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Package 665/671HostnameOS / ArchBUILDCHECKBUILD BIN
xcms 1.36.0
Ralf Tautenhahn
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/xcms
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: xcms
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch xcms_1.36.0.tar.gz
StartedAt: 2013-05-01 11:53:02 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:01:43 -0700 (Wed, 01 May 2013)
EllapsedTime: 521.2 seconds
RetCode: 0
Status:  OK 
CheckDir: xcms.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/xcms.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'xcms/DESCRIPTION' ... OK
* this is package 'xcms' version '1.36.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'Rmpi'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'xcms' can be installed ... [23s/26s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'xcms/R/unix/zzz.R':
  .onLoad calls:
    require(methods)

File 'xcms/R/windows/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

fitGauss: warning in nls(d ˜ SSgauss(td, mu, sigma, h), algo = "port"):
  partial argument match of 'algo' to 'algorithm'
joinOverlappingPeaks: warning in which(upper.tri(matrix(0, Ngp, Ngp)),
  arr = TRUE): partial argument match of 'arr' to 'arr.ind'
joinOverlappingPeaks: warning in which(upper.tri(matrix(0, lcc, lcc)),
  arr = TRUE): partial argument match of 'arr' to 'arr.ind'
plot.xcmsEIC: warning in rgb(rgbvec[1], rgbvec[2], rgbvec[3], max =
  255): partial argument match of 'max' to 'maxColorValue'
.onLoad : <anonymous>: no visible global function definition for
  'mpi.comm.size'
.onLoad : <anonymous>: no visible global function definition for
  'mpi.close.Rslaves'
.onLoad : <anonymous>: no visible global function definition for
  'mpi.finalize'
.xcmsFragments.plotTree: no visible global function definition for
  'edgemode<-'
.xcmsFragments.plotTree: no visible global function definition for
  'addEdge'
KeggSearch: no visible global function definition for
  'search.compounds.by.mass'
fillPeaksChromPar: no visible binding for global variable 'i'
fillPeaksChromPar: no visible binding for global variable 'object'
running: multiple local function definitions for 'funct' with different
  formal arguments
xcmsClusterApply: no visible global function definition for
  'checkCluster'
xcmsClusterApply : submit: no visible global function definition for
  'sendCall'
xcmsClusterApply: no visible global function definition for
  'recvOneResult'
xcmsClusterApply: no visible global function definition for
  'checkForRemoteErrors'
xcmsPapply: no visible global function definition for 'mpi.comm.size'
xcmsPapply: no visible global function definition for
  'mpi.spawn.Rslaves'
xcmsPapply: no visible global function definition for 'mpi.comm.rank'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.send.Robj'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.recv.Robj'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.any.source'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.any.tag'
xcmsPapply : papply_int_slavefunction: no visible global function
  definition for 'mpi.get.sourcetag'
xcmsPapply: no visible global function definition for
  'mpi.bcast.Robj2slave'
xcmsPapply: no visible global function definition for 'mpi.bcast.cmd'
xcmsPapply: no visible global function definition for 'mpi.recv.Robj'
xcmsPapply: no visible global function definition for 'mpi.any.source'
xcmsPapply: no visible global function definition for 'mpi.any.tag'
xcmsPapply: no visible global function definition for
  'mpi.get.sourcetag'
xcmsPapply: no visible global function definition for 'mpi.send.Robj'
xcmsParallelSetup: no visible global function definition for
  'mpi.spawn.Rslaves'
xcmsParallelSetup: no visible global function definition for
  'mpi.comm.size'
xcmsParallelSetup: no visible global function definition for
  'mpi.comm.rank'
xcmsSet: no visible global function definition for 'mpi.close.Rslaves'
* checking Rd files ... NOTE
prepare_Rd: split.xcmsRaw.Rd:18-20: Dropping empty section \usage
prepare_Rd: split.xcmsSet.Rd:19-21: Dropping empty section \usage
prepare_Rd: xcmsSet.Rd:51-53: Dropping empty section \note
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [4s/5s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'doRUnit.R' [366s/389s]
 [366s/390s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/xcms.Rcheck/00check.log'
for details.

xcms.Rcheck/00install.out:

* installing *source* package 'xcms' ...
