Merge branch 'master' into fix/6898-ignore-tzone

Author: MichaelChirico

.ci/.lintr.R

@@ -16,6 +16,13 @@ linters = c(dt_linters, all_linters(
   # system_time_linter = undesirable_function_linter(c(
   #   system.time = "Only run timings in benchmark.Rraw"
   # )),
+  undesirable_function_linter(c(
+    cat = "Use catf to enable translations",
+    message = "Use messagef to avoid fragmented translations.",
+    warning = "Use warningf to avoid fragmented translations.",
+    stop = "Use stopf to avoid fragmented translations.",
+    NULL
+  )),
   # undesirable_function_linter(modify_defaults(
   #   default_undesirable_functions,
   #   ifelse = "Use fifelse instead.",

.ci/README.md

@@ -12,7 +12,7 @@ Test jobs:
 - `test-lin-rel-cran` - `--as-cran` on Linux, strict test for final status of `R CMD check`.
 - `test-lin-dev-gcc-strict-cran` - `--as-cran` on Linux, `r-devel` built with `-enable-strict-barrier --disable-long-double`, test for compilation warnings, test for new NOTEs/WARNINGs from `R CMD check`.
 - `test-lin-dev-clang-cran` - same as `gcc-strict` job but R built with `clang` and  no `--enable-strict-barrier --disable-long-double` flags.
-- `test-lin-ancient-cran` - Stated R dependency version (currently 3.3.0) on Linux.
+- `test-lin-ancient-cran` - Stated R dependency version (currently 3.4.0) on Linux.
 - `test-lin-dev-san` - `r-devel` on Linux built with `clang -fsanitize=address,undefined` (including LeakSanitizer), test for sanitizer output in tests and examples.
 - `test-win-rel` - `r-release` on Windows.
 - `test-win-dev` - `r-devel` on Windows.

.ci/atime/tests.R

@@ -13,6 +13,7 @@ for (extra.arg in extra.args.6107){
       tmp_csv = tempfile()
       fwrite(DT, tmp_csv)
     },
+    FasterIO = "60a01fa65191c44d7997de1843e9a1dfe5be9f72", # First commit of the PR (https://github.com/Rdatatable/data.table/pull/6925/commits) that reduced time usage
     Slow = "e9087ce9860bac77c51467b19e92cf4b72ca78c7", # Parent of the merge commit (https://github.com/Rdatatable/data.table/commit/a77e8c22e44e904835d7b34b047df2eff069d1f2) of the PR (https://github.com/Rdatatable/data.table/pull/6107) that fixes the issue
     Fast = "a77e8c22e44e904835d7b34b047df2eff069d1f2") # Merge commit of the PR (https://github.com/Rdatatable/data.table/pull/6107) that fixes the issue
   this.test$expr = str2lang(sprintf("data.table::fread(tmp_csv, %s)", extra.arg))
@@ -128,6 +129,18 @@ test.list <- atime::atime_test_list(
       paste0('useDynLib(', new.Package_))
   },
 
+  # Constant overhead improvement https://github.com/Rdatatable/data.table/pull/6925
+  # Test case adapted from https://github.com/Rdatatable/data.table/pull/7022#discussion_r2107900643
+  "fread disk overhead improved in #6925" = atime::atime_test(
+    N = 2^seq(0, 20), # smaller N because we are doing multiple fread calls.
+    setup = {
+      fwrite(iris[1], iris.csv <- tempfile())
+    },
+    expr = replicate(N, data.table::fread(iris.csv)),
+    Fast = "60a01fa65191c44d7997de1843e9a1dfe5be9f72", # First commit of the PR (https://github.com/Rdatatable/data.table/pull/6925/commits) that reduced time usage
+    Slow = "e25ea80b793165094cea87d946d2bab5628f70a6" # Parent of the first commit (https://github.com/Rdatatable/data.table/commit/60a01fa65191c44d7997de1843e9a1dfe5be9f72)
+  ),
+
   # Performance regression discussed in https://github.com/Rdatatable/data.table/issues/4311
   # Test case adapted from https://github.com/Rdatatable/data.table/pull/4440#issuecomment-632842980 which is the fix PR.
   "shallow regression fixed in #4440" = atime::atime_test(
@@ -177,8 +190,9 @@ test.list <- atime::atime_test_list(
   # Fixed in https://github.com/Rdatatable/data.table/pull/4558
   "DT[by] fixed in #4558" = atime::atime_test(
     setup = {
+      N9 <- as.integer(N * 0.9)
       d <- data.table(
-        id = sample(c(seq.int(N * 0.9), sample(N * 0.9, N * 0.1, TRUE))),
+        id = sample(c(seq.int(N9), sample(N9, N-N9, TRUE))),
         v1 = sample(5L, N, TRUE),
         v2 = sample(5L, N, TRUE)
       )
@@ -251,5 +265,15 @@ test.list <- atime::atime_test_list(
     Before = "f339aa64c426a9cd7cf2fcb13d91fc4ed353cd31", # Parent of the first commit https://github.com/Rdatatable/data.table/commit/fcc10d73a20837d0f1ad3278ee9168473afa5ff1 in the PR https://github.com/Rdatatable/data.table/pull/6393/commits with major change to fwrite with gzip.
     PR = "3630413ae493a5a61b06c50e80d166924d2ef89a"), # Close-to-last merge commit in the PR.
 
