OPENMS_LOG_WARN writes to std::cerr now

src/openms/source/APPLICATIONS/OpenSwathBase.cpp

@@ -294,6 +294,7 @@ namespace OpenMS
       else if (out_chrom_type == FileTypes::CHROMPARQUET)
       {
 #ifndef WITH_PARQUET
+        (void*)&source_file; // to suppress unused variable warning
         throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
 #else
         auto * chromConsumer = new MSChromatogramParquetConsumer(out_chrom, run_id, source_file, transition_exp);

src/openms/source/CONCEPT/LogStream.cpp

@@ -609,7 +609,7 @@ namespace OpenMS
   {
     Logger::LogStream g_log_fatal(new Logger::LogStreamBuf("FATAL_ERROR", &red), true, &cerr);
     Logger::LogStream g_log_error(new Logger::LogStreamBuf("ERROR", &red), true, &cerr);
-    Logger::LogStream g_log_warn(new Logger::LogStreamBuf("WARNING", &yellow), true, &cout);
+    Logger::LogStream g_log_warn(new Logger::LogStreamBuf("WARNING", &yellow), true, &cerr);
     Logger::LogStream g_log_info(new Logger::LogStreamBuf("INFO", nullptr), true, &cout);
     // OPENMS_LOG_DEBUG is disabled by default, but will be enabled in TOPPAS.cpp or TOPPBase.cpp if started in debug mode (--debug or -debug X)
     Logger::LogStream g_log_debug(new Logger::LogStreamBuf("DEBUG", &magenta), false); // last param should be 'true', but segfaults...

src/tests/topp/FileInfo_17_output.txt

@@ -3,9 +3,6 @@
 
 File name: C:/dev/openms/src/tests/topp/FileInfo_17_input.fasta
 File type: fasta
-Warning: Duplicate header, #7, ID: crab_chick = #2, ID: crab_chick
-Warning: Duplicate header, #10, ID: crab_squac = #9, ID: crab_squac
-Warning: Duplicate sequence, #10, ID: crab_squac == #9, ID: crab_squac
 
 Number of sequences   : 11
 Sequence length distribution:

src/topp/FileInfo.cpp

@@ -814,27 +814,16 @@ class TOPPFileInfo : public TOPPBase
         return ILLEGAL_PARAMETERS;
       }
 
-      std::cout << "Checking mzML file for valid indices ... " << std::endl;
+      os << "Checking mzML file for valid indices ... " << std::endl;
       Internal::IndexedMzMLHandler ifile;
       ifile.openFile(in);
       if (ifile.getParsingSuccess())
       {
-        // Validate that we can access each single spectrum and chromatogram
-        for (int i = 0; i < (int)ifile.getNrSpectra(); i++)
-        {
-          OpenMS::Interfaces::SpectrumPtr p = ifile.getSpectrumById(i);
-        }
-        for (int i = 0; i < (int)ifile.getNrChromatograms(); i++)
-        {
-          OpenMS::Interfaces::ChromatogramPtr p = ifile.getChromatogramById(i);
-        }
-
-        std::cout << "Found a valid indexed mzML XML File with " << ifile.getNrSpectra() << " spectra and " << ifile.getNrChromatograms() << " chromatograms." << std::endl
-                  << std::endl;
+        os << "Found a valid indexed mzML XML File with " << ifile.getNrSpectra() << " spectra and " << ifile.getNrChromatograms() << " chromatograms.\n";
       }
       else
       {
-        std::cout << "Could not detect a valid index for the mzML file " << in << "\nEither the index is not present or is not correct." << std::endl;
+        os << "Could not detect a valid index for the mzML file " << in << "\nEither the index is not present or is not correct.\n";
         return ILLEGAL_PARAMETERS;
       }
     }
@@ -861,7 +850,7 @@ class TOPPFileInfo : public TOPPBase
       Size dup_header(0);
       Size dup_seq(0);
 
-      typedef std::unordered_map<size_t, vector<ptrdiff_t> > SHashmap;
+      using SHashmap = std::unordered_map<size_t, vector<ptrdiff_t> >;
       SHashmap m_headers;
       SHashmap m_seqs;
 
@@ -918,7 +907,7 @@ class TOPPFileInfo : public TOPPBase
             vector<ptrdiff_t>::const_iterator iter = find_if(it_id->second.begin(), it_id->second.end(), [&loopiter, &entries](const ptrdiff_t& idx) { return entries[idx].headerMatches(*loopiter); });
             if (iter != it_id->second.end())
             {
-              os << "Warning: Duplicate header, #" << std::distance(entries.begin(), loopiter) << ", ID: " << loopiter->identifier << " = #" << *iter << ", ID: " << entries[*iter].identifier << '\n';
+              OPENMS_LOG_WARN << "Warning: Duplicate header, #" << std::distance(entries.begin(), loopiter) << ", ID: " << loopiter->identifier << " = #" << *iter << ", ID: " << entries[*iter].identifier << '\n';
               ++dup_header;
             }
 
@@ -935,7 +924,8 @@ class TOPPFileInfo : public TOPPBase
             vector<ptrdiff_t>::const_iterator iter = find_if(it_id->second.begin(), it_id->second.end(), [&loopiter, &entries](const ptrdiff_t& idx) { return entries[idx].sequenceMatches(*loopiter); });
             if (iter != it_id->second.end())
             {
-              os << "Warning: Duplicate sequence, #" << std::distance(entries.begin(), loopiter) << ", ID: " << loopiter->identifier << " == #" << *iter << ", ID: " << entries[*iter].identifier << '\n';
+              OPENMS_LOG_WARN << "Warning: Duplicate sequence, #" << std::distance(entries.begin(), loopiter) << ", ID: " << loopiter->identifier
+                              << " == #" << *iter << ", ID: " << entries[*iter].identifier << '\n';
               ++dup_seq;
             }