** libs
rm -f massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c massifquant/xcms_massifquant.cpp -o massifquant/xcms_massifquant.o
massifquant/xcms_massifquant.cpp:46:25: warning: implicit conversion changes signedness: 'uint32_t' (aka 'unsigned int') to 'int' [-Wsign-conversion]
    int totalScanNums = dkeep.getTotalScanNumbers();
        ˜˜˜˜˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/xcms_massifquant.cpp:122:6: warning: unused variable 'scanLength' [-Wunused-variable]
        int scanLength = int(featInfo.at(5) - featInfo.at(4) + 1);
            ^
massifquant/xcms_massifquant.cpp:33:58: warning: unused variable 'vstcenter' [-Wunused-variable]
    SEXP peaklist,entrylist,list_names,vmz,vmzmin,vmzmax,vstcenter,vscmin,vscmax,vintensity,vintenmax, vlength;
                                                         ^
massifquant/xcms_massifquant.cpp:33:93: warning: unused variable 'vintenmax' [-Wunused-variable]
    SEXP peaklist,entrylist,list_names,vmz,vmzmin,vmzmax,vstcenter,vscmin,vscmax,vintensity,vintenmax, vlength;
                                                                                            ^
massifquant/xcms_massifquant.cpp:76:12: warning: unused variable 'maxScanNums' [-Wunused-variable]
    double maxScanNums = double(scanrangeTo);
           ^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c massifquant/TrMgr.cpp -o massifquant/TrMgr.o
massifquant/TrMgr.cpp:16:19: warning: implicit conversion turns floating-point number into integer: 'const double' to 'int' [-Wconversion]
    currMissedMax(cmm),
                 ˜^˜˜
massifquant/TrMgr.cpp:26:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        delete trks[i];
               ˜˜˜˜ ^
massifquant/TrMgr.cpp:63:12: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    return picIdx.size();
    ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:67:12: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    return actIdx.size();
    ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:71:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    return trks[i];
           ˜˜˜˜ ^
massifquant/TrMgr.cpp:84:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return trks[picIdx.at(i)]->getFeatureInfo(scanTime);
               ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:84:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        return trks[picIdx.at(i)]->getFeatureInfo(scanTime);
                    ˜˜˜˜˜˜    ^
massifquant/TrMgr.cpp:100:10: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    trks[actIdx.at(i)]->predictCentroid();
    ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:101:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    centIdx = trks[actIdx.at(i)]->claimDataIdx(mData,iData,predDist,minTrLen, scanBack);
              ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:176:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      restructFoundIdx.push_back(actIdx.at(collideIdx.at(0)));
                                 ˜˜˜˜˜˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:191:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    restructFoundIdx.push_back(actIdx.at(collideIdx.at(bestIdx)));
                               ˜˜˜˜˜˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:191:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    restructFoundIdx.push_back(actIdx.at(collideIdx.at(bestIdx)));
                                         ˜˜˜˜˜˜˜˜˜˜    ^˜˜˜˜˜˜
massifquant/TrMgr.cpp:192:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    moreMissIdx = collideIdx != collideIdx.at(bestIdx);
                                ˜˜˜˜˜˜˜˜˜˜    ^˜˜˜˜˜˜
massifquant/TrMgr.cpp:197:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        missActIdx.push_back(actIdx.at(collideIdx.at(*it_miss)));
                             ˜˜˜˜˜˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:197:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        missActIdx.push_back(actIdx.at(collideIdx.at(*it_miss)));
                                       ˜˜˜˜˜˜˜˜˜˜    ^˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:132:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int origLen  = predDatIdx.size();
      ˜˜˜˜˜˜˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:137:18: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int chgdLen =  predDatIdx.size();
      ˜˜˜˜˜˜˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:213:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        trks[*it]->incrementMiss();
        ˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:216:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (trks[*it]->getCurrMissed() > currMissedMax ||
            ˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:217:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            trks[*it]->getCurrMissed() > trks[*it]->getTrLen() ||
            ˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:217:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            trks[*it]->getCurrMissed() > trks[*it]->getTrLen() ||
                                         ˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:218:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            (trks[*it]->getPredCounts()/2) > trks[*it]->getTrLen()) {
             ˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:218:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            (trks[*it]->getPredCounts()/2) > trks[*it]->getTrLen()) {
                                             ˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:230:14: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (trks[i]->getTrLen() < minTrLen) {
        ˜˜˜˜ ^
massifquant/TrMgr.cpp:233:21: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        delete trks[i];
               ˜˜˜˜ ^
massifquant/TrMgr.cpp:234:14: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        trks[i] = NULL;
        ˜˜˜˜ ^
massifquant/TrMgr.cpp:238:36: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    std::list<double> iList = trks[i]->getIntensityList();
                              ˜˜˜˜ ^
massifquant/TrMgr.cpp:243:21: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        delete trks[i];
               ˜˜˜˜ ^
massifquant/TrMgr.cpp:244:14: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        trks[i] = NULL;
