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Replace Rcpp::Rcerr with Rf_warningcall (issue #164)

- Replace Rcpp::Rcerr with Rf_warningcall for most functions.
- Also replace Rprintf with Rf_warningcall if backend not initialized.

jotsetung authored on 17/05/2018 11:52:44
Showing 2 changed files

src/RcppPwiz.cpp index 73bcb69ff0..54a7d94f91 100644
src/RcppRamp.cpp index 3d67d98460..04b8177c30 100644

src/RcppPwiz.cpp

History View file @ f8520e7ab9

@@ -84,7 +84,7 @@ int RcppPwiz::getLastScan() const {
     SpectrumListPtr slp = msd->run.spectrumListPtr;
     return slp->size();
   }
-  Rprintf("Warning: pwiz not yet initialized.\n ");
+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
   return -1;
 }
 
@@ -93,7 +93,7 @@ int RcppPwiz::getLastChrom() const {
     ChromatogramListPtr clp = msd->run.chromatogramListPtr;
     return clp->size();
   }
-  Rprintf("Warning: pwiz not yet initialized.\n ");
+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
   return -1;
 }
 
@@ -160,7 +160,7 @@ Rcpp::List RcppPwiz::getInstrumentInfo ( )
         }
       return(instrumentInfo);
     }
-  Rprintf("Warning: pwiz not yet initialized.\n ");
+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
   return instrumentInfo;
 }
 
@@ -306,7 +306,7 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)
       
       return header;
     }
-  Rprintf("Warning: pwiz not yet initialized.\n ");
+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
   return Rcpp::DataFrame::create( );
 }
 
@@ -324,7 +324,7 @@ Rcpp::DataFrame RcppPwiz::getAllScanHeaderInfo ( )
         }
       return allScanHeaderInfo ;
     }
-  Rprintf("Warning: pwiz not yet initialized.\n ");
+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
   return Rcpp::DataFrame::create( );
 }
 
@@ -362,7 +362,7 @@ Rcpp::List RcppPwiz::getPeakList ( int whichScan )
 				Rcpp::_["peaks"]  = peaks
 				) ;
     }
-  Rprintf("Warning: pwiz not yet initialized.\n ");
+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
   return Rcpp::List::create( );
 }
 
@@ -756,10 +756,10 @@ Rcpp::DataFrame RcppPwiz::getChromatogramsInfo( int whichChrom )
   if (msd != NULL) {
     ChromatogramListPtr clp = msd->run.chromatogramListPtr;
     if (clp.get() == 0) {
-      Rcpp::Rcerr << "The direct support for chromatogram info is only available in mzML format." << std::endl;
+      Rf_warningcall(R_NilValue, "The direct support for chromatogram info is only available in mzML format.");
       return Rcpp::DataFrame::create();
     } else if (clp->size() == 0) {
-      Rcpp::Rcerr << "No available chromatogram info." << std::endl;
+      Rf_warningcall(R_NilValue, "No available chromatogram info.");
       return Rcpp::DataFrame::create();
     } else if ( (whichChrom < 0) || (whichChrom > clp->size()) ) {
       Rprintf("Index whichChrom out of bounds [0 ... %d].\n", (clp->size())-1);
@@ -783,7 +783,7 @@ Rcpp::DataFrame RcppPwiz::getChromatogramsInfo( int whichChrom )
     }
     return(chromatogramsInfo);
   }
-  Rprintf("Warning: pwiz not yet initialized.\n ");
+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
   return Rcpp::DataFrame::create( );
 }
 
@@ -794,10 +794,10 @@ Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichCh
     CVID nativeIdFormat_ = id::getDefaultNativeIDFormat(*msd); // Ask CHRIS if I'm correctly dereferencing this...
     ChromatogramListPtr clp = msd->run.chromatogramListPtr;
     if (clp.get() == 0) {
-      Rcpp::Rcerr << "The direct support for chromatogram info is only available in mzML format." << std::endl;
+      Rf_warningcall(R_NilValue, "The direct support for chromatogram info is only available in mzML format.");
       return Rcpp::DataFrame::create();
     } else if (clp->size() == 0) {
-      Rcpp::Rcerr << "No available chromatogram info." << std::endl;
+      Rf_warningcall(R_NilValue, "No available chromatogram info.");
       return Rcpp::DataFrame::create();
     }
 
