Merge remote-tracking branch 'upstream/master' into fix_fwrite_length

Author: philippechataignon

.devcontainer/r-devel-alpine/Dockerfile

@@ -0,0 +1,22 @@
+FROM docker.io/rhub/r-minimal:devel
+
+RUN apk update \
+  && apk add --no-cache \
+     gcc git musl-dev openmp pkgconf tzdata zlib-dev \
+  && echo 'options("repos"="https://cloud.r-project.org")' >> /usr/local/lib/R/etc/Rprofile.site
+
+ENV TZDIR=/usr/share/zoneinfo
+
+COPY DESCRIPTION .
+
+RUN Rscript -e '                                          \ 
+read.dcf("DESCRIPTION", c("Imports", "Suggests")) |>      \
+  tools:::.split_dependencies() |>                        \
+  names() |>                                              \
+  setdiff(tools:::.get_standard_package_names()$base) |>  \
+  install.packages(repos="https://cloud.r-project.org")   \
+'
+
+# setup cc()
+WORKDIR /root
+COPY .devcontainer/.Rprofile .

.devcontainer/r-devel-alpine/devcontainer.json

@@ -0,0 +1,9 @@
+{
+    "build": { "dockerfile": "Dockerfile", "context": "../.." },
+    "customizations": { "vscode": {
+       "extensions": [
+        "REditorSupport.r",
+        "ms-vscode.cpptools-extension-pack"
+       ]
+    }}
+  }

NEWS.md

@@ -125,7 +125,7 @@ rowwiseDT(
 
 15. Joins of `integer64` and `double` columns succeed when the `double` column has lossless `integer64` representation, [#4167](https://github.com/Rdatatable/data.table/issues/4167) and [#6625](https://github.com/Rdatatable/data.table/issues/6625). Previously, this only worked when the double column had lossless _32-bit_ integer representation. Thanks @MichaelChirico for the reports and fix.
 
-17. `DT[order(...)]` better matches `base::order()` behavior by (1) recognizing the `method=` argument (and erroring since this is not supported) and (2) accepting a vector of `TRUE`/`FALSE` in `decreasing=` as an alternative to using `-a` to convey "sort `a` decreasing", [#4456](https://github.com/Rdatatable/data.table/issues/4456). Thanks @jangorecki for the FR and @MichaelChirico for the PR.
+16. `DT[order(...)]` better matches `base::order()` behavior by (1) recognizing the `method=` argument (and erroring since this is not supported) and (2) accepting a vector of `TRUE`/`FALSE` in `decreasing=` as an alternative to using `-a` to convey "sort `a` decreasing", [#4456](https://github.com/Rdatatable/data.table/issues/4456). Thanks @jangorecki for the FR and @MichaelChirico for the PR.
 
 17. Assignment with `:=` to an S4 slot of an under-allocated data.table now works, [#6704](https://github.com/Rdatatable/data.table/issues/6704). Thanks @MichaelChirico for the report and fix.
 
@@ -153,6 +153,8 @@ rowwiseDT(
 
 11. Deprecation of `fread(autostart=)` has been upgraded to an error. It has been warning since v1.11.0 (6 years ago). The argument will be removed in the next release.
 
+12. Deprecation of `droplevels(in.place=TRUE)` (warning since v1.16.0) has been upgraded from warning to error. The argument will be removed in the next release.
+
 # data.table [v1.16.4](https://github.com/Rdatatable/data.table/milestone/36) 4 December 2024
 
 ## BUG FIXES

R/fdroplevels.R

@@ -8,10 +8,9 @@ fdroplevels = function(x, exclude = if (anyNA(levels(x))) NULL else NA, ...) {
   return(ans)
 }
 
-droplevels.data.table = function(x, except=NULL, exclude, in.place=FALSE, ...){
-  stopifnot(is.logical(in.place))
-  if (isTRUE(in.place)) warningf("droplevels() with in.place=TRUE is deprecated. Use setdroplevels() instead.")
-  if (!in.place) x = copy(x)
+droplevels.data.table = function(x, except=NULL, exclude, in.place=NULL, ...){
+  if (!is.null(in.place)) stopf("droplevels() with in.place=TRUE is deprecated. Use setdroplevels() instead.")
+  x = copy(x)
   if (missing(exclude)) exclude = NULL
   setdroplevels(x, except, exclude)[]
 }

