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Package 142/671HostnameOS / ArchBUILDCHECKBUILD BIN
CNVtools 1.54.0
Chris Barnes
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/CNVtools
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  WARNINGS 
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  WARNINGS  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS [ OK ]

Summary

Package: CNVtools
Version: 1.54.0
Command: rm -rf CNVtools.buildbin-libdir && mkdir CNVtools.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CNVtools_1.54.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CNVtools.buildbin-libdir
StartedAt: 2013-05-01 12:16:24 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 12:16:34 -0700 (Wed, 01 May 2013)
EllapsedTime: 10.1 seconds
RetCode: 0
Status:  OK 
PackageFile: CNVtools_1.54.0.tgz
PackageFileSize: 865 KiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CNVtools.buildbin-libdir CNVtools_1.54.0.tar.gz'
>>>>>>> 

* installing *source* package 'CNVtools' ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c fitmodel.cpp -o fitmodel.o
In file included from fitmodel.cpp:2:
./fitmodel.h:161:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    return(index[i1] < index[i2]);
           ˜˜˜˜˜ ^˜
./fitmodel.h:161:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    return(index[i1] < index[i2]);
                       ˜˜˜˜˜ ^˜
./fitmodel.h:166:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != (int) index.size(); i++) w[i] = i;
                                                  ˜ ^
fitmodel.cpp:17:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  ret.assign(length*7, 0.);
  ˜˜˜        ˜˜˜˜˜˜^˜
fitmodel.cpp:20:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ret[ i + 0*length ] = posterior[i]; 
    ˜˜˜  ˜˜^˜˜˜˜˜˜˜˜˜
fitmodel.cpp:21:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ret[ i + 1*length]  = mean[i]; 
    ˜˜˜  ˜˜^˜˜˜˜˜˜˜˜˜
fitmodel.cpp:22:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ret[ i + 2*length]  = variance[i]; 
    ˜˜˜  ˜˜^˜˜˜˜˜˜˜˜˜
fitmodel.cpp:23:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ret[ i + 3*length]  = logp[i]; 
    ˜˜˜  ˜˜^˜˜˜˜˜˜˜˜˜
fitmodel.cpp:24:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ret[ i + 4*length]  = alpha[i]; 
    ˜˜˜  ˜˜^˜˜˜˜˜˜˜˜˜
fitmodel.cpp:25:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ret[ i + 5*length]  = proba_disease[i]; 
    ˜˜˜  ˜˜^˜˜˜˜˜˜˜˜˜
fitmodel.cpp:26:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    ret[ i + 6*length]  = nu[i];
    ˜˜˜  ˜˜^˜˜˜˜˜˜˜˜˜
fitmodel.cpp:60:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      alphas[i][j] = 0.;
      ˜˜˜˜˜˜ ^
fitmodel.cpp:60:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      alphas[i][j] = 0.;
      ˜˜˜˜˜˜    ^
fitmodel.cpp:66:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      alphas[ cohort[i] - 1 ][ cn[i] ] += posterior[i];
      ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:66:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      alphas[ cohort[i] - 1 ][ cn[i] ] += posterior[i];
      ˜˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:69:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    vector<double> n(ncohorts,0.);
                   ˜ ^˜˜˜˜˜˜˜
fitmodel.cpp:72:4: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        n[i] += alphas[i][j];
        ˜ ^
fitmodel.cpp:72:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        n[i] += alphas[i][j];
                ˜˜˜˜˜˜ ^
fitmodel.cpp:72:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        n[i] += alphas[i][j];
                ˜˜˜˜˜˜    ^
fitmodel.cpp:77:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        alphas[i][j] /= n[i];
        ˜˜˜˜˜˜ ^
fitmodel.cpp:77:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        alphas[i][j] /= n[i];
        ˜˜˜˜˜˜    ^
fitmodel.cpp:77:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        alphas[i][j] /= n[i];
                        ˜ ^
fitmodel.cpp:78:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (alphas[i][j] < min_n/nind) alphas[i][j] = 0.;  //I want at least min_n individuals per group  
            ˜˜˜˜˜˜ ^
fitmodel.cpp:78:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (alphas[i][j] < min_n/nind) alphas[i][j] = 0.;  //I want at least min_n individuals per group  
            ˜˜˜˜˜˜    ^
fitmodel.cpp:78:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (alphas[i][j] < min_n/nind) alphas[i][j] = 0.;  //I want at least min_n individuals per group  
                                       ˜˜˜˜˜˜ ^
fitmodel.cpp:78:43: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (alphas[i][j] < min_n/nind) alphas[i][j] = 0.;  //I want at least min_n individuals per group  
                                       ˜˜˜˜˜˜    ^
fitmodel.cpp:81:68: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) alpha[i] = alphas[ cohort[i] - 1 ][ cn[i] ];
                                                 ˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:81:75: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) alpha[i] = alphas[ cohort[i] - 1 ][ cn[i] ];
                                                 ˜˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:86:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      alphas[0][ cn[i] ] += posterior[i];
      ˜˜˜˜˜˜     ^˜˜˜˜
fitmodel.cpp:90:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != ncomp; i++)  sum += alphas[0][i];
                                             ˜˜˜˜˜˜    ^
fitmodel.cpp:92:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      alphas[0][i] /= sum;
      ˜˜˜˜˜˜    ^
fitmodel.cpp:93:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (alphas[0][i] < min_n/nind) alphas[0][i] = 0.;  //I want at least min_n individuals per group  
          ˜˜˜˜˜˜    ^
fitmodel.cpp:93:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (alphas[0][i] < min_n/nind) alphas[0][i] = 0.;  //I want at least min_n individuals per group  
                                     ˜˜˜˜˜˜    ^
fitmodel.cpp:95:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) alpha[i] = alphas[0][ cn[i] ];
                                                 ˜˜˜˜˜˜     ^˜˜˜˜
fitmodel.cpp:297:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  vector<vector<double> > n(ncohorts, vector<double>(ncomp, 0 ));
                          ˜ ^˜˜˜˜˜˜˜
fitmodel.cpp:301:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  for (int i = 0; i != length; i++) means[ cohort[i] - 1][ cn[i] ] = mean[i];
                                    ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:301:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  for (int i = 0; i != length; i++) means[ cohort[i] - 1][ cn[i] ] = mean[i];
                                    ˜˜˜˜˜                  ^˜˜˜˜
fitmodel.cpp:306:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[i][j] = 0;
      ˜˜˜˜˜˜˜˜˜ ^
fitmodel.cpp:306:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[i][j] = 0;
      ˜˜˜˜˜˜˜˜˜    ^
