Merge branch 'master' into truehash

Author: aitap

.gitattributes

@@ -8,3 +8,16 @@
 #   want to preserve the line endings robustly
 inst/tests/** -text
 inst/tests/*.Rraw text eol=lf linguist-language=R
+# Ensure GitHub  linguist only considers source code files
+#   for language statistics
+docs/** linguist-documentation
+man/** linguist-documentation
+tests/** linguist-vendored
+vignettes/** linguist-vendored
+po/** linguist-vendored
+.github/** linguist-vendored
+.ci/** linguist-vendored
+.dev/** linguist-vendored
+.devcontainer/** linguist-vendored
+.graphics/** linguist-vendored
+.Rproj.user/** linguist-vendored

R/frollapply.R

@@ -297,38 +297,22 @@ frollapply = function(X, N, FUN, ..., by.column=TRUE, fill=NA, align=c("right","
       tight = function(i, dest, src, n) FUN(.Call(CmemcpyDT, dest, src, i, n), ...)
     }
   } else {
-    #has.growable = base::getRversion() >= "3.4.0"
-    ## this is now always TRUE
-    ## we keep this branch, it may be useful when getting rid of SET_GROWABLE_BIT and SETLENGTH #6180
-    has.growable = TRUE
-    cpy = if (has.growable) function(x) .Call(Csetgrowable, copy(x)) else copy
+    cpy = function(x) .Call(CcopyAsGrowable, x)
     ansMask = function(len, n) {
       mask = seq_len(len) >= n
       mask[is.na(mask)] = FALSE ## test 6010.206
       mask
     }
     if (by.column) {
-      allocWindow = function(x, n) x[seq_len(max(n, na.rm=TRUE))]
-      if (has.growable) {
-        tight = function(i, dest, src, n) FUN(.Call(CmemcpyVectoradaptive, dest, src, i, n), ...) # CmemcpyVectoradaptive handles k[i]==0
-      } else {
-        tight = function(i, dest, src, n) {stopf("internal error: has.growable should be TRUE, implement support for n==0"); FUN(src[(i-n[i]+1L):i], ...)} # nocov
-      }
+      allocWindow = function(x, n) cpy(x[seq_len(max(n, na.rm=TRUE))])
+      tight = function(i, dest, src, n) FUN(.Call(CmemcpyVectoradaptive, dest, src, i, n), ...) # CmemcpyVectoradaptive handles k[i]==0
     } else {
       if (!list.df) {
-        allocWindow = function(x, n) x[seq_len(max(n, na.rm=TRUE)), , drop=FALSE]
-      } else {
-        allocWindow = function(x, n) lapply(x, `[`, seq_len(max(n)))
-      }
-      if (has.growable) {
-        tight = function(i, dest, src, n) FUN(.Call(CmemcpyDTadaptive, dest, src, i, n), ...) # CmemcpyDTadaptive handles k[i]==0
+        allocWindow = function(x, n) cpy(x[seq_len(max(n, na.rm=TRUE)), , drop=FALSE])
       } else {
-        if (!list.df) { # nocov
-          tight = function(i, dest, src, n) {stopf("internal error: has.growable should be TRUE, implement support for n==0"); FUN(src[(i-n[i]+1L):i, , drop=FALSE], ...)} # nocov
-        } else {
-          tight = function(i, dest, src, n) {stopf("internal error: has.growable should be TRUE, implement support for n==0"); FUN(lapply(src, `[`, (i-n[i]+1L):i), ...)} # nocov
-        }
+        allocWindow = function(x, n) cpy(lapply(x, `[`, seq_len(max(n))))
       }
+      tight = function(i, dest, src, n) FUN(.Call(CmemcpyDTadaptive, dest, src, i, n), ...) # CmemcpyDTadaptive handles k[i]==0
     }
   }
   ## prepare templates for errors and warnings

inst/tests/tests.Rraw

@@ -19453,7 +19453,7 @@ test(2290.4, DT[, `:=`(a = 2, c := 3)], error="It looks like you re-used `:=` in
 df = data.frame(a=1:3)
 setDT(df)
 attr(df, "att") = 1
-test(2291.1, set(df, NULL, "new", "new"), error="attributes .* have been reassigned")
+test(2291.1, set(df, NULL, "new", "new"), error="either been loaded from disk.*or constructed manually.*Please run setDT.*setalloccol.*on it first")
 
 # ns-qualified bysub error, #6493
 DT = data.table(a = 1)

src/assign.c

@@ -1,28 +1,5 @@
 #include "data.table.h"
 
