ffdf and wrappers simply append to the template
(and no longer treat templates with onw row different)
o parameter 'drop' for ff_array now behaves more like in standard R arrays
o new fftempdir handling (suggested by William Dunlap)
o .onLoad no longer sets an undefined options("fftempdir") to tempdir()
but to standardPathFile(file.path(tempdir(), "ff")), hence by default
.onUnload will not unlink tempdir() but will unlink
standardPathFile(file.path(tempdir(), "ff"))
o .onLoad will create the fftempdir if it does not exists,
but only if dirname(fftempdir) exists, if it does not exists
it will consider fftempdir undefined (see above)
o .onLoad sets a new options("fftempkeep")
to TRUE if the fftempdir already existed
and to FALSE if it was created by .onLoad
o .onUnload will unlink fftempdir only if options("fftempkeep")==FALSE
hence you can during a session can decide to keep a user-defined
fftempdir (won't work across R sessions if it was a subdiretory of
tempdir() because this is unlinked anyhow at terminating R).
o furthermore .onUnload will now only set options("fftempdir") to NULL
if it was equal to standardPathFile(file.path(tempdir(), "ff"))
and hence preserve any (other) value that was set before .onLoad
o clone.default() and clone.list() are no longer exported from ff
(covered by clone.default in package bit)
MAINTENANCE
o ff has been changed for R_useDynamicSymbols(dll, FALSE)
BUG FIXES
o read.table.ffdf and wrappers now can handle Coltype "ordered" from template
o getset.ff and readwrite.ff now return the proper vmode
o getset.ff and readwrite.ff now repects add=TRUE
o getset.ff and readwrite.ff with add=TRUE now longer returns values above the vmode domain
o reducing the length of ff-objects with packed vmodes
(boolean, logical, quad, nibble, byte, ubyte, short, ushort)
will now fill non-used parts of the file such that
subsequent enlarging the length of the ff-object will
all be initialized with the same value
(note that the filling depends on the presence of a names attribtute,
with names filling uses .vNA, without names filling uses 0)
o .onUnload no longer fails when fftempkeep=NULL
CHANGES IN ff VERSION 2.2.15
USER VISIBLE CHANGES
o S3 methods are no longer exported
o The generics maxindex() and poslength() have been moved to package bit,
also their methods for 'bit', 'bitwhich', 'ri' and their default methods.
o chunk.bit has been removed.
o ff vectors can now have length=0 (and filesize=0) (with the help of Martijn Schuemje)
o ff() now has default length=0 and default vmode=logical (wish of Martijn Schuemje)
o ffdf data.frames can now have nrow=0 (and filesizes=0)
o get.ff and set.ff no longer throw an error for zero-length index
o get.ff (and [[.ff) now return the appropriate vmode
o read.table.ffdf and its wrappers no longer overwrite one-row-templates
in argument 'x' (since now zero-row-templates are possible)
BUG FIXES
o maxlength of ff with vmodes having .ffbytes < 1 now are multiples of 1/.ffbytes
o default pattern with given filename is now file.path(filename)$path, "ff") instead of the path alone
o [[.ff now calls get.ff and no longer set..ff (reported by me :-)
CHANGES IN ff VERSION 2.2.14
USER VISIBLE CHANGES
o The $x component in hybrid indices now has class 'rlepack'.
If you have stored hi's of older versions you can convert them by
i <- as.hi(i)
BUG FIXES
o ram2ramcode() no longer gives wrong warnings
(reported by Fabian Werner)
CHANGES IN ff VERSION 2.2.13
USER VISIBLE CHANGES
o clone.default no longer switches to clone.ff if dot-arguments are used.
MAINTENANCE
o clone(), clone.default() and clone.list() were moved to package bit
o clone(), clone.default() and clone.list() are also exported from ff
(wish of CRAN maintainers)
o several compiler warnings have been removed
BUG FIXES
o On opening an ff vector the C-code now properly assignes the 'readonly'
value to fresh memory. Changing the readonly status of an ff *could*
have unwanted side effects in R <= 3.0.2 and definitely *would* have
for R >= 3.1.0. Big thanks to Luke Tierney for spotting this!
o the C-code of the shellsorts at loop termination no longer reads at
incs[SHELLARRAYSIZE] (UBSAN)
CHANGES IN ff VERSION 2.2.12
USER VISIBLE CHANGES
o new function file.move used instead of file.rename in order to
allow moving files across filesystem boundaries
o filename<-.ff now copies and deletes if file.rename cannot move
across filesystem boundaries (suggested by Milan Bouchet-Valat)
CHANGES IN ff VERSION 2.2.11
USER VISIBLE CHANGES
o Methods 'open.ff' and 'open.ffdf' gain a new parameter 'assert' by which 'open' can be used to assert openness.
