@@ -2,7 +2,7 @@ Package: mzR

 Type: Package

 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files

        (mass spectrometry data)

-Version: 2.27.2

+Version: 2.29.2

 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer

 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,

             Laurent Gatto <laurent.gatto@uclouvain.be>,

@@ -1,3 +1,13 @@

+CHANGES IN VERSION 2.29.2

+-------------------------

+ o Update to Proteowizard 3_0_21263

+ o Removed RAMP backend, dropping ability to read mzData

+

+CHANGES IN VERSION 2.29.1

+-------------------------

+ o Pwiz backend partially re-written to avoid segfault on macOS

+   (https://github.com/sneumann/xcms/issues/422).

+

 CHANGES IN VERSION 2.27.2

 -------------------------

  o Remove support for the ramp backend.

@@ -50,10 +50,12 @@ setMethod("detector", "mzRpwiz",

 setMethod("header", c("mzRpwiz", "missing"),

           function(object) {

-              res <- object@backend$getAllScanHeaderInfo()

-              res$filterString <- as.character(res$filterString)

-              res$spectrumId <- as.character(res$spectrumId)

-              res

+              scans <- seq_len(object@backend$getLastScan())

+              ## res <- object@backend$getAllScanHeaderInfo()

+              ## res$filterString <- as.character(res$filterString)

+              ## res$spectrumId <- as.character(res$spectrumId)

+              ## res

+              header(object, scans)

           })

 setMethod("header", c("mzRpwiz", "numeric"),

@@ -3,6 +3,7 @@

 RcppPwiz::RcppPwiz()

 {

   msd = NULL;

+  nativeIdFormat = CVID_Unknown;

   instrumentInfo = Rcpp::List::create();

   chromatogramsInfo = Rcpp::DataFrame::create();

   isInCacheInstrumentInfo = FALSE;

@@ -15,12 +16,13 @@ RcppPwiz::~RcppPwiz()

   RcppPwiz::close();

 }

-void RcppPwiz::open(const string& fileName)

+// void RcppPwiz::open(const string& fileName)

+void RcppPwiz::open(Rcpp::StringVector fileName)

 {

-  filename = fileName;

-  msd = new MSDataFile(fileName);

-

+  filename = Rcpp::as<std::string>(fileName(0));

+  msd = new MSDataFile(filename);

+  nativeIdFormat = id::getDefaultNativeIDFormat(*msd);

 }

 /* Release all memory on close. */

@@ -30,6 +32,7 @@ void RcppPwiz::close()

     {

       delete msd;

       msd = NULL;

+      nativeIdFormat = CVID_Unknown;

       instrumentInfo = Rcpp::List::create();

       chromatogramsInfo = Rcpp::DataFrame::create();

       isInCacheInstrumentInfo = FALSE;

@@ -127,12 +130,45 @@ Rcpp::List RcppPwiz::getInstrumentInfo ( )

   return instrumentInfo;

 }

+int RcppPwiz::getAcquisitionNumber(string id, size_t index) const

+{

+  // const SpectrumIdentity& si = msd->run.spectrumListPtr->spectrumIdentity(index);

+  string scanNumber = id::translateNativeIDToScanNumber(nativeIdFormat, id);

+  if (scanNumber.empty())

+    return static_cast<int>(index) + 1;

+  else

+    return lexical_cast<int>(scanNumber);

+}

+

+// Using this function instead of pwiz translateNativeIDToScanNumber because

+// it randomly causes segfaults on macOS.

+// int RcppPwiz::getAcquisitionNumber(string id, size_t index) const

+// {

+//   if (id.find("controllerType") != std::string::npos) {

+//     if (id.find("controllerType=0 controllerNumber=1") == std::string::npos)

+//       return static_cast<int>(index) + 1;

+//   }

+//   string e;

+//   std::smatch match;

+//   if (id.find("scan=") != std::string::npos)

+//     e ="scan=(\\d+)";

+//   else if (id.find("index=") != std::string::npos)

+//     e = "index=(\\d+)";

+//   else if (id.find("spectrum=") != std::string::npos)

+//     e = "spectrum=(\\d+)";