fitmodel.cpp:312:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      n[ 0 ][ cn[i] ] += posterior[i];
      ˜       ^˜˜˜˜
fitmodel.cpp:313:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double res = signal[i] - means[ cohort[i] - 1 ][ cn[i] ];
                               ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:313:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double res = signal[i] - means[ cohort[i] - 1 ][ cn[i] ];
                               ˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:314:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[ 0 ][ cn[i] ] += posterior[i]*res*res;
      ˜˜˜˜˜˜˜˜˜       ^˜˜˜˜
fitmodel.cpp:317:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      n[ cohort[i] - 1][ cn[i] ] += posterior[i];
      ˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:317:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      n[ cohort[i] - 1][ cn[i] ] += posterior[i];
      ˜                  ^˜˜˜˜
fitmodel.cpp:318:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double res = signal[i] - means[ cohort[i] - 1 ][ cn[i] ];
                               ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:318:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double res = signal[i] - means[ cohort[i] - 1 ][ cn[i] ];
                               ˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:319:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[ cohort[i] - 1][ cn[i] ] += posterior[i]*res*res;
      ˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:319:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[ cohort[i] - 1][ cn[i] ] += posterior[i]*res*res;
      ˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜
fitmodel.cpp:327:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        temp += shrinkage*n[ 0 ][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[ 0 ][j]); 
                          ˜      ^
fitmodel.cpp:327:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        temp += shrinkage*n[ 0 ][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[ 0 ][j]); 
                                     ˜˜˜˜˜ ^
fitmodel.cpp:327:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        temp += shrinkage*n[ 0 ][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[ 0 ][j]); 
                                     ˜˜˜˜˜    ^
fitmodel.cpp:327:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        temp += shrinkage*n[ 0 ][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[ 0 ][j]); 
                                                            ˜˜˜˜˜ ^
fitmodel.cpp:327:63: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        temp += shrinkage*n[ 0 ][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[ 0 ][j]); 
                                                            ˜˜˜˜˜    ^
fitmodel.cpp:327:96: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        temp += shrinkage*n[ 0 ][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[ 0 ][j]); 
                                                                                               ˜      ^
fitmodel.cpp:329:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[ 0 ][j] = (scale + temp + variances[ 0 ][j])/( dof + n[ 0 ][j] + 3 );
      ˜˜˜˜˜˜˜˜˜      ^
fitmodel.cpp:329:58: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[ 0 ][j] = (scale + temp + variances[ 0 ][j])/( dof + n[ 0 ][j] + 3 );
                                          ˜˜˜˜˜˜˜˜˜      ^
fitmodel.cpp:329:77: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[ 0 ][j] = (scale + temp + variances[ 0 ][j])/( dof + n[ 0 ][j] + 3 );
                                                                     ˜      ^
fitmodel.cpp:336:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double temp = scale + shrinkage*n[i][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[i][j]) + variances[i][j]; 
                                        ˜ ^
fitmodel.cpp:336:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double temp = scale + shrinkage*n[i][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[i][j]) + variances[i][j]; 
                                        ˜    ^
fitmodel.cpp:336:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double temp = scale + shrinkage*n[i][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[i][j]) + variances[i][j]; 
                                                 ˜˜˜˜˜ ^
fitmodel.cpp:336:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double temp = scale + shrinkage*n[i][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[i][j]) + variances[i][j]; 
                                                 ˜˜˜˜˜    ^
fitmodel.cpp:336:72: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double temp = scale + shrinkage*n[i][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[i][j]) + variances[i][j]; 
                                                                        ˜˜˜˜˜ ^
fitmodel.cpp:336:75: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double temp = scale + shrinkage*n[i][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[i][j]) + variances[i][j]; 
                                                                        ˜˜˜˜˜    ^
fitmodel.cpp:336:103: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double temp = scale + shrinkage*n[i][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[i][j]) + variances[i][j]; 
                                                                                                           ˜ ^
fitmodel.cpp:336:106: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double temp = scale + shrinkage*n[i][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[i][j]) + variances[i][j]; 
                                                                                                           ˜    ^
fitmodel.cpp:336:122: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double temp = scale + shrinkage*n[i][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[i][j]) + variances[i][j]; 
                                                                                                                      ˜˜˜˜˜˜˜˜˜ ^
fitmodel.cpp:336:125: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        double temp = scale + shrinkage*n[i][j]*(means[i][j] - mean_p)*(means[i][j] - mean_p)/(shrinkage + n[i][j]) + variances[i][j]; 
                                                                                                                      ˜˜˜˜˜˜˜˜˜    ^
fitmodel.cpp:337:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        variances[i][j] = temp/( dof + n[i][j] + 3 );
        ˜˜˜˜˜˜˜˜˜ ^
fitmodel.cpp:337:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        variances[i][j] = temp/( dof + n[i][j] + 3 );
        ˜˜˜˜˜˜˜˜˜    ^
fitmodel.cpp:337:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        variances[i][j] = temp/( dof + n[i][j] + 3 );
                                       ˜ ^
fitmodel.cpp:337:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        variances[i][j] = temp/( dof + n[i][j] + 3 );