BUG FIXES
o ff no longer segfaults when using closed ff objects, e.g. if an integer ff index was used and index or object was closed (reported by Jan Wijffels)
o ffdf[DuplicatedRows,] works now (reported by Debabrata Midya)
CHANGES IN ff VERSION 2.2.10
BUG FIXES
o .Call("R_bit_as_hi") now again addresses package="bit" as it
should be (reported by Martijn Tennekes)
CHANGES IN ff VERSION 2.2.9
USER VISIBLE CHANGES
o Functions 'ramsort', 'ramorder', 'is.sorted' and 'na.count' are now generic
in package 'bit'.
BUG FIXES
o in ffdf argument 'ff_join' now also allows naming columns by name as documented (reported by Suharto Anggono)
CHANGES IN ff VERSION 2.2.8
BUG FIXES
o read.table.ffdf no longer overwrites the comment.char explicitely given
and finally sets comment.char="" if it was not given (now as documented,
reported by Julin Maloof)
o ffsort no longer stops when sorting an fffactor with keysort
o fforder no longer creates NA when ordering an fffactor (reported by Jan Wijffels)
o .Call("R_bit_as_hi") now correctly addresses package="ff"
CHANGES IN ff VERSION 2.2.7
BUG FIXES
o Fixed memory allocation error in keysort
CHANGES IN ff VERSION 2.2.6
MAINTENANCE
o Removed .Internal calls to as.vector
BUG FIXES
o fixed a bug in insertion sort for integers that could have affected function ramsort
CHANGES IN ff VERSION 2.2.5
MAINTENANCE
o Removed assignInNamespace("[.AsIs" ... since no longer neccessary and
just causing CHECK warnings
CHANGES IN ff VERSION 2.2.4
BUG FIXES
o ff again compiles on NEtBSD (reported by Thomas Vaughan)
o as.integer.hi() now correctly returns integer() for an empty subscript (reported by Ivan Zhang)
o ffsave now respects argument 'envir'
o ffsave now generates as default for rootpath the root of the drive on which the ff data is (not the current drive)
o ffload no longer tries to create the archive directory if not existing
o ffload no longer tries to create the directory of the stored rootpath if different from the new rootpath (wish of Ivan Zhang)
(let us know if this creates problems with case spelling of the old rootpath)
CHANGES IN ff VERSION 2.2.2
USER VISIBLE CHANGES
o In read.table.ffdf arguments 'colClasses' and 'col.names' are now
enforced also during 'next.rows' chunks. If they are not provided
by the user, they are derived now BEFORE argument 'transFUN' is
applied. This allows dropping columns in transFUN - and still
having all columns info ready for next chunk's call.
o all calls to 'seq.int' have been replaced by 'seq_along' or 'seq_len'
o most calls to 'cat' have been replaced by 'message' or 'packageStartupMessage'
BUG FIXES
o fforder no longer creates an integer overflow (thanks to Edwin de Jonge)
CHANGES IN ff VERSION 2.2.0
NEW FEATURES
o ff now supports the 64 bit Windows and Sun versions of R
(thanks to Brian Ripley)
o ff now supports sorting and ordering of ff vectors and dataframes
(see ramsort, ffsort, ffdfsort, ramorder, fforder, ffdforder)
o ff now supports ff vectors as subscripts of ff objects
(currently positive integers only, booleans are planned)
o New option 'ffmaxbytes' which allows certain ff procedures like sorting
using larger limit of RAM than 'ffbatchbytes' in chunked processing.
Such higher limit is useful for (single-R-process) sorting compared to
some multi-R-process chunked processing. It is a good idea to reduce
'ffmaxbytes' on slaves or avoid ff sorting there completely.
o New generic 'pagesize' with method 'pagesize.ff' which returns the
current pagesize as defined on opening the ff object.
USER VISIBLE CHANGES
o [.ff now returns with the same vmode as the ff-object
o Certain operations are faster now because we worked around
unnecessary copying triggered by many of R's assignment functions.
For example reading a factor from a (well-cached) file is now 20%
faster and thus as fast as just creating this factor in-RAM using
levels()<- and class()<- assignments.
(consider this tuning temporary, hoping for a generic fix in base R)
o ff() can now open files larger than .Machine$integer.max elements
(but gives access only to the first .Machine$integer.max elements)
o ff now has default pattern NULL translating to the pattern in 'filename'
(and only to the previous default 'ff' if no filename is given)
o ff now sets the pattern in synch with a requested 'filename'
o clone.ff now always creates a file consistent with the previous pattern
o clone.ff now always creates a finalizer consistent with the file location
o clone.ffdf has a new argument 'nrow' which allows to create an empty copy
with a different number of rows (currently requires 'initdata=NULL')
o clone.default now deep-copies lists and atomic vectors
DEPRECATED
o virtual window support is deprecated. Let us know if you urgently need this and why.