        ˜˜˜˜ ^
massifquant/TrMgr.cpp:250:21: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        delete trks[i];
               ˜˜˜˜ ^
massifquant/TrMgr.cpp:251:14: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        trks[i] = NULL;
        ˜˜˜˜ ^
massifquant/TrMgr.cpp:266:28: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        bool change = trks[i]->performScanBack();
                      ˜˜˜˜ ^
massifquant/TrMgr.cpp:268:18: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            trks[i]->computeMyXbar();
            ˜˜˜˜ ^
massifquant/TrMgr.cpp:289:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        trks[*it_f]->makeZeroCurrMissed();
        ˜˜˜˜ ^˜˜˜˜
massifquant/TrMgr.cpp:290:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        trks[*it_f]->incrementTrLen();
        ˜˜˜˜ ^˜˜˜˜
massifquant/TrMgr.cpp:291:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        trks[*it_f]->innovateCentroid(mData.at(*it_d),
        ˜˜˜˜ ^˜˜˜˜
massifquant/TrMgr.cpp:291:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        trks[*it_f]->innovateCentroid(mData.at(*it_d),
                                      ˜˜˜˜˜    ^˜˜˜˜
massifquant/TrMgr.cpp:292:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                                    iData.at(*it_d),
                                    ˜˜˜˜˜    ^˜˜˜˜
massifquant/TrMgr.cpp:295:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        mData[*it_d] = CLAIMEDPT;
        ˜˜˜˜˜ ^˜˜˜˜
massifquant/TrMgr.cpp:296:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        iData[*it_d] = CLAIMEDPT;
        ˜˜˜˜˜ ^˜˜˜˜
massifquant/TrMgr.cpp:314:30: warning: implicit conversion changes signedness: 'unsigned int' to 'const int' [-Wsign-conversion]
                currScanIdx, i,
                             ^
massifquant/TrMgr.cpp:330:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (trks[*it]->getTrLen() < 5) {
            ˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:335:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        std::list<double> iList = trks[*it]->getIntensityList();
                                  ˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:355:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            bool change = trks[*it]->performScanBack();
                          ˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:357:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
                trks[*it]->computeMyXbar();
                ˜˜˜˜ ^˜˜
massifquant/TrMgr.cpp:370:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        trks[*it_pic]->displayContents();
        ˜˜˜˜ ^˜˜˜˜˜˜
massifquant/TrMgr.cpp:392:14: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (d.at(*it) < tmpmin) {
        ˜    ^˜˜
massifquant/TrMgr.cpp:394:21: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      tmpmin = d.at(*it);
               ˜    ^˜˜
massifquant/TrMgr.cpp:414:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        totalCents +=  trks[picIdx.at(i)]->getTrLen();
                       ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:417:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        std::list<int> iscanList = trks[picIdx.at(i)]->getScanList();
                                   ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:418:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        std::list<int> icentList = trks[picIdx.at(i)]->getCentroidList();
                                   ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:419:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        std::list<double> imzList = trks[picIdx.at(i)]->getMzList();
                                    ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:420:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        std::list<double> iintensityList = trks[picIdx.at(i)]->getIntensityList();
                                           ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:445:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        int istart = trks[picIdx.at(i)]->getStartScanIdx();
                     ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:468:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        picIdx[j] = it->second;
        ˜˜˜˜˜˜ ^
massifquant/TrMgr.cpp:486:25: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            delete trks[eIdx.at(i)];
                   ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:487:18: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            trks[eIdx.at(i)] = NULL;
            ˜˜˜˜ ^˜˜˜˜˜˜˜˜˜
massifquant/TrMgr.cpp:508:10: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    trks[i]->computeMyXbar();
    ˜˜˜˜ ^
massifquant/TrMgr.cpp:509:10: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    trks[i]->computeMyS2();
    ˜˜˜˜ ^
massifquant/TrMgr.cpp:510:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    double mzTol = ppm*trks[i]->getXbar()/10e5;
                       ˜˜˜˜ ^
massifquant/TrMgr.cpp:512:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    double peakDeviance = fabs(computeAnyXbar(diff(trks[i]->getMzList())));
                                                   ˜˜˜˜ ^
massifquant/TrMgr.cpp:522:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    std::list<double> mzList = trks[i]->getMzList();
                               ˜˜˜˜ ^
massifquant/TrMgr.cpp:526:29: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    int n = mzList.size() - midIdx;
                          ˜ ^˜˜˜˜˜
massifquant/TrMgr.cpp:529:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        std::vector<double> seizmo(n);
                            ˜˜˜˜˜˜ ^
massifquant/TrMgr.cpp:531:25: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        for (size_t j = midIdx; j < mzVec.size(); ++j) {
                    ˜   ^˜˜˜˜˜
massifquant/TrMgr.cpp:532:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            seizmo[k] = fabs(rmz.at(j) - mzVec.at(j));
            ˜˜˜˜˜˜ ^
massifquant/TrMgr.cpp:526:27: warning: implicit conversion loses integer precision: 'unsigned long' to 'int' [-Wshorten-64-to-32]
    int n = mzList.size() - midIdx;
        ˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