@@ -821,8 +821,8 @@ Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichCh
     for (int i = 0; i < N_chrom; i++) {
       int current_chrom = whichChrom[i];
       if (current_chrom < 0 || current_chrom > N) {
+	Rf_warningcall(R_NilValue, "Provided index out of bounds.");
 	Rcpp::Rcerr << "Provided index out of bounds" << std::endl;
-	return Rcpp::DataFrame::create();
       }
       ChromatogramPtr ch = clp->chromatogram(current_chrom - 1, false);
       chromatogramId[i] = ch->id;
@@ -877,7 +877,7 @@ Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichCh
     chromHeader.attr("names") = names;
     return chromHeader;
   }
-  Rprintf("Warning: pwiz not yet initialized.\n ");
+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
   return Rcpp::DataFrame::create( );
 }
 
@@ -885,14 +885,14 @@ Rcpp::DataFrame RcppPwiz::getAllChromatogramHeaderInfo ( ) {
   if (msd != NULL) {
     ChromatogramListPtr clp = msd->run.chromatogramListPtr;
     if (clp.get() == 0) {
-      Rcpp::Rcerr << "The direct support for chromatogram info is only available in mzML format." << std::endl;
+      Rf_warningcall(R_NilValue, "The direct support for chromatogram info is only available in mzML format.");
       return Rcpp::DataFrame::create();
     }
     int N = clp->size();
     if (N > 0) {
       return getChromatogramHeaderInfo(Rcpp::seq(1, N));
     } else {
-      Rprintf("Warning: pwiz not yet initialized.\n ");
+      Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
     }
   }
   return Rcpp::DataFrame::create( );
@@ -921,7 +921,7 @@ Rcpp::NumericMatrix RcppPwiz::get3DMap ( std::vector<int> scanNumbers, double wh
         }
 
       int j=0;
-      Rprintf("%d\n",1);
+      //Rprintf("%d\n",1);
       for (int i = 0; i < scanNumbers.size(); i++)
         {
 	  SpectrumPtr s = slp->spectrum(scanNumbers[i] - 1, true);
@@ -945,7 +945,7 @@ Rcpp::NumericMatrix RcppPwiz::get3DMap ( std::vector<int> scanNumbers, double wh
       return(map3d);
     }
 
-  Rprintf("Warning: pwiz not yet initialized.\n ");
+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
   return Rcpp::NumericMatrix(0,0);
 }
 
@@ -953,6 +953,6 @@ string RcppPwiz::getRunStartTimeStamp() {
   if (msd != NULL) {
     return msd->run.startTimeStamp;
   }
-  Rprintf("Warning: pwiz not yet initialized.\n ");
+  Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
   return "";
 }

src/RcppRamp.cpp

History View file @ f8520e7ab9

@@ -55,7 +55,7 @@ Rcpp::StringVector RcppRamp::getFilename (  )
     {
         return filename;
     }
-    Rprintf("Warning: Ramp not yet initialized.\n ");
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
     return filename;
 }
 
@@ -86,7 +86,7 @@ Rcpp::List RcppRamp::getRunInfo (  )
         }
         return runInfo;
     }
-    Rprintf("Warning: Ramp not yet initialized.\n");
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
     return runInfo;
 }
 
@@ -130,7 +130,7 @@ Rcpp::List RcppRamp::getInstrumentInfo ( )
         }
         return(instrumentInfo);
     }
-    Rprintf("Warning: Ramp not yet initialized.\n ");
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
     return instrumentInfo;
 }
 
@@ -200,7 +200,7 @@ Rcpp::List RcppRamp::getScanHeaderInfo ( int whichScan  )
 
         return  header;
     }
-    Rprintf("Warning: Ramp not yet initialized.\n ");
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
     return Rcpp::List::create( );
 }
 
@@ -322,7 +322,7 @@ Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo ( )
         }
         return(allScanHeaderInfo);
     }
-    Rprintf("Warning: Ramp not yet initialized.\n ");
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
     return Rcpp::DataFrame::create( );
 }
 