-static void finalizer(SEXP p)
-{
-  SEXP x;
-  R_len_t n, l, tl;
-  if(!R_ExternalPtrAddr(p)) internal_error(__func__, "didn't receive an ExternalPtr"); // # nocov
-  p = R_ExternalPtrTag(p);
-  if (!isString(p)) internal_error(__func__, "ExternalPtr doesn't see names in tag"); // # nocov
-  l = LENGTH(p);
-  tl = TRUELENGTH(p);
-  if (l<0 || tl<l) internal_error(__func__, "l=%d, tl=%d", l, tl); // # nocov
-  n = tl-l;
-  if (n==0) {
-    // gc's ReleaseLargeFreeVectors() will have reduced R_LargeVallocSize by the correct amount
-    // already, so nothing to do (but almost never the case).
-    return;
-  }
-  x = PROTECT(allocVector(INTSXP, 50));  // 50 so it's big enough to be on LargeVector heap. See NodeClassSize in memory.c:allocVector
-                                         // INTSXP rather than VECSXP so that GC doesn't inspect contents after LENGTH (thanks to Karl Miller, Jul 2015)
-  SETLENGTH(x,50+n*2*sizeof(void *)/4);  // 1*n for the names, 1*n for the VECSXP itself (both are over allocated).
-  UNPROTECT(1);
-  return;
-}
-
 void setselfref(SEXP x) {
   if(!INHERITS(x, char_datatable))  return; // #5286
   SEXP p;
@@ -38,7 +15,6 @@ void setselfref(SEXP x) {
       R_NilValue
     ))
   ));
-  R_RegisterCFinalizerEx(p, finalizer, FALSE);
   UNPROTECT(2);
 
 /*
@@ -64,39 +40,8 @@ void setselfref(SEXP x) {
 */
 }
 
-/* There are two reasons the finalizer doesn't restore the LENGTH to TRUELENGTH. i) The finalizer
-happens too late after GC has already released the memory, and ii) copies by base R (e.g.
-[<- in write.table just before test 894) allocate at length LENGTH but copy the TRUELENGTH over.
-If the finalizer sets LENGTH to TRUELENGTH, that's a fail as it wasn't really allocated at
-TRUELENGTH when R did the copy.
-Karl Miller suggested an ENVSXP so that restoring LENGTH in finalizer should work. This is the
-closest I got to getting it to pass all tests :
-
-  SEXP env = PROTECT(allocSExp(ENVSXP));
-  defineVar(SelfRefSymbol, x, env);
-  defineVar(R_NamesSymbol, getAttrib(x, R_NamesSymbol), env);
-  setAttrib(x, SelfRefSymbol, p = R_MakeExternalPtr(
-    R_NilValue,         // for identical() to return TRUE. identical() doesn't look at tag and prot
-    R_NilValue, //getAttrib(x, R_NamesSymbol), // to detect if names has been replaced and its tl lost, e.g. setattr(DT,"names",...)
-    PROTECT(            // needed when --enable-strict-barrier it seems, iiuc. TO DO: test under that flag and remove if not needed.
-      env               // wrap x in env to avoid an infinite loop in object.size() if prot=x were here
-    )
-  ));
-  R_RegisterCFinalizerEx(p, finalizer, FALSE);
-  UNPROTECT(2);
-
-Then in finalizer:
-  SETLENGTH(names, tl)
-  SETLENGTH(dt, tl)
-
-and that finalizer indeed now happens before the GC releases memory (thanks to the env wrapper).
-
-However, we still have problem (ii) above and it didn't pass tests involving base R copies.
-
-We really need R itself to start setting TRUELENGTH to be the allocated length and then
-for GC to release TRUELENGTH not LENGTH.  Would really tidy this up.
-
-Moved out of ?setkey Details section in 1.12.2 (Mar 2019). Revisit this w.r.t. to recent versions of R.
+/*
+  Moved out of ?setkey Details section in 1.12.2 (Mar 2019). Revisit this w.r.t. to recent versions of R.
   The problem (for \code{data.table}) with the copy by \code{key<-} (other than
   being slower) is that \R doesn't maintain the over-allocated truelength, but it
   looks as though it has. Adding a column by reference using \code{:=} after a
@@ -126,15 +71,9 @@ static int _selfrefok(SEXP x, Rboolean checkNames, Rboolean verbose) {
   tag = R_ExternalPtrTag(v);
   if (!(isNull(tag) || isString(tag))) internal_error(__func__, ".internal.selfref tag is neither NULL nor a character vector"); // # nocov
   names = getAttrib(x, R_NamesSymbol);
-  if (names!=tag && isString(names) && !ALTREP(names))  // !ALTREP for #4734
-    SET_TRUELENGTH(names, LENGTH(names));
-    // R copied this vector not data.table; it's not actually over-allocated. It looks over-allocated
-    // because R copies the original vector's tl over despite allocating length.
   prot = R_ExternalPtrProtected(v);
   if (TYPEOF(prot) != EXTPTRSXP)   // Very rare. Was error(_(".internal.selfref prot is not itself an extptr")).
     return 0;                      // # nocov ; see http://stackoverflow.com/questions/15342227/getting-a-random-internal-selfref-error-in-data-table-for-r
-  if (x!=R_ExternalPtrAddr(prot) && !ALTREP(x))
-    SET_TRUELENGTH(x, LENGTH(x));  // R copied this vector not data.table, it's not actually over-allocated
   return checkNames ? names==tag : x==R_ExternalPtrAddr(prot);
 }
 
