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If you are viewing this file on CRAN, please check latest news on GitHub here.

Changes in v1.11.5 (in development)

NEW FEATURES

  1. For convenience when using rbindlist(lapply(files,fread)) and some files are empty, fread now reads empty input as a null-data.table with warning, rather than error, #2898. For consistency, fwrite(data.table(NULL)) now creates an empty file and warns, instead of error, too.

  2. setcolorder(DT) without further arguments now defaults to moving the key columns to be first, #2895. Thanks to @jsams for the PR.

BUG FIXES

  1. fread now respects the order of columns passed to select= when column numbers are used, #2986. It already respected the order when column names are used. Thanks @privefl for raising the issue.

  2. gmin and gmax no longer fail on ordered factors, #1947. Thanks to @mcieslik-mctp for identifying and @mbacou for the nudge.

  3. as.ITime.character now properly handles NA when attempting to detect the format of non-NA values in vector. Thanks @polyjian for reporting, closes #2940.

  4. as.matrix(DT, rownames="id") now works when DT has a single row, #2930. Thanks to @malcook for reporting and @sritchie73 for fixing. The root cause was the dual meaning of the rownames= argument: i) a single column name/number (most common), or ii) rowname values length 1 for the single row. For clarity and safety, rownames.value= has been added. Old usage (i.e. length(rownames)>1) continues to work for now but will issue a warning in a future release, and then error in a release after that.

  5. Fixed regression in v1.11.0 (May 2018) caused by PR #2389 which introduced partial key retainment on := assigns. This broke the joining logic that assumed implicitly that assigning always drops keys completely. Consequently, join and subset results could be wrong when matching character to factor columns with existing keys, #2881. Thanks to @ddong63 for reporting and to @MarkusBonsch for fixing. Missing test added to ensure this doesn't arise again.

  6. as.IDate.numeric no longer ignores "origin", #2880. Thanks to David Arenburg for reporting and fixing.

NOTES

  1. The type coercion warning message has been improved, #2989. Thanks to @sarahbeeysian on Twitter for highlighting. For example, given the follow statements:
  DT = data.table(id=1:3)
  DT[2, id:="foo"]

the warning message has changed from :

Coerced character RHS to integer to match the column's type. Either change the target column ['id'] to
character first (by creating a new character vector length 3 (nrows of entire table) and assign that;
i.e. 'replace' column), or coerce RHS to integer (e.g. 1L, NA_[real|integer]_, as.*, etc) to make your
intent clear and for speed. Or, set the column type correctly up front when you create the table and
stick to it, please.

to :

Coerced character RHS to integer to match the type of the target column (column 1 named 'id'). If the
target column's type integer is correct, it's best for efficiency to avoid the coercion and create the
RHS as type integer. To achieve that consider R's type postfix: typeof(0L) vs typeof(0), and typeof(NA)
vs typeof(NA_integer_) vs typeof(NA_real_). You can wrap the RHS with as.integer() to avoid this
warning, but that will still perform the coercion. If the target column's type is not correct, it's
best to revisit where the DT was created and fix the column type there; e.g., by using colClasses= in
fread(). Otherwise, you can change the column type now by plonking a new column (of the desired type)
over the top of it; e.g. DT[, `id`:=as.character(`id`)]. If the RHS of := has nrow(DT) elements then
the assignment is called a column plonk and is the way to change a column's type. Column types can be
observed with sapply(DT,typeof).

Further, if a coercion from double to integer is performed, fractional data such as 3.14 is now detected and the truncation to 3 is warned about if and only if truncation has occurred.

DT = data.table(v=1:3)
DT[2, v:=3.14]
Warning message:
  Coerced double RHS to integer to match the type of the target column (column 1 named 'v'). One or
  more RHS values contain fractions which have been lost; e.g. item 1 with value 3.140000 has been
  truncated to 3.
  1. split.data.table method is now properly exported, #2920. But we don't recommend it because split copies all the pieces into new memory.

  2. Setting indices on columns which are part of the key will now create those indices.

Changes in v1.11.4 (on CRAN 27 May 2018)

  1. Empty RHS of := is no longer an error when the i clause returns no rows to assign to anyway, #2829. Thanks to @cguill95 for reporting and to @MarkusBonsch for fixing.

  2. Fixed runaway memory usage with R-devel (R > 3.5.0), #2882. Thanks to many people but in particular to Trang Nguyen for making the breakthrough reproducible example, Paul Bailey for liaising, and Luke Tierney for then pinpointing the issue. It was caused by an interaction of two or more data.table threads operating on new compact vectors in the ALTREP framework, such as the sequence 1:n. This interaction could result in R's garbage collector turning off, and hence the memory explosion. Problems may occur in R 3.5.0 too but we were only able to reproduce in R > 3.5.0. The R code in data.table's implementation benefits from ALTREP (for loops in R no longer allocate their range vector input, for example) but are not so appropriate as data.table columns. Sequences such as 1:n are common in test data but not very common in real-world datasets. Therefore, there is no need for data.table to support columns which are ALTREP compact sequences. The data.table() function already expanded compact vectors (by happy accident) but setDT() did not (it now does). If, somehow, a compact vector still reaches the internal parallel regions, a helpful error will now be generated. If this happens, please report it as a bug.

  3. Tests 1590.3 & 1590.4 now pass when users run test.data.table() on Windows, #2856. Thanks to Avraham Adler for reporting. Those tests were passing on AppVeyor, win-builder and CRAN's Windows because R CMD check sets LC_COLLATE=C as documented in R-exts$1.3.1, whereas by default on Windows LC_COLLATE is usually a regional Windows-1252 dialect such as English_United States.1252.

  4. Around 1 billion very small groups (of size 1 or 2 rows) could result in "Failed to realloc working memory" even when plenty of memory is available, #2777. Thanks once again to @jsams for the detailed report as a follow up to bug fix 40 in v1.11.0.

