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Supporting removal of STRICT_R_HEADERS in 4.5.0 #272

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merged 4 commits into from
Nov 14, 2024
Merged

Supporting removal of STRICT_R_HEADERS in 4.5.0 #272

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51246bc
Cleaned up legacy function definitions
yaccos Nov 12, 2024
d3605c7
Added a missing bracket
yaccos Nov 12, 2024
df0aaea
Replaced CRLF endlines with LF endlines
yaccos Nov 13, 2024
0f97073
undo indentation
HenrikBengtsson Nov 14, 2024
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: matrixStats
Version: 1.4.1-9001
Version: 1.4.1-9002
Depends:
R (>= 2.12.0)
R (>= 3.4.0)
Suggests:
utils,
base64enc,
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3 changes: 2 additions & 1 deletion NEWS.md
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@@ -1,6 +1,7 @@
# Version (development version)

* ...
* Minimum version requirement lifted to 3.4.0 due to
removal of the flag `STRICT_R_HEADERS` in R 4.5.0.


# Version 1.4.1 [2024-09-06]
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34 changes: 3 additions & 31 deletions src/000.types.h
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Original file line number Diff line number Diff line change
@@ -1,6 +1,9 @@
#include <Rinternals.h> /* R_xlen_t, ... */
#include <Rversion.h> /* R_VERSION, R_Version() */

/* Needed if compiled prior to 4.5.0 with STRICT_R_HEADERS */
#include <float.h>

#ifndef R_INT_MIN
#define R_INT_MIN -INT_MAX
#endif
Expand Down Expand Up @@ -35,37 +38,6 @@
#endif



/* Backward compatibility with R (< 3.0.0)
As in <R>/src/include/Rinternals.h */
#ifndef R_XLEN_T_MAX
typedef int R_xlen_t;
#define R_XLEN_T_MAX R_LEN_T_MAX
#ifndef xlength
#define xlength length
#endif
#endif


/* With strict headers (the default in R (>=4.5.0)),
* the prefixed variants R_Calloc and R_Free
* must be used instead of Calloc and Free. However, the prefixed variants
* do not exist prior to R 3.4.0, so we check whether strict headers are used and
* apply the legacy functions if not.
* If future versions of R remove the un-prefixed variants, this workaround will fail.
* In such a case, we must enforce the prefixed variants and increase the version
* requirement of the package to R 3.4.0.
*
*/
#if (R_VERSION >= R_Version(4, 5, 0))
#define R_CALLOC(num, size) R_Calloc(num, size)
#define R_FREE(ptr) R_Free(ptr)
#else
#define R_CALLOC(num, size) Calloc(num, size)
#define R_FREE(ptr) Free(ptr)
#endif


/* define NA_R_XLEN_T */
#ifdef LONG_VECTOR_SUPPORT
#define R_XLEN_T_MIN -R_XLEN_T_MAX-1
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6 changes: 3 additions & 3 deletions src/diff2_lowlevel_template.h
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Expand Up @@ -68,11 +68,11 @@ void CONCAT_MACROS(diff2, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nx,
}
}

ans[ii] = X_DIFF(xvalue2, xvalue1);
ans[ii] = X_DIFF(xvalue2, xvalue1);
}
} else {
/* Allocate temporary work vector (to hold intermediate differences) */
tmp = R_CALLOC(nidxs - lag, X_C_TYPE);
tmp = R_Calloc(nidxs - lag, X_C_TYPE);

/* (a) First order of differences */
for (ii=0; ii < nidxs-lag; ii++) {
Expand Down Expand Up @@ -115,7 +115,7 @@ void CONCAT_MACROS(diff2, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nx,
}

/* Deallocate temporary work vector */
R_FREE(tmp);
R_Free(tmp);
} /* if (differences ...) */
}

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4 changes: 2 additions & 2 deletions src/rowDiffs_lowlevel_template.h
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Expand Up @@ -229,7 +229,7 @@ void CONCAT_MACROS(rowDiffs, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nrow, R_xlen_t
nrow_tmp = nrows - lag;
ncol_tmp = ncols;
}
tmp = R_CALLOC(nrow_tmp*ncol_tmp, X_C_TYPE);
tmp = R_Calloc(nrow_tmp*ncol_tmp, X_C_TYPE);

/* (a) First order of differences */
DIFF_X_MATRIX_TYPE(x, nrow, rows, nrows, rowsHasNA, cols, ncols, colsHasNA, byrow, lag, tmp, nrow_tmp, ncol_tmp);
Expand All @@ -253,7 +253,7 @@ void CONCAT_MACROS(rowDiffs, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nrow, R_xlen_t
DIFF_X_MATRIX(tmp, nrow_tmp, ncol_tmp, byrow, lag, ans, nrow_ans, ncol_ans);

/* Deallocate temporary work matrix */
R_FREE(tmp);
R_Free(tmp);
} /* if (differences ...) */
}

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6 changes: 3 additions & 3 deletions src/validateIndices_lowlevel_template.h
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Expand Up @@ -95,7 +95,7 @@ R_xlen_t* CONCAT_MACROS(validateIndices, X_C_SIGNATURE)(X_C_TYPE *idxs, R_xlen_t

// state < 0
// use filter as bitset to find out all required idxs
Rboolean *filter = R_CALLOC(maxIdx, Rboolean);
Rboolean *filter = R_Calloc(maxIdx, Rboolean);
count = maxIdx;
memset(filter, 0, maxIdx*sizeof(Rboolean)); // set to FALSE
for (ii = 0; ii < nidxs; ++ ii) {
Expand All @@ -110,7 +110,7 @@ R_xlen_t* CONCAT_MACROS(validateIndices, X_C_SIGNATURE)(X_C_TYPE *idxs, R_xlen_t