@@ -361,7 +361,7 @@ Rcpp::List RcppRamp::getPeakList ( int whichScan )
                    Rcpp::_["peaks"]  = peaks
                ) ;
     }
-    Rprintf("Warning: Ramp not yet initialized.\n ");
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
     return Rcpp::List::create( );
 }
 
@@ -384,7 +384,7 @@ Rcpp::NumericMatrix RcppRamp::get3DMap ( std::vector<int> scanNumbers, double wh
         }
         // map3d = 0.0;
         int j=0;
-        Rprintf("%d\n",1);
+        //Rprintf("%d\n",1);
         for (int i = 0; i < scanNumbers.size(); i++)
         {
             rampPeakList *pl = ramp->getPeakList( scanNumbers[i] );
@@ -415,7 +415,7 @@ Rcpp::NumericMatrix RcppRamp::get3DMap ( std::vector<int> scanNumbers, double wh
         }
         return(map3d);
     }
-    Rprintf("Warning: Ramp not yet initialized.\n ");
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
     return Rcpp::NumericMatrix(0,0);
 }
 
@@ -425,7 +425,7 @@ int RcppRamp::getLastScan() const
     {
         return ramp->getLastScan();
     }
-    Rprintf("Warning: Ramp not yet initialized.\n ");
+    Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
     return -1;
 }
 