Changes in v1.11.2 (on CRAN 8 May 2018)

  1. test.data.table() created/overwrote variable x in .GlobalEnv, #2828; i.e. a modification of user's workspace which is not allowed. Thanks to @etienne-s for reporting.

  2. as.chron methods for IDate and ITime have been removed, #2825. as.chron still works since IDate inherits from Date. We are not sure why we had specific methods in the first place. It may have been from a time when IDate did not inherit from Date, perhaps. Note that we don't use chron ourselves in our own work.

  3. Fixed SETLENGTH() cannot be applied to an ALTVEC object starting in R-devel (R 3.6.0) on 1 May 2018, a few hours after 1.11.0 was accepted on CRAN, #2820. Many thanks to Luke Tierney for pinpointing the problem.

  4. Fixed some rare memory faults in fread() and rbindlist() found with gctorture2() and rchk, #2841.

Changes in v1.11.0 (on CRAN 1 May 2018)

NOTICE OF INTENDED FUTURE POTENTIAL BREAKING CHANGES

  1. fread()'s na.strings= argument :

    "NA"                                      # old default
    getOption("datatable.na.strings", "NA")   # this release; i.e. the same; no change yet
    getOption("datatable.na.strings", "")     # future release

    This option controls how ,, is read in character columns. It does not affect numeric columns which read ,, as NA regardless. We would like ,,=>NA for consistency with numeric types, and ,"",=>empty string to be the standard default for fwrite/fread character columns so that fread(fwrite(DT))==DT without needing any change to any parameters. fwrite has never written NA as "NA" in case "NA" is a valid string in the data; e.g., 2 character id columns sometimes do. Instead, fwrite has always written ,, by default for an <NA> in a character columns. The use of R's getOption() allows users to move forward now, using options(datatable.fread.na.strings=""), or restore old behaviour when the default's default is changed in future, using options(datatable.fread.na.strings="NA").

  2. fread() and fwrite()'s logical01= argument :

    logical01 = FALSE                         # old default
    getOption("datatable.logical01", FALSE)   # this release; i.e. the same; no change yet
    getOption("datatable.logical01", TRUE)    # future release

    This option controls whether a column of all 0's and 1's is read as integer, or logical directly to avoid needing to change the type afterwards to logical or use colClasses. 0/1 is smaller and faster than "TRUE"/"FALSE", which can make a significant difference to space and time the more logical columns there are. When the default's default changes to TRUE for fread we do not expect much impact since all arithmetic operators that are currently receiving 0's and 1's as type integer (think sum()) but instead could receive logical, would return exactly the same result on the 0's and 1's as logical type. However, code that is manipulating column types using is.integer or is.logical on fread's result, could require change. It could be painful if DT[(logical_column)] (i.e. DT[logical_column==TRUE]) changed behaviour due to logical_column no longer being type logical but integer. But that is not the change proposed. The change is the other way around; i.e., a previously integer column holding only 0's and 1's would now be type logical. Since it's that way around, we believe the scope for breakage is limited. We think a lot of code is converting 0/1 integer columns to logical anyway, either using colClasses= or afterwards with an assign. For fwrite, the level of breakage depends on the consumer of the output file. We believe 0/1 is a better more standard default choice to move to. See notes below about improvements to fread's sampling for type guessing, and automatic rereading in the rare cases of out-of-sample type surprises.

These options are meant for temporary use to aid your migration, #2652. You are not meant to set them to the old default and then not migrate your code that is dependent on the default. Either set the argument explicitly so your code is not dependent on the default, or change the code to cope with the new default. Over the next few years we will slowly start to remove these options, warning you if you are using them, and return to a simple default. See the history of NEWS and NEWS.0 for past migrations that have, generally speaking, been successfully managed in this way. For example, at the end of NOTES for this version (below in this file) is a note about the usage of datatable.old.unique.by.key now warning, as you were warned it would do over a year ago. When that change was introduced, the default was changed and that option provided an option to restore the old behaviour. These fread/fwrite changes are even more cautious and not even changing the default's default yet. Giving you extra warning by way of this notice to move forward. And giving you a chance to object.

NEW FEATURES

  1. fread():