configure

@@ -34,15 +34,11 @@ else
     NOZLIB=0
     lib=`pkg-config --libs zlib`
     cflag=`pkg-config --cflags zlib`
-    expr -- "$lib" : ".*-lz$" >> config.log  # -- for FreeBSD, #4652
+    echo "$lib" | grep -qE '[-]lz($| )' >> config.log
     if [ $? -ne 0 ]; then
-      expr -- "$lib" : ".*-lz " >> config.log
-      # would use \b in one expr but MacOS does not support \b
-      if [ $? -ne 0 ]; then
-        echo "*** pkg-config is installed and 'pkg-config --exists zlib' succeeds but"
-        echo "*** 'pkg-config --libs zlib' returns '${lib}' which does not include the standard -lz."
-        msg=1
-      fi
+      echo "*** pkg-config is installed and 'pkg-config --exists zlib' succeeds but"
+      echo "*** 'pkg-config --libs zlib' returns '${lib}' which does not include the standard -lz."
+      msg=1
     fi
   fi
 fi

inst/tests/tests.Rraw

@@ -8449,11 +8449,9 @@ baseR = base::order(c(x2,x1,x1,x2))
   # are so relaxed now that they barely testing anything. It appears base R behaviour is undefined in this rare case of identical strings in different encodings.
 test(1590.04, identical(baseR, INT(1,4,2,3)) || identical(baseR, INT(2,3,1,4)) || identical(baseR, 1:4))
 Encoding(x2) = "unknown"
-# TODO(#6350): Decide if this test should be adjusted for Alpine Linux, or just dropped.
-if (!file.exists("/etc/alpine-release")) {
-  test(1590.05, x1!=x2)
-  test(1590.06, forderv(    c(x2,x1,x1,x2)), INT(1,4,2,3))  # consistent with Windows-1252 result, tested further below
-}
+# test(1590.05, x1!=x2) # Skip this test of R's own behavior since R itself does not give platform-consistent results, #6350
+# TODO(#6350): Restore this test. On Alpine, forder() finds this input to be sorted, but we want to be platform-independent.
+if (!file.exists("/etc/alpine-release")) test(1590.06, forderv(    c(x2,x1,x1,x2)), INT(1,4,2,3))  # consistent with Windows-1252 result, tested further below
 baseR = base::order(c(x2,x1,x1,x2))
 test(1590.07, identical(baseR, INT(1,4,2,3)) || identical(baseR, INT(2,3,1,4)) || identical(baseR, 1:4))
 Sys.setlocale("LC_CTYPE", ctype)
@@ -17794,7 +17792,7 @@ if (base::getRversion() >= "3.4.0") {
 }
 test(2214.06, droplevels(DT)[["a"]], droplevels(DT[1:5,a]))
 test(2214.07, droplevels(DT, 1)[["a"]], x[1:5])
-test(2214.08, droplevels(DT, in.place=TRUE), DT, warning="droplevels() with in.place=TRUE is deprecated.")
+test(2214.08, droplevels(DT, in.place=TRUE), error="droplevels() with in.place=TRUE is deprecated.")
 # support ordered factors in fdroplevels
 o = factor(letters[1:10], ordered=TRUE)
 test(2214.09, fdroplevels(o[1:5]), droplevels(o[1:5]))

man/fdroplevels.Rd

@@ -12,13 +12,13 @@
 fdroplevels(x, exclude = if (anyNA(levels(x))) NULL else NA, \dots)
 setdroplevels(x, except = NULL, exclude = NULL)
 
-\method{droplevels}{data.table}(x, except = NULL, exclude, in.place = FALSE, \dots)
+\method{droplevels}{data.table}(x, except = NULL, exclude, in.place = NULL, \dots)
 }
 \arguments{
   \item{x}{ \code{factor} or \code{data.table} where unused levels should be dropped. }
   \item{exclude}{ A \code{character} vector of factor levels which are dropped no matter of presented or not. }
   \item{except}{ An \code{integer} vector of indices of data.table columns which are not modified by dropping levels. }
-  \item{in.place}{ logical (default is \code{FALSE}). If \code{TRUE} levels of factors of \code{data.table} are modified in-place. }
+  \item{in.place}{ Deprecated. Use \code{setdroplevels} for in-place modification. }
   \item{\dots}{ further arguments passed to methods }
 }