                                       ˜    ^
fitmodel.cpp:345:69: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) variance[i] = variances[ 0 ][ cn[i] ];
                                                    ˜˜˜˜˜˜˜˜˜       ^˜˜˜˜
fitmodel.cpp:348:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) variance[i] = variances[ cohort[i] - 1][ cn[i] ];
                                                    ˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:348:80: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) variance[i] = variances[ cohort[i] - 1][ cn[i] ];
                                                    ˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜
fitmodel.cpp:357:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  vector<vector<double> > n(ncohorts, vector<double>(ncomp, 0 ));
                          ˜ ^˜˜˜˜˜˜˜
fitmodel.cpp:362:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[i][j] = 0;
      ˜˜˜˜˜ ^
fitmodel.cpp:362:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[i][j] = 0;
      ˜˜˜˜˜    ^
fitmodel.cpp:367:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    n[ cohort[i] - 1][ cn[i] ] += posterior[i];
    ˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:367:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    n[ cohort[i] - 1][ cn[i] ] += posterior[i];
    ˜                  ^˜˜˜˜
fitmodel.cpp:368:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    means[ cohort[i] - 1][ cn[i] ] += posterior[i]*signal[i];
    ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:368:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    means[ cohort[i] - 1][ cn[i] ] += posterior[i]*signal[i];
    ˜˜˜˜˜                  ^˜˜˜˜
fitmodel.cpp:373:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[i][j] = (means[i][j] + shrinkage*mean_p)/( n[i][j] + shrinkage );
      ˜˜˜˜˜ ^
fitmodel.cpp:373:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[i][j] = (means[i][j] + shrinkage*mean_p)/( n[i][j] + shrinkage );
      ˜˜˜˜˜    ^
fitmodel.cpp:373:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[i][j] = (means[i][j] + shrinkage*mean_p)/( n[i][j] + shrinkage );
                     ˜˜˜˜˜ ^
fitmodel.cpp:373:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[i][j] = (means[i][j] + shrinkage*mean_p)/( n[i][j] + shrinkage );
                     ˜˜˜˜˜    ^
fitmodel.cpp:373:58: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[i][j] = (means[i][j] + shrinkage*mean_p)/( n[i][j] + shrinkage );
                                                       ˜ ^
fitmodel.cpp:373:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[i][j] = (means[i][j] + shrinkage*mean_p)/( n[i][j] + shrinkage );
                                                       ˜    ^
fitmodel.cpp:378:64: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  for (int i = 0; i != length; i++) mean[i] = means[ cohort[i] - 1][ cn[i] ];
                                              ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:378:70: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  for (int i = 0; i != length; i++) mean[i] = means[ cohort[i] - 1][ cn[i] ];
                                              ˜˜˜˜˜                  ^˜˜˜˜
fitmodel.cpp:416:24: warning: implicit conversion turns floating-point number into integer: 'const double' to 'bool' [-Wconversion]
    double p_disease = disease_status[i] ? proba_disease[i] : 1. - proba_disease[i];
           ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fitmodel.cpp:466:26: warning: implicit conversion turns floating-point number into integer: 'const double' to 'bool' [-Wconversion]
      double p_disease = disease_status[i] ? proba_disease[i] : 1. - proba_disease[i];
             ˜˜˜˜˜˜˜˜˜   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fitmodel.cpp:496:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  vector<vector<double> > n(ncohorts, vector<double>(ncomp, 0 ));
                          ˜ ^˜˜˜˜˜˜˜
fitmodel.cpp:501:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[i][j] = 0;
      ˜˜˜˜˜ ^
fitmodel.cpp:501:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[i][j] = 0;
      ˜˜˜˜˜    ^
fitmodel.cpp:509:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      n[ 0 ][ cn[i] ] += posterior[i]*u[i];
      ˜       ^˜˜˜˜
fitmodel.cpp:510:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[ 0 ][ cn[i] ] += posterior[i]*u[i]*signal[i];
      ˜˜˜˜˜       ^˜˜˜˜
fitmodel.cpp:514:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (n[0][j] > 0) means[ 0 ][j] /= n[ 0 ][j]; else means[0][j] = -99.;
          ˜    ^
fitmodel.cpp:514:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (n[0][j] > 0) means[ 0 ][j] /= n[ 0 ][j]; else means[0][j] = -99.;
                       ˜˜˜˜˜      ^
fitmodel.cpp:514:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (n[0][j] > 0) means[ 0 ][j] /= n[ 0 ][j]; else means[0][j] = -99.;
                                        ˜      ^
fitmodel.cpp:514:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (n[0][j] > 0) means[ 0 ][j] /= n[ 0 ][j]; else means[0][j] = -99.;
                                                        ˜˜˜˜˜    ^
fitmodel.cpp:518:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) mean[i] = means[ 0 ][ cn[i] ];
                                                ˜˜˜˜˜       ^˜˜˜˜
fitmodel.cpp:524:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      n[ cohort[i] - 1][ cn[i] ] += posterior[i]*u[i];
      ˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:524:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      n[ cohort[i] - 1][ cn[i] ] += posterior[i]*u[i];
      ˜                  ^˜˜˜˜
fitmodel.cpp:525:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[ cohort[i] - 1][ cn[i] ] += posterior[i]*u[i]*signal[i];
      ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:525:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[ cohort[i] - 1][ cn[i] ] += posterior[i]*u[i]*signal[i];
      ˜˜˜˜˜                  ^˜˜˜˜
fitmodel.cpp:530:8: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] > 0) means[i][j] /= n[i][j]; else means[i][j] = -99.;
            ˜ ^
fitmodel.cpp:530:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] > 0) means[i][j] /= n[i][j]; else means[i][j] = -99.;
            ˜    ^
fitmodel.cpp:530:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] > 0) means[i][j] /= n[i][j]; else means[i][j] = -99.;
                         ˜˜˜˜˜ ^
fitmodel.cpp:530:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] > 0) means[i][j] /= n[i][j]; else means[i][j] = -99.;
                         ˜˜˜˜˜    ^
fitmodel.cpp:530:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] > 0) means[i][j] /= n[i][j]; else means[i][j] = -99.;
                                        ˜ ^
fitmodel.cpp:530:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] > 0) means[i][j] /= n[i][j]; else means[i][j] = -99.;
                                        ˜    ^