    • Efficiency savings at C level including parallelization announced here; e.g. a 9GB 2 column integer csv input is 50s down to 12s to cold load on a 4 core laptop with 16GB RAM and SSD. Run echo 3 >/proc/sys/vm/drop_caches first to measure cold load time. Subsequent load time (after file has been cached by OS on the first run) 40s down to 6s.
    • The fread for small data page has been revised.
    • Memory maps lazily; e.g. reading just the first 10 rows with nrow=10 is 12s down to 0.01s from cold for the 9GB file. Large files close to your RAM limit may work more reliably too. The progress meter will commence sooner and more consistently.
    • fread has always jumped to the middle and to the end of the file for a much improved column type guess. The sample size is increased from 100 rows at 10 jump jump points (1,000 rows) to 100 rows at 100 jumps points (10,000 row sample). In the rare case of there still being out-of-sample type exceptions, those columns are now automatically reread so you don't have to use colClasses yourself.
    • Large number of columns support; e.g. 12,000 columns tested.
    • Quoting rules are more robust and flexible. See point 10 on the wiki page here.
    • Numeric data that has been quoted is now detected and read as numeric.
    • The ability to position autostart anywhere inside one of multiple tables in a single file is removed with warning. It used to search upwards from that line to find the start of the table based on a consistent number of columns. People appear to be using skip="string" or skip=nrow to find the header row exactly, which is retained and simpler. It was too difficult to retain search-upwards-autostart together with skipping/filling blank lines, filling incomplete rows and parallelization too. If there is any header info above the column names, it is still auto detected and auto skipped (particularly useful when loading a set of files where the column names start on different lines due to a varying height messy header).
    • dec=',' is now implemented directly so there is no dependency on locale. The options datatable.fread.dec.experiment and datatable.fread.dec.locale have been removed.
    • \\r\\r\\n line endings are now handled such as produced by base::download.file() when it doubles up \\r. Other rare line endings (\\r and \\n\\r) are now more robust.
    • Mixed line endings are now handled; e.g. a file formed by concatenating a Unix file and a Windows file so that some lines end with \\n while others end with \\r\\n.
    • Improved automatic detection of whether the first row is column names by comparing the types of the fields on the first row against the column types ascertained by the 10,000 rows sample (or colClasses if provided). If a numeric column has a string value at the top, then column names are deemed present.
    • Detects GB-18030 and UTF-16 encodings and in verbose mode prints a message about BOM detection.
    • Detects and ignores trailing ^Z end-of-file control character sometimes created on MS DOS/Windows, #1612. Thanks to Gergely Daróczi for reporting and providing a file.
    • Added ability to recognize and parse hexadecimal floating point numbers, as used for example in Java. Thanks for @scottstanfield #2316 for the report.
    • Now handles floating-point NaN values in a wide variety of formats, including NaN, sNaN, 1.#QNAN, NaN1234, #NUM! and others, #1800. Thanks to Jori Liesenborgs for highlighting and the PR.
    • If negative numbers are passed to select= the out-of-range error now suggests drop= instead, #2423. Thanks to Michael Chirico for the suggestion.
    • sep=NULL or sep="" (i.e., no column separator) can now be used to specify single column input reliably like base::readLines, #1616. sep='\\n' still works (even on Windows where line ending is actually \\r\\n) but NULL or "" are now documented and recommended. Thanks to Dmitriy Selivanov for the pull request and many others for comments. As before, sep=NA is not valid; use the default "auto" for automatic separator detection. sep='\\n' is now deprecated and in future will start to warn when used.
    • Single-column input with blank lines is now valid and the blank lines are significant (representing NA). The blank lines are significant even at the very end, which may be surprising on first glance. The change is so that fread(fwrite(DT))==DT for single-column inputs containing NA which are written as blank. There is no change when ncol>1; i.e., input stops with detailed warning at the first blank line, because a blank line when ncol>1 is invalid input due to no separators being present. Thanks to @skanskan, Michael Chirico, @franknarf1 and Pasha for the testing and discussions, #2106.
    • Too few column names are now auto filled with default column names, with warning, #1625. If there is just one missing column name it is guessed to be for the first column (row names or an index), otherwise the column names are filled at the end. Similarly, too many column names now automatically sets fill=TRUE, with warning.
    • skip= and nrow= are more reliable and are no longer affected by invalid lines outside the range specified. Thanks to Ziyad Saeed and Kyle Chung for reporting, #1267.
    • Ram disk (/dev/shm) is no longer used for the output of system command input. Although faster when it worked, it was causing too many device full errors; e.g., #1139 and zUMIs/19. Thanks to Kyle Chung for reporting. Standard tempdir() is now used. If you wish to use ram disk, set TEMPDIR to /dev/shm; see ?tempdir.
    • Detecting whether a very long input string is a file name or data is now much faster, #2531. Many thanks to @javrucebo for the detailed report, benchmarks and suggestions.
    • A column of TRUE/FALSEs is ok, as well as True/Falses and true/falses, but mixing styles (e.g. TRUE/false) is not and will be read as type character.
    • New argument index to compliment the existing key argument for applying secondary orderings out of the box for convenience, #2633.
    • A warning is now issued whenever incorrectly quoted fields have been detected and fixed using a non-standard quote rule. fread has always used these advanced rules but now it warns that it is using them. Most file writers correctly quote fields if the field contains the field separator, but a common error is not to also quote fields that contain a quote and then escape those quotes, particularly if that quote occurs at the start of the field. The ability to detect and fix such files is referred to as self-healing. Ambiguities are resolved using the knowledge that the number of columns is constant, and therefore this ability is not available when fill=TRUE. This feature can be improved in future by using column type consistency as well as the number of fields.
    txt = 'A,B\n1,hello\n2,"howdy" said Joe\n3,bonjour\n'
    cat(txt)
    # A,B
    # 1,hello
    # 2,"howdy" said Joe
    # 3,bonjour
    fread(txt)
           A                B
       <int>           <char>
    1:     1            hello
    2:     2 "howdy" said Joe
    3:     3          bonjour
    Warning message:
    In fread(txt) : Found and resolved improper quoting
    • Many thanks to @yaakovfeldman, Guillermo Ponce, Arun Srinivasan, Hugh Parsonage, Mark Klik, Pasha Stetsenko, Mahyar K, Tom Crockett, @cnoelke, @qinjs, @etienne-s, Mark Danese, Avraham Adler, @franknarf1, @MichaelChirico, @tdhock, Luke Tierney, Ananda Mahto, @memoryfull, @brandenkmurray for testing dev and reporting these regressions before release to CRAN: #1464, #1671, #1888, #1895, #2070, #2073, #2087, #2091, #2092, #2107, #2118, #2123, #2167, #2194, #2196, #2201, #2222, #2228, #2238, #2246, #2251, #2265, #2267, #2285, #2287, #2299, #2322, #2347, #2352, #2370, #2371, #2395, #2404, #2446, #2453, #2457, #2464, #2481, #2499, #2512, #2515, #2516, #2518, #2520, #2523, #2526, #2535, #2542, #2548, #2561, #2600, #2625, #2666, #2697, #2735, #2744.
  2. fwrite():

    • empty strings are now always quoted (,"",) to distinguish them from NA which by default is still empty (,,) but can be changed using na= as before. If na= is provided and quote= is the default 'auto' then quote= is set to TRUE so that if the na= value occurs in the data, it can be distinguished from NA. Thanks to Ethan Welty for the request #2214 and Pasha for the code change and tests, #2215.
    • logical01 has been added and the old name logicalAsInt retained. Pease move to the new name when convenient for you. The old argument name (logicalAsInt) will slowly be deprecated over the next few years. The default is unchanged: FALSE, so logical is still written as "TRUE"/"FALSE" in full by default. We intend to change the default's default in future to TRUE; see the notice at the top of these release notes.
  3. Added helpful message when subsetting by a logical column without wrapping it in parentheses, #1844. Thanks @dracodoc for the suggestion and @MichaelChirico for the PR.

