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Changelog

Source: NEWS.md

filearray 0.2.4

  • Partition files are written to a temporary file and then renamed into place, so other processes loading the same array no longer fail with “File size too small” while a partition is being created or filled
  • filearray_load only treats files named <n>.farr as partitions
  • Writes lock the partitions they change, so several processes (for example parallel, callr or mirai workers, or several applications) can write to one array without losing each other’s data: sub-assignment (x[...] <- value), fill_partition, initialize_partition, set_partition, fmap, fmap_element_wise and filearray_bind wait while another process holds one of their partitions. Reading takes no locks, except that functions that must first create missing partitions (such as max or sum) lock the partitions they create
  • Added lock_partition(parts, timeout) and unlock_partition(parts) methods to hold partitions over several operations (for example to check whether a partition has been computed and write it only if not); lock_partition waits and retries until the partitions are free or timeout seconds have passed
  • Locks are byte-range locks on an empty file .filearray.lock in the array directory, released by the operating system when a process exits. options(filearray.lock = FALSE) (environment variable FILEARRAY_LOCK) turns off automatic locking; options(filearray.lock.timeout = <seconds>) (FILEARRAY_LOCK_TIMEOUT) limits how long writes wait, by default without limit
  • A missing partition is created only if no other process has created it in the meantime, and every partition write uses its own temporary file, so concurrent writers no longer replace each other’s partitions or share a temporary file
  • fmap stops when the mapping function raises an error or is interrupted, instead of warning “cannot finish map” and returning a partly written result
  • delete() releases the locks the session holds on the array before removing it
  • Added with_filelock(expr, lockfile, timeout, on_unsupported) to evaluate code while holding an exclusive lock on any lock file, so that only one R session at a time runs it; other sessions wait. It is not tied to file arrays, so other packages can use it. on_unsupported chooses what happens when the lock cannot be taken: warn (default), stop, or ignore
  • Partition locks never make a write fail when the lock itself cannot be taken: any error while locking (for example a stale network file handle or too many open files, not only file systems without lock support) now warns once and the write proceeds, and an invalid filearray.lock.timeout option or FILEARRAY_LOCK_TIMEOUT value warns once and is ignored instead of stopping every write
  • Fixed mapreduce (and so sum, max, min, range and fwhich) reading only the first slice of every partition after the first when partition_size is greater than 1, which gave wrong results and wrong fwhich indices
  • fmap2 reports the error raised by the mapping function instead of “Unknown error.”
  • Errors and interrupts raised in the functions passed to fmap, fmap2 and mapreduce now reach the caller unchanged on Linux builds that compile packages with libc++ while R itself loads libstdc++ (for example through ICU). Before, they arrived as “c++ exception (unknown reason)” and could corrupt memory and crash the R session

filearray 0.2.3

CRAN release: 2026-08-21

  • as_filearray takes RAVE file array proxy

filearray 0.2.2

CRAN release: 2026-05-23

  • Fixed out-of-bound indexing leading to segfault along certain margins
  • Fixed ASAN issue that may cause run-time error: signed integer overflow: 9223372036854775807 + 1 cannot be represented in type int64_t (load.cpp:636:51)

filearray 0.2.1

CRAN release: 2026-03-23

  • Fixed incorrect NA propagation in complex array collapse: NaN == NaN is always FALSE per IEEE 754, so NA detection now uses ISNAN() instead of == NA_REAL. Also added a missing “result already NA” short-circuit guard matching the non-complex path.
  • Fixed x[] failure on R-devel (>= 4.6.0): replaced tryCatch({ ...elt(1) }) in fa_subset1 with check_missing_dots(), which correctly detects a missing first argument without relying on the error-throwing behavior of ...elt() that changed in R-devel.
  • Replaced deprecated Rf_findVarInFrame (removed in R 4.5.0) with a compatibility wrapper farr_findVarInFrame that uses R_existsVarInFrame + R_getVarEx on R >= 4.5.0 and falls back to Rf_findVarInFrame on older R.
  • Fixed multiple unprotected SEXP variables flagged by rchk: result in test_farr_findVarInFrame_, dots in check_missing_dots, and dims in dropDimension.