...	...	@@ -84,7 +84,7 @@ int RcppPwiz::getLastScan() const {
84	84	SpectrumListPtr slp = msd->run.spectrumListPtr;
85	85	return slp->size();
86	86	}
87		- Rprintf("Warning: pwiz not yet initialized.\n ");
	87	+ Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
88	88	return -1;
89	89	}
90	90
...	...	@@ -93,7 +93,7 @@ int RcppPwiz::getLastChrom() const {
93	93	ChromatogramListPtr clp = msd->run.chromatogramListPtr;
94	94	return clp->size();
95	95	}
96		- Rprintf("Warning: pwiz not yet initialized.\n ");
	96	+ Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
97	97	return -1;
98	98	}
99	99
...	...	@@ -160,7 +160,7 @@ Rcpp::List RcppPwiz::getInstrumentInfo ( )
160	160	}
161	161	return(instrumentInfo);
162	162	}
163		- Rprintf("Warning: pwiz not yet initialized.\n ");
	163	+ Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
164	164	return instrumentInfo;
165	165	}
166	166
...	...	@@ -306,7 +306,7 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan)
306	306
307	307	return header;
308	308	}
309		- Rprintf("Warning: pwiz not yet initialized.\n ");
	309	+ Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
310	310	return Rcpp::DataFrame::create( );
311	311	}
312	312
...	...	@@ -324,7 +324,7 @@ Rcpp::DataFrame RcppPwiz::getAllScanHeaderInfo ( )
324	324	}
325	325	return allScanHeaderInfo ;
326	326	}
327		- Rprintf("Warning: pwiz not yet initialized.\n ");
	327	+ Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
328	328	return Rcpp::DataFrame::create( );
329	329	}
330	330
...	...	@@ -362,7 +362,7 @@ Rcpp::List RcppPwiz::getPeakList ( int whichScan )
362	362	Rcpp::_["peaks"] = peaks
363	363	) ;
364	364	}
365		- Rprintf("Warning: pwiz not yet initialized.\n ");
	365	+ Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
366	366	return Rcpp::List::create( );
367	367	}
368	368
...	...	@@ -756,10 +756,10 @@ Rcpp::DataFrame RcppPwiz::getChromatogramsInfo( int whichChrom )
756	756	if (msd != NULL) {
757	757	ChromatogramListPtr clp = msd->run.chromatogramListPtr;
758	758	if (clp.get() == 0) {
759		- Rcpp::Rcerr << "The direct support for chromatogram info is only available in mzML format." << std::endl;
	759	+ Rf_warningcall(R_NilValue, "The direct support for chromatogram info is only available in mzML format.");
760	760	return Rcpp::DataFrame::create();
761	761	} else if (clp->size() == 0) {
762		- Rcpp::Rcerr << "No available chromatogram info." << std::endl;
	762	+ Rf_warningcall(R_NilValue, "No available chromatogram info.");
763	763	return Rcpp::DataFrame::create();
764	764	} else if ( (whichChrom < 0) \|\| (whichChrom > clp->size()) ) {
765	765	Rprintf("Index whichChrom out of bounds [0 ... %d].\n", (clp->size())-1);
...	...	@@ -783,7 +783,7 @@ Rcpp::DataFrame RcppPwiz::getChromatogramsInfo( int whichChrom )
783	783	}
784	784	return(chromatogramsInfo);
785	785	}
786		- Rprintf("Warning: pwiz not yet initialized.\n ");
	786	+ Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
787	787	return Rcpp::DataFrame::create( );
788	788	}
789	789
...	...	@@ -794,10 +794,10 @@ Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichCh
794	794	CVID nativeIdFormat_ = id::getDefaultNativeIDFormat(*msd); // Ask CHRIS if I'm correctly dereferencing this...
795	795	ChromatogramListPtr clp = msd->run.chromatogramListPtr;
796	796	if (clp.get() == 0) {
797		- Rcpp::Rcerr << "The direct support for chromatogram info is only available in mzML format." << std::endl;
	797	+ Rf_warningcall(R_NilValue, "The direct support for chromatogram info is only available in mzML format.");
798	798	return Rcpp::DataFrame::create();
799	799	} else if (clp->size() == 0) {
800		- Rcpp::Rcerr << "No available chromatogram info." << std::endl;
	800	+ Rf_warningcall(R_NilValue, "No available chromatogram info.");
801	801	return Rcpp::DataFrame::create();
802	802	}
803	803
...	...	@@ -821,8 +821,8 @@ Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichCh
821	821	for (int i = 0; i < N_chrom; i++) {
822	822	int current_chrom = whichChrom[i];
823	823	if (current_chrom < 0 \|\| current_chrom > N) {
	824	+ Rf_warningcall(R_NilValue, "Provided index out of bounds.");
824	825	Rcpp::Rcerr << "Provided index out of bounds" << std::endl;
825		- return Rcpp::DataFrame::create();
826	826	}
827	827	ChromatogramPtr ch = clp->chromatogram(current_chrom - 1, false);
828	828	chromatogramId[i] = ch->id;
...	...	@@ -877,7 +877,7 @@ Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichCh
877	877	chromHeader.attr("names") = names;
878	878	return chromHeader;
879	879	}
880		- Rprintf("Warning: pwiz not yet initialized.\n ");
	880	+ Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
881	881	return Rcpp::DataFrame::create( );
882	882	}
883	883
...	...	@@ -885,14 +885,14 @@ Rcpp::DataFrame RcppPwiz::getAllChromatogramHeaderInfo ( ) {
885	885	if (msd != NULL) {
886	886	ChromatogramListPtr clp = msd->run.chromatogramListPtr;
887	887	if (clp.get() == 0) {
888		- Rcpp::Rcerr << "The direct support for chromatogram info is only available in mzML format." << std::endl;
	888	+ Rf_warningcall(R_NilValue, "The direct support for chromatogram info is only available in mzML format.");
889	889	return Rcpp::DataFrame::create();
890	890	}
891	891	int N = clp->size();
892	892	if (N > 0) {
893	893	return getChromatogramHeaderInfo(Rcpp::seq(1, N));
894	894	} else {
895		- Rprintf("Warning: pwiz not yet initialized.\n ");
	895	+ Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
896	896	}
897	897	}
898	898	return Rcpp::DataFrame::create( );
...	...	@@ -921,7 +921,7 @@ Rcpp::NumericMatrix RcppPwiz::get3DMap ( std::vector<int> scanNumbers, double wh
921	921	}
922	922
923	923	int j=0;
924		- Rprintf("%d\n",1);
	924	+ //Rprintf("%d\n",1);
925	925	for (int i = 0; i < scanNumbers.size(); i++)
926	926	{
927	927	SpectrumPtr s = slp->spectrum(scanNumbers[i] - 1, true);
...	...	@@ -945,7 +945,7 @@ Rcpp::NumericMatrix RcppPwiz::get3DMap ( std::vector<int> scanNumbers, double wh
945	945	return(map3d);
946	946	}
947	947
948		- Rprintf("Warning: pwiz not yet initialized.\n ");
	948	+ Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
949	949	return Rcpp::NumericMatrix(0,0);
950	950	}
951	951
...	...	@@ -953,6 +953,6 @@ string RcppPwiz::getRunStartTimeStamp() {
953	953	if (msd != NULL) {
954	954	return msd->run.startTimeStamp;
955	955	}
956		- Rprintf("Warning: pwiz not yet initialized.\n ");
	956	+ Rf_warningcall(R_NilValue, "pwiz not yet initialized.");
957	957	return "";
958	958	}

