Merge branch 'master' into fread_quote_sep

Author: ben-schwen

.github/workflows/R-CMD-check-occasional.yaml

@@ -1,6 +1,7 @@
 on:
   schedule:
    - cron: '17 13 23 * *' # 23rd of month at 13:17 UTC
+  workflow_dispatch:
 
 # A more complete suite of checks to run monthly; each PR/merge need not pass all these, but they should pass before CRAN release
 name: R-CMD-check-occasional

.github/workflows/R-CMD-check.yaml

@@ -5,6 +5,7 @@ on:
     branches:
       - master
   pull_request:
+  workflow_dispatch:
 
 name: R-CMD-check
 

.github/workflows/code-quality.yaml

@@ -2,11 +2,44 @@ on:
   push:
     branches: [master]
   pull_request:
+  workflow_dispatch:
 
 name: code-quality
 
 jobs:
+  changes:
+    runs-on: ubuntu-latest
+    outputs:
+      r:  ${{ steps.filter.outputs.r }}
+      c:  ${{ steps.filter.outputs.c }}
+      po: ${{ steps.filter.outputs.po }}
+      md: ${{ steps.filter.outputs.md }}
+      rd: ${{ steps.filter.outputs.rd }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # ensure diff against base is available for PRs
+      - uses: dorny/paths-filter@v3
+        id: filter
+        with:
+          filters: |
+            r:
+              - '**/*.R'
+              - '**/*.Rmd'
+            c:
+              - '**/*.c'
+              - '**/*.h'
+            po:
+              - 'po/**/*.po'
+            md:
+              - '**/*.md'
+              - '**/*.Rmd'
+            rd:
+              - 'man/**/*.Rd'
+
   lint-r:
+    needs: changes
+    if: needs.changes.outputs.r == 'true' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -31,6 +64,8 @@ jobs:
           LINTR_ERROR_ON_LINT: true
           R_LINTR_LINTER_FILE: .ci/.lintr
   lint-c:
+    needs: changes
+    if: needs.changes.outputs.c == 'true' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -42,6 +77,8 @@ jobs:
         run: |
           Rscript .ci/lint.R .ci/linters/c src '[.][ch]$'
   lint-po:
+    needs: changes
+    if: needs.changes.outputs.po == 'true' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -55,13 +92,17 @@ jobs:
         run: |
           Rscript .ci/lint.R .ci/linters/po po '[.]po$'
   lint-md:
+    needs: changes
+    if: needs.changes.outputs.md == 'true' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
       - uses: r-lib/actions/setup-r@v2
       - name: Lint
         run: Rscript .ci/lint.R .ci/linters/md . '[.]R?md$'
   lint-rd:
+    needs: changes
+    if: needs.changes.outputs.rd == 'true' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

.github/workflows/performance-tests.yml

@@ -10,6 +10,7 @@ on:
       - 'R/**'
       - 'src/**'
       - '.ci/atime/**'
+  workflow_dispatch:
 
 jobs:
   comment:

.github/workflows/rchk.yaml

@@ -18,7 +18,14 @@
 on:
   push:
     branches: [master]
+    paths:
+      - '.github/workflows/rchk.yaml'
+      - 'src/**'
   pull_request:
+    paths:
+      - '.github/workflows/rchk.yaml'
+      - 'src/**'
+  workflow_dispatch:
 
 name: 'rchk'
 

.github/workflows/test-coverage.yaml

@@ -3,7 +3,20 @@
 on:
   push:
     branches: [master]
+    paths:
+      - '.github/workflows/test-coverage.yaml'
+      - 'inst/tests/**'
+      - 'R/**'
+      - 'src/**'
+      - 'tests/**'
   pull_request:
+    paths:
+      - '.github/workflows/test-coverage.yaml'
+      - 'inst/tests/**'
+      - 'R/**'
+      - 'src/**'
+      - 'tests/**'
+  workflow_dispatch:
 
 name: test-coverage.yaml
 

DESCRIPTION

@@ -104,5 +104,6 @@ Authors@R: c(
   person("Reino", "Bruner",        role="ctb"),
   person(given="@badasahog",       role="ctb", comment="GitHub user"),
   person("Vinit", "Thakur",        role="ctb"),
-  person("Mukul", "Kumar",         role="ctb")
+  person("Mukul", "Kumar",         role="ctb"),
+  person("Ildikó", "Czeller",      role="ctb")
   )