filearray 0.2.0

CRAN release: 2025-04-01

  • Additional audo_set_headers to function filearray_load_or_create to avoid automatically setting headers, with default being TRUE for compatibility concerns

filearray 0.1.9

CRAN release: 2024-11-08

  • Fixed CRAN check issue brought by testthat update, which requires bit64 when checking int64 arrays. Added bit64 to Suggests field to mitigate this check error

filearray 0.1.8

CRAN release: 2024-09-03

  • Fixed a bug where C++ errors are not correctly thrown due to a recent Rcpp update. This bug may cause erroneous code to execute ignoring try-catch statement and imbalanced protecting stacks (fwhich, mapreduce)

filearray 0.1.7

CRAN release: 2024-07-16

  • Removed non-API R C interface
  • Allows subsetAssign to assign when value length is 1 (thanks @talegari issue #9)
  • Allows more flexible fwhich function with functional val input and options to include corresponding values as part of return (thanks @talegari issue #10)
  • Fixed mapreduce bug when partition length is way larger than the buffer size, causing buffer to stop updating
  • Fixed other C++ issues, such as unused buffer allocation in subset-assign, and min_ offset in sub_vec_range. These issues are not considered bugs since they don’t affect the results, but the performance is slightly increased after fix.
  • Replaced dipsaus with more updated ravetools in the vignette performance profiling
  • Updated examples to get rid of warning messages and out-dated arguments.

filearray 0.1.6

CRAN release: 2023-06-23

  • Removed c++11 from system requirement and Makevars
  • Used TinyThreads instead of OpenMP to get parallel working on OSX
  • Added as_filearray method, and support optional float
  • Added array proxy class, allowing arrays to lazy-evaluate simple operators
  • Allows user-defined temporary file array path
  • Fixed fmap issues, using better guesses for default .input_size
  • Fixed a memory bug caused when partition margin has elements greater than 1 and when FARR_subset_sequential is used
  • Used fastmap to avoid environment look-up
  • fa_eval_ops allows dimension names
  • Larger default buffer size to allow 2^20 in single partition
  • Disabled single indexing
  • Fixed endian issue on big-endian platforms

filearray 0.1.5

CRAN release: 2022-10-16

  • Fixed a bug when trying to read array data sequentially. The bug is caused by buffer size being greater than the array length, making in a pointer that controls the partition number exceed the end of vector, resulting in undefined behavior. The functions affected are: fmap, fmap2. The bug has been fixed and passed valgrind memory check.

filearray 0.1.4

CRAN release: 2022-08-06

  • Fixed a bug when allocated memory is one byte short than requested. The bug would crash R when triggered in certain cases.
  • Removed limit to the maximum number of partitions when writing. The previous implementation creates and opens related file descriptors all at once before writing. This setup will raise errors when the number of connections reach to certain limit, often defined by the operating systems. This update only opens the connection on demand. The performance might be impacted when writing to disk, but in return, the program will be more robust
  • Fixed subset function environment not resolved correctly when using formula
  • Added filearray_load_or_create as an alternative to filearray_checkload by automatically replace existing obsolete array files if the headers, dimensions, or data types don’t match. Also on_missing argument is provided to allow array initialization if new array is created.

filearray 0.1.3

CRAN release: 2022-01-28

  • Automatically detect whether symbolic-link works and show warnings
  • Warnings can be suppressed
  • Allow extra headers to be set in meta file
  • Added header signature method
  • Fixed symbolic-link issues on Windows when partition sizes are 0
  • Added check-load function filearray_checkload to validate header
  • Fixed collapse method when dimnames are set
  • Fixed an unprotected variable in C++ code
  • filearray_bind can use cache if the header signatures agree
  • filearray_bind can choose to force overwrite
  • Added package digest to Imports
  • Fixed a typo and several small bugs

filearray 0.1.2

CRAN release: 2021-11-25

  • Removed flush in saving data to let system decide when to flush to hard drive
  • Allowed array to expand along the partition margin
  • Fixed dimension name getting dropped under certain situations
  • Use 2 cores by default when R CMD check is detected

filearray 0.1.1

CRAN release: 2021-09-19

  • Added OpenMP flag in the MakeVars
  • Fixed critical bugs that could cause segfaults
  • Can store complex and float data types
  • Re-implemented read/write functions to use memory map
  • Allowed dimnames to be set
  • Added generics subset to subset using dimnames
  • Added vignette to compare performance
  • Added speed comparisons in README.md
  • Added collapse to calculate marginal summation with little memory overhead
  • Added fmap, fmap2 to apply functions to one or multiple file arrays with little memory overhead (also very fast)
  • Fixed ‘unprotected’ issues warned by rchk

filearray 0.1.0

CRAN release: 2021-09-08

  • Added a NEWS.md file to track changes to the package.
  • Initial implementation