  4. tables gains index argument for supplementary metadata about data.tables in memory (or any optionally specified environment), part of #1648. Thanks due variously to @jangorecki, @rsaporta, @MichaelChirico for ideas and work towards PR.

  5. Improved auto-detection of character inputs' formats to as.ITime to mirror the logic in as.POSIXlt.character, #1383 Thanks @franknarf1 for identifying a discrepancy and @MichaelChirico for investigating.

  6. setcolorder() now accepts less than ncol(DT) columns to be moved to the front, #592. Thanks @MichaelChirico for the PR. This also incidentally fixed #2007 whereby explicitly setting select = NULL in fread errored; thanks to @rcapell for reporting that and @dselivanov and @MichaelChirico for investigating and providing a new test.

  7. Three new Grouping Sets functions: rollup, cube and groupingsets, #1377. Allows to aggregation on various grouping levels at once producing sub-totals and grand total.

  8. as.data.table() gains new method for arrays to return a useful data.table, #1418.

  9. print.data.table() (all via master issue #1523):

    • gains print.keys argument, FALSE by default, which displays the keys and/or indices (secondary keys) of a data.table. Thanks @MichaelChirico for the PR, Yike Lu for the suggestion and Arun for honing that idea to its present form.

    • gains col.names argument, "auto" by default, which toggles which registers of column names to include in printed output. "top" forces data.frame-like behavior where column names are only ever included at the top of the output, as opposed to the default behavior which appends the column names below the output as well for longer (>20 rows) tables. "none" shuts down column name printing altogether. Thanks @MichaelChirico for the PR, Oleg Bondar for the suggestion, and Arun for guiding commentary.

    • list columns would print the first 6 items in each cell followed by a comma if there are more than 6 in that cell. Now it ends ",..." to make it clearer, part of #1523. Thanks to @franknarf1 for drawing attention to an issue raised on Stack Overflow by @TMOTTM here.

  10. setkeyv accelerated if key already exists #2331. Thanks to @MarkusBonsch for the PR.

  11. Keys and indexes are now partially retained up to the key column assigned to with ':=' #2372. They used to be dropped completely if any one of the columns was affected by :=. Tanks to @MarkusBonsch for the PR.

  12. Faster as.IDate and as.ITime methods for POSIXct and numeric, #1392. Thanks to Jan Gorecki for the PR.

  13. unique(DT) now returns DT early when there are no duplicates to save RAM, #2013. Thanks to Michael Chirico for the PR, and thanks to @mgahan for pointing out a reversion in na.omit.data.table before release, #2660.

  14. uniqueN() is now faster on logical vectors. Thanks to Hugh Parsonage for PR#2648.

    N = 1e9
                                          was      now
    x = c(TRUE,FALSE,NA,rep(TRUE,N))
    uniqueN(x) == 3                      5.4s    0.00s
    x = c(TRUE,rep(FALSE,N), NA)
    uniqueN(x,na.rm=TRUE) == 2           5.4s    0.00s
    x = c(rep(TRUE,N),FALSE,NA)
    uniqueN(x) == 3                      6.7s    0.38s
    
  15. Subsetting optimization with keys and indices is now possible for compound queries like DT[a==1 & b==2], #2472. Thanks to @MichaelChirico for reporting and to @MarkusBonsch for the implementation.

  16. melt.data.table now offers friendlier functionality for providing value.name for list input to measure.vars, #1547. Thanks @MichaelChirico and @franknarf1 for the suggestion and use cases, @jangorecki and @mrdwab for implementation feedback, and @MichaelChirico for ultimate implementation.

  17. update.dev.pkg is new function to update package from development repository, it will download package sources only when newer commit is available in repository. data.table::update.dev.pkg() defaults updates data.table, but any package can be used.

  18. Item 1 in NEWS for v1.10.2 on CRAN in Jan 2017 included :

    When j is a symbol prefixed with .. it will be looked up in calling scope and its value taken to be column names or numbers. When you see the .. prefix think one-level-up, like the directory .. in all operating systems means the parent directory. In future the .. prefix could be made to work on all symbols apearing anywhere inside DT[...].

    The response has been positive (this tweet and FR#2655) and so this prefix is now expanded to all symbols appearing in j= as a first step; e.g. :

    cols = "colB"
    DT[, c(..cols, "colC")]   # same as DT[, .(colB,colC)]
    DT[, -..cols]             # all columns other than colB

    Thus, with= should no longer be needed in any cases. Please change to using the .. prefix and over the next few years we will start to formally deprecate and remove the with= parameter. If this is well received, the .. prefix could be expanded to symbols appearing in i= and by=, too. Note that column names should not now start with ... If a symbol ..var is used in j= but ..var exists as a column name, the column still takes precedence, for backwards compatibility. Over the next few years, data.table will start issuing warnings/errors when it sees column names starting with ... This affects one CRAN package out of 475 using data.table, so we do not believe this restriction to be unreasonable. Our main focus here which we believe .. achieves is to resolve the more common ambiguity when var is in calling scope and var is a column name too. Further, we have not forgotten that in the past we recommended prefixing the variable in calling scope with .. yourself. If you did that and ..var exists in calling scope, that still works, provided neither var exists in calling scope nor ..var exists as a column name. Please now remove the .. prefix on ..var in calling scope to tidy this up. In future data.table will start to warn/error on such usage.

  19. setindexv can now assign multiple (separate) indices by accepting a list in the cols argument.

