Merge pull request #780 from sneumann/fix/issue778

Fix/issue778 using Rf_error()

.editorconfig

@@ -6,7 +6,7 @@ root = true
 charset = utf-8
 end_of_line = lf
 trim_trailing_whitespace = true
-insert_final_newline = false
+insert_final_newline = true
 
 [*.R]
 indent_style = space
@@ -18,4 +18,4 @@ indent_style = tab
 
 [.travis.yml]
 indent_style = space
-indent_size = 2
+indent_size = 2

.github/workflows/check-bioc.yml

@@ -54,8 +54,8 @@ jobs:
       matrix:
         config:
           - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.4', bioc: 'devel'}
-          - { os: windows-latest, r: '4.4', bioc: 'devel'}
+          - { os: macOS-latest, r: '4.4', bioc: '3.20'}
+          - { os: windows-latest, r: '4.4', bioc: '3.20'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: xcms
-Version: 4.5.0
+Version: 4.5.1
 Title: LC-MS and GC-MS Data Analysis
 Description: Framework for processing and visualization of chromatographically
     separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF,

NEWS.md

@@ -1,3 +1,9 @@
+# xcms 4.5.1
+
+## Changes in version 4.5.1
+
+- Fix compile errors with R-4.5
+
 # xcms 4.3
 
 ## Changes in version 4.3.4

src/binners.c

@@ -72,11 +72,11 @@ SEXP binYonX(SEXP x, SEXP y, SEXP breaks, SEXP nBins, SEXP binSize,
   base_value = REAL(baseValue)[0];
 
   if (from_idx < 0 || to_idx < 0)
-    error("'fromIdx' and 'toIdx' have to be >= 0!");
+    Rf_error("'fromIdx' and 'toIdx' have to be >= 0!");
   if (from_idx > to_idx)
-    error("'fromIdx' has to be smaller than 'toIdx'!");
+    Rf_error("'fromIdx' has to be smaller than 'toIdx'!");
   if (to_idx >= LENGTH(x))
-    error("'toIdx' can not be larger than length(x)!");
+    Rf_error("'toIdx' can not be larger than length(x)!");
 
   /* Define from_x and to_x */
   if (ISNA(REAL(fromX)[0])) {
@@ -95,12 +95,12 @@ SEXP binYonX(SEXP x, SEXP y, SEXP breaks, SEXP nBins, SEXP binSize,
     n_bin = (LENGTH(breaks) - 1);
     p_brks = REAL(breaks);
     if (n_bin < 1)
-      error("Not enough breaks defined!");
+      Rf_error("Not enough breaks defined!");
   } else if (INTEGER(nBins)[0] != NA_INTEGER) {
     /* Calculating breaks based on the number of bins. */
     n_bin = asInteger(nBins);
     if (n_bin <= 0)
-      error("'nBins' must be larger 1!");
+      Rf_error("'nBins' must be larger 1!");
     PROTECT(brks = allocVector(REALSXP, n_bin + 1));
     count_protect++;
     /* Calculate the breaks */
@@ -110,7 +110,7 @@ SEXP binYonX(SEXP x, SEXP y, SEXP breaks, SEXP nBins, SEXP binSize,
     /* Calculating breaks based on bin size. */
     bin_size = REAL(binSize)[0];
     if (bin_size < 0)
-      error("'binSize' has to be > 0!");
+      Rf_error("'binSize' has to be > 0!");
     if (shift_by_half_bin_size > 0) {
       from_x = from_x - (bin_size / 2);
       to_x = to_x + (bin_size / 2);
@@ -224,7 +224,7 @@ SEXP binYonX_multi(SEXP x, SEXP y, SEXP breaks, SEXP nBins, SEXP binSize,
   SEXP res, from_idx, to_idx, current_res;
   int n_subsets, *p_subset_from_idx, *p_subset_to_idx;
   if (LENGTH(subsetFromIdx) != LENGTH(subsetToIdx)) {
-    error("Arguments 'subsetFromIdx' and 'subsetToIdx' have to have the same length!");
+    Rf_error("Arguments 'subsetFromIdx' and 'subsetToIdx' have to have the same length!");
   }
   n_subsets = LENGTH(subsetFromIdx);
   p_subset_from_idx = INTEGER(subsetFromIdx);