...	...	@@ -55,7 +55,7 @@ Rcpp::StringVector RcppRamp::getFilename ( )
55	55	{
56	56	return filename;
57	57	}
58		- Rprintf("Warning: Ramp not yet initialized.\n ");
	58	+ Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
59	59	return filename;
60	60	}
61	61
...	...	@@ -86,7 +86,7 @@ Rcpp::List RcppRamp::getRunInfo ( )
86	86	}
87	87	return runInfo;
88	88	}
89		- Rprintf("Warning: Ramp not yet initialized.\n");
	89	+ Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
90	90	return runInfo;
91	91	}
92	92
...	...	@@ -130,7 +130,7 @@ Rcpp::List RcppRamp::getInstrumentInfo ( )
130	130	}
131	131	return(instrumentInfo);
132	132	}
133		- Rprintf("Warning: Ramp not yet initialized.\n ");
	133	+ Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
134	134	return instrumentInfo;
135	135	}
136	136
...	...	@@ -200,7 +200,7 @@ Rcpp::List RcppRamp::getScanHeaderInfo ( int whichScan )
200	200
201	201	return header;
202	202	}
203		- Rprintf("Warning: Ramp not yet initialized.\n ");
	203	+ Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
204	204	return Rcpp::List::create( );
205	205	}
206	206
...	...	@@ -322,7 +322,7 @@ Rcpp::DataFrame RcppRamp::getAllScanHeaderInfo ( )
322	322	}
323	323	return(allScanHeaderInfo);
324	324	}
325		- Rprintf("Warning: Ramp not yet initialized.\n ");
	325	+ Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
326	326	return Rcpp::DataFrame::create( );
327	327	}
328	328
...	...	@@ -361,7 +361,7 @@ Rcpp::List RcppRamp::getPeakList ( int whichScan )
361	361	Rcpp::_["peaks"] = peaks
362	362	) ;
363	363	}
364		- Rprintf("Warning: Ramp not yet initialized.\n ");
	364	+ Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
365	365	return Rcpp::List::create( );
366	366	}
367	367
...	...	@@ -384,7 +384,7 @@ Rcpp::NumericMatrix RcppRamp::get3DMap ( std::vector<int> scanNumbers, double wh
384	384	}
385	385	// map3d = 0.0;
386	386	int j=0;
387		- Rprintf("%d\n",1);
	387	+ //Rprintf("%d\n",1);
388	388	for (int i = 0; i < scanNumbers.size(); i++)
389	389	{
390	390	rampPeakList *pl = ramp->getPeakList( scanNumbers[i] );
...	...	@@ -415,7 +415,7 @@ Rcpp::NumericMatrix RcppRamp::get3DMap ( std::vector<int> scanNumbers, double wh
415	415	}
416	416	return(map3d);
417	417	}
418		- Rprintf("Warning: Ramp not yet initialized.\n ");
	418	+ Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
419	419	return Rcpp::NumericMatrix(0,0);
420	420	}
421	421
...	...	@@ -425,7 +425,7 @@ int RcppRamp::getLastScan() const
425	425	{
426	426	return ramp->getLastScan();
427	427	}
428		- Rprintf("Warning: Ramp not yet initialized.\n ");
	428	+ Rf_warningcall(R_NilValue, "Ramp not yet initialized.");
429	429	return -1;
430	430	}
431	431