  20. as.matrix.data.table method now has an additional rownames argument allowing for a single column to be used as the rownames after conversion to a matrix. Thanks to @sritchie73 for the suggestion, use cases, #2692 and implementation PR#2702 and @MichaelChirico for additional use cases.

BUG FIXES

  1. The new quote rules handles this single field "Our Stock Screen Delivers an Israeli Software Company (MNDO, CTCH)<\/a> SmallCapInvestor.com - Thu, May 19, 2011 10:02 AM EDT<\/cite><\/div>Yesterday in \""Google, But for Finding Great Stocks\"", I discussed the value of stock screeners as a powerful tool", #2051. Thanks to @scarrascoso for reporting. Example file added to test suite.

  2. fwrite() creates a file with permissions that now play correctly with Sys.umask(), #2049. Thanks to @gnguy for reporting.

  3. fread() no longer holds an open lock on the file when a line outside the large sample has too many fields and generates an error, #2044. Thanks to Hugh Parsonage for reporting.

  4. Setting j = {} no longer results in an error, #2142. Thanks Michael Chirico for the pull request.

  5. Segfault in rbindlist() when one or more items are empty, #2019. Thanks Michael Lang for the pull request. Another segfault if the result would be more than 2bn rows, thanks to @jsams's comment in #2340.

  6. Error printing 0-length ITime and NA objects, #2032 and #2171. Thanks Michael Chirico for the pull requests and @franknarf1 for pointing out a shortcoming of the initial fix.

  7. as.IDate.POSIXct error with NULL timezone, #1973. Thanks @lbilli for reporting and Michael Chirico for the pull request.

  8. Printing a null data.table with print no longer visibly outputs NULL, #1852. Thanks @aaronmcdaid for spotting and @MichaelChirico for the PR.

  9. data.table now works with Shiny Reactivity / Flexdashboard. The error was typically something like col not found in DT[col==val]. Thanks to Dirk Eddelbuettel leading Matt through reproducible steps and @sergeganakou and Richard White for reporting. Closes #2001 and shiny/#1696.

  10. The as.IDate.POSIXct method passed tzone along but was not exported. So tzone is now taken into account by as.IDate too as well as IDateTime, #977 and #1498. Tests added.

  11. Named logical vector now select rows as expected from single row data.table. Thanks to @skranz for reporting. Closes #2152.

  12. fread()'s rare Internal error: Sampling jump point 10 is before the last jump ended has been fixed, #2157. Thanks to Frank Erickson and Artem Klevtsov for reporting with example files which are now added to the test suite.

  13. CJ() no longer loses attribute information, #2029. Thanks to @MarkusBonsch and @royalts for the pull request.

  14. split.data.table respects factor ordering in by argument, #2082. Thanks to @MichaelChirico for identifying and fixing the issue.

  15. .SD would incorrectly include symbol on lhs of := when .SDcols is specified and get() appears in j. Thanks @renkun-ken for reporting and the PR, and @ProfFancyPants for reporing a regression introduced in the PR. Closes #2326 and #2338.

  16. Integer values that are too large to fit in int64 will now be read as strings #2250.

  17. Internal-only .shallow now retains keys correctly, #2336. Thanks to @MarkusBonsch for reporting, fixing (PR #2337) and adding 37 tests. This much advances the journey towards exporting shallow(), #2323.

  18. isoweek calculation is correct regardless of local timezone setting (Sys.timezone()), #2407. Thanks to @MoebiusAV and @SimonCoulombe for reporting and @MichaelChirico for fixing.

  19. Fixed as.xts.data.table to support all xts supported time based index clasess #2408. Thanks to @ebs238 for reporting and for the PR.

  20. A memory leak when a very small number such as 0.58E-2141 is bumped to type character is resolved, #918.

  21. The edge case setnames(data.table(), character(0)) now works rather than error, #2452.

  22. Order of rows returned in non-equi joins were incorrect in certain scenarios as reported under #1991. This is now fixed. Thanks to @Henrik-P for reporting.

  23. Non-equi joins work as expected when x in x[i, on=...] is a 0-row data.table. Closes #1986.

  24. Non-equi joins along with by=.EACHI returned incorrect result in some rare cases as reported under #2360. This is fixed now. This fix also takes care of #2275. Thanks to @ebs238 for the nice minimal reproducible report, @Mihael for asking on SO and to @Frank for following up on SO and filing an issue.

  25. by=.EACHI works now when list columns are being returned and some join values are missing, #2300. Thanks to @jangorecki and @franknarf1 for the reproducible examples which have been added to the test suite.

  26. Indices are now retrieved by exact name, #2465. This prevents usage of wrong indices as well as unexpected row reordering in join results. Thanks to @pannnda for reporting and providing a reproducible example and to @MarkusBonsch for fixing.

  27. setnames of whole table when original table had NA names skipped replacing those, #2475. Thanks to @franknarf1 and BenoitLondon on StackOverflow for the report and @MichaelChirico for fixing.

  28. CJ() works with multiple empty vectors now #2511. Thanks to @MarkusBonsch for fixing.

  29. := assignment of one vector to two or more columns, e.g. DT[, c("x", "y") := 1:10], failed to copy the 1:10 data causing errors later if and when those columns were updated by reference, #2540. This is an old issue (#185) that had been fixed but reappeared when code was refactored. Thanks to @patrickhowerter for the detailed report with reproducible example and to @MarkusBonsch for fixing and strengthening tests so it doesn't reappear again.

  30. "Negative length vectors not allowed" error when grouping median and var fixed, #2046 and #2111. Thanks to @caneff and @osofr for reporting and to @kmillar for debugging and explaining the cause.

  31. Fixed a bug on Windows where data.tables containing non-UTF8 strings in keys were not properly sorted, #2462, #1826 and StackOverflow. Thanks to @shrektan for reporting and fixing.

  32. x. prefixes during joins sometimes resulted in a "column not found" error. This is now fixed. Closes #2313. Thanks to @franknarf1 for the MRE.