fitmodel.cpp:530:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] > 0) means[i][j] /= n[i][j]; else means[i][j] = -99.;
                                                      ˜˜˜˜˜ ^
fitmodel.cpp:530:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] > 0) means[i][j] /= n[i][j]; else means[i][j] = -99.;
                                                      ˜˜˜˜˜    ^
fitmodel.cpp:535:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) mean[i] = means[ cohort[i] - 1][ cn[i] ];
                                                ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:535:72: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) mean[i] = means[ cohort[i] - 1][ cn[i] ];
                                                ˜˜˜˜˜                  ^˜˜˜˜
fitmodel.cpp:550:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  vector<vector<double> > n(ncohorts, vector<double>(ncomp, 0 ));
                          ˜ ^˜˜˜˜˜˜˜
fitmodel.cpp:554:54: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  for (int i = 0; i != length; i++) means[ cohort[i] - 1][ cn[i] ] = mean[i];
                                    ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:554:60: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  for (int i = 0; i != length; i++) means[ cohort[i] - 1][ cn[i] ] = mean[i];
                                    ˜˜˜˜˜                  ^˜˜˜˜
fitmodel.cpp:559:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[i][j] = 0;
      ˜˜˜˜˜˜˜˜˜ ^
fitmodel.cpp:559:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[i][j] = 0;
      ˜˜˜˜˜˜˜˜˜    ^
fitmodel.cpp:566:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double res = signal[i] - means[ cohort[i] - 1 ][ cn[i] ];
                               ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:566:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double res = signal[i] - means[ cohort[i] - 1 ][ cn[i] ];
                               ˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:576:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      n[ cohort[i] - 1][ 0 ] += posterior[i];
      ˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:577:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double res = signal[i] - means[ cohort[i] - 1 ][ cn[i] ];
                               ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:577:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double res = signal[i] - means[ cohort[i] - 1 ][ cn[i] ];
                               ˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:578:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[ cohort[i] - 1 ][ 0 ] += posterior[i]*u[i]*res*res;
      ˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:582:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (n[i][0] >= 2) variances[ i ][ 0 ] /= n[ i ][ 0 ]; else variances[ i ][ 0 ] = 0.0001;
          ˜ ^
fitmodel.cpp:582:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (n[i][0] >= 2) variances[ i ][ 0 ] /= n[ i ][ 0 ]; else variances[ i ][ 0 ] = 0.0001;
                        ˜˜˜˜˜˜˜˜˜  ^
fitmodel.cpp:582:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (n[i][0] >= 2) variances[ i ][ 0 ] /= n[ i ][ 0 ]; else variances[ i ][ 0 ] = 0.0001;
                                               ˜  ^
fitmodel.cpp:582:77: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (n[i][0] >= 2) variances[ i ][ 0 ] /= n[ i ][ 0 ]; else variances[ i ][ 0 ] = 0.0001;
                                                                 ˜˜˜˜˜˜˜˜˜  ^
fitmodel.cpp:584:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) variance[i] = variances[ cohort[i] - 1][ 0 ];
                                                    ˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:589:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      n[ 0 ][ cn[i] ] += posterior[i];
      ˜       ^˜˜˜˜
fitmodel.cpp:590:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double res = signal[i] - means[ cohort[i] - 1 ][ cn[i] ];
                               ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:590:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double res = signal[i] - means[ cohort[i] - 1 ][ cn[i] ];
                               ˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:591:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[ 0 ][ cn[i] ] += posterior[i]*u[i]*res*res;
      ˜˜˜˜˜˜˜˜˜       ^˜˜˜˜
fitmodel.cpp:594:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (n[0][j] >= 2) variances[ 0 ][j] /= n[ 0 ][j]; else variances[ 0 ][j] = 0.0001;
          ˜    ^
fitmodel.cpp:594:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (n[0][j] >= 2) variances[ 0 ][j] /= n[ 0 ][j]; else variances[ 0 ][j] = 0.0001;
                        ˜˜˜˜˜˜˜˜˜      ^
fitmodel.cpp:594:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (n[0][j] >= 2) variances[ 0 ][j] /= n[ 0 ][j]; else variances[ 0 ][j] = 0.0001;
                                             ˜      ^
fitmodel.cpp:594:77: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (n[0][j] >= 2) variances[ 0 ][j] /= n[ 0 ][j]; else variances[ 0 ][j] = 0.0001;
                                                             ˜˜˜˜˜˜˜˜˜      ^
fitmodel.cpp:596:69: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) variance[i] = variances[ 0 ][ cn[i] ];
                                                    ˜˜˜˜˜˜˜˜˜       ^˜˜˜˜
fitmodel.cpp:601:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      n[ cohort[i] - 1][ cn[i] ] += posterior[i];
      ˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:601:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      n[ cohort[i] - 1][ cn[i] ] += posterior[i];
      ˜                  ^˜˜˜˜
fitmodel.cpp:602:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double res = signal[i] - means[ cohort[i] - 1 ][ cn[i] ];
                               ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:602:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double res = signal[i] - means[ cohort[i] - 1 ][ cn[i] ];
                               ˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:603:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[ cohort[i] - 1][ cn[i] ] += posterior[i]*u[i]*res*res;
      ˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:603:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[ cohort[i] - 1][ cn[i] ] += posterior[i]*u[i]*res*res;
      ˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜
fitmodel.cpp:608:8: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] >= 2) variances[i][j] /= n[i][j]; else variances[i][j] = 0.0001;  //this may be an issue: not enough points in a specific cohort to estimate the variance of this component
            ˜ ^
fitmodel.cpp:608:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] >= 2) variances[i][j] /= n[i][j]; else variances[i][j] = 0.0001;  //this may be an issue: not enough points in a specific cohort to estimate the variance of this component
            ˜    ^