@@ -151,7 +90,7 @@ static SEXP shallow(SEXP dt, SEXP cols, R_len_t n)
   // called from alloccol where n is checked carefully, or from shallow() at R level
   // where n is set to truelength (i.e. a shallow copy only with no size change)
   int protecti=0;
-  SEXP newdt = PROTECT(allocVector(VECSXP, n)); protecti++;   // to do, use growVector here?
+  SEXP newdt = PROTECT(R_allocResizableVector(VECSXP, n)); protecti++;   // to do, use growVector here?
   SHALLOW_DUPLICATE_ATTRIB(newdt, dt);
 
   // TO DO: keepattr() would be faster, but can't because shallow isn't merely a shallow copy. It
@@ -169,7 +108,7 @@ static SEXP shallow(SEXP dt, SEXP cols, R_len_t n)
   setAttrib(newdt, sym_sorted, duplicate(sorted));
 
   SEXP names = PROTECT(getAttrib(dt, R_NamesSymbol)); protecti++;
-  SEXP newnames = PROTECT(allocVector(STRSXP, n)); protecti++;
+  SEXP newnames = PROTECT(R_allocResizableVector(STRSXP, n)); protecti++;
   const int l = isNull(cols) ? LENGTH(dt) : length(cols);
   if (isNull(cols)) {
     for (int i=0; i<l; ++i) SET_VECTOR_ELT(newdt, i, VECTOR_ELT(dt,i));
@@ -186,13 +125,9 @@ static SEXP shallow(SEXP dt, SEXP cols, R_len_t n)
       for (int i=0; i<l; ++i) SET_STRING_ELT( newnames, i, STRING_ELT(names,INTEGER(cols)[i]-1) );
     }
   }
+  R_resizeVector(newdt,l);
+  R_resizeVector(newnames,l);
   setAttrib(newdt, R_NamesSymbol, newnames);
-  // setAttrib appears to change length and truelength, so need to do that first _then_ SET next,
-  // otherwise (if the SET were were first) the 100 tl is assigned to length.
-  SETLENGTH(newnames,l);
-  SET_TRUELENGTH(newnames,n);
-  SETLENGTH(newdt,l);
-  SET_TRUELENGTH(newdt,n);
   setselfref(newdt);
   UNPROTECT(protecti);
   return(newdt);
@@ -260,7 +195,7 @@ SEXP alloccol(SEXP dt, R_len_t n, Rboolean verbose)
   // if (TRUELENGTH(getAttrib(dt,R_NamesSymbol))!=tl)
   //    internal_error(__func__, "tl of dt passes checks, but tl of names (%d) != tl of dt (%d)", tl, TRUELENGTH(getAttrib(dt,R_NamesSymbol))); // # nocov
 
-  tl = TRUELENGTH(dt);
+  tl = R_maxLength(dt);
   // R <= 2.13.2 and we didn't catch uninitialized tl somehow
   if (tl<0) internal_error(__func__, "tl of class is marked but tl<0"); // # nocov
   if (tl>0 && tl<l) internal_error(__func__, "tl (%d) < l (%d) but tl of class is marked", tl, l); // # nocov
@@ -310,11 +245,11 @@ SEXP shallowwrapper(SEXP dt, SEXP cols) {
   if (!selfrefok(dt, FALSE)) {
     int n = isNull(cols) ? length(dt) : length(cols);
     return(shallow(dt, cols, n));
-  } else return(shallow(dt, cols, TRUELENGTH(dt)));
+  } else return(shallow(dt, cols, R_maxLength(dt)));
 }
 