  33. setattr() no longer segfaults when setting 'class' to empty character vector, #2386. Thanks to @hatal175 for reporting and to @MarkusBonsch for fixing.

  34. Fixed cases where the result of merge.data.table() would contain duplicate column names if by.x was also in names(y). merge.data.table() gains the no.dups argument (default TRUE) to match the correpsonding patched behaviour in base:::merge.data.frame(). Now, when by.x is also in names(y) the column name from y has the corresponding suffixes added to it. by.x remains unchanged for backwards compatibility reasons. In addition, where duplicate column names arise anyway (i.e. suffixes = c("", "")) merge.data.table() will now throw a warning to match the behaviour of base:::merge.data.frame(). Thanks to @sritchie73 for reporting and fixing PR#2631 and PR#2653

  35. CJ() now fails with proper error message when results would exceed max integer, #2636.

  36. NA in character columns now display as <NA> just like base R to distinguish from "" and "NA".

  37. getDTthreads() could return INT_MAX (2 billion) after an explicit call to setDTthreads(0), PR#2708.

  38. Fixed a bug on Windows that data.table may break if the garbage collecting was triggered when sorting a large number of non-ASCII characters. Thanks to @shrektan for reporting and fixing PR#2678, #2674.

  39. Internal aliasing of . to list was over-aggressive in applying list even when . was intended within bquote, #1912. Thanks @MichaelChirico for reporting/filing and @ecoRoland for suggesting and testing a fix.

  40. Attempt to allocate a wildly large amount of RAM (16EB) when grouping by key and there are close to 2 billion 1-row groups, #2777. Thanks to @jsams for the detailed report.

  41. Fix a bug that print(dt, class=TRUE) shows only topn - 1 rows. Thanks to @heavywatal for reporting #2803 and filing PR#2804.

NOTES

  1. The license has been changed from GPL to MPL (Mozilla Public License). All contributors were consulted and approved. PR#2456 details the reasons for the change.

  2. ?data.table makes explicit the option of using a logical vector in j to select columns, #1978. Thanks @Henrik-P for the note and @MichaelChirico for filing.

  3. Test 1675.1 updated to cope with a change in R-devel in June 2017 related to factor() and NA levels.

  4. Package ezknitr has been added to the whitelist of packages that run user code and should be consider data.table-aware, #2266. Thanks to Matt Mills for testing and reporting.

  5. Printing with quote = TRUE now quotes column names as well, #1319. Thanks @jan-glx for the suggestion and @MichaelChirico for the PR.

  6. Added a blurb to ?melt.data.table explicating the subtle difference in behavior of the id.vars argument vis-a-vis its analog in reshape2::melt, #1699. Thanks @MichaelChirico for uncovering and filing.

  7. Added some clarification about the usage of on to ?data.table, #2383. Thanks to @peterlittlejohn for volunteering his confusion and @MichaelChirico for brushing things up.

  8. Clarified that "data.table always sorts in C-locale" means that upper-case letters are sorted before lower-case letters by ordering in data.table (e.g. setorder, setkey, DT[order(...)]). Thanks to @hughparsonage for the pull request editing the documentation. Note this makes no difference in most cases of data; e.g. ids where only uppercase or lowercase letters are used ("AB123"<"AC234" is always true, regardless), or country names and words which are consistently capitalized. For example, "America" < "Brazil" is not affected (it's always true), and neither is "america" < "brazil" (always true too); since the first letter is consistently capitalized. But, whether "america" < "Brazil" (the words are not consistently capitalized) is true or false in base R depends on the locale of your R session. In America it is true by default and false if you i) type Sys.setlocale(locale="C"), ii) the R session has been started in a C locale for you which can happen on servers/services (the locale comes from the environment the R session is started in). However, "america" < "Brazil" is always, consistently false in data.table which can be a surprise because it differs to base R by default in most regions. It is false because "B"<"a" is true because all upper-case letters come first, followed by all lower case letters (the ascii number of each letter determines the order, which is what is meant by C-locale).

  9. data.table's dependency has been moved forward from R 3.0.0 (Apr 2013) to R 3.1.0 (Apr 2014; i.e. 3.5 years old). We keep this dependency as old as possible for as long as possible as requested by users in managed environments. Thanks to Jan Gorecki, the test suite from latest dev now runs on R 3.1.0 continously, as well as R-release (currently 3.4.2) and latest R-devel snapshot. Our CRAN release procedures also double check with this stated dependency before release to CRAN. The primary motivation for the bump to R 3.1.0 was allowing one new test which relies on better non-copying behaviour in that version, #2484. It also allows further internal simplifications. Thanks to @MichaelChirico for fixing another test that failed on R 3.1.0 due to slightly different behaviour of base::read.csv in R 3.1.0-only which the test was comparing to, #2489.

  10. New vignette added: Importing data.table - focused on using data.table as a dependency in R packages. Answers most commonly asked questions and promote good practices.

  11. As warned in v1.9.8 release notes below in this file (on CRAN 25 Nov 2016) it has been 1 year since then and so use of options(datatable.old.unique.by.key=TRUE) to restore the old default is now deprecated with warning. The new warning states that this option still works and repeats the request to pass by=key(DT) explicitly to unique(), duplicated(), uniqueN() and anyDuplicated() and to stop using this option. In another year, this warning will become error. Another year after that the option will be removed.

  12. As set2key() and key2() have been warning since v1.9.8 on CRAN Nov 2016, their warnings have now been upgraded to errors. Note that when they were introduced in version 1.9.4 (Oct 2014) they were marked as 'experimental' in NEWS item 4. They will be removed in one year.

Was warning: set2key() will be deprecated in the next relase. Please use setindex() instead.
Now error: set2key() is now deprecated. Please use setindex() instead.
  1. The option datatable.showProgress is no longer set to a default value when the package is loaded. Instead, the default= argument of getOption is used by both fwrite and fread. The default is the result of interactive() at the time of the call. Using getOption in this way is intended to be more helpful to users looking at args(fread) and ?fread.