67 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c massifquant/Tracker.cpp -o massifquant/Tracker.o
massifquant/Tracker.cpp:171:13: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    trLen = scanList.size();
          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from massifquant/Tracker.cpp:8:
massifquant/Tracker.h:49:16: warning: private field 'r_val_i' is not used [-Wunused-private-field]
        double r_val_i;
               ^
massifquant/Tracker.h:50:16: warning: private field 'p_val_i' is not used [-Wunused-private-field]
        double p_val_i;
               ^
massifquant/Tracker.h:53:16: warning: private field 'r_val_m' is not used [-Wunused-private-field]
        double r_val_m;
               ^
massifquant/Tracker.h:54:16: warning: private field 'p_val_m' is not used [-Wunused-private-field]
        double p_val_m;
               ^
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c massifquant/SegProc.cpp -o massifquant/SegProc.o
massifquant/SegProc.cpp:18:37: warning: implicit conversion turns floating-point number into integer: 'double' to 'size_type' (aka 'unsigned long') [-Wconversion]
    segClusters = std::vector<int> (origTrNum, 0);
                  ˜˜˜               ^˜˜˜˜˜˜˜˜
massifquant/SegProc.cpp:34:15: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    int ppm = busybody.getPpm();
        ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/SegProc.cpp:61:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (candIdx.size() == 0 || segClusters.at(i) != 0) { continue; }
                                   ˜˜˜˜˜˜˜˜˜˜˜    ^
massifquant/SegProc.cpp:62:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        segClusters[i] = 1;
        ˜˜˜˜˜˜˜˜˜˜˜ ^
massifquant/SegProc.cpp:90:46: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'const int' [-Wshorten-64-to-32]
        compareMeans(busybody, *it_i, edges, segIdx.size());
        ˜˜˜˜˜˜˜˜˜˜˜˜                         ^˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/SegProc.cpp:95:32: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'const value_type' (aka 'const int') [-Wshorten-64-to-32]
            unionIdx.push_back(segIdx.size());
            ˜˜˜˜˜˜˜˜           ^˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/SegProc.cpp:182:25: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            cleanSegIdx[segCounts + k] = iSegs2Union.at(k);
                        ^˜˜˜˜˜˜˜˜ ˜
massifquant/SegProc.cpp:185:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        cleanUnionIdx[cleanCounts] = segCounts;
        ˜˜˜˜˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
massifquant/SegProc.cpp:146:27: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
            int jCounts = jSIdx.size();
                ˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜
massifquant/SegProc.cpp:148:26: warning: implicit conversion loses integer precision: 'const unsigned long' to 'int' [-Wshorten-64-to-32]
            int maxSet = max(iSegs2Union.size(), jSIdx.size());
                ˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/SegProc.cpp:281:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            erasedPicIdx[j] = *it;
            ˜˜˜˜˜˜˜˜˜˜˜˜ ^
11 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c massifquant/DataKeeper.cpp -o massifquant/DataKeeper.o
massifquant/DataKeeper.cpp:22:14: warning: implicit conversion changes signedness: 'int' to 'uint32_t' (aka 'unsigned int') [-Wsign-conversion]
 num_scans = lastScan;
           ˜ ^˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:45:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int start_pos = scan_idx.at(s);
                    ˜˜˜˜˜˜˜˜    ^
massifquant/DataKeeper.cpp:46:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int stop_pos = scan_idx.at(s + 1);
                   ˜˜˜˜˜˜˜˜    ˜˜^˜˜
massifquant/DataKeeper.cpp:52:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        the_scan[copyvec_idx] = mz.at(i);
        ˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:52:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        the_scan[copyvec_idx] = mz.at(i);
                                ˜˜    ^
massifquant/DataKeeper.cpp:65:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int start_pos = scan_idx.at(s);
                    ˜˜˜˜˜˜˜˜    ^
massifquant/DataKeeper.cpp:66:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int stop_pos = scan_idx.at(s + 1);
                   ˜˜˜˜˜˜˜˜    ˜˜^˜˜
massifquant/DataKeeper.cpp:73:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        mzScan[copyvec_idx] = mz.at(i);
        ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:73:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        mzScan[copyvec_idx] = mz.at(i);
                              ˜˜    ^
massifquant/DataKeeper.cpp:74:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        intenScan[copyvec_idx] = intensity.at(i);
        ˜˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:74:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        intenScan[copyvec_idx] = intensity.at(i);
                                 ˜˜˜˜˜˜˜˜˜    ^
massifquant/DataKeeper.cpp:99:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        mzScan = std::vector<double>(N);
                 ˜˜˜                 ^
massifquant/DataKeeper.cpp:100:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        intenScan = std::vector<double>(N);
                    ˜˜˜                 ^
massifquant/DataKeeper.cpp:104:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            mzScan[i] = pmz[idx - 1];
            ˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:105:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            intenScan[i] = sqrt(pinten[idx - 1]);
            ˜˜˜˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:118:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int start_pos = scan_idx.at(s);
                    ˜˜˜˜˜˜˜˜    ^
massifquant/DataKeeper.cpp:119:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int stop_pos = scan_idx.at(s + 1);
                   ˜˜˜˜˜˜˜˜    ˜˜^˜˜
massifquant/DataKeeper.cpp:124:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        the_scan[copyvec_idx] = intensity.at(i);
        ˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:124:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        the_scan[copyvec_idx] = intensity.at(i);