 SEXP truelength(SEXP x) {
-  return ScalarInteger(isNull(x) ? 0 : TRUELENGTH(x));
+  return ScalarInteger(isNull(x) || !R_isResizable(x) ? 0 : R_maxLength(x));
 }
 
 SEXP selfrefokwrapper(SEXP x, SEXP verbose) {
@@ -509,10 +444,10 @@ SEXP assign(SEXP dt, SEXP rows, SEXP cols, SEXP newcolnames, SEXP values)
   // modify DT by reference. Other than if new columns are being added and the allocVec() fails with
   // out-of-memory. In that case the user will receive hard halt and know to rerun.
   if (length(newcolnames)) {
-    oldtncol = TRUELENGTH(dt);   // TO DO: oldtncol can be just called tl now, as we won't realloc here any more.
+    if (!R_isResizable(dt)) error(_("This data.table has either been loaded from disk (e.g. using readRDS()/load()) or constructed manually (e.g. using structure()). Please run setDT() or setalloccol() on it first (to pre-allocate space for new columns) before assigning by reference to it."));   // #2996
+    oldtncol = R_maxLength(dt);   // TO DO: oldtncol can be just called tl now, as we won't realloc here any more.
 
     if (oldtncol<oldncol) {
-      if (oldtncol==0) error(_("This data.table has either been loaded from disk (e.g. using readRDS()/load()) or constructed manually (e.g. using structure()). Please run setDT() or setalloccol() on it first (to pre-allocate space for new columns) before assigning by reference to it."));   // #2996
       internal_error(__func__, "oldtncol(%d) < oldncol(%d)", oldtncol, oldncol); // # nocov
     }
     if (oldtncol>oldncol+10000L) warning(_("truelength (%d) is greater than 10,000 items over-allocated (length = %d). See ?truelength. If you didn't set the datatable.alloccol option very large, please report to data.table issue tracker including the result of sessionInfo()."),oldtncol, oldncol);
@@ -522,13 +457,14 @@ SEXP assign(SEXP dt, SEXP rows, SEXP cols, SEXP newcolnames, SEXP values)
       error(_("It appears that at some earlier point, names of this data.table have been reassigned. Please ensure to use setnames() rather than names<- or colnames<-. Otherwise, please report to data.table issue tracker."));  // # nocov
       // Can growVector at this point easily enough, but it shouldn't happen in first place so leave it as
       // strong error message for now.
-    else if (TRUELENGTH(names) != oldtncol)
+    else if (R_maxLength(names) != oldtncol)
       // Use (long long) to cast R_xlen_t to a fixed type to robustly avoid -Wformat compiler warnings, see #5768, PRId64 didn't work
-      internal_error(__func__, "selfrefnames is ok but tl names [%lld] != tl [%d]", (long long)TRUELENGTH(names), oldtncol);  // # nocov
+      internal_error(__func__, "selfrefnames is ok but maxLength(names) [%lld] != maxLength(dt) [%d]", (long long)R_maxLength(names), oldtncol);  // # nocov
     if (!selfrefok(dt, verbose)) // #6410 setDT(dt) and subsequent attr<- can lead to invalid selfref
       error(_("It appears that at some earlier point, attributes of this data.table have been reassigned. Please use setattr(DT, name, value) rather than attr(DT, name) <- value. If that doesn't apply to you, please report your case to the data.table issue tracker."));
-    SETLENGTH(dt, oldncol+LENGTH(newcolnames));
-    SETLENGTH(names, oldncol+LENGTH(newcolnames));
+    R_resizeVector(dt, oldncol+LENGTH(newcolnames));
+    R_resizeVector(names, oldncol+LENGTH(newcolnames));
+    setAttrib(dt, R_NamesSymbol, names);
     for (int i=0; i<LENGTH(newcolnames); ++i)
       SET_STRING_ELT(names,oldncol+i,STRING_ELT(newcolnames,i));
     // truelengths of both already set by alloccol
@@ -726,8 +662,9 @@ SEXP assign(SEXP dt, SEXP rows, SEXP cols, SEXP newcolnames, SEXP values)
       SET_VECTOR_ELT(dt, i, R_NilValue);
       SET_STRING_ELT(names, i, NA_STRING);  // release reference to the CHARSXP
     }
-    SETLENGTH(dt,    ndt-ndelete);
-    SETLENGTH(names, ndt-ndelete);
+    R_resizeVector(dt,    ndt-ndelete);
+    R_resizeVector(names, ndt-ndelete);
+    setAttrib(dt, R_NamesSymbol, names);
     if (LENGTH(names)==0) {
       // That was last column deleted, leaving NULL data.table, so we need to reset .row_names, so that it really is the NULL data.table.
       PROTECT(nullint=allocVector(INTSXP, 0)); protecti++;