src/fastMatch.c

@@ -29,7 +29,7 @@ SEXP fastMatch(SEXP x, SEXP y, SEXP xidx, SEXP yidx, SEXP xolength, SEXP tol) {
 
     struct idxStruct * pidxS =  (struct idxStruct *) calloc(nx,  sizeof(struct idxStruct));
     if (pidxS == NULL)
-        error("fastMatch/calloc: memory could not be allocated ! (%lu bytes)\n", nx  * sizeof(struct idxStruct) );
+        Rf_error("fastMatch/calloc: memory could not be allocated ! (%lu bytes)\n", nx  * sizeof(struct idxStruct) );
     for (xi=0;xi < nx;xi++)
          pidxS[xi].from = ny+1;
 

src/massifquant/nmath.h

@@ -46,11 +46,11 @@ double  gamma_cody(double);
 #ifndef MATHLIB_STANDALONE
 
 #include <R_ext/Error.h>
-# define MATHLIB_ERROR(fmt,x)       error(fmt,x);
-# define MATHLIB_WARNING(fmt,x)     warning(fmt,x)
-# define MATHLIB_WARNING2(fmt,x,x2) warning(fmt,x,x2)
-# define MATHLIB_WARNING3(fmt,x,x2,x3)  warning(fmt,x,x2,x3)
-# define MATHLIB_WARNING4(fmt,x,x2,x3,x4) warning(fmt,x,x2,x3,x4)
+# define MATHLIB_ERROR(fmt,x)       Rf_error(fmt,x);
+# define MATHLIB_WARNING(fmt,x)     Rf_warning(fmt,x)
+# define MATHLIB_WARNING2(fmt,x,x2) Rf_warning(fmt,x,x2)
+# define MATHLIB_WARNING3(fmt,x,x2,x3)  Rf_warning(fmt,x,x2,x3)
+# define MATHLIB_WARNING4(fmt,x,x2,x3,x4) Rf_warning(fmt,x,x2,x3,x4)
 
 #include <R_ext/Arith.h>
 #define ML_POSINF   R_PosInf
@@ -199,4 +199,4 @@ void attribute_hidden bratio(double a, double b, double x, double y,
         double *w, double *w1, int *ierr, int log_p);
 
 
-#endif /* MATHLIB_PRIVATE_H */
+#endif /* MATHLIB_PRIVATE_H */

src/massifquant/xcms_massifquant.cpp

@@ -59,7 +59,7 @@ extern "C" SEXP massifquant(SEXP mz, SEXP intensity, SEXP scanindex,
     }
 
     if ((scanrangeFrom <  firstScan) || (scanrangeFrom > totalScanNums) || (scanrangeTo < firstScan) || (scanrangeTo > totalScanNums))
-        error("Error in scanrange \n");
+        Rf_error("Error in scanrange \n");
 
     //show the progress please
     Rprintf("\n Detecting Kalman ROI's ... \n percent finished: ");
@@ -112,17 +112,17 @@ extern "C" SEXP massifquant(SEXP mz, SEXP intensity, SEXP scanindex,
     Rprintf(" %d\n", 100);
 
     const char *names[N_NAMES] = {"mz", "mzmin", "mzmax", "scmin", "scmax", "length", "intensity"};
-    PROTECT(list_names = allocVector(STRSXP, N_NAMES));
+    PROTECT(list_names = Rf_allocVector(STRSXP, N_NAMES));
     for(int j = 0; j < N_NAMES; j++)
-        SET_STRING_ELT(list_names, j,  mkChar(names[j]));
+        SET_STRING_ELT(list_names, j,  Rf_mkChar(names[j]));
 