NAMESPACE

@@ -58,6 +58,8 @@ export(frollmax)
 export(frollmin)
 export(frollprod)
 export(frollmedian)
+export(frollvar)
+export(frollsd)
 export(frollapply)
 export(frolladapt)
 export(nafill)

NEWS.md

@@ -38,6 +38,11 @@
 
 1. `data.table(x=1, <expr>)`, where `<expr>` is an expression resulting in a 1-column matrix without column names, will eventually have names `x` and `V2`, not `x` and `V1`, consistent with `data.table(x=1, <expr>)` where `<expr>` results in an atomic vector, for example `data.table(x=1, cbind(1))` and `data.table(x=1, 1)` will both have columns named `x` and `V2`. In this release, the matrix case continues to be named `V1`, but the new behavior can be activated by setting `options(datatable.old.matrix.autoname)` to `FALSE`. See point 5 under Bug Fixes for more context; this change will provide more internal consistency as well as more consistency with `data.frame()`.
 
+2. The behavior of `week()` will be changed in a future release to calculate weeks sequentially (days 1-7 as week 1), which is a potential breaking change. For now, the current "legacy" behavior, where week numbers advance every 7th day of the year (e.g., day 7 starts week 2), remains the default, and a deprecation warning will be issued when the old and new behaviors differ. Users can control this behavior with the temporary option `options(datatable.week = "...")`:
+    *   `"sequential"`: Opt-in to the new, sequential behavior (no warning).
+    *   `"legacy"`: Continue using the legacy behavior but suppress the deprecation warning.
+See [#2611](https://github.com/Rdatatable/data.table/issues/2611) for details. Thanks @MichaelChirico for the report and @venom1204 for the implementation.
+    
 ### NEW FEATURES
 
 1. New `sort_by()` method for data.tables, [#6662](https://github.com/Rdatatable/data.table/issues/6662). It uses `forder()` to improve upon the data.frame method and also matches `DT[order(...)]` behavior with respect to locale. Thanks @rikivillalba for the suggestion and PR.
@@ -246,7 +251,7 @@
     #9: 2025-09-22     9         8           9.0
     ```
 
-19. New rolling functions: `frollmin`, `frollprod` and `frollmedian`, have been implemented, towards [#2778](https://github.com/Rdatatable/data.table/issues/2778). Thanks to @jangorecki for implementation. Implementation of rolling median is based on a novel algorithm "sort-median" described by [@suomela](https://github.com/suomela) in his 2014 paper [Median Filtering is Equivalent to Sorting](https://arxiv.org/abs/1406.1717). "sort-median" scales very well, not only for size of input vector but also for size of rolling window.
+19. Other new rolling functions: `frollmin`, `frollprod`, `frollmedian`, `frollvar` and `frollsd`, have been implemented, resolving long standing issue [#2778](https://github.com/Rdatatable/data.table/issues/2778). Thanks to @jangorecki for implementation. Implementation of rolling median is based on a novel algorithm "sort-median" described by [@suomela](https://github.com/suomela) in his 2014 paper [Median Filtering is Equivalent to Sorting](https://arxiv.org/abs/1406.1717). "sort-median" scales very well, not only for size of input vector but also for size of rolling window.
     ```r
     rollmedian = function(x, n) {
       ans = rep(NA_real_, nx<-length(x))
@@ -291,6 +296,7 @@
     #   user  system elapsed
     #  0.028   0.000   0.005
     ```
+    20. `fread()` now supports the `comment.char` argument to skip trailing comments or comment-only lines, consistent with `read.table()`, [#856](https://github.com/Rdatatable/data.table/issues/856). The default remains `comment.char = ""` (no comment parsing) for backward compatibility and performance, in contrast to `read.table(comment.char = "#")`. Thanks to @arunsrinivasan and many others for the suggestion and @ben-schwen for the implementation.
 