BUG FIXES
o read.table.ffdf now also works if transFUN filters and returns less rows
BUG FIXES at 2.1.4
o [<-.ffdf no longer does calculate the number of elements in an ffdf
which could led to an integer overflow
BUG FIXES at 2.1.3
o ffsafe now always closes ffdf objects - also partially closed ones
o ffsafe no longer passes arguments 'add' and 'move' to 'save'
o ffsafe and friends now work around the fact that under windows getwd()
can report the same path in upper and lower case versions.
CHANGES IN ff VERSION 2.1.2
NEW FEATURES
o New functions ffsave, ffsave.image, ffinfo and ffload allow to save
and load ff and ffdf objects together with all associated ff files
in a ff archive. Incremental save and selective load are supported.
o read.table.ffdf now supports reading fixed-width format by specifying
FUN="read.fwf". But beware, read.fwf reads fwf, writes csv, then calls
read.table to read csv (Anyone feels challenged to provide faster
csv and fwf reader?)
o read.table.ffdf will now treat an argument 'x' with 1 row special:
instead of appending it will overwrite the first row. This is working
around the fact that it is currently not possible to create ff vectors
having length zero and ffdf data.frames with zero rows.
o read.table.ffdf and write.table.ffdf have a new argument 'transFUN'
which allows filtering and other modifications on-the-fly of the
data.frames processed in each chunk.
o argument 'ff_args' in read.table.ffdf has been renamed to 'asffdf_args'
o New 'chunk' methods for classes 'bit' and 'ff_vector'
USER VISIBLE CHANGES
o The filename of each ff object is now always stored with absolute path
and assignments to pattern<- "./foo" will now expand "." to getwd()
o as.ffdf.data.frame now passes '...' to ffdf like the other as.ffdf
methods do. From now on use 'col_args' for passing arguments to ff
(first ff columns are created, then ffdf is called to bind them).
o New argument 'RECORDBYTES' for chunk methods. Position of dots argument
moved to last position.
o The low-level access-functions 'get.ff', 'set.ff' and 'getset.ff' now
accept vectors (not only scalars) of positive subscript positions. This
allows to evaluate the benefit of the hybrid index preprocessing done in
'[.ff', '[<-.ff' and 'swap.ff'.
BUG FIXES
o Fixed problems with negative subscripts (discovered by Trishank
Kuppusamy): [.ff_array and [<-.ff_array no longer skip over -1 in a
non-packed negative index, and hybrid indexing no longer reverts the
order of assigned or returned values (for negative subscripts we now
always set hi$ix=NULL and hi$re=FALSE).
o as.hi.ri no longer blows RAM by expanding the sequence ri[[1]]:ri[[2]]
o [.ffdf now requires less RAM because it avoids as.data.frame
o as.hi.which now call as.hi.integer and works
o chunk.default no longer uses seq.int or seq because these were buggy
o now also compiles under latest max os snow leopard
o default for options("ffbatchbytes") is now 1% of RAM under windows and
16MB on other OSes (was much too small on other)
CHANGES IN ff VERSION 2.1.0
NEW LICENCING
o Dual licencing has been removed, all ff functionality is now
available under GPL-2 (and some under the ISC license version
of free BSD)
NEW FEATURES
o New packed vmodes 'boolean', 'quad', 'nibble', 'byte', 'ubyte',
'short', 'ushort' and 'single' allow efficient storage of integer or
factor data.
o New class 'ffdf' supports data.frame structure with several
options for physical storage of virtual columns.
o New functions 'read.table.ffdf' and 'write.table.ffdf' for reading/
writing csv files into/from ffdf objects.
o Improved handling of files and finalizers (see user visible changes).
o New generic function 'chunk' from package 'bit' with a first method
'chunk.ffdf' that supports automated chunking suitable for parallel
processing.
o New subscript types from package 'bit' are supported: 'bit',
'bitwhich' and 'ri' for chunked processing.
o New coercing functions between 'ff' and 'bit': as.ff.bit, as.bit.ff
as.hi.bit, as.bit.hi, as.hi.bitwhich, as.bitwhich.hi, as.hi.ri.
o The generics 'maxindex' and 'poslength' now also have methods
for classes 'bit', 'bitwhich' and 'ri' from package 'bit',
implemented via bit's corresponding generics 'length' and 'sum'
o Function 'ff' has a new parameter 'update'=TRUE that can be used
to create ff objects like 'initdata' without actually filling
it with initdata (used by ffdf)
o In function 'update' parameter 'delete' now accepts a tri-bool:
update(delete=NA) will do fast update by file exchange without
deleting the source file.