                                ˜˜˜˜˜˜˜˜˜    ^
massifquant/DataKeeper.cpp:132:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int start_pos = scan_idx.at(s);
                    ˜˜˜˜˜˜˜˜    ^
massifquant/DataKeeper.cpp:133:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int stop_pos = scan_idx.at(s + 1);
                   ˜˜˜˜˜˜˜˜    ˜˜^˜˜
massifquant/DataKeeper.cpp:139:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        the_scan[copyvec_idx] = mz.at(i);
        ˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:139:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        the_scan[copyvec_idx] = mz.at(i);
                                ˜˜    ^
massifquant/DataKeeper.cpp:147:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int start_pos = scan_idx.at(s);
                    ˜˜˜˜˜˜˜˜    ^
massifquant/DataKeeper.cpp:148:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    int stop_pos = scan_idx.at(s + 1);
                   ˜˜˜˜˜˜˜˜    ˜˜^˜˜
massifquant/DataKeeper.cpp:153:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        the_scan[copyvec_idx] = intensity.at(i);
        ˜˜˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:153:46: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        the_scan[copyvec_idx] = intensity.at(i);
                                ˜˜˜˜˜˜˜˜˜    ^
massifquant/DataKeeper.cpp:180:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        mzScan = std::vector<double>(N);
                 ˜˜˜                 ^
massifquant/DataKeeper.cpp:181:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        intenScan = std::vector<double>(N);
                    ˜˜˜                 ^
massifquant/DataKeeper.cpp:186:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            mzScan[i] = pmz[idx - 1];
            ˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:187:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            intenScan[i] = pinten[idx - 1];
            ˜˜˜˜˜˜˜˜˜ ^
massifquant/DataKeeper.cpp:295:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            mMaxFeat.push_back(mGhost.at(neighborIdx.at(imaxIdx)));
                               ˜˜˜˜˜˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:295:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            mMaxFeat.push_back(mGhost.at(neighborIdx.at(imaxIdx)));
                                         ˜˜˜˜˜˜˜˜˜˜˜    ^˜˜˜˜˜˜
massifquant/DataKeeper.cpp:321:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    double mzApex = mz.at(apexIdx);
                    ˜˜    ^˜˜˜˜˜˜
massifquant/DataKeeper.cpp:395:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            mMaxFeat.push_back(mGhost.at(neighborIdx.at(imaxIdx)));
                               ˜˜˜˜˜˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/DataKeeper.cpp:395:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            mMaxFeat.push_back(mGhost.at(neighborIdx.at(imaxIdx)));
                                         ˜˜˜˜˜˜˜˜˜˜˜    ^˜˜˜˜˜˜
In file included from massifquant/DataKeeper.cpp:4:
massifquant/DataKeeper.h:36:26: warning: private field 'scbuf' is not used [-Wunused-private-field]
        struct scanBuf * scbuf;
                         ^
37 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c massifquant/OpOverload.cpp -o massifquant/OpOverload.o
massifquant/OpOverload.cpp:32:7: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    C[j] = A[j] + B[j];
    ˜ ^
massifquant/OpOverload.cpp:32:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    C[j] = A[j] + B[j];
           ˜ ^
massifquant/OpOverload.cpp:32:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    C[j] = A[j] + B[j];
                  ˜ ^
massifquant/OpOverload.cpp:29:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int m = A.size();
      ˜   ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:42:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        C[j] = A[j] + B[j];
        ˜ ^
massifquant/OpOverload.cpp:42:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        C[j] = A[j] + B[j];
               ˜ ^
massifquant/OpOverload.cpp:42:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        C[j] = A[j] + B[j];
                      ˜ ^
massifquant/OpOverload.cpp:39:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int m = A.size();
      ˜   ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:52:7: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    C[j] = A[j] -  b;
    ˜ ^
massifquant/OpOverload.cpp:52:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    C[j] = A[j] -  b;
           ˜ ^
massifquant/OpOverload.cpp:49:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int m = A.size();
      ˜   ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:63:7: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    C[j] = A[j] / b;
    ˜ ^
massifquant/OpOverload.cpp:63:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    C[j] = A[j] / b;
           ˜ ^
massifquant/OpOverload.cpp:60:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int m = A.size();
      ˜   ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:75:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (A.at(i) >= b)
        ˜    ^
massifquant/OpOverload.cpp:76:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      C.at(i) = 1;
      ˜    ^
massifquant/OpOverload.cpp:72:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int m = A.size();
      ˜   ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:86:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (A.at(i) <= b)
        ˜    ^
massifquant/OpOverload.cpp:87:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      C.at(i) = 1;
      ˜    ^
massifquant/OpOverload.cpp:83:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int m = A.size();
      ˜   ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:97:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (A.at(i) == b)
        ˜    ^
massifquant/OpOverload.cpp:94:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int m = A.size();
      ˜   ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:168:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (A.at(i) > b)
        ˜    ^
massifquant/OpOverload.cpp:169:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      C.at(i) = 1;