  2. print.data.table() invisibly returns its first argument instead of NULL. This behavior is compatible with the standard print.data.frame() and tibble's print.tbl_df(). Thanks to @heavywatal for PR#2807

Changes in v1.10.4-3 (on CRAN 20 Oct 2017)

  1. Fixed crash/hang on MacOS when parallel::mclapply is used and data.table is merely loaded, #2418. Oddly, all tests including test 1705 (which tests mclapply with data.table) passed fine on CRAN. It appears to be some versions of MacOS or some versions of libraries on MacOS, perhaps. Many thanks to Martin Morgan for reporting and confirming this fix works. Thanks also to @asenabouth, Joe Thorley and Danton Noriega for testing, debugging and confirming that automatic parallelism inside data.table (such as fwrite) works well even on these MacOS installations. See also news items below for 1.10.4-1 and 1.10.4-2.

Changes in v1.10.4-2 (on CRAN 12 Oct 2017)

  1. OpenMP on MacOS is now supported by CRAN and included in CRAN's package binaries for Mac. But installing v1.10.4-1 from source on MacOS failed when OpenMP was not enabled at compile time, #2409. Thanks to Liz Macfie and @fupangpangpang for reporting. The startup message when OpenMP is not enabled has been updated.

  2. Two rare potential memory faults fixed, thanks to CRAN's automated use of latest compiler tools; e.g. clang-5 and gcc-7

Changes in v1.10.4-1 (on CRAN 09 Oct 2017)

  1. The nanotime v0.2.0 update on CRAN 22 June 2017 changed from integer64 to S4 and broke fwrite of nanotime columns. Fixed to work with nanotime both before and after v0.2.0.

  2. Pass R-devel changes related to deparse(,backtick=) and factor().

  3. Internal NAMED()==2 now MAYBE_SHARED(), #2330. Back-ported to pass under the stated dependency, R 3.0.0.

  4. Attempted improvement on Mac-only when the parallel package is used too (which forks), #2137. Intel's OpenMP implementation appears to leave threads running after the OpenMP parallel region (inside data.table) has finished unlike GNU libgomp. So, if and when parallel's fork is invoked by the user after data.table has run in parallel already, instability occurs. The problem only occurs with Mac package binaries from CRAN because they are built by CRAN with Intel's OpenMP library. No known problems on Windows or Linux and no known problems on any platform when parallel is not used. If this Mac-only fix still doesn't work, call setDTthreads(1) immediately after library(data.table) which has been reported to fix the problem by putting data.table into single threaded mode earlier.

  5. When fread() and print() see integer64 columns are present but package bit64 is not installed, the warning is now displayed as intended. Thanks to a question by Santosh on r-help and forwarded by Bill Dunlap.

Changes in v1.10.4 (on CRAN 01 Feb 2017)

BUG FIXES

  1. The new specialized nanotime writer in fwrite() type punned using *(long long *)&REAL(column)[i] which, strictly, is undefined behavour under C standards. It passed a plethora of tests on linux (gcc 5.4 and clang 3.8), win-builder and 6 out 10 CRAN flavours using gcc. But failed (wrong data written) with the newest version of clang (3.9.1) as used by CRAN on the failing flavors, and solaris-sparc. Replaced with the union method and added a grep to CRAN_Release.cmd.

Changes in v1.10.2 (on CRAN 31 Jan 2017)

NEW FEATURES

  1. When j is a symbol prefixed with .. it will be looked up in calling scope and its value taken to be column names or numbers.

    myCols = c("colA","colB")
    DT[, myCols, with=FALSE]
    DT[, ..myCols]              # same

    When you see the .. prefix think one-level-up like the directory .. in all operating systems meaning the parent directory. In future the .. prefix could be made to work on all symbols apearing anywhere inside DT[...]. It is intended to be a convenient way to protect your code from accidentally picking up a column name. Similar to how x. and i. prefixes (analogous to SQL table aliases) can already be used to disambiguate the same column name present in both x and i. A symbol prefix rather than a ..() function will be easier for us to optimize internally and more convenient if you have many variables in calling scope that you wish to use in your expressions safely. This feature was first raised in 2012 and long wished for, #633. It is experimental.

  2. When fread() or print() see integer64 columns are present, bit64's namespace is now automatically loaded for convenience.

  3. fwrite() now supports the new nanotime type by Dirk Eddelbuettel, #1982. Aside: data.table already automatically supported nanotime in grouping and joining operations via longstanding support of its underlying integer64 type.

  4. indices() gains a new argument vectors, default FALSE. This strsplits the index names by __ for you, #1589.

    DT = data.table(A=1:3, B=6:4)
    setindex(DT, B)
    setindex(DT, B, A)
    indices(DT)
    [1] "B"    "B__A"
    indices(DT, vectors=TRUE)
    [[1]]
    [1] "B"
    [[2]]
    [1] "B" "A"

BUG FIXES

  1. Some long-standing potential instability has been discovered and resolved many thanks to a detailed report from Bill Dunlap and Michael Sannella. At C level any call of the form setAttrib(x, install(), allocVector()) can be unstable in any R package. Despite setAttrib() PROTECTing its inputs, the 3rd argument (allocVector) can be executed first only for its result to to be released by install()'s potential GC before reaching setAttrib's PROTECTion of its inputs. Fixed by either PROTECTing or pre-install()ing. Added to CRAN_Release.cmd procedures: i) greps to prevent usage of this idiom in future and ii) running data.table's test suite with gctorture(TRUE).

  2. A new potential instability introduced in the last release (v1.10.0) in GForce optimized grouping has been fixed by reverting one change from malloc to R_alloc. Thanks again to Michael Sannella for the detailed report.