*ansNidxs = count;
if (count == 0) {
R_FREE(filter);
R_Free(filter);
return NULL;
}

Expand All @@ -123,7 +123,7 @@ R_xlen_t* CONCAT_MACROS(validateIndices, X_C_SIGNATURE)(X_C_TYPE *idxs, R_xlen_t

// fill required idxs into ans
// NOTE: braces is needed here, because of macro-defined function
RETURN_VALIDATED_ANS(R_xlen_t, upperBound, !filter[ii], ii, R_FREE(filter););
RETURN_VALIDATED_ANS(R_xlen_t, upperBound, !filter[ii], ii, R_Free(filter););
}


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42 changes: 21 additions & 21 deletions src/weightedMedian_lowlevel_template.h
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Expand Up @@ -32,7 +32,7 @@ double CONCAT_MACROS(weightedMedian, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nx, do
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* Weights */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
wtmp =R_CALLOC(nidxs, double);
wtmp =R_Calloc(nidxs, double);

/* Check for missing, negative, and infinite weights */
nxt = 0;
Expand All @@ -48,7 +48,7 @@ double CONCAT_MACROS(weightedMedian, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nx, do
weight = R_INDEX_GET(w, ((idxs == NULL) ? (ii) : idxs[ii]), NA_REAL, 1);
if (ISNAN(weight)) {
if (!narm) {
R_FREE(wtmp);
R_Free(wtmp);
return NA_REAL;
}
} else if (weight <= 0) {
Expand All @@ -66,7 +66,7 @@ double CONCAT_MACROS(weightedMedian, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nx, do
value = R_INDEX_GET(x, ((idxs == NULL) ? (jj) : idxs[jj]), X_NA, idxsHasNA);
if (X_ISNAN(value)) {
if (!narm) {
R_FREE(wtmp);
R_Free(wtmp);
return NA_REAL;
}
} else {
Expand All @@ -76,7 +76,7 @@ double CONCAT_MACROS(weightedMedian, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nx, do
}
} else if (ISNAN(weight)) {
if (!narm) {
R_FREE(wtmp);
R_Free(wtmp);
return NA_REAL;
}
}
Expand All @@ -88,7 +88,7 @@ double CONCAT_MACROS(weightedMedian, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nx, do
value = R_INDEX_GET(x, ((idxs == NULL) ? (ii) : idxs[ii]), X_NA, idxsHasNA);
if (X_ISNAN(value)) {
if (!narm) {
R_FREE(wtmp);
R_Free(wtmp);
return NA_REAL;
}
} else {
Expand All @@ -106,15 +106,15 @@ double CONCAT_MACROS(weightedMedian, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nx, do

/* Nothing to do? */
if (nxt == 0) {
R_FREE(wtmp);
R_Free(wtmp);
return NA_REAL;
}


/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* Copy (x,w) to work with and calculate total weight */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
xtmp =R_CALLOC(nxt, X_C_TYPE);
xtmp =R_Calloc(nxt, X_C_TYPE);
jj = 0;
wtotal = 0;
for (ii=0; ii < nidxs; ii++) {
Expand All @@ -138,8 +138,8 @@ double CONCAT_MACROS(weightedMedian, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nx, do
/* Early stopping? */
if (nx == 1) {
res = (double)x[0];
R_FREE(xtmp);
R_FREE(wtmp);
R_Free(xtmp);
R_Free(wtmp);
return res;
}

Expand All @@ -165,8 +165,8 @@ double CONCAT_MACROS(weightedMedian, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nx, do
res = ((double)x[half-1] + (double)x[half]) / 2;
}

R_FREE(xtmp);
R_FREE(wtmp);
R_Free(xtmp);
R_Free(wtmp);
return res;
}

Expand All @@ -176,12 +176,12 @@ double CONCAT_MACROS(weightedMedian, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nx, do
/* one) according to the reordered vector. */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* (a) Sort x */
idxs_int =R_CALLOC(nx, int);
idxs_int =R_Calloc(nx, int);
for (ii = 0; ii < nx; ii++) idxs_int[ii] = ii;
X_QSORT_I(x, idxs_int, 1, nx);

/* (b) Normalized cumulative weights */
wcum =R_CALLOC(nx, double);
wcum =R_Calloc(nx, double);
tmp_d2 = 0;
/* Index where cumulative weight passed 1/2 */
half = nx+1; /* Default is last */
Expand Down Expand Up @@ -209,16 +209,16 @@ double CONCAT_MACROS(weightedMedian, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nx, do
}
}
}
R_FREE(wtmp);
R_FREE(idxs_int);
R_Free(wtmp);
R_Free(idxs_int);


/* Two special cases where more than half of the total weight is at
a) the first, or b) the last value */
if (half == 0 || half == nx) {
res = (double)x[half];
R_FREE(wcum);
R_FREE(xtmp);
R_Free(wcum);
R_Free(xtmp);
return res;
}

Expand All @@ -242,8 +242,8 @@ double CONCAT_MACROS(weightedMedian, X_C_SIGNATURE)(X_C_TYPE *x, R_xlen_t nx, do
/* The corresponding x value */
res = dx + x[half];

R_FREE(wcum);
R_FREE(xtmp);
R_Free(wcum);
R_Free(xtmp);

return res;
}
Expand Down Expand Up @@ -290,8 +290,8 @@ printf("x[half+(-1:1)]=c(%g, %g, %g)\n", x[half-1-1], x[half-1], x[half-1+1]);
}
}

R_FREE(wcum);
R_FREE(xtmp);
R_Free(wcum);
R_Free(xtmp);

return res;
}
Expand Down