fitmodel.cpp:608:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] >= 2) variances[i][j] /= n[i][j]; else variances[i][j] = 0.0001;  //this may be an issue: not enough points in a specific cohort to estimate the variance of this component
                          ˜˜˜˜˜˜˜˜˜ ^
fitmodel.cpp:608:33: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] >= 2) variances[i][j] /= n[i][j]; else variances[i][j] = 0.0001;  //this may be an issue: not enough points in a specific cohort to estimate the variance of this component
                          ˜˜˜˜˜˜˜˜˜    ^
fitmodel.cpp:608:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] >= 2) variances[i][j] /= n[i][j]; else variances[i][j] = 0.0001;  //this may be an issue: not enough points in a specific cohort to estimate the variance of this component
                                             ˜ ^
fitmodel.cpp:608:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] >= 2) variances[i][j] /= n[i][j]; else variances[i][j] = 0.0001;  //this may be an issue: not enough points in a specific cohort to estimate the variance of this component
                                             ˜    ^
fitmodel.cpp:608:63: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] >= 2) variances[i][j] /= n[i][j]; else variances[i][j] = 0.0001;  //this may be an issue: not enough points in a specific cohort to estimate the variance of this component
                                                           ˜˜˜˜˜˜˜˜˜ ^
fitmodel.cpp:608:66: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] >= 2) variances[i][j] /= n[i][j]; else variances[i][j] = 0.0001;  //this may be an issue: not enough points in a specific cohort to estimate the variance of this component
                                                           ˜˜˜˜˜˜˜˜˜    ^
fitmodel.cpp:611:74: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) variance[i] = variances[ cohort[i] - 1][ cn[i] ];
                                                    ˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:611:80: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) variance[i] = variances[ cohort[i] - 1][ cn[i] ];
                                                    ˜˜˜˜˜˜˜˜˜                  ^˜˜˜˜
fitmodel.cpp:628:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  vector<vector<double> > n(ncohorts, vector<double>(ncomp, 0 )); //sum(z[,i])  
                          ˜ ^˜˜˜˜˜˜˜
fitmodel.cpp:629:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  vector<vector<double> > val(ncohorts, vector<double>(ncomp, 0 )); //sum( z[,i]*(log(u[,i]) - u[,i]) )
                          ˜˜˜ ^˜˜˜˜˜˜˜
fitmodel.cpp:667:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      n[ cohort[i] - 1][ 0 ] += posterior[i];
      ˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:668:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      val[ cohort[i] - 1 ][ 0 ] += posterior[i]*( log(u[i]) - u[i] ); 
      ˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:672:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      val[i][ 0 ] = val[ i ][ 0 ]/n[ i ][ 0 ];
      ˜˜˜ ^
fitmodel.cpp:672:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      val[i][ 0 ] = val[ i ][ 0 ]/n[ i ][ 0 ];
                    ˜˜˜  ^
fitmodel.cpp:672:38: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      val[i][ 0 ] = val[ i ][ 0 ]/n[ i ][ 0 ];
                                  ˜  ^
fitmodel.cpp:676:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if( nus[ i ][ 0 ] >= numax ) continue;
          ˜˜˜  ^
fitmodel.cpp:678:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double xx = (nus[ i ][ 0 ] + 1)/2; 
                   ˜˜˜  ^
fitmodel.cpp:679:25: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      tvalue = 1 + val[ i ][ 0 ] + gmath::psi(xx) - log( xx );
                   ˜˜˜  ^
fitmodel.cpp:685:7: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        nus[ i ][ 0 ] =  zeroin(rmin, rmax, function_to_find_root, 0.05);
        ˜˜˜  ^
fitmodel.cpp:692:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) nu[i] = nus[ cohort[i] - 1][ 0 ];
                                              ˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:697:15: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      n[ 0 ][ cn[i] ] += posterior[i];
      ˜       ^˜˜˜˜
fitmodel.cpp:698:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      val[ 0 ][ cn[i] ] += posterior[i]*( log(u[i]) - u[i] );
      ˜˜˜       ^˜˜˜˜
fitmodel.cpp:702:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      val[ 0 ][j] = val[ 0 ][j]/n[ 0 ][j];
      ˜˜˜      ^
fitmodel.cpp:702:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      val[ 0 ][j] = val[ 0 ][j]/n[ 0 ][j];
                    ˜˜˜      ^
fitmodel.cpp:702:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      val[ 0 ][j] = val[ 0 ][j]/n[ 0 ][j];
                                ˜      ^
fitmodel.cpp:706:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if( nus[ 0 ][ j ] >= numax ) continue;
          ˜˜˜       ^
fitmodel.cpp:708:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      double xx = (nus[ 0 ][ j ] + 1)/2;
                   ˜˜˜       ^
fitmodel.cpp:709:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      tvalue = 1 + val[ 0 ][ j ] + gmath::psi(xx) - log( xx );
                   ˜˜˜       ^
fitmodel.cpp:715:12: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        nus[ 0 ][ j ] =  zeroin(rmin, rmax, function_to_find_root, 0.05);
        ˜˜˜       ^
fitmodel.cpp:722:57: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) nu[i] = nus[ 0 ][ cn[i] ];
                                              ˜˜˜       ^˜˜˜˜
fitmodel.cpp:727:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      n[ cohort[i] - 1][ cn[i] ] += posterior[i];
      ˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:727:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      n[ cohort[i] - 1][ cn[i] ] += posterior[i];
      ˜                  ^˜˜˜˜
fitmodel.cpp:728:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      val[ cohort[i] - 1 ][ cn[i] ] += posterior[i]*( log(u[i]) - u[i] ); 
      ˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:728:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      val[ cohort[i] - 1 ][ cn[i] ] += posterior[i]*( log(u[i]) - u[i] ); 
      ˜˜˜                   ^˜˜˜˜
fitmodel.cpp:733:8: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] > 0) val[i][j] /= n[i][j];
            ˜ ^
fitmodel.cpp:733:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] > 0) val[i][j] /= n[i][j];
            ˜    ^
fitmodel.cpp:733:23: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] > 0) val[i][j] /= n[i][j];
                         ˜˜˜ ^
fitmodel.cpp:733:26: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] > 0) val[i][j] /= n[i][j];
                         ˜˜˜    ^
fitmodel.cpp:733:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] > 0) val[i][j] /= n[i][j];
                                      ˜ ^
fitmodel.cpp:733:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[i][j] > 0) val[i][j] /= n[i][j];