+//   else if (id.find("scanId=") != std::string::npos)

+//     e = "scanId=(\\d+)";

+//   else return static_cast<int>(index) + 1;

+//   if (std::regex_search(id, match, std::regex(e)))

+//     return lexical_cast<int>(match[1]);

+//   else return static_cast<int>(index) + 1;

+// }

+

 Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan) {

   if (msd != NULL) {

     SpectrumListPtr slp = msd->run.spectrumListPtr;

-    int N = slp->size();

-    int N_scans = whichScan.size();

-    CVID nativeIdFormat = id::getDefaultNativeIDFormat(*msd);

+    size_t N = slp->size();

+    size_t N_scans = whichScan.size();

     Rcpp::IntegerVector seqNum(N_scans); // number in sequence observed file (1-based)

     Rcpp::IntegerVector acquisitionNum(N_scans); // scan number as declared in File (may be gaps)

     Rcpp::IntegerVector msLevel(N_scans);

@@ -165,23 +201,20 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan) {

     Rcpp::NumericVector scanWindowLowerLimit(N_scans);

     Rcpp::NumericVector scanWindowUpperLimit(N_scans);

-    for (int i = 0; i < N_scans; i++) {

+    for (size_t i = 0; i < N_scans; i++) {

       int current_scan = whichScan[i];

-      SpectrumPtr sp = slp->spectrum(current_scan - 1, false);

+      size_t current_index = static_cast<size_t>(current_scan - 1);

+      // SpectrumPtr sp = slp->spectrum(current_index, false);

+      SpectrumPtr sp = slp->spectrum(current_index, DetailLevel_FullMetadata);

       Scan dummy;

       Scan& scan = sp->scanList.scans.empty() ? dummy : sp->scanList.scans[0];

+      if (scan.empty())

+	Rprintf("Scan with index %d empty.\n", current_scan);

       // seqNum

       seqNum[i] = current_scan;

-      // acquisitionNum

-      string id = sp->id;

-      string scanNumber = id::translateNativeIDToScanNumber(nativeIdFormat, id);

-      if (scanNumber.empty()) {

-	acquisitionNum[i] = current_scan;

-      } else {

-	acquisitionNum[i] = lexical_cast<int>(scanNumber);

-      }

+      acquisitionNum[i] = getAcquisitionNumber(sp->id, current_index);

       // spectrumId

-      spectrumId[i] = sp->id;

+      spectrumId[i] = Rcpp::String(sp->id);

       // msLevel

       msLevel[i] = sp->cvParam(MS_ms_level).valueAs<int>();

       // peaksCount

@@ -231,14 +264,8 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan) {

 	collisionEnergy[i] = precursor.activation.cvParam(MS_collision_energy).valueAs<double>();

 	// precursorScanNum

 	size_t precursorIndex = slp->find(precursor.spectrumID);

-	if (precursorIndex < slp->size()) {

-	  const SpectrumIdentity& precursorSpectrum = slp->spectrumIdentity(precursorIndex);

-	  string precursorScanNumber = id::translateNativeIDToScanNumber(nativeIdFormat, precursorSpectrum.id);

-	  if (precursorScanNumber.empty()) {

-	    precursorScanNum[i] = precursorIndex + 1;

-	  } else {

-	    precursorScanNum[i] = lexical_cast<int>(precursorScanNumber);

-	  }

+	if (precursorIndex < N) {

+	  precursorScanNum[i] = getAcquisitionNumber(precursor.spectrumID, precursorIndex);

 	} else {

 	  precursorScanNum[i] = NA_INTEGER;

 	}

@@ -277,7 +304,7 @@ Rcpp::DataFrame RcppPwiz::getScanHeaderInfo (Rcpp::IntegerVector whichScan) {

     Rcpp::List header(31);

     std::vector<std::string> names;

-    int i = 0;

+    size_t i = 0;

     names.push_back("seqNum");

     header[i++] = Rcpp::wrap(seqNum);

     names.push_back("acquisitionNum");

@@ -352,7 +379,7 @@ Rcpp::DataFrame RcppPwiz::getAllScanHeaderInfo ( ) {

   if (msd != NULL) {

     if (!isInCacheAllScanHeaderInfo) {

       SpectrumListPtr slp = msd->run.spectrumListPtr;