USER VISIBLE CHANGES
o Package 'ff' now depends on package 'bit' (1.1.1 or higher),
which offers many functions useful for subsetting 'ff' (see there).
o Functions 'bbatch', 'repfromto' and 'repfromto<-' have been
moved to file 'chunkutil.R' in package 'bit' where they
support the new generic function 'chunk'. See also utility function
'vecseq' which allows to generate concatenated multiple sequences and
return them as a call.
o ff files created via "pattern" (without giving an explicit filename)
now have by default extension 'ff' which can be changed via
options("ffextension"). The old behaviour without extension can be
restored by setting options(ffextension=NULL) AFTER loading package ff.
o If an option("fffinalizer") is defined, ff(finalizer=NULL) now takes
it from there. If not defined, ff() behaves as before: if the file
location equals option("fftempdir") it chooses 'delete', otherwise
it chooses 'close'.
o ff args 'pattern' and 'filename' allow more detailed control
where to create ff files. 'pattern' now also accepts a rootname
with a path. 'filename' now can be given in three forms: with an
explicit path to create there, with a preceding "./" to create in
getwd() and without path to create in getOption("fftempdir").
o New assignment generic 'filename<-' renames/moves the underlying file
AND changes the finalizer if the location is changed in or out of
fftempdir. New assignment generic 'pattern<-' does similar renaming by
giving a pattern and also has a method that renames/moves all files of
a ffdf dataframe.
o The finalizer logic has been changed. The finalizer function (which
name is stored in the ff object) is now attached at finalize-time
(not at create-time) by attaching a single 'finalize' function at
create-time (for details see ?finalize). As a benefit we can access and
change the finalizer through new functions 'finalizer' and
'finalizer<-'. Finalizers are now expected to set the finalizer name to
NULL and the 'open' method makes use of this information: 'open' will
activate a 'close' finalizer, but only if there was no finalizer
activated. Finalized ff objects will have no memory about which
finalizer they had, and 'clone' of a finalized ff will no longer copy
the finalizer.
o 'length<-.ff' will now change the length of the existing ff
file. For increased ff size it no longer needs to copy contents
and will no longer guarantee to fill the new elements with NA,
see the help page. For decreased ff size it will physically reduce
the filesize. These operations carried out by file.resize are extremely
fast and save disk space.
o 'dim<-.ff' will now allow changing the fastest rotating dimension
and automatically adjust the length (dimorder retained,
dimnames removed).
o The default in all ff access functions has been changed from
pack=TRUE to pack=FALSE. Packing an evaluated index is only
efficient if the index is re-used.
('hi' and 'as.hi' still have default pack=TRUE)
o '[.ff_array' used with one subscript like in ff[i] will now return the
elements of the array taken from their virtual positions (more
compatible with R standard behaviour. If you want to access elements in
their physical order, you can remove the 'dim' attribute by
'dim(ff) <- NULL' and then use ff[i].
o 'as.hi' and 'hiparse' now take an argument 'envir' rather than
'parents' to specify in which frame to evaluate
o Assigning NA of length 1 to a signed ff factor no longer gives
a warning (ram2ffcode no longer warns here)
o "levels<-.ff" now warns if the number of levels was reduced, but no
longer if it was increased
BUG FIXES
o 'bbatch' now balances better
o 'vw<-.ff_array' no longer complains about a wrong value
when vw had been set before
o 'maxffmode' now also returns only one .ffmode if a single vmode was
passed in
o '[.ff' and friends now also find their (unevaluated) index arguments
if the call was inherited via 'NextMethod'
o '[.AsIs' now returns a class based on the class AFTER subscripting
not the the class of the un-subscripted object (BUG in R Base)
o 'update.ff' now handles factors correctly
o Closing and re-opening ff files will no longer trigger attempts to
delete ff files with a 'delete' finalizer multiple times
KNOWN PROBLEMS / TODOs
o bootstrapping rows from matrix with dimorder=c(2,1) is (under Win32)
not faster than bootstrapping rows from a ffdf build physically on
top of vectors: the fs-cache has problems handling larger matrix
compared to smaller vectors. Therefore we consider partitioning of
ff objects in a future release.
o ff objects can be nicely used in multi-core processing, however be
aware that there is yet no locking mechanism against concurrent writes
(often locking is not needed).
o NAs are mapped to TRUE in 'bit' and to FALSE in 'ff' booleans. Might be aligned
in a future release. Don't use bit or ff booleans if you have NAs
- or map NAs explicitely.