-    PROTECT(peaklist = allocVector(VECSXP, busybody.getPicCounts()));
+    PROTECT(peaklist = Rf_allocVector(VECSXP, busybody.getPicCounts()));
     for (int i=0;i<busybody.getPicCounts();i++) {
 
         std::vector<double> featInfo = busybody.iterOverFeatures(i, pscantime);
 	//jo int scanLength = int(featInfo.at(5) - featInfo.at(4) + 1);
 
-        PROTECT(entrylist = allocVector(VECSXP, N_NAMES));
+        PROTECT(entrylist = Rf_allocVector(VECSXP, N_NAMES));
 
         //allow for new vars declared to be passed out
         PROTECT(vmz = NEW_NUMERIC(1));
@@ -153,7 +153,7 @@ extern "C" SEXP massifquant(SEXP mz, SEXP intensity, SEXP scanindex,
         SET_VECTOR_ELT(entrylist, 5, vlength);
         SET_VECTOR_ELT(entrylist, 6, vintensity);
 
-        setAttrib(entrylist, R_NamesSymbol, list_names); //attaching the vector names
+        Rf_setAttrib(entrylist, R_NamesSymbol, list_names); //attaching the vector names
         SET_VECTOR_ELT(peaklist, i, entrylist);
         UNPROTECT(N_NAMES + 1); //entrylist + values
     }

src/mzROI.c

@@ -76,7 +76,7 @@ struct mzROIStruct * checkmzROIBufSize(struct mzROIStruct *mzROI, const unsigned
 
     mzROI = (struct mzROIStruct *) realloc(mzROI, newLength * sizeof(struct mzROIStruct));
     if (mzROI == NULL)
-        error("findmzROI/realloc: buffer memory could not be allocated ! (%lu bytes)\n", newLength * sizeof(struct mzROIStruct) );
+        Rf_error("findmzROI/realloc: buffer memory could not be allocated ! (%lu bytes)\n", newLength * sizeof(struct mzROIStruct) );
 
     mzLength->mzROITotal = newLength;
   }
@@ -99,7 +99,7 @@ struct mzROIStruct * checkmzvalBufSize(struct mzROIStruct *mzval, const unsigned
 
     mzval = (struct mzROIStruct *) realloc(mzval, newLength * sizeof(struct mzROIStruct));
     if (mzval == NULL)
-      error("findmzROI/realloc: buffer memory could not be allocated ! (%lu bytes)\n", newLength * sizeof(struct mzROIStruct));
+      Rf_error("findmzROI/realloc: buffer memory could not be allocated ! (%lu bytes)\n", newLength * sizeof(struct mzROIStruct));
 
     mzLength->mzvalTotal = newLength;
   }
@@ -202,7 +202,7 @@ struct mzROIStruct * insertpeak(const double fMass, const double fInten,
 
     if (ddiff <= ddev)
     { // match (smaller than defined ppm) -> extend this ROI
-          if ( (i > hpos) || (i<lpos) ) error("! scan: %d \n",scan);
+          if ( (i > hpos) || (i<lpos) ) Rf_error("! scan: %d \n",scan);
           wasfound = TRUE;
           //recursive m/z mean update
           mzval[i].mz = ((mzval[i].length * mzval[i].mz) + fMass) / (mzval[i].length + 1);
@@ -311,7 +311,7 @@ int i,p,del=0;
       }
         if (entries > ctScan) {
             #ifdef DEBUG
-                error("Warning : entries > ctScan (is this centroid data ?) i: %d m: %3.4f  %d entries, lastscan %d   (ctScan=%d)\n",i,mzval[i].mz,mzval[i].length,lastscan,ctScan);
+                Rf_error("Warning : entries > ctScan (is this centroid data ?) i: %d m: %3.4f  %d entries, lastscan %d   (ctScan=%d)\n",i,mzval[i].mz,mzval[i].length,lastscan,ctScan);
             #endif
           (*scerr)++;
         }
@@ -328,7 +328,7 @@ int i,p,del=0;
     p=0;
     struct mzROIStruct * tmp = (struct mzROIStruct *) calloc(mzLength->mzval - del,  sizeof(struct mzROIStruct));
     if (tmp == NULL)
-      error("findmzROI/cleanup: buffer memory could not be allocated ! (%lu bytes)\n", (mzLength->mzval - del) * sizeof(struct mzROIStruct));
+      Rf_error("findmzROI/cleanup: buffer memory could not be allocated ! (%lu bytes)\n", (mzLength->mzval - del) * sizeof(struct mzROIStruct));
     for (i=0; i < mzLength->mzval; i++) {
         if (mzval[i].deleteMe == FALSE) {
             tmp[p].mz = mzval[i].mz;
@@ -379,7 +379,7 @@ struct scanBuf * getScan(int scan, double *pmz, double *pintensity, int *pscanin
         scanbuf->thisScan= (struct scanStruct  *) calloc(N, sizeof(struct scanStruct));
         // scanbuf->thisScan= (struct scanStruct  *) malloc(N * sizeof(struct scanStruct));
         if (scanbuf->thisScan == NULL)
-	    error("findmzROI/getThisScan: Memory could not be allocated!\n");
+	    Rf_error("findmzROI/getThisScan: Memory could not be allocated!\n");
 