-  tests=extra.test.list)
+  # Test case created directly using the atime code below (not adapted from any other benchmark), based on the PR, Removes unnecessary data.table call from as.data.table.array https://github.com/Rdatatable/data.table/pull/7010 
+  "as.data.table.array improved in #7010" = atime::atime_test(
+    setup = {
+      dims = c(N, 1, 1)
+      arr = array(seq_len(prod(dims)), dim=dims)
+    },
+    expr = data.table:::as.data.table.array(arr, na.rm=FALSE),
+    Slow = "73d79edf8ff8c55163e90631072192301056e336",   # Parent of the first commit in the PR (https://github.com/Rdatatable/data.table/commit/8397dc3c993b61a07a81c786ca68c22bc589befc)
+    Fast = "8397dc3c993b61a07a81c786ca68c22bc589befc"),  # Commit in the PR (https://github.com/Rdatatable/data.table/pull/7019/commits) that removes inefficiency
+
+    tests=extra.test.list)
 # nolint end: undesirable_operator_linter.

.ci/linters/cocci/malloc_return_value_cast.cocci

@@ -4,3 +4,9 @@ expression E;
 @@
 - (T)
   malloc(E)
+
+- (T)
+  calloc(_, E)
+
+- (T)
+  realloc(_, E)

.dev/CRAN_Release.cmd

@@ -95,17 +95,6 @@ grep "PROTECT_PTR" ./src/*.c
 # No use of long long, instead use int64_t. TODO
 # grep "long long" ./src/*.c
 
-// No use of llu, lld, zd or zu
-grep -nE "(llu|lld|zd|zu)" src/*.[hc]
-// Comment moved here from fread.c on 19 Nov 2019
-// [Moved from fread.c on 19 Nov 2019] On Windows variables of type `size_t` cannot be printed
-// with "%zu" in the `snprintf()` function. For those variables we used to cast them into
-// `unsigned long long int` before printing, and defined (llu) to make the cast shorter.
-// We're now observing warnings from gcc-8 with -Wformat-extra-args, #4062. So
-// now we're more strict and cast to [u]int64_t and use PRIu64/PRId64 from <inttypes.h>
-// In many cases the format specifier is passed to our own macro (e.g. DTPRINT) or to Rprintf(),
-// error() etc, and even if they don't call sprintf() now, they could in future.
-
 # No tabs in C or R code (sorry, Richard Hendricks)
 grep -P "\t" ./R/*.R
 grep -P "\t" ./src/*.c
@@ -235,23 +224,23 @@ system.time(test.data.table(script="*.Rraw"))  # apx 8h = froll 3h + nafill 1m +
 
 
 ###############################################
-#  R 3.3.0 (stated dependency)
+#  R 3.4.0 (stated dependency)
 ###############################################
 
 ### ONE TIME BUILD
 sudo apt-get -y build-dep r-base
 cd ~/build
-wget http://cran.stat.ucla.edu/src/base/R-3/R-3.3.0.tar.gz
-tar xvf R-3.3.0.tar.gz
-cd R-3.3.0
+wget http://cran.stat.ucla.edu/src/base/R-3/R-3.4.0.tar.gz
+tar xvf R-3.4.0.tar.gz
+cd R-3.4.0
 CFLAGS="-fcommon" FFLAGS="-fallow-argument-mismatch" ./configure --without-recommended-packages
 make
-alias R330=~/build/R-3.3.0/bin/R
+alias R340=~/build/R-3.4.0/bin/R
 ### END ONE TIME BUILD
 
 cd ~/GitHub/data.table
-R330 CMD INSTALL ./data.table_1.16.99.tar.gz
-R330
+R340 CMD INSTALL ./data.table_1.16.99.tar.gz
+R340
 require(data.table)
 test.data.table(script="*.Rraw")
 