                                      ˜    ^
fitmodel.cpp:739:9: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[ i ][ j ] > 0) {
            ˜  ^
fitmodel.cpp:739:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        if (n[ i ][ j ] > 0) {
            ˜       ^
fitmodel.cpp:740:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          if( nus[ i ][ j ] >= numax ) continue;
              ˜˜˜  ^
fitmodel.cpp:740:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          if( nus[ i ][ j ] >= numax ) continue;
              ˜˜˜       ^
fitmodel.cpp:743:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          double xx = (nus[ i ][ j ] + 1)/2;
                       ˜˜˜  ^
fitmodel.cpp:743:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          double xx = (nus[ i ][ j ] + 1)/2;
                       ˜˜˜       ^
fitmodel.cpp:744:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          tvalue = 1 + val[ i ][ j ] + gmath::psi(xx) - log( xx );
                       ˜˜˜  ^
fitmodel.cpp:744:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
          tvalue = 1 + val[ i ][ j ] + gmath::psi(xx) - log( xx );
                       ˜˜˜       ^
fitmodel.cpp:750:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            nus[ i ][ j ] =  zeroin(rmin, rmax, function_to_find_root, 0.05);
            ˜˜˜  ^
fitmodel.cpp:750:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
            nus[ i ][ j ] =  zeroin(rmin, rmax, function_to_find_root, 0.05);
            ˜˜˜       ^
fitmodel.cpp:755:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        } else { nus[ i ][ j ] = 10;}  //some default values when proba of class is 0
                 ˜˜˜  ^
fitmodel.cpp:755:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
        } else { nus[ i ][ j ] = 10;}  //some default values when proba of class is 0
                 ˜˜˜       ^
fitmodel.cpp:758:62: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) nu[i] = nus[ cohort[i] - 1][ cn[i] ];  
                                              ˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:758:68: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != length; i++) nu[i] = nus[ cohort[i] - 1][ cn[i] ];  
                                              ˜˜˜                  ^˜˜˜˜
fitmodel.cpp:787:27: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      cout << "\t" << nus[i][j]; 
                      ˜˜˜ ^
fitmodel.cpp:787:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      cout << "\t" << nus[i][j]; 
                      ˜˜˜    ^
fitmodel.cpp:801:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      nus[i][j] = -99.0;
      ˜˜˜ ^
fitmodel.cpp:801:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      nus[i][j] = -99.0;
      ˜˜˜    ^
fitmodel.cpp:802:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[i][j] = -99.;
      ˜˜˜˜˜˜˜˜˜ ^
fitmodel.cpp:802:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[i][j] = -99.;
      ˜˜˜˜˜˜˜˜˜    ^
fitmodel.cpp:803:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[i][j] = -99.;
      ˜˜˜˜˜ ^
fitmodel.cpp:803:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[i][j] = -99.;
      ˜˜˜˜˜    ^
fitmodel.cpp:804:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postLogit[j] = 0.;
      ˜˜˜˜˜˜˜˜˜ ^
fitmodel.cpp:805:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postTable[i][j] = -1.;
      ˜˜˜˜˜˜˜˜˜ ^
fitmodel.cpp:805:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postTable[i][j] = -1.;
      ˜˜˜˜˜˜˜˜˜    ^
fitmodel.cpp:812:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postLogit2[ s ][ j ] = -0.1;
      ˜˜˜˜˜˜˜˜˜˜  ^
fitmodel.cpp:812:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postLogit2[ s ][ j ] = -0.1;
      ˜˜˜˜˜˜˜˜˜˜       ^
fitmodel.cpp:813:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      proba_d[ s ][ j ] = 0.;
      ˜˜˜˜˜˜˜  ^
fitmodel.cpp:813:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      proba_d[ s ][ j ] = 0.;
      ˜˜˜˜˜˜˜       ^
fitmodel.cpp:821:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (posterior[i] > postTable [cohort[i] - 1 ][ cn[i] ] ) {
                       ˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:821:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (posterior[i] > postTable [cohort[i] - 1 ][ cn[i] ] ) {
                       ˜˜˜˜˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:822:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[ cohort[i] - 1 ][ cn[i] ] = variance[i];
      ˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:822:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[ cohort[i] - 1 ][ cn[i] ] = variance[i];
      ˜˜˜˜˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:823:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[ cohort[i] - 1 ][ cn[i] ] = mean[i];
      ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:823:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[ cohort[i] - 1 ][ cn[i] ] = mean[i];
      ˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:824:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postTable [cohort[i] - 1 ][ cn[i] ] = posterior[i];
      ˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:824:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postTable [cohort[i] - 1 ][ cn[i] ] = posterior[i];
      ˜˜˜˜˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:825:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      nus[ cohort[i] - 1 ][ cn[i] ] = nu[i];
      ˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:825:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      nus[ cohort[i] - 1 ][ cn[i] ] = nu[i];
      ˜˜˜                   ^˜˜˜˜
fitmodel.cpp:829:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (posterior[i] > postLogit2[ s ][ cn[i] ]) {
                       ˜˜˜˜˜˜˜˜˜˜  ^
fitmodel.cpp:829:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (posterior[i] > postLogit2[ s ][ cn[i] ]) {
                       ˜˜˜˜˜˜˜˜˜˜       ^˜˜˜˜
fitmodel.cpp:830:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      proba_d[ s ][ cn[i] ] = proba_disease[i];
      ˜˜˜˜˜˜˜  ^
fitmodel.cpp:830:21: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      proba_d[ s ][ cn[i] ] = proba_disease[i];
      ˜˜˜˜˜˜˜       ^˜˜˜˜
fitmodel.cpp:831:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postLogit2[ s ][ cn[i] ] = posterior[i];
      ˜˜˜˜˜˜˜˜˜˜  ^
fitmodel.cpp:831:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postLogit2[ s ][ cn[i] ] = posterior[i];
      ˜˜˜˜˜˜˜˜˜˜       ^˜˜˜˜
fitmodel.cpp:834:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (posterior[i] > postLogit[ cn[i] ]) {
                       ˜˜˜˜˜˜˜˜˜  ^˜˜˜˜
fitmodel.cpp:835:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postLogit[ cn[i] ] = posterior[i];
      ˜˜˜˜˜˜˜˜˜  ^˜˜˜˜
fitmodel.cpp:836:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      alpha_m[ cn[i] ] = alpha[i];
      ˜˜˜˜˜˜˜  ^˜˜˜˜