      ˜    ^
massifquant/OpOverload.cpp:165:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int m = A.size();
      ˜   ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:179:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (A.at(i) >= b)
        ˜    ^
massifquant/OpOverload.cpp:180:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      C.at(i) = 1;
      ˜    ^
massifquant/OpOverload.cpp:176:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int m = A.size();
      ˜   ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:190:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (A.at(i) <= b)
        ˜    ^
massifquant/OpOverload.cpp:191:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      C.at(i) = 1;
      ˜    ^
massifquant/OpOverload.cpp:187:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int m = A.size();
      ˜   ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:211:7: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    C[j] = A[j]*B[j];
    ˜ ^
massifquant/OpOverload.cpp:211:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    C[j] = A[j]*B[j];
           ˜ ^
massifquant/OpOverload.cpp:211:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    C[j] = A[j]*B[j];
                ˜ ^
massifquant/OpOverload.cpp:208:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int m = A.size();
      ˜   ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:221:7: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    C[j] = A[j] + B[j];
    ˜ ^
massifquant/OpOverload.cpp:221:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    C[j] = A[j] + B[j];
           ˜ ^
massifquant/OpOverload.cpp:221:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    C[j] = A[j] + B[j];
                  ˜ ^
massifquant/OpOverload.cpp:218:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int m = A.size();
      ˜   ^˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:233:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        Asubset[i] = A.at(*it); //assign it the current value;
        ˜˜˜˜˜˜˜ ^
massifquant/OpOverload.cpp:233:27: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        Asubset[i] = A.at(*it); //assign it the current value;
                     ˜    ^˜˜
massifquant/OpOverload.cpp:228:11: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
  int m = subidx.size();
      ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:246:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        Asubset[i] = A.at(*it); //assign it the current value;
        ˜˜˜˜˜˜˜ ^
massifquant/OpOverload.cpp:246:27: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        Asubset[i] = A.at(*it); //assign it the current value;
                     ˜    ^˜˜
massifquant/OpOverload.cpp:241:13: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
    int m = subidx.size();
        ˜   ^˜˜˜˜˜˜˜˜˜˜˜˜
massifquant/OpOverload.cpp:260:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        seq[count] = i;
        ˜˜˜ ^˜˜˜˜
massifquant/OpOverload.cpp:328:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if ( mzvals.at(mid) < val){
             ˜˜˜˜˜˜    ^˜˜
massifquant/OpOverload.cpp:344:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (val < mzvals.at(mid) ){
                  ˜˜˜˜˜˜    ^˜˜
48 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c obiwarp/mat.cpp -o obiwarp/mat.o
obiwarp/mat.cpp:416:45: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        fwrite((int*)(_dat), sizeof(int), _m*_n, fh);
        ˜˜˜˜˜˜                            ˜˜^˜˜
obiwarp/mat.cpp:824:51: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        fwrite((double*)(_dat), sizeof(double), _m*_n, fh);
        ˜˜˜˜˜˜                                  ˜˜^˜˜
obiwarp/mat.cpp:1242:49: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        fwrite((float*)(_dat), sizeof(float), _m*_n, fh);
        ˜˜˜˜˜˜                                ˜˜^˜˜
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c obiwarp/vec.cpp -o obiwarp/vec.o
obiwarp/vec.cpp:406:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort(_dat, _n, sizeof(int), intCompare);
    ˜˜˜˜˜       ^˜
obiwarp/vec.cpp:1423:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort(_dat, _n, sizeof(double), doubleCompare);
    ˜˜˜˜˜       ^˜
obiwarp/vec.cpp:2440:17: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    qsort(_dat, _n, sizeof(float), floatCompare);
    ˜˜˜˜˜       ^˜
3 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c obiwarp/xcms_dynprog.cpp -o obiwarp/xcms_dynprog.o
In file included from obiwarp/xcms_dynprog.cpp:6:
obiwarp/xcms_dynprog.h:69:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                val = pow(i,order);
                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜
obiwarp/xcms_dynprog.cpp:482:21: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
  sum_sq_res_yeqx = VecF::sum_sq_res_yeqx(nVals, nValsNew);
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
obiwarp/xcms_dynprog.cpp:534:10: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
  return VecF::sum_sq_res_yeqx(nVals, nValsNew);
  ˜˜˜˜˜˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
obiwarp/xcms_dynprog.cpp:582:34: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                  ((sum_x[n] * sum_y[m])/cols))/cols;
                  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
obiwarp/xcms_dynprog.cpp:724:18: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
      tmp(m,n) = sqrt(sum);
               ˜ ^˜˜˜˜˜˜˜˜
obiwarp/xcms_dynprog.cpp:921:16: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
  float _avg = smat.avg();
        ˜˜˜˜   ^˜˜˜˜˜˜˜˜˜
6 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c obiwarp/xcms_lmat.cpp -o obiwarp/xcms_lmat.o
obiwarp/xcms_lmat.cpp:41:19: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
      tm_tmp[i] = pscantime[i];
                ˜ ^˜˜˜˜˜˜˜˜˜˜˜
obiwarp/xcms_lmat.cpp:50:19: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
      mz_tmp[i] = mz[i];
                ˜ ^˜˜˜˜
obiwarp/xcms_lmat.cpp:59:20: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
      mat_tmp[i] = intensity[i];
                 ˜ ^˜˜˜˜˜˜˜˜˜˜˜
obiwarp/xcms_lmat.cpp:129:17: warning: implicit conversion loses integer precision: 'size_t' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32]
      int len = strlen( str );
          ˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜
4 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c xcms_obiwarp.cpp -o xcms_obiwarp.o
In file included from xcms_obiwarp.cpp:12:
./obiwarp/xcms_dynprog.h:69:23: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                val = pow(i,order);
                    ˜ ^˜˜˜˜˜˜˜˜˜˜˜
xcms_obiwarp.cpp:101:28: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
    dyn.linear_less_before(*REAL(gap_extend), *REAL(gap_init), gp_length, gp_array);
    ˜˜˜                    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xcms_obiwarp.cpp:101:47: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
    dyn.linear_less_before(*REAL(gap_extend), *REAL(gap_init), gp_length, gp_array);
    ˜˜˜                                       ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xcms_obiwarp.cpp:111:5: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                  *REAL(factor_diag), *REAL(factor_gap), *INTEGER(AS_INTEGER(local_alignment)), *REAL(init_penalty));
                  ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xcms_obiwarp.cpp:111:25: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                  *REAL(factor_diag), *REAL(factor_gap), *INTEGER(AS_INTEGER(local_alignment)), *REAL(init_penalty));
                                      ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xcms_obiwarp.cpp:111:83: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
                  *REAL(factor_diag), *REAL(factor_gap), *INTEGER(AS_INTEGER(local_alignment)), *REAL(init_penalty));
                                                                                                ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
6 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c fastMatch.c -o fastMatch.o
fastMatch.c:30:61: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
    struct idxStruct * pidxS =  (struct idxStruct *) calloc(nx,  sizeof(struct idxStruct));
                                                     ˜˜˜˜˜˜ ^˜
fastMatch.c:32:81: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        error("fastMatch/calloc: memory could not be allocated ! (%d bytes)\n", nx  * sizeof(struct idxStruct) );
                                                                                ^˜  ˜
2 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c mzClust_hclust.c -o mzClust_hclust.o
mzClust_hclust.c:29:27: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
        clust = (int *) malloc(n * m * sizeof(int));
                               ˜˜^˜˜ ˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c mzROI.c -o mzROI.o
mzROI.c:68:37: warning: implicit conversion turns floating-point number into integer: 'double' to 'unsigned int' [-Wconversion]
    newLength= mzLength->mzROITotal * ROI_ALLOC_INC;
             ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mzROI.c:91:38: warning: implicit conversion turns floating-point number into integer: 'double' to 'unsigned int' [-Wconversion]
     newLength= mzLength->mzvalTotal * MZVAL_ALLOC_INC;
              ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mzROI.c:181:58: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
  int lpos = lower_bound( fMass - ddev,mzval,0,mzLength->mzval);
             ˜˜˜˜˜˜˜˜˜˜˜                       ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
mzROI.c:182:67: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
  int hpos = upper_bound( fMass + ddev,mzval,lpos,mzLength->mzval - lpos);
             ˜˜˜˜˜˜˜˜˜˜˜                          ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
mzROI.c:182:69: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  int hpos = upper_bound( fMass + ddev,mzval,lpos,mzLength->mzval - lpos);
                                                                  ˜ ^˜˜˜
mzROI.c:185:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      lpos = mzLength->mzval -1;
           ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
mzROI.c:187:30: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      hpos = mzLength->mzval -1 ;
           ˜ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
mzROI.c:203:28: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
          mzval[i].scmax = scan;
                         ˜ ^˜˜˜
mzROI.c:217:74: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        int lpos = lowerBound( fMass - ddev,scanbuf->nextScan,0,scanbuf->nextScanLength);
                   ˜˜˜˜˜˜˜˜˜˜                                   ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
mzROI.c:218:92: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        int hpos = upperBound( fMass + ddev,scanbuf->nextScan,lpos,scanbuf->nextScanLength - lpos);
                   ˜˜˜˜˜˜˜˜˜˜                                      ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
mzROI.c:218:94: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        int hpos = upperBound( fMass + ddev,scanbuf->nextScan,lpos,scanbuf->nextScanLength - lpos);
                                                                                           ˜ ^˜˜˜
mzROI.c:237:53: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        int i = lower_bound(fMass,mzval,0,mzLength->mzval);
                ˜˜˜˜˜˜˜˜˜˜˜               ˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
mzROI.c:241:33: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
        int n = mzLength->mzval - i;
            ˜   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
mzROI.c:241:35: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        int n = mzLength->mzval - i;
                                ˜ ^
mzROI.c:244:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            memmove(mzval + i +1, mzval + i, n*sizeof(struct mzROIStruct));
                                             ^˜
/usr/include/secure/_string.h:63:42: note: expanded from macro 'memmove'
   ? __builtin___memmove_chk (dest, src, len, __darwin_obsz0 (dest))    \
                                         ^
mzROI.c:244:46: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
            memmove(mzval + i +1, mzval + i, n*sizeof(struct mzROIStruct));
                                             ^˜
/usr/include/secure/_string.h:64:39: note: expanded from macro 'memmove'