.dev/README.md

@@ -1,5 +1,25 @@
 # data.table developer
 
+Inside this repository we provide some tools to improves development experience. Most notable is the `cc()` helper function that recompiles C sources, reloads R sources, and runs tests.
+
+Typical development workflow will then look like:
+
+0. `git checkout -b [branch]`
+1. edit package files
+2. run `R`
+3. call `cc(TRUE)`
+4. (if needed) go to point 1.
+
+Once we (and tests) are satisfied with changes, we then run complete package checks:
+
+0. in shell terminal
+1. run `make build`
+2. run `make check`
+3. (optionally) run on `r-devel`, e.g. `R=~/build/R-devel/bin/R make check`
+4. (optionally) run on ancient R, e.g. `R=~/build/R-340/bin/R make check`
+5. `git commit -m '[changes description]'`
+6. `git push [remote] [branch]`
+
 ## Setup
 
 To use the optional helper function `cc()`, one needs to set up the project path and source `.dev/cc.R` to use `cc()` conveniently. This works through creating an additional `.Rprofile` in the `data.table` directory.

.devcontainer/r-ancient-gcc/Dockerfile

@@ -1,4 +1,4 @@
-FROM registry.gitlab.com/jangorecki/dockerfiles/r-3.3.0
+FROM registry.gitlab.com/jangorecki/dockerfiles/r-3.4.0
 
 RUN apt-get -qq update \
   && apt-get install -y --no-install-recommends git

.github/CONTRIBUTING.md

@@ -76,6 +76,10 @@ See [`?test`](https://rdatatable.gitlab.io/data.table/reference/test.html).
 1. **[Squashing Github pull requests into a single commit](http://eli.thegreenplace.net/2014/02/19/squashing-github-pull-requests-into-a-single-commit)**.
 1. **[Github help](https://help.github.com/articles/using-pull-requests/)** - you'll need the *fork and pull* model.
 
+#### Performance testing
+
+If your PR may have an effect on time/memory usage, please consider adding a performance test, either in the same PR, or a follow-up PR. Note that first-time contributors _must_ do so in a follow-up PR, since the tests are only run on PRs from branches created directly in the Rdatatable/data.table repo. See the [Performance testing](https://github.com/Rdatatable/data.table/wiki/Performance-testing) wiki page for details.
+
 Minimal first time PR
 ---------------------
 

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

@@ -15,7 +15,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macOS-latest, windows-latest, ubuntu-latest]
-        r: ['devel', 'release', '3.3', '3.4', '3.5', '3.6', '4.0', '4.1', '4.2', '4.3']
+        r: ['devel', 'release', '3.4', '3.5', '3.6', '4.0', '4.1', '4.2', '4.3']
         locale: ['en_US.utf8', 'zh_CN.utf8', 'lv_LV.utf8'] # Chinese for translations, Latvian for collate order (#3502)
         exclude:
           # only run non-English locale CI on Ubuntu
@@ -28,8 +28,6 @@ jobs:
           - os: windows-latest
             locale: 'lv_LV.utf8'
           # macOS/arm64 only available for R>=4.1.0
-          - os: macOS-latest
-            r: '3.3'
           - os: macOS-latest
             r: '3.4'
           - os: macOS-latest

.gitlab-ci.yml

@@ -203,13 +203,13 @@ test-lin-dev-clang-cran:
 # stated dependency on R
 test-lin-ancient-cran:
   <<: *test-lin
-  image: registry.gitlab.com/rdatatable/dockerfiles/r-3.3.0
+  image: registry.gitlab.com/rdatatable/dockerfiles/r-3.4.0
   variables:
     _R_CHECK_FORCE_SUGGESTS_: "FALSE" # can be removed if all dependencies are available (knitr, xts, etc.)
   script:
     - *install-deps
     # knitr requires evaluate, which requires R 3.6.0.
-    # Restore checking vignettes if upgrading our R dependency means knitr can be installed.
+    # Restore checking vignettes if upgrading our R dependency means knitr can be installed, or when we switch to litedown.
     - R CMD check --no-manual --no-build-vignettes --ignore-vignettes $(ls -1t data.table_*.tar.gz | head -n 1)
 
 # run the main checks with Address(+Leak),UBSanitizer enabled