-      int N = slp->size();

+      size_t N = slp->size();

       allScanHeaderInfo = getScanHeaderInfo(Rcpp::seq(1, N));

       isInCacheAllScanHeaderInfo = TRUE;	    

@@ -366,21 +393,23 @@ Rcpp::DataFrame RcppPwiz::getAllScanHeaderInfo ( ) {

 Rcpp::List RcppPwiz::getPeakList(Rcpp::IntegerVector whichScan) {

   if (msd != NULL) {

     SpectrumListPtr slp = msd->run.spectrumListPtr;

-    int n_scans = slp->size();

-    int n_want = whichScan.size();

+    size_t n_scans = slp->size();

+    size_t n_want = whichScan.size();

     int current_scan;

     SpectrumPtr sp;

     BinaryDataArrayPtr mzs,ints;

     std::vector<double> data;

     Rcpp::NumericVector data_matrix;

     Rcpp::List res(n_want);

-    for (int i = 0; i < n_want; i++) {

+    for (size_t i = 0; i < n_want; i++) {

       current_scan = whichScan[i];

       if (current_scan < 1 || current_scan > n_scans) {

 	Rprintf("Index whichScan out of bounds [1 ... %d].\n", n_scans);

 	return Rcpp::List::create( );

       }

-      sp = slp->spectrum(current_scan - 1, true);

+      size_t current_index = static_cast<size_t>(current_scan - 1);

+      // sp = slp->spectrum(current_index, true);

+      sp = slp->spectrum(current_index, DetailLevel_FullData);

       mzs = sp->getMZArray();

       ints = sp->getIntensityArray();

       if (!mzs.get() || !ints.get()) {

@@ -847,7 +876,7 @@ Rcpp::DataFrame RcppPwiz::getChromatogramsInfo( int whichChrom )

 Rcpp::DataFrame RcppPwiz::getChromatogramHeaderInfo (Rcpp::IntegerVector whichChrom)

 {

   if (msd != NULL) {

-    CVID nativeIdFormat_ = id::getDefaultNativeIDFormat(*msd);

+    // CVID nativeIdFormat_ = id::getDefaultNativeIDFormat(*msd);

     ChromatogramListPtr clp = msd->run.chromatogramListPtr;

     if (clp.get() == 0) {

       Rf_warningcall(R_NilValue, "The direct support for chromatogram info is only available in mzML format.");

@@ -980,7 +1009,7 @@ Rcpp::NumericMatrix RcppPwiz::get3DMap ( std::vector<int> scanNumbers, double wh

       //Rprintf("%d\n",1);

       for (int i = 0; i < scanNumbers.size(); i++)

         {

-	  SpectrumPtr s = slp->spectrum(scanNumbers[i] - 1, true);

+	  SpectrumPtr s = slp->spectrum(scanNumbers[i] - 1, DetailLevel_FullMetadata);

 	  vector<MZIntensityPair> pairs;

 	  s->getMZIntensityPairs(pairs);

@@ -28,6 +28,7 @@

 #include <fstream>

 #include <string>

 #include <iostream>

+#include <regex>

 #if defined(__MINGW32__)

 #include <windows.h>

@@ -49,18 +50,21 @@ private:

     Rcpp::DataFrame allScanHeaderInfo;

     bool isInCacheAllScanHeaderInfo;

     string filename;

+    CVID nativeIdFormat;

     void addSpectrumList(MSData& msd,

 			 Rcpp::DataFrame& spctr_header,

 			 Rcpp::List& spctr_data,

 			 bool rtime_seconds);

     void addDataProcessing(MSData& msd, Rcpp::StringVector soft_proc);

-

+    int getAcquisitionNumber(string id, size_t index) const;

+  

 public:

     RcppPwiz();

     virtual ~RcppPwiz();

-    void open(const string& fileNames);

+    // void open(const string& fileNames);

+    void open(Rcpp::StringVector fileNames);

     void close();

     /* void writeMSfile(const string& filenames, const string& format); */

     void writeSpectrumList(const string& file, const string& format,