  3. fwrite() could write floating point values incorrectly, #1968. A thread-local variable was incorrectly thread-global. This variable's usage lifetime is only a few clock cycles so it needed large data and many threads for several threads to overlap their usage of it and cause the problem. Many thanks to @mgahan and @jmosser for finding and reporting.

NOTES

  1. fwrite()'s ..turbo option has been removed as the warning message warned. If you've found a problem, please report it.

  2. No known issues have arisen due to DT[,1] and DT[,c("colA","colB")] now returning columns as introduced in v1.9.8. However, as we've moved forward by setting options('datatable.WhenJisSymbolThenCallingScope'=TRUE) introduced then too, it has become clear a better solution is needed. All 340 CRAN and Bioconductor packages that use data.table have been checked with this option on. 331 lines would need to be changed in 59 packages. Their usage is elegant, correct and recommended, though. Examples are DT[1, encoding] in quanteda and DT[winner=="first", freq] in xgboost. These are looking up the columns encoding and freq respectively and returning them as vectors. But if, for some reason, those columns are removed from DT and encoding or freq are still variables in calling scope, their values in calling scope would be returned. Which cannot be what was intended and could lead to silent bugs. That was the risk we were trying to avoid.
    options('datatable.WhenJisSymbolThenCallingScope') is now removed. A migration timeline is no longer needed. The new strategy needs no code changes and has no breakage. It was proposed and discussed in point 2 here, as follows.
    When j is a symbol (as in the quanteda and xgboost examples above) it will continue to be looked up as a column name and returned as a vector, as has always been the case. If it's not a column name however, it is now a helpful error explaining that data.table is different to data.frame and what to do instead (use .. prefix or with=FALSE). The old behaviour of returning the symbol's value in calling scope can never have been useful to anybody and therefore not depended on. Just as the DT[,1] change could be made in v1.9.8, this change can be made now. This change increases robustness with no downside. Rerunning all 340 CRAN and Bioconductor package checks reveal 2 packages throwing the new error: partools and simcausal. Their maintainers have been informed that there is a likely bug on those lines due to data.table's (now remedied) weakness. This is exactly what we wanted to reveal and improve.

  3. As before, and as we can see is in common use in CRAN and Bioconductor packages using data.table, DT[,myCols,with=FALSE] continues to lookup myCols in calling scope and take its value as column names or numbers. You can move to the new experimental convenience feature DT[, ..myCols] if you wish at leisure.

Changes in v1.10.0 (on CRAN 3 Dec 2016)

BUG FIXES

  1. fwrite(..., quote='auto') already quoted a field if it contained a sep or \n, or sep2[2] when list columns are present. Now it also quotes a field if it contains a double quote (") as documented, #1925. Thanks to Aki Matsuo for reporting. Tests added. The qmethod tests did test escaping embedded double quotes, but only when sep or \n was present in the field as well to trigger the quoting of the field.

  2. Fixed 3 test failures on Solaris only, #1934. Two were on both sparc and x86 and related to a tzone attribute difference between as.POSIXct and as.POSIXlt even when passed the default tz="". The third was on sparc only: a minor rounding issue in fwrite() of 1e-305.

  3. Regression crash fixed when 0's occur at the end of a non-empty subset of an empty table, #1937. Thanks Arun for tracking down. Tests added. For example, subsetting the empty DT=data.table(a=character()) with DT[c(1,0)] should return a 1 row result with one NA since 1 is past the end of nrow(DT)==0, the same result as DT[1].

  4. Fixed newly reported crash that also occurred in old v1.9.6 when by=.EACHI, nomatch=0, the first item in i has no match AND j has a function call that is passed a key column, #1933. Many thanks to Reino Bruner for finding and reporting with a reproducible example. Tests added.

  5. Fixed fread() error occurring for a subset of Windows users: showProgress is not type integer but type 'logical'., #1944 and #1111. Our tests cover this usage (it is just default usage), pass on AppVeyor (Windows), win-builder (Windows) and CRAN's Windows so perhaps it only occurs on a specific and different version of Windows to all those. Thanks to @demydd for reporting. Fixed by using strictly logical type at R level and Rboolean at C level, consistently throughout.

  6. Combining on= (new in v1.9.6) with by= or keyby= gave incorrect results, #1943. Many thanks to Henrik-P for the detailed and reproducible report. Tests added.

  7. New function rleidv was ignoring its cols argument, #1942. Thanks Josh O'Brien for reporting. Tests added.

NOTES

  1. It seems OpenMP is not available on CRAN's Mac platform; NOTEs appeared in CRAN checks for v1.9.8. Moved Rprintf from init.c to packageStartupMessage to avoid the NOTE as requested urgently by Professor Ripley. Also fixed the bad grammar of the message: 'single threaded' now 'single-threaded'. If you have a Mac and run macOS or OS X on it (I run Ubuntu on mine) please contact CRAN maintainers and/or Apple if you'd like CRAN's Mac binary to support OpenMP. Otherwise, please follow these instructions for OpenMP on Mac which people have reported success with.

  2. Just to state explicitly: data.table does not now depend on or require OpenMP. If you don't have it (as on CRAN's Mac it appears but not in general on Mac) then data.table should build, run and pass all tests just fine.

  3. There are now 5,910 raw tests as reported by test.data.table(). Tests cover 91% of the 4k lines of R and 89% of the 7k lines of C. These stats are now known thanks to Jim Hester's Covr package and Codecov.io. If anyone is looking for something to help with, creating tests to hit the missed lines shown by clicking the R and src folders at the bottom here would be very much appreciated.

  4. The FAQ vignette has been revised given the changes in v1.9.8. In particular, the very first FAQ.

  5. With hindsight, the last release v1.9.8 should have been named v1.10.0 to convey it wasn't just a patch release from .6 to .8 owing to the 'potentially breaking changes' items. Thanks to @neomantic for correctly pointing out. The best we can do now is now bump to 1.10.0.

Old news from v1.9.8 (Nov 2016) back to v1.2 (Aug 2008) has been moved to NEWS.0.md