   : __inline_memmove_chk (dest, src, len))
                                      ^
mzROI.c:249:30: warning: implicit conversion turns floating-point number into integer: 'const double' to 'unsigned int' [-Wconversion]
        mzval[i].intensity = fInten;
                           ˜ ^˜˜˜˜˜
mzROI.c:250:26: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
        mzval[i].scmin = scan;
                       ˜ ^˜˜˜
mzROI.c:251:26: warning: implicit conversion changes signedness: 'const int' to 'unsigned int' [-Wsign-conversion]
        mzval[i].scmax = scan;
                       ˜ ^˜˜˜
mzROI.c:279:26: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
             p=mzLength->mzROI;
              ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜
mzROI.c:280:46: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
             mzROI=checkmzROIBufSize(mzROI, p+1 , mzLength);
                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜        ˜^˜
mzROI.c:319:80: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    struct mzROIStruct * tmp = (struct mzROIStruct *) calloc(mzLength->mzval - del,  sizeof(struct mzROIStruct));
                                                                             ˜ ^˜˜
mzROI.c:321:106: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
      error("findmzROI/cleanup: buffer memory could not be allocated ! (%d bytes)\n", (mzLength->mzval - del) * sizeof(struct mzROIStruct));
                                                                                                       ˜ ^˜˜
mzROI.c:349:23: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
    mzLength->mzval = p;
                    ˜ ^
mzROI.c:369:58: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
        scanbuf->thisScan= (struct scanStruct  *) calloc(N, sizeof(struct scanStruct));
                                                  ˜˜˜˜˜˜ ^
mzROI.c:374:33: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
        scanbuf->thisScanLength=N;
                               ˜^
mzROI.c:402:50: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            scanbuf->nextScan= (double *) calloc(N, sizeof(double));
                                          ˜˜˜˜˜˜ ^
mzROI.c:405:37: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
            scanbuf->nextScanLength=N;
                                   ˜^
mzROI.c:551:21: warning: implicit conversion loses floating-point precision: 'double' to 'float' [-Wconversion]
  pickOptions.dev = REAL(dev)[0];
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜
mzROI.c:552:28: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  pickOptions.minEntries = INTEGER(minEntries)[0];
                         ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mzROI.c:553:32: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  pickOptions.minimumIntValues=INTEGER(prefilter)[0];
                              ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mzROI.c:554:26: warning: implicit conversion changes signedness: 'int' to 'unsigned int' [-Wsign-conversion]
  pickOptions.minimumInt=INTEGER(prefilter)[1];
                        ˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
mzROI.c:645:45: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      INTEGER_POINTER(vscmin)[0] = mzROI[i].scmin;
                                 ˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
mzROI.c:646:45: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      INTEGER_POINTER(vscmax)[0] = mzROI[i].scmax;
                                 ˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜
mzROI.c:647:46: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      INTEGER_POINTER(vlength)[0] = mzROI[i].length;
                                  ˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜
mzROI.c:648:49: warning: implicit conversion changes signedness: 'unsigned int' to 'int' [-Wsign-conversion]
      INTEGER_POINTER(vintensity)[0] = mzROI[i].intensity;
                                     ˜ ˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜
36 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c util.c -o util.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c xcms.c -o xcms.o
xcms.c:67:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    ibase = floor(*basespace/dx);
          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xcms.c:72:13: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
    ipost = round((xvals[ix] - *xstart)/dx);
          ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xcms.c:95:21: warning: implicit conversion turns floating-point number into integer: 'double' to 'int' [-Wconversion]
            ipost = round((xvals[ix] - *xstart)/dx);
                  ˜ ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
xcms.c:276:53: warning: implicit conversion changes signedness: 'int' to 'unsigned long' [-Wsign-conversion]
    double * sortBuf = (double *) malloc((*mrad*2+1)*(*nrad*2+1)*sizeof(double));
                                         ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
xcms.c:291:28: warning: implicit conversion changes signedness: 'int' to 'size_t' (aka 'unsigned long') [-Wsign-conversion]
            qsort(sortBuf, bufLen, sizeof(double), CompareDouble);
            ˜˜˜˜˜          ^˜˜˜˜˜
5 warnings generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o xcms.so massifquant/xcms_massifquant.o massifquant/TrMgr.o massifquant/Tracker.o massifquant/SegProc.o massifquant/DataKeeper.o massifquant/OpOverload.o obiwarp/mat.o obiwarp/vec.o obiwarp/xcms_dynprog.o obiwarp/xcms_lmat.o xcms_obiwarp.o fastMatch.o mzClust_hclust.o mzROI.o util.o xcms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/xcms.Rcheck/xcms/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xcms)

xcms.Rcheck/xcms-Ex.timings:

nameusersystemelapsed
AutoLockMass-methods0.0100.0020.012
descendZero0.0130.0010.015
findMZ0.0090.0010.009
findneutral0.0060.0010.007
group.mzClust0.0100.0010.011
group.nearest0.1200.0030.122
medianFilter0.0070.0000.007
netCdfSource-class0.0120.0000.013
peakTable-methods0.0120.0020.014
profGenerate0.0100.0010.012
profStep-methods0.0130.0020.014
ramp0.0130.0010.128
rampSource-class0.0080.0010.009
rectUnique0.0220.0010.024
stitch-methods0.0180.0020.020
xcmsPapply0.0080.0010.010
xcmsRaw0.0140.0020.015