 ### BUG FIXES
 
@@ -332,8 +338,13 @@
 
 19. Ellipsis elements like `..1` are correctly excluded when searching for variables in "up-a-level" syntax inside `[`, [#5460](https://github.com/Rdatatable/data.table/issues/5460). Thanks @ggrothendieck for the report and @MichaelChirico for the fix.
 
-20. `fread()` auto-detects separators for single-column files consisting solely of quoted values (e.g. `"this_that"\n"2025-01-01 00:00:01"`), [#7366](https://github.com/Rdatatable/data.table/issues/7366). Thanks @arunsrinivasan
-for the report and @ben-schwen for the fix.
+20. `forderv` could segfault on keys with long runs of identical bytes (e.g., many duplicate columns) because the single-group branch tail-recursed radix-by-radix until the C stack ran out, [#4300](https://github.com/Rdatatable/data.table/issues/4300). This is a major problem since sorting is extensively used in `data.table`. Thanks @quantitative-technologies for the report and @ben-schwen for the fix.
+
+21. `[` now preserves existing key(s) when new columns are added before them, instead of incorrectly setting a new column as key, [#7364](https://github.com/Rdatatable/data.table/issues/7364). Thanks @czeildi for the bug report and the fix.
+
+22. `setDTthreads(percent=)` and `setDTthreads(threads=)` now respect `OMP_NUM_THREADS` and `omp_get_max_threads()`, ensuring consistency with `setDTthreads()` (no arguments) when OpenMP environment variables are set, [#7165](https://github.com/Rdatatable/data.table/issues/7165). Previously, explicitly setting a thread count or percentage would ignore these OpenMP limits, potentially exceeding the user's intended thread cap. Thanks to @bastistician for the report and @ben-schwen for the fix.
+
+20. `fread()` auto-detects separators for single-column files consisting solely of quoted values (e.g. `"this_that"\n"2025-01-01 00:00:01"`), [#7366](https://github.com/Rdatatable/data.table/issues/7366). Thanks @arunsrinivasan for the report and @ben-schwen for the fix.
 
 ### NOTES
 
@@ -531,6 +542,8 @@ rowwiseDT(
 
 21. `setDT(get0('var'))` now correctly modifies `var` by reference, consistent with the long-standing behavior of `setDT(get('var'))`, [#6864](https://github.com/Rdatatable/data.table/issues/6864). Thanks to @rikivillalba for the report and @venom1204 for the fix.
 
+22. `fread()` could fail to read Mac CSV files (with `\r` line endings) if the file contained any `\n` character, such as a final `\r\n`. This was fixed by detecting the predominant line ending in a sample of the file, [#4186](https://github.com/Rdatatable/data.table/issues/4186). Thanks to @MPagel for the report and @ben-schwen for the fix.
+
 ### NOTES
 
 1. There is a new vignette on joins! See `vignette("datatable-joins")`. Thanks to Angel Feliz for authoring it! Feedback welcome. This vignette has been highly requested since 2017: [#2181](https://github.com/Rdatatable/data.table/issues/2181).

R/data.table.R

@@ -1448,7 +1448,7 @@ replace_dot_alias = function(e) {
         if (SD_only)
           jvnames = jnames = sdvars
         else
-          jnames = as.character(Filter(is.name, jsub)[-1L])
+          jnames = vapply_1c(jsub, function(x) if (is.name(x)) as.character(x) else NA_character_)[-1L]
         key_idx = chmatch(key, jnames)
         missing_keys = which(is.na(key_idx))
         if (length(missing_keys) && missing_keys[1L] == 1L) return(NULL)