         scanbuf->thisScanLength=N;
 
@@ -411,7 +411,7 @@ struct scanBuf * getScan(int scan, double *pmz, double *pintensity, int *pscanin
         if (N > 0) {
             scanbuf->nextScan= (double *) calloc(N, sizeof(double));
             if (scanbuf->nextScan == NULL)
-                error("findmzROI/getNextScan: Memory could not be allocated!\n");
+                Rf_error("findmzROI/getNextScan: Memory could not be allocated!\n");
             scanbuf->nextScanLength=N;
 
             for (idx=idx1;idx <= idx2; idx++)
@@ -463,7 +463,7 @@ SEXP getEIC(SEXP mz, SEXP intensity, SEXP scanindex, SEXP mzrange, SEXP scanrang
   scanrangeFrom = INTEGER(scanrange)[0];
   scanrangeTo = INTEGER(scanrange)[1];
   if ((scanrangeFrom <  firstScan) || (scanrangeFrom > ilastScan) || (scanrangeTo < firstScan) || (scanrangeTo > ilastScan))
-     error("Error in scanrange \n");
+     Rf_error("Error in scanrange \n");
   char *names[2] = {"scan", "intensity"};
   PROTECT(list_names = allocVector(STRSXP, 2));
   for(i = 0; i < 2; i++)
@@ -508,7 +508,7 @@ SEXP getMZ(SEXP mz, SEXP intensity, SEXP scanindex, SEXP mzrange, SEXP scanrange
   scanrangeFrom = INTEGER(scanrange)[0];
   scanrangeTo = INTEGER(scanrange)[1];
   if ((scanrangeFrom <  firstScan) || (scanrangeFrom > ilastScan) || (scanrangeTo < firstScan) || (scanrangeTo > ilastScan))
-     error("Error in scanrange \n");
+     Rf_error("Error in scanrange \n");
 
   buflength = scanrangeTo - scanrangeFrom +1;
   PROTECT(res = NEW_NUMERIC(buflength));
@@ -563,7 +563,7 @@ SEXP getWeightedMZ(SEXP mz, SEXP intensity, SEXP scanindex, SEXP mzrange,
   scanrangeTo = INTEGER(scanrange)[1];
   if ((scanrangeFrom < firstScan) || (scanrangeFrom > ilastScan) ||
       (scanrangeTo < firstScan) || (scanrangeTo > ilastScan))
-    error("Error in scanrange \n");
+    Rf_error("Error in scanrange \n");
 
   buflength = scanrangeTo - scanrangeFrom +1;
   PROTECT(res = NEW_NUMERIC(buflength));
@@ -626,11 +626,11 @@ SEXP findmzROI(SEXP mz, SEXP intensity, SEXP scanindex, SEXP mzrange,
 
   struct mzROIStruct * mzROI = (struct mzROIStruct *) calloc(ROI_INIT_LENGTH,  sizeof(struct mzROIStruct));
   if (mzROI == NULL)
-      error("findmzROI/calloc: buffer memory could not be allocated ! (%lu bytes)\n",ROI_INIT_LENGTH  * sizeof(struct mzROIStruct) );
+      Rf_error("findmzROI/calloc: buffer memory could not be allocated ! (%lu bytes)\n",ROI_INIT_LENGTH  * sizeof(struct mzROIStruct) );
 
   struct mzROIStruct * mzval = (struct mzROIStruct *) calloc(MZVAL_INIT_LENGTH,  sizeof(struct mzROIStruct));
   if (mzval == NULL)
-      error("findmzROI/calloc: buffer memory could not be allocated ! (%lu bytes)\n",MZVAL_INIT_LENGTH  * sizeof(struct mzROIStruct) );
+      Rf_error("findmzROI/calloc: buffer memory could not be allocated ! (%lu bytes)\n",MZVAL_INIT_LENGTH  * sizeof(struct mzROIStruct) );
 
   mzLength.mzvalTotal = MZVAL_INIT_LENGTH;
   mzLength.mzROITotal = ROI_INIT_LENGTH;
@@ -678,7 +678,7 @@ SEXP findmzROI(SEXP mz, SEXP intensity, SEXP scanindex, SEXP mzrange,
           fInten = scanbuf->thisScan[p].intensity;
 
           if (fMass < lastMass)
-            error("m/z sort assumption violated ! (scan %d, p %d, current %2.4f (I=%2.2f), last %2.4f) \n",ctScan,p,fMass,fInten,lastMass);
+            Rf_error("m/z sort assumption violated ! (scan %d, p %d, current %2.4f (I=%2.2f), last %2.4f) \n",ctScan,p,fMass,fInten,lastMass);
           lastMass = fMass;
 
           if (fInten > inoise)

src/xcms_obiwarp.cpp

@@ -39,16 +39,16 @@ extern "C" SEXP R_set_from_xcms(SEXP valscantime, SEXP scantime, SEXP mzrange, S
     double *pscantime2, *pmz2, *pintensity2;
     SEXP corrected;
 
-    PROTECT(valscantime = coerceVector(valscantime, INTSXP));
-    mzrange = coerceVector(mzrange, INTSXP);
+    PROTECT(valscantime = Rf_coerceVector(valscantime, INTSXP));
+    mzrange = Rf_coerceVector(mzrange, INTSXP);
     pvalscantime = INTEGER(valscantime)[0];
     pmzrange = INTEGER(mzrange)[0];
     pscantime = REAL(scantime);
     pmz = REAL(mz);
     pintensity = REAL(intensity);
 
-    PROTECT(valscantime2 = coerceVector(valscantime2, INTSXP));
-    mzrange2 = coerceVector(mzrange2, INTSXP);
+    PROTECT(valscantime2 = Rf_coerceVector(valscantime2, INTSXP));
+    mzrange2 = Rf_coerceVector(mzrange2, INTSXP);
     pvalscantime2 = INTEGER(valscantime2)[0];
     pmzrange2 = INTEGER(mzrange2)[0];
     pscantime2 = REAL(scantime2);
@@ -120,13 +120,13 @@ extern "C" SEXP R_set_from_xcms(SEXP valscantime, SEXP scantime, SEXP mzrange, S
     lmat2.tm_axis_vals(nOut, nOutF);
     lmat2.warp_tm(nOutF, mOutF);
 
-    PROTECT(corrected = allocVector(REALSXP, length(scantime2)));
-    for(int i=0; i < length(scantime2);i++){
+    PROTECT(corrected = Rf_allocVector(REALSXP, Rf_length(scantime2)));
+    for(int i=0; i < Rf_length(scantime2);i++){
       REAL(corrected)[i] = lmat2.tm()->back()[i];
     }
 
     UNPROTECT(3);
 
     return corrected;
 
-}
+}