fitmodel.cpp:843:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    myRank * hope = new myRank(means[ i ]);
                               ˜˜˜˜˜  ^
fitmodel.cpp:852:42: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variance[j] = variances[ cohort[j] - 1 ][ ranks[cohort[j] - 1][ cn[j] ] ];
                    ˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:852:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variance[j] = variances[ cohort[j] - 1 ][ ranks[cohort[j] - 1][ cn[j] ] ];
                    ˜˜˜˜˜˜˜˜˜                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fitmodel.cpp:852:65: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variance[j] = variances[ cohort[j] - 1 ][ ranks[cohort[j] - 1][ cn[j] ] ];
                                                ˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:852:71: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variance[j] = variances[ cohort[j] - 1 ][ ranks[cohort[j] - 1][ cn[j] ] ];
                                                ˜˜˜˜˜                 ^˜˜˜˜
fitmodel.cpp:853:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      nu[j] = nus[ cohort[j] - 1 ][ ranks[cohort[j] - 1][ cn[j] ] ];
              ˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:853:37: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      nu[j] = nus[ cohort[j] - 1 ][ ranks[cohort[j] - 1][ cn[j] ] ];
              ˜˜˜                   ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fitmodel.cpp:853:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      nu[j] = nus[ cohort[j] - 1 ][ ranks[cohort[j] - 1][ cn[j] ] ];
                                    ˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:853:59: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      nu[j] = nus[ cohort[j] - 1 ][ ranks[cohort[j] - 1][ cn[j] ] ];
                                    ˜˜˜˜˜                 ^˜˜˜˜
fitmodel.cpp:854:34: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      mean[j] = means[ cohort[j] - 1 ][    ranks[cohort[j]-1][cn[j]] ];
                ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:854:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      mean[j] = means[ cohort[j] - 1 ][    ranks[cohort[j]-1][cn[j]] ];
                ˜˜˜˜˜                      ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fitmodel.cpp:854:59: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      mean[j] = means[ cohort[j] - 1 ][    ranks[cohort[j]-1][cn[j]] ];
                                           ˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜
fitmodel.cpp:854:63: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      mean[j] = means[ cohort[j] - 1 ][    ranks[cohort[j]-1][cn[j]] ];
                                           ˜˜˜˜˜              ^˜˜˜˜
fitmodel.cpp:855:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      alpha[j] = alpha_m [  ranks[cohort[j]-1][cn[j]]   ];
                 ˜˜˜˜˜˜˜    ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fitmodel.cpp:855:44: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      alpha[j] = alpha_m [  ranks[cohort[j]-1][cn[j]]   ];
                            ˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜
fitmodel.cpp:855:48: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      alpha[j] = alpha_m [  ranks[cohort[j]-1][cn[j]]   ];
                            ˜˜˜˜˜              ^˜˜˜˜
fitmodel.cpp:857:51: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      proba_disease[j] = proba_d[ assoc_strata[j] - 1 ][    ranks[cohort[j]-1][cn[j]]  ];
                         ˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:857:61: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      proba_disease[j] = proba_d[ assoc_strata[j] - 1 ][    ranks[cohort[j]-1][cn[j]]  ];
                         ˜˜˜˜˜˜˜                            ^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
fitmodel.cpp:857:76: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      proba_disease[j] = proba_d[ assoc_strata[j] - 1 ][    ranks[cohort[j]-1][cn[j]]  ];
                                                            ˜˜˜˜˜ ˜˜˜˜˜˜˜˜˜^˜
fitmodel.cpp:857:80: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      proba_disease[j] = proba_d[ assoc_strata[j] - 1 ][    ranks[cohort[j]-1][cn[j]]  ];
                                                            ˜˜˜˜˜              ^˜˜˜˜
fitmodel.cpp:867:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[i][j] = 0.0001;
      ˜˜˜˜˜˜˜˜˜ ^
fitmodel.cpp:867:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      variances[i][j] = 0.0001;
      ˜˜˜˜˜˜˜˜˜    ^
fitmodel.cpp:868:11: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      nus[i][j] = -99.;
      ˜˜˜ ^
fitmodel.cpp:868:14: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      nus[i][j] = -99.;
      ˜˜˜    ^
fitmodel.cpp:869:13: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[i][j] = -99.;
      ˜˜˜˜˜ ^
fitmodel.cpp:869:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[i][j] = -99.;
      ˜˜˜˜˜    ^
fitmodel.cpp:870:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postLogit[j] = 0.;
      ˜˜˜˜˜˜˜˜˜ ^
fitmodel.cpp:871:17: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postTable[i][j] = 0;
      ˜˜˜˜˜˜˜˜˜ ^
fitmodel.cpp:871:20: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postTable[i][j] = 0;
      ˜˜˜˜˜˜˜˜˜    ^
fitmodel.cpp:877:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postLogit2[ i ][ j ]  = -0.1;
      ˜˜˜˜˜˜˜˜˜˜  ^
fitmodel.cpp:877:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postLogit2[ i ][ j ]  = -0.1;
      ˜˜˜˜˜˜˜˜˜˜       ^
fitmodel.cpp:883:45: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (posterior[i] > postTable [cohort[i] - 1 ][ cn[i] ] ) {
                       ˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:883:52: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (posterior[i] > postTable [cohort[i] - 1 ][ cn[i] ] ) {
                       ˜˜˜˜˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:884:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      nus[ cohort[i] - 1 ][ cn[i] ] = nu[i];
      ˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:884:29: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      nus[ cohort[i] - 1 ][ cn[i] ] = nu[i];
      ˜˜˜                   ^˜˜˜˜
fitmodel.cpp:885:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (variance[i] > 0) variances[ cohort[i] - 1 ][ cn[i] ] = variance[i];
                           ˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:885:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      if (variance[i] > 0) variances[ cohort[i] - 1 ][ cn[i] ] = variance[i];
                           ˜˜˜˜˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:886:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[ cohort[i] - 1 ][ cn[i] ] = mean[i];
      ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:886:31: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      means[ cohort[i] - 1 ][ cn[i] ] = mean[i];
      ˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:887:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postTable [cohort[i] - 1 ][ cn[i] ] = posterior[i];
      ˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:887:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postTable [cohort[i] - 1 ][ cn[i] ] = posterior[i];
      ˜˜˜˜˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:890:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (posterior[i] > postLogit[ cn[i] ]) {
                       ˜˜˜˜˜˜˜˜˜  ^˜˜˜˜
fitmodel.cpp:891:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postLogit[ cn[i] ] = posterior[i];
      ˜˜˜˜˜˜˜˜˜  ^˜˜˜˜
fitmodel.cpp:895:36: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (posterior[i] > postLogit2[ s ][ cn[i] ]) {
                       ˜˜˜˜˜˜˜˜˜˜  ^
fitmodel.cpp:895:41: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if (posterior[i] > postLogit2[ s ][ cn[i] ]) {
                       ˜˜˜˜˜˜˜˜˜˜       ^˜˜˜˜
fitmodel.cpp:897:16: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      proba_d[ s ] [ cn[i] ] = proba_disease[i];
      ˜˜˜˜˜˜˜  ^
fitmodel.cpp:897:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      proba_d[ s ] [ cn[i] ] = proba_disease[i];
      ˜˜˜˜˜˜˜        ^˜˜˜˜
fitmodel.cpp:898:19: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postLogit2[ s ][ cn[i] ] = posterior[i];      
      ˜˜˜˜˜˜˜˜˜˜  ^
fitmodel.cpp:898:24: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
      postLogit2[ s ][ cn[i] ] = posterior[i];      
      ˜˜˜˜˜˜˜˜˜˜       ^˜˜˜˜
fitmodel.cpp:906:28: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    nu[i] = nus[ cohort[i] - 1 ][ cn[i] ];
            ˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:906:35: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    nu[i] = nus[ cohort[i] - 1 ][ cn[i] ];
            ˜˜˜                   ^˜˜˜˜
fitmodel.cpp:907:40: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    variance[i] = variances[ cohort[i] - 1 ][ cn[i] ];
                  ˜˜˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:907:47: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    variance[i] = variances[ cohort[i] - 1 ][ cn[i] ];
                  ˜˜˜˜˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:908:32: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    mean[i] = means[ cohort[i] - 1 ][ cn[i] ];
              ˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:908:39: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    mean[i] = means[ cohort[i] - 1 ][ cn[i] ];
              ˜˜˜˜˜                   ^˜˜˜˜
fitmodel.cpp:909:49: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    proba_disease[i] = proba_d[ assoc_strata[i] - 1 ][ cn[i] ];
                       ˜˜˜˜˜˜˜  ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜˜
fitmodel.cpp:909:56: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    proba_disease[i] = proba_d[ assoc_strata[i] - 1 ][ cn[i] ];
                       ˜˜˜˜˜˜˜                         ^˜˜˜˜
fitmodel.cpp:968:22: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
  vector<double> def(ncomp, 0.0);
                 ˜˜˜ ^˜˜˜˜
295 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c glm_test.cpp -o glm_test.o
In file included from glm_test.cpp:2:
./fitmodel.h:161:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    return(index[i1] < index[i2]);
           ˜˜˜˜˜ ^˜
./fitmodel.h:161:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    return(index[i1] < index[i2]);
                       ˜˜˜˜˜ ^˜
./fitmodel.h:166:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != (int) index.size(); i++) w[i] = i;
                                                  ˜ ^
glm_test.cpp:84:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'bool' [-Wconversion]
    if (!(pi)) {wi = ri = 0.0;}
        ˜ ^˜
glm_test.cpp:151:10: warning: implicit conversion turns floating-point number into integer: 'double' to 'bool' [-Wconversion]
          if (!(pi && (weights[i]>0.0))) {wi = ri = 0.0;} else {
                ^˜ ˜˜
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 mla.cpp -o mla.o
mla.cpp:60:11: warning: implicit conversion turns floating-point number into integer: 'double' to 'bool' [-Wconversion]
      if (swt[s]) 
      ˜˜  ^˜˜˜˜˜
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 routine.cpp -o routine.o
In file included from routine.cpp:2:
./fitmodel.h:161:18: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    return(index[i1] < index[i2]);
           ˜˜˜˜˜ ^˜
./fitmodel.h:161:30: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    return(index[i1] < index[i2]);
                       ˜˜˜˜˜ ^˜
./fitmodel.h:166:53: warning: implicit conversion changes signedness: 'int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    for (int i = 0; i != (int) index.size(); i++) w[i] = i;
                                                  ˜ ^
routine.cpp:110:22: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    array_strat_var[ strat_var[i] ]++;
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜  ^˜˜˜˜˜˜˜˜˜˜˜
routine.cpp:111:27: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if ( array_strat_var[ strat_var[i] ] == 1 ) nstrat_var++;
         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜  ^˜˜˜˜˜˜˜˜˜˜˜
routine.cpp:118:23: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    array_strat_mean[ strat_mean[i] ]++;
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜  ^˜˜˜˜˜˜˜˜˜˜˜˜
routine.cpp:119:28: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if ( array_strat_mean[ strat_mean[i] ] == 1 ) nstrat_mean++;
         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜  ^˜˜˜˜˜˜˜˜˜˜˜˜
routine.cpp:126:24: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    array_strat_assoc[ strat_assoc[i] ]++;
    ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜  ^˜˜˜˜˜˜˜˜˜˜˜˜˜
routine.cpp:127:29: warning: implicit conversion changes signedness: 'const int' to 'size_type' (aka 'unsigned long') [-Wsign-conversion]
    if ( array_strat_assoc[ strat_assoc[i] ] == 1 ) nstrat_assoc++;
         ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜  ^˜˜˜˜˜˜˜˜˜˜˜˜˜
9 warnings generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c zeroin.c -o zeroin.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o CNVtools.so fitmodel.o glm_test.o mla.o routine.o zeroin.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/CNVtools.buildbin-libdir/CNVtools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CNVtools)


>>>>>>> 
>>>>>>> FIXING LINKS FOR CNVtools.buildbin-libdir/CNVtools/libs//CNVtools.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "CNVtools.buildbin-libdir/CNVtools/libs//CNVtools.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "CNVtools.buildbin-libdir/CNVtools/libs//CNVtools.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "CNVtools.buildbin-libdir/CNVtools/libs//CNVtools.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "CNVtools.buildbin-libdir/CNVtools/libs//CNVtools.so"