fix: add additional C++ fixes

Author: jorainer

.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 }}

src/massifquant/nmath.h

@@ -47,10 +47,10 @@ double  gamma_cody(double);
 
 #include <R_ext/Error.h>
 # define MATHLIB_ERROR(fmt,x)       Rf_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_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/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;
 
-}
+}