src/data.table.h

@@ -87,6 +87,23 @@
 # endif
 #endif
 
+// TODO(R>=4.6.0): remove the SVN revision check
+#if R_VERSION < R_Version(4, 6, 0) || R_SVN_REVISION < 89077
+# define BACKPORT_RESIZABLE_API
+# define R_allocResizableVector(type, maxlen) R_allocResizableVector_(type, maxlen)
+# define R_duplicateAsResizable(x) R_duplicateAsResizable_(x)
+# define R_maxLength(x) R_maxLength_(x)
+  static inline R_xlen_t R_maxLength_(SEXP x) {
+    return IS_GROWABLE(x) ? TRUELENGTH(x) : XLENGTH(x);
+  }
+# define R_isResizable(x) R_isResizable_(x)
+  static inline bool R_isResizable_(SEXP x) {
+    // IS_GROWABLE checks for XLENGTH < TRUELENGTH instead
+    return (LEVELS(x) & 0x20) && XLENGTH(x) <= TRUELENGTH(x);
+  }
+# define R_resizeVector(x, newlen) R_resizeVector_(x, newlen)
+#endif
+
 // init.c
 extern SEXP char_integer64;
 extern SEXP char_ITime;
@@ -281,7 +298,7 @@ SEXP memcpyVector(SEXP dest, SEXP src, SEXP offset, SEXP size);
 SEXP memcpyDT(SEXP dest, SEXP src, SEXP offset, SEXP size);
 SEXP memcpyVectoradaptive(SEXP dest, SEXP src, SEXP offset, SEXP size);
 SEXP memcpyDTadaptive(SEXP dest, SEXP src, SEXP offset, SEXP size);
-SEXP setgrowable(SEXP x);
+SEXP copyAsGrowable(SEXP x);
 
 // nafill.c
 void nafillDouble(double *x, uint_fast64_t nx, unsigned int type, double fill, bool nan_is_na, ans_t *ans, bool verbose);
@@ -321,6 +338,11 @@ bool perhapsDataTable(SEXP x);
 SEXP perhapsDataTableR(SEXP x);
 SEXP frev(SEXP x, SEXP copyArg);
 NORET void internal_error(const char *call_name, const char *format, ...);
+#ifdef BACKPORT_RESIZABLE_API
+SEXP R_allocResizableVector_(SEXPTYPE type, R_xlen_t maxlen);
+SEXP R_duplicateAsResizable_(SEXP x);
+void R_resizeVector_(SEXP x, R_xlen_t newlen);
+#endif
 
 // types.c
 char *end(char *start);

src/dogroups.c

@@ -324,8 +324,9 @@ SEXP dogroups(SEXP dt, SEXP dtcols, SEXP groups, SEXP grpcols, SEXP jiscols, SEX
           // Even if we could know reliably to switch from allocNAVectorLike to allocVector for slight speedup, user code could still
           // contain a switched halt, and in that case we'd want the groups not yet done to have NA rather than 0 or uninitialized.
           // Increment length only if the allocation passes, #1676. But before SET_VECTOR_ELT otherwise attempt-to-set-index-n/n R error
-          SETLENGTH(dtnames, LENGTH(dtnames)+1);
-          SETLENGTH(dt, LENGTH(dt)+1);
+          R_resizeVector(dtnames, LENGTH(dtnames)+1);
+          R_resizeVector(dt, LENGTH(dt)+1);
+          setAttrib(dt, R_NamesSymbol, dtnames);
           SET_VECTOR_ELT(dt, colj, target);
           UNPROTECT(1);
           SET_STRING_ELT(dtnames, colj, STRING_ELT(newnames, colj-origncol));
@@ -515,7 +516,7 @@ SEXP growVector(SEXP x, const R_len_t newlen)
   SEXP newx;
   R_len_t len = length(x);
   if (isNull(x)) error(_("growVector passed NULL"));
-  PROTECT(newx = allocVector(TYPEOF(x), newlen));   // TO DO: R_realloc(?) here?
+  PROTECT(newx = R_allocResizableVector(TYPEOF(x), newlen));   // TO DO: R_realloc(?) here?
   if (newlen < len) len=newlen;   // i.e. shrink
   if (!len) { // cannot memcpy invalid pointer, #6819
     SHALLOW_DUPLICATE_